From 5bfa7add51ed28a8445143ec668b16eef74448b1 Mon Sep 17 00:00:00 2001
From: gbayarri <genis.bayarri@irbbarcelona.org>
Date: Tue, 21 Jan 2025 16:21:50 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bioexcel?=
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             <a class="nav" href="z_97f47455ed834d2d_test_correlation_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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 </footer>
diff --git a/coverage/z_100f5897bddc1993_test_averages_py.html b/coverage/z_100f5897bddc1993_test_averages_py.html
index 67698828..f62252ba 100644
--- a/coverage/z_100f5897bddc1993_test_averages_py.html
+++ b/coverage/z_100f5897bddc1993_test_averages_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_bimodality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -114,7 +114,7 @@ <h2>
             <a class="nav" href="z_100f5897bddc1993_test_bimodality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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diff --git a/coverage/z_100f5897bddc1993_test_bimodality_py.html b/coverage/z_100f5897bddc1993_test_bimodality_py.html
index e264e8d7..e95cc4ad 100644
--- a/coverage/z_100f5897bddc1993_test_bimodality_py.html
+++ b/coverage/z_100f5897bddc1993_test_bimodality_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_timeseries_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -110,7 +110,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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+            created at 2025-01-21 16:21 +0000
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diff --git a/coverage/z_100f5897bddc1993_test_timeseries_py.html b/coverage/z_100f5897bddc1993_test_timeseries_py.html
index 1ec88f2b..229b1261 100644
--- a/coverage/z_100f5897bddc1993_test_timeseries_py.html
+++ b/coverage/z_100f5897bddc1993_test_timeseries_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_timeseries_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -112,7 +112,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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+            created at 2025-01-21 16:21 +0000
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diff --git a/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html b/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html
index 5c64b3dc..0f1a5c94 100644
--- a/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html
+++ b/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cda7f8e8576a7189_test_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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@@ -115,7 +115,7 @@ <h2>
             <a class="nav" href="z_cda7f8e8576a7189_test_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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diff --git a/coverage/z_159731231e5c9c9d___init___py.html b/coverage/z_159731231e5c9c9d___init___py.html
index de927252..a8e3a4d1 100644
--- a/coverage/z_159731231e5c9c9d___init___py.html
+++ b/coverage/z_159731231e5c9c9d___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d_bipopulations_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -94,7 +94,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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 </footer>
diff --git a/coverage/z_159731231e5c9c9d_bipopulations_py.html b/coverage/z_159731231e5c9c9d_bipopulations_py.html
index b477346b..056df67c 100644
--- a/coverage/z_159731231e5c9c9d_bipopulations_py.html
+++ b/coverage/z_159731231e5c9c9d_bipopulations_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d_canonicalag_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -204,7 +204,7 @@ <h2>
     <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -270,13 +270,13 @@ <h2>
     <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -386,7 +386,7 @@ <h2>
             <a class="nav" href="z_159731231e5c9c9d_canonicalag_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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diff --git a/coverage/z_159731231e5c9c9d_canonicalag_py.html b/coverage/z_159731231e5c9c9d_canonicalag_py.html
index 11c2c00c..b72d4320 100644
--- a/coverage/z_159731231e5c9c9d_canonicalag_py.html
+++ b/coverage/z_159731231e5c9c9d_canonicalag_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d_puckering_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -204,7 +204,7 @@ <h2>
     <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -278,13 +278,13 @@ <h2>
     <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -401,7 +401,7 @@ <h2>
             <a class="nav" href="z_159731231e5c9c9d_puckering_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_159731231e5c9c9d_puckering_py.html b/coverage/z_159731231e5c9c9d_puckering_py.html
index 1f6d981f..5e5d0a9c 100644
--- a/coverage/z_159731231e5c9c9d_puckering_py.html
+++ b/coverage/z_159731231e5c9c9d_puckering_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -196,7 +196,7 @@ <h2>
     <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -263,13 +263,13 @@ <h2>
     <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -370,7 +370,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91___init___py.html b/coverage/z_3afbcd666ed82c91___init___py.html
index 07ecd10b..2118c59b 100644
--- a/coverage/z_3afbcd666ed82c91___init___py.html
+++ b/coverage/z_3afbcd666ed82c91___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -95,7 +95,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_averages_py.html b/coverage/z_3afbcd666ed82c91_dna_averages_py.html
index 1e4df842..488c66b0 100644
--- a/coverage/z_3afbcd666ed82c91_dna_averages_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_averages_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_bimodality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -209,7 +209,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -226,7 +226,7 @@ <h2>
     <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -242,12 +242,12 @@ <h2>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="str">f"{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">+</span><span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">-</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{sequence[i:i+1+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">+</span><span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="key">while</span> <span class="nam">any</span><span class="op">(</span><span class="nam">pd</span><span class="op">.</span><span class="nam">Index</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">.</span><span class="nam">duplicated</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -269,19 +269,19 @@ <h2>
     <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">means</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Sequence Base Pair "</span> <span class="str">f"{'Step' if self.baselen==1 else ''}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Sequence Base Pair "</span> <span class="fst">f"</span><span class="op">{</span><span class="str">'Step'</span> <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">==</span><span class="num">1</span> <span class="key">else</span> <span class="str">''</span><span class="op">}</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="str">"Base Pair "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="str">f"{'Step' if self.baselen==1 else ''} "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="str">f"Helical Parameter: {self.helpar_name.capitalize()}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="str">'Step'</span> <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">==</span><span class="num">1</span> <span class="key">else</span> <span class="str">''</span><span class="op">}</span><span class="fst"> </span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="fst">f"</span><span class="fst">Helical Parameter: </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">            <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">                <span class="str">f"Base Pair {'Step' if self.baselen==1 else ''}"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">                <span class="fst">f"</span><span class="fst">Base Pair </span><span class="op">{</span><span class="str">'Step'</span> <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">==</span><span class="num">1</span> <span class="key">else</span> <span class="str">''</span><span class="op">}</span><span class="fst">"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">                <span class="str">"mean"</span><span class="op">:</span> <span class="nam">means</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">                <span class="str">"std"</span><span class="op">:</span> <span class="nam">stds</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
@@ -369,7 +369,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_bimodality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html b/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
index 47214220..22904fb2 100644
--- a/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_timeseries_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -208,7 +208,7 @@ <h2>
     <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="com"># get  unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -300,8 +300,8 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">vlines</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean2'</span><span class="op">]</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="nam">ylim</span><span class="op">,</span> <span class="nam">colors</span><span class="op">=</span><span class="str">"r"</span><span class="op">,</span> <span class="nam">linestyles</span><span class="op">=</span><span class="str">"dashed"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">ylabel</span><span class="op">(</span><span class="str">"Density"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">xlabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">title</span><span class="op">(</span><span class="str">f"Distribution of {self.helpar_name} states"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">xlabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">title</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Distribution of </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst"> states</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -426,7 +426,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_timeseries_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html b/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
index ed72ff3d..a2ce00f3 100644
--- a/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_timeseries_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -185,7 +185,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="com"># get base length from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -229,7 +229,7 @@ <h2>
     <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_basepairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">cols</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">cols</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 1}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">1</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -237,7 +237,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="key">elif</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_basepairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">cols</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">1</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">cols</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence)}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -254,7 +254,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="com"># create indices list</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">indices</span> <span class="op">=</span> <span class="nam">cols</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="com"># create subunits list from cols</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i-1:i+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">-</span><span class="num">1</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="com"># clean subunits (leave only basepairs)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="nam">pattern</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="str">r"\d+_[A-Za-z]{2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="com"># get removed items</span>&nbsp;</span><span class="r"></span></p>
@@ -277,7 +277,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="com"># trick for getting the index column from the .ser file</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">            <span class="nam">indices</span><span class="op">.</span><span class="nam">insert</span><span class="op">(</span><span class="num">0</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="com"># create subunits list from cols</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i:i+1+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">+</span><span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
@@ -293,64 +293,64 @@ <h2>
     <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="com"># unstack columns to prevent errors from repeated base pairs</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="nam">column_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="op">[</span><span class="nam">col</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">unstack</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">dropna</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">reset_index</span><span class="op">(</span><span class="nam">drop</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">            <span class="nam">column_data</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="nam">col</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Computing base number {col}..."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Computing base number </span><span class="op">{</span><span class="nam">col</span><span class="op">}</span><span class="fst">...</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">            <span class="com"># column series</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">series_colfn</span> <span class="op">=</span> <span class="str">f"series_{self.helpar_name}_{col}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">series_colfn</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">series_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">col</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">column_data</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.csv"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">            <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{series_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">reduced_data</span> <span class="op">=</span> <span class="nam">column_data</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="op">:</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">plot</span><span class="op">(</span><span class="nam">reduced_data</span><span class="op">.</span><span class="nam">index</span><span class="op">,</span> <span class="nam">reduced_data</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Time (Snapshots)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">                <span class="str">f"Helical Parameter vs Time: {self.helpar_name.capitalize()} "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">                <span class="fst">f"</span><span class="fst">Helical Parameter vs Time: </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> </span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">                <span class="str">"(base pair "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                <span class="str">f"{'step' if self.baselen==1 else ''} {col})"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="str">'step'</span> <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">==</span><span class="num">1</span> <span class="key">else</span> <span class="str">''</span><span class="op">}</span><span class="fst"> </span><span class="op">{</span><span class="nam">col</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">            <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">                <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">            <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">            <span class="com"># columns histogram</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">            <span class="nam">hist_colfn</span> <span class="op">=</span> <span class="str">f"hist_{self.helpar_name}_{col}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">            <span class="nam">hist_colfn</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">hist_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">col</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">            <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">            <span class="nam">ybins</span><span class="op">,</span> <span class="nam">x</span><span class="op">,</span> <span class="nam">_</span> <span class="op">=</span> <span class="nam">axs</span><span class="op">.</span><span class="nam">hist</span><span class="op">(</span><span class="nam">column_data</span><span class="op">,</span> <span class="nam">bins</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">bins</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">            <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">:</span> <span class="nam">x</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="str">"density"</span><span class="op">:</span> <span class="nam">ybins</span><span class="op">}</span><span class="op">)</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">                <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">            <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"Density"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">            <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">                <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">            <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -424,7 +424,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_timeseries_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html b/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html
index ff9e7fa8..446e5146 100644
--- a/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -187,26 +187,26 @@ <h2>
     <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="com"># Check that the type is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="key">not</span> <span class="key">in</span> <span class="op">[</span><span class="str">"series"</span><span class="op">,</span> <span class="str">"hist"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Type {self.type} not valid. Valid types are: series, hist."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Type </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">}</span><span class="fst"> not valid. Valid types are: series, hist.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># Check that the parameter is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">parameter</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Parameter {self.parameter} not valid. Valid parameters are: {constants.helical_parameters}."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Parameter </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">parameter</span><span class="op">}</span><span class="fst"> not valid. Valid parameters are: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="com"># Check that the sequence is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">pattern</span> <span class="op">=</span> <span class="str">r'^[ACGT]+$'</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">re</span><span class="op">.</span><span class="nam">match</span><span class="op">(</span><span class="nam">pattern</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Sequence {self.sequence} not valid. Only 'A', 'C', 'G' or 'T' bases allowed."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Sequence </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">}</span><span class="fst"> not valid. Only 'A', 'C', 'G' or 'T' bases allowed.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># Check that the index is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">index</span> <span class="op">&lt;</span> <span class="num">1</span> <span class="key">or</span> <span class="nam">self</span><span class="op">.</span><span class="nam">index</span> <span class="op">>=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">1</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Index {self.index} not valid. It should be between 0 and {len(self.sequence) - 2}."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Index </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">index</span><span class="op">}</span><span class="fst"> not valid. It should be between 0 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -214,39 +214,39 @@ <h2>
     <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">bp</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">index</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">+</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">index</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="com"># Get the filename</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">filename</span> <span class="op">=</span> <span class="str">f"{self.type}_{self.parameter}_{self.index}_{bp}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">csv_file</span> <span class="op">=</span> <span class="str">f"{filename}.csv"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">jpg_file</span> <span class="op">=</span> <span class="str">f"{filename}.jpg"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">filename</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">parameter</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">index</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">bp</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">csv_file</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">filename</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">jpg_file</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">filename</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># Unzip the file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="key">with</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_zip_file"</span><span class="op">]</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">zip_ref</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="com"># Check if the csv file exists in the zip file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="key">if</span> <span class="nam">csv_file</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">                <span class="com"># Extract the file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'{csv_file} exists, copying into {self.stage_io_dict["out"]["output_path_csv"]}.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">csv_file</span><span class="op">}</span><span class="fst"> exists, copying into </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path_csv"</span><span class="op">]</span><span class="op">}</span><span class="fst">.</span><span class="fst">'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">                <span class="key">with</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">open</span><span class="op">(</span><span class="nam">csv_file</span><span class="op">)</span> <span class="key">as</span> <span class="nam">source</span><span class="op">,</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path_csv"</span><span class="op">]</span><span class="op">,</span> <span class="str">"wb"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">target</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                    <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfileobj</span><span class="op">(</span><span class="nam">source</span><span class="op">,</span> <span class="nam">target</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"File {csv_file} not found in the zip file."</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">File </span><span class="op">{</span><span class="nam">csv_file</span><span class="op">}</span><span class="fst"> not found in the zip file.</span><span class="fst">"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="com"># Check if the jpg file exists in the zip file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="key">if</span> <span class="nam">jpg_file</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                <span class="com"># Extract the file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'{jpg_file} exists, copying into {self.stage_io_dict["out"]["output_path_jpg"]}.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">jpg_file</span><span class="op">}</span><span class="fst"> exists, copying into </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path_jpg"</span><span class="op">]</span><span class="op">}</span><span class="fst">.</span><span class="fst">'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                <span class="key">with</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">open</span><span class="op">(</span><span class="nam">jpg_file</span><span class="op">)</span> <span class="key">as</span> <span class="nam">source</span><span class="op">,</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path_jpg"</span><span class="op">]</span><span class="op">,</span> <span class="str">"wb"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">target</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfileobj</span><span class="op">(</span><span class="nam">source</span><span class="op">,</span> <span class="nam">target</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"File {jpg_file} not found in the zip file."</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">File </span><span class="op">{</span><span class="nam">jpg_file</span><span class="op">}</span><span class="fst"> not found in the zip file.</span><span class="fst">"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="com"># Write the list of files</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_list_path"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_list_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">f</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">                    <span class="key">for</span> <span class="nam">name</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">f"{name}\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">name</span><span class="op">}</span><span class="fst">\n</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="com"># self.run_biobb()</span>&nbsp;</span><span class="r"></span></p>
@@ -322,7 +322,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc___init___py.html b/coverage/z_64e03be4370b7ecc___init___py.html
index 9f576d5d..945c395b 100644
--- a/coverage/z_64e03be4370b7ecc___init___py.html
+++ b/coverage/z_64e03be4370b7ecc___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc_intrabpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -98,7 +98,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc_intrabpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html b/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
index 5b9e4ccd..d75be5be 100644
--- a/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc_intrahpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -242,15 +242,15 @@ <h2>
     <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">propel</span> <span class="op">=</span> <span class="nam">propel</span><span class="op">[</span><span class="nam">propel</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">opening</span> <span class="op">=</span> <span class="nam">opening</span><span class="op">[</span><span class="nam">opening</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="str">f"{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
@@ -286,7 +286,7 @@ <h2>
     <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">ser2_shifted</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="nam">corr_data</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="str">f"{ser1.name}/{ser2.name}"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span><span class="op">}</span><span class="fst">/</span><span class="op">{</span><span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span><span class="op">}</span><span class="fst">"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">result_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">.</span><span class="nam">from_dict</span><span class="op">(</span><span class="nam">results</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -462,7 +462,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc_intrahpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html b/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
index 44524197..a9d9c5f0 100644
--- a/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc_intraseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -295,7 +295,7 @@ <h2>
     <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">                    <span class="str">f"{corr_matrix[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">corr_matrix</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -305,7 +305,7 @@ <h2>
     <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="str">"Helical Parameter Correlation "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="str">f"for Base Pair Step \'{self.base}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="fst">f"</span><span class="fst">for Base Pair Step \'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">base</span><span class="op">}</span><span class="fst">\'</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -432,7 +432,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc_intraseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html b/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
index 1aa8ee8b..fe54c560 100644
--- a/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -201,7 +201,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -225,9 +225,9 @@ <h2>
     <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from strands</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
@@ -245,7 +245,7 @@ <h2>
     <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                    <span class="nam">j</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                    <span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">                    <span class="str">f"{corr_data[corr_data.columns[j]].iloc[i]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">corr_data</span><span class="op">[</span><span class="nam">corr_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -255,7 +255,7 @@ <h2>
     <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span> <span class="str">f"for Helical Parameter '{self.helpar_name}'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span> <span class="fst">f"</span><span class="fst">for Helical Parameter '</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -350,7 +350,7 @@ <h2>
             <a class="nav" href="z_9de9475b0a6fab52___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4___init___py.html b/coverage/z_74fa14c6d0e940a4___init___py.html
index 291fa928..b66eb01c 100644
--- a/coverage/z_74fa14c6d0e940a4___init___py.html
+++ b/coverage/z_74fa14c6d0e940a4___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4_biobb_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -95,7 +95,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_biobb_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html b/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html
index bb0fb40c..c928a311 100644
--- a/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html
+++ b/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4_biobb_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
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@@ -205,8 +205,8 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">                <span class="key">if</span> <span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"Strand  1"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">" "</span><span class="op">)</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                        <span class="str">f"using sequence {self.sequence} "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                        <span class="str">f"from {self.stage_io_dict['in']['input_lis_file']}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                        <span class="fst">f"</span><span class="fst">using sequence </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">}</span><span class="fst"> </span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                        <span class="fst">f"</span><span class="fst">from </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="com"># define temporary file name</span>&nbsp;</span><span class="r"></span></p>
@@ -218,29 +218,29 @@ <h2>
     <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">}</span><span class="fst"> &lt;&lt;! </span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="str">"  lis=canal_output,"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending sequence of bases to be searched to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  seq={self.bases},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="fst">f"</span><span class="fst">  seq=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">bases</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">nastr</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Adding null values string specification to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  nastr={self.nastr},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="fst">f"</span><span class="fst">  nastr=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">nastr</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="nam">instructions</span> <span class="op">+</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="str">f"  cormin={self.cormin},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="str">f"  lev1={self.lev1},lev2={self.lev2},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="str">f"  itst={self.itst},itnd={self.itnd},itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="str">f"  histo={self.histo},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="str">f"  series={self.series},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="str">f"  corr={self.corr},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  cormin=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">cormin</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  lev1=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">lev1</span><span class="op">}</span><span class="fst">,lev2=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">lev2</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itst=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itst</span><span class="op">}</span><span class="fst">,itnd=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span><span class="op">}</span><span class="fst">,itdel=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  histo=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">histo</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  series=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">series</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  corr=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">corr</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="str">"&amp;end"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="str">f"{tmp_cda_path} {self.sequence}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">tmp_cda_path</span><span class="op">}</span><span class="fst"> </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="str">"!"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -329,7 +329,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_biobb_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html b/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
index bdff8f71..e54ee993 100644
--- a/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
+++ b/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4_biobb_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -217,7 +217,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">ion_type_options</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="op">(</span><span class="str">"Invalid value for property type! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                              <span class="str">f"Option include: {ion_type_options}"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                              <span class="fst">f"</span><span class="fst">Option include: </span><span class="op">{</span><span class="nam">ion_type_options</span><span class="op">}</span><span class="fst">"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="com"># define temporary file names</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">input_cdi_file</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cdi_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
@@ -230,29 +230,29 @@ <h2>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">}</span><span class="fst"> &lt;&lt;! </span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="str">"  lis=canion_output,"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="str">f"  dat={input_cdi_file[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="str">f"  axfrm={input_afr_file[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="str">f"  solute={input_avg_struc[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="str">f"  type={self.type},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="str">f"  dlow={self.dlow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="str">f"  dhig={self.dhig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="str">f"  rlow={self.rlow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="str">f"  rhig={self.rhig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="str">f"  alow={self.alow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="str">f"  ahig={self.ahig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="str">f"  itst={self.itst},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="str">f"  itnd={self.itnd},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">f"  itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">f"  rmsf={self.rmsf},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">f"  circ={self.circ},"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  dat=</span><span class="op">{</span><span class="nam">input_cdi_file</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">4</span><span class="op">]</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  axfrm=</span><span class="op">{</span><span class="nam">input_afr_file</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">4</span><span class="op">]</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  solute=</span><span class="op">{</span><span class="nam">input_avg_struc</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">4</span><span class="op">]</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  type=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  dlow=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">dlow</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  dhig=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">dhig</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  rlow=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">rlow</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  rhig=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">rhig</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  alow=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">alow</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  ahig=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">ahig</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itst=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itst</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itnd=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itdel=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  rmsf=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">rmsf</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  circ=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">circ</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending sequence of bases to be searched to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  seq={self.bases},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="fst">f"</span><span class="fst">  seq=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">bases</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"&amp;end"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -341,7 +341,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_biobb_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html b/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
index 492d1c55..d1625ff7 100644
--- a/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
+++ b/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4_canal_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -216,7 +216,7 @@ <h2>
     <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">range1_end</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">":"</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">s2start</span> <span class="op">=</span> <span class="nam">range1_end</span> <span class="op">+</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">s2end</span> <span class="op">=</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">range1_end</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="op">=</span> <span class="str">f"{s2end}:{s2start}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">s2end</span><span class="op">}</span><span class="fst">:</span><span class="op">{</span><span class="nam">s2start</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># check standard library files location if not provided</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -228,14 +228,14 @@ <h2>
     <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">                    <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">list</span><span class="op">(</span><span class="nam">curves_aux_path</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"standard_*.lib"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">!=</span> <span class="num">3</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                        <span class="key">raise</span> <span class="nam">FileNotFoundError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                            <span class="str">"One or all standard library files "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                            <span class="str">f"missing from {curves_aux_path}! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                            <span class="fst">f"</span><span class="fst">missing from </span><span class="op">{</span><span class="nam">curves_aux_path</span><span class="op">}</span><span class="fst">! </span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                            <span class="str">"Check files standard_b.lib, "</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">                            <span class="str">"standard_s.lib and standard_i.lib exist."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="op">=</span> <span class="nam">curves_aux_path</span> <span class="op">/</span> <span class="str">"standard"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                    <span class="key">raise</span> <span class="nam">FileNotFoundError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                        <span class="str">".curvesplus directory not found in "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                        <span class="str">f"{os.getenv('CONDA_PREFIX')} !"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                        <span class="fst">f"</span><span class="op">{</span><span class="nam">os</span><span class="op">.</span><span class="nam">getenv</span><span class="op">(</span><span class="str">'CONDA_PREFIX'</span><span class="op">)</span><span class="op">}</span><span class="fst"> !</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                        <span class="str">"Please indicate where standard_*.lib files are "</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                        <span class="str">"located with the stdlib_path property."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                <span class="com"># copy standard library files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
@@ -267,30 +267,30 @@ <h2>
     <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">}</span><span class="fst"> &lt;&lt;! </span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="str">f"  file={tmp_struc_input},"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  file=</span><span class="op">{</span><span class="nam">tmp_struc_input</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending provided topology to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">                <span class="str">f"  ftop={tmp_top_input},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">                <span class="fst">f"</span><span class="fst">  ftop=</span><span class="op">{</span><span class="nam">tmp_top_input</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="nam">instructions</span> <span class="op">+</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">            <span class="str">"  lis='curves_output',"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">            <span class="str">f"  lib={relative_lib_path},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">            <span class="str">f"  ions={self.ions},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">            <span class="str">f"  test={self.test},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">            <span class="str">f"  line={self.line},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="str">f"  fit={self.fit},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="str">f"  axfrm={self.axfrm},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="str">f"  itst={self.itst},itnd={self.itnd},itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  lib=</span><span class="op">{</span><span class="nam">relative_lib_path</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  ions=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">ions</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  test=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">test</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  line=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">line</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  fit=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">fit</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  axfrm=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">axfrm</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itst=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itst</span><span class="op">}</span><span class="fst">,itnd=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span><span class="op">}</span><span class="fst">,itdel=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="str">"&amp;end"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="str">"2 1 -1 0 0"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="str">f"{self.s1range}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="str">f"{self.s2range}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="str">"!"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -393,7 +393,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_canal_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html b/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html
index 85edd2b4..17c977f5 100644
--- a/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html
+++ b/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -197,7 +197,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="com"># Check that the type is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">extensions</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Type {self.type} not valid. Valid types are: {', '.join(extensions.keys())}."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Type </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">}</span><span class="fst"> not valid. Valid types are: </span><span class="op">{</span><span class="str">', '</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">extensions</span><span class="op">.</span><span class="nam">keys</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">}</span><span class="fst">.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -207,7 +207,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="com"># Check that the correlation is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="nam">pattern</span> <span class="op">=</span> <span class="str">r'\d+_\d+'</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="nam">re</span><span class="op">.</span><span class="nam">match</span><span class="op">(</span><span class="nam">pattern</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">correlation</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Correlation {self.correlation} not valid. It should match the pattern &lt;number_number>."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Correlation </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">correlation</span><span class="op">}</span><span class="fst"> not valid. It should match the pattern &lt;number_number>.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">sufix</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
@@ -219,32 +219,32 @@ <h2>
     <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                                        <span class="str">"opening"</span><span class="op">,</span> <span class="str">"phaseC"</span><span class="op">,</span> <span class="str">"phaseW"</span><span class="op">,</span> <span class="str">"propel"</span><span class="op">,</span> <span class="str">"reg"</span><span class="op">,</span> <span class="str">"rise"</span><span class="op">,</span> <span class="str">"roll"</span><span class="op">,</span> <span class="str">"shear"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                                        <span class="str">"shift"</span><span class="op">,</span> <span class="str">"slide"</span><span class="op">,</span> <span class="str">"stagger"</span><span class="op">,</span> <span class="str">"stretch"</span><span class="op">,</span> <span class="str">"tbend"</span><span class="op">,</span> <span class="str">"tilt"</span><span class="op">,</span> <span class="str">"tip"</span><span class="op">,</span> <span class="str">"twist"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">                                        <span class="str">"xdisp"</span><span class="op">,</span> <span class="str">"ydisp"</span><span class="op">,</span> <span class="str">"zetaC"</span><span class="op">,</span> <span class="str">"zetaW"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Parameter {self.helpar_name} not valid. Valid parameters are: alphaC, alphaW, ampC, ampW, ax-bend, betaC, betaW, buckle, chiC, chiW, curv, deltaC, deltaW, epsilC, epsilW, gammaC, gammaW, h-ris, h-twi, inclin, majd, majw, mind, minw, opening, phaseC, phaseW, propel, reg, rise, roll, shear, shift, slide, stagger, stretch, tbend, tilt, tip, twist, xdisp, ydisp, zetaC, zetaW."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Parameter </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst"> not valid. Valid parameters are: alphaC, alphaW, ampC, ampW, ax-bend, betaC, betaW, buckle, chiC, chiW, curv, deltaC, deltaW, epsilC, epsilW, gammaC, gammaW, h-ris, h-twi, inclin, majd, majw, mind, minw, opening, phaseC, phaseW, propel, reg, rise, roll, shear, shift, slide, stagger, stretch, tbend, tilt, tip, twist, xdisp, ydisp, zetaC, zetaW.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">sufix</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="com"># Generate the filename</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">filename</span> <span class="op">=</span> <span class="str">f"canal_output_{sufix}.{extensions[self.type]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">filename</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">canal_output_</span><span class="op">{</span><span class="nam">sufix</span><span class="op">}</span><span class="fst">.</span><span class="op">{</span><span class="nam">extensions</span><span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># Unzip the file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="key">with</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_zip_file"</span><span class="op">]</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">zip_ref</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="com"># Check if the file exists in the zip file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="key">if</span> <span class="nam">filename</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">                <span class="com"># Extract the file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'{filename} exists, copying into {self.stage_io_dict["out"]["output_path"]}.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">filename</span><span class="op">}</span><span class="fst"> exists, copying into </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">}</span><span class="fst">.</span><span class="fst">'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                <span class="key">with</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">open</span><span class="op">(</span><span class="nam">filename</span><span class="op">)</span> <span class="key">as</span> <span class="nam">source</span><span class="op">,</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"wb"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">target</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                    <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfileobj</span><span class="op">(</span><span class="nam">source</span><span class="op">,</span> <span class="nam">target</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"File {filename} not found in the zip file."</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">File </span><span class="op">{</span><span class="nam">filename</span><span class="op">}</span><span class="fst"> not found in the zip file.</span><span class="fst">"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="com"># Write the list of files</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_list_path"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_list_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">f</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                    <span class="key">for</span> <span class="nam">name</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">f"{name}\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">name</span><span class="op">}</span><span class="fst">\n</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="com"># self.run_biobb()</span>&nbsp;</span><span class="r"></span></p>
@@ -315,7 +315,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_76997f7c8cf1ed45___init___py.html b/coverage/z_76997f7c8cf1ed45___init___py.html
index eeb535b6..48fa3d70 100644
--- a/coverage/z_76997f7c8cf1ed45___init___py.html
+++ b/coverage/z_76997f7c8cf1ed45___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -108,7 +108,7 @@ <h2>
             <a class="nav" href="z_159731231e5c9c9d___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html b/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
index 2fe467e1..6d0ea88d 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canal_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -111,7 +111,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_canal_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8030ef0ea5bfd6aa_test_canal_unzip_py.html b/coverage/z_8030ef0ea5bfd6aa_test_canal_unzip_py.html
index daf093b1..4be5cd49 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_canal_unzip_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_canal_unzip_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -113,7 +113,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
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 </footer>
diff --git a/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html b/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html
index 3102009e..b4aab9c5 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -111,7 +111,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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 </footer>
diff --git a/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html b/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html
index 7a329efa..ee3e19c5 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -113,7 +113,7 @@ <h2>
             <a class="nav" href="z_100f5897bddc1993_test_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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diff --git a/coverage/z_833b0317e3c43dca___init___py.html b/coverage/z_833b0317e3c43dca___init___py.html
index c072ffdb..54cc23fb 100644
--- a/coverage/z_833b0317e3c43dca___init___py.html
+++ b/coverage/z_833b0317e3c43dca___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -89,7 +89,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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     </div>
 </footer>
diff --git a/coverage/z_833b0317e3c43dca_common_py.html b/coverage/z_833b0317e3c43dca_common_py.html
index ad1a87be..0d8fea6a 100644
--- a/coverage/z_833b0317e3c43dca_common_py.html
+++ b/coverage/z_833b0317e3c43dca_common_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_constants_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -119,7 +119,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca_constants_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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 </footer>
diff --git a/coverage/z_833b0317e3c43dca_constants_py.html b/coverage/z_833b0317e3c43dca_constants_py.html
index 6c80fc82..43e6fe38 100644
--- a/coverage/z_833b0317e3c43dca_constants_py.html
+++ b/coverage/z_833b0317e3c43dca_constants_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_loader_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -162,7 +162,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca_loader_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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     </div>
 </footer>
diff --git a/coverage/z_833b0317e3c43dca_loader_py.html b/coverage/z_833b0317e3c43dca_loader_py.html
index 64552fb6..b1b5abbd 100644
--- a/coverage/z_833b0317e3c43dca_loader_py.html
+++ b/coverage/z_833b0317e3c43dca_loader_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_transform_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -133,7 +133,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca_transform_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_833b0317e3c43dca_transform_py.html b/coverage/z_833b0317e3c43dca_transform_py.html
index 831d0dee..bd035b23 100644
--- a/coverage/z_833b0317e3c43dca_transform_py.html
+++ b/coverage/z_833b0317e3c43dca_transform_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -102,7 +102,7 @@ <h2>
             <a class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f___init___py.html b/coverage/z_8a2a7f872cf1434f___init___py.html
index c9ac5e7a..a4239721 100644
--- a/coverage/z_8a2a7f872cf1434f___init___py.html
+++ b/coverage/z_8a2a7f872cf1434f___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interbpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -97,7 +97,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f_interbpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html b/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
index 0272aa72..7f71bb2f 100644
--- a/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interhpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -242,15 +242,15 @@ <h2>
     <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">roll</span> <span class="op">=</span> <span class="nam">roll</span><span class="op">[</span><span class="nam">roll</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">twist</span> <span class="op">=</span> <span class="nam">twist</span><span class="op">[</span><span class="nam">twist</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="str">f"{self.sequence[i:i+3]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">3</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{self.sequence[i:i+3]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">3</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
@@ -286,7 +286,7 @@ <h2>
     <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">ser2_shifted</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="nam">corr_data</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="str">f"{ser1.name}/{ser2.name}"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span><span class="op">}</span><span class="fst">/</span><span class="op">{</span><span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span><span class="op">}</span><span class="fst">"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">result_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">.</span><span class="nam">from_dict</span><span class="op">(</span><span class="nam">results</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -466,7 +466,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f_interhpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html b/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
index a0444ce0..aa2bc86a 100644
--- a/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -293,7 +293,7 @@ <h2>
     <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">                    <span class="str">f"{corr_matrix[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">corr_matrix</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -303,7 +303,7 @@ <h2>
     <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="str">"Helical Parameter Correlation "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">            <span class="str">f"for Base Pair Step \'{self.basepair}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">            <span class="fst">f"</span><span class="fst">for Base Pair Step \'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">basepair</span><span class="op">}</span><span class="fst">\'</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -430,7 +430,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f_interseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html b/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
index 0c4a6302..7f198d80 100644
--- a/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -205,7 +205,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -229,9 +229,9 @@ <h2>
     <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from strands</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
@@ -249,7 +249,7 @@ <h2>
     <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">                    <span class="nam">j</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">                    <span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">                    <span class="str">f"{corr_data[corr_data.columns[j]].iloc[i]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">corr_data</span><span class="op">[</span><span class="nam">corr_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -259,7 +259,7 @@ <h2>
     <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span> <span class="str">f"for Helical Parameter '{self.helpar_name}'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span> <span class="fst">f"</span><span class="fst">for Helical Parameter '</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -354,7 +354,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
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 </footer>
diff --git a/coverage/z_957b841f7413f0a1___init___py.html b/coverage/z_957b841f7413f0a1___init___py.html
index d0971fef..3ef4a567 100644
--- a/coverage/z_957b841f7413f0a1___init___py.html
+++ b/coverage/z_957b841f7413f0a1___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_020f76a90aa51c7b_test_bipopulations_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -89,7 +89,7 @@ <h2>
             <a class="nav" href="z_020f76a90aa51c7b_test_bipopulations_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
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 </footer>
diff --git a/coverage/z_97f47455ed834d2d_test_correlation_py.html b/coverage/z_97f47455ed834d2d_test_correlation_py.html
index 001d9e10..2aee258d 100644
--- a/coverage/z_97f47455ed834d2d_test_correlation_py.html
+++ b/coverage/z_97f47455ed834d2d_test_correlation_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -209,7 +209,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
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 </footer>
diff --git a/coverage/z_9de9475b0a6fab52___init___py.html b/coverage/z_9de9475b0a6fab52___init___py.html
index 8374775f..14d7cfbd 100644
--- a/coverage/z_9de9475b0a6fab52___init___py.html
+++ b/coverage/z_9de9475b0a6fab52___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52_average_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -93,7 +93,7 @@ <h2>
             <a class="nav" href="z_9de9475b0a6fab52_average_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
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diff --git a/coverage/z_9de9475b0a6fab52_average_stiffness_py.html b/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
index 292e86d6..360a6a96 100644
--- a/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
+++ b/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52_basepair_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -209,7 +209,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -224,7 +224,7 @@ <h2>
     <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -239,10 +239,10 @@ <h2>
     <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># calculate average stiffness</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">cov</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">cov</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -255,15 +255,15 @@ <h2>
     <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Sequence Base Pair"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="str">"Base Pair Helical Parameter Stiffness: "</span> <span class="str">f"{self.helpar_name.capitalize()}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="str">"Base Pair Helical Parameter Stiffness: "</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">data</span><span class="op">=</span><span class="nam">avg_stiffness</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">columns</span><span class="op">=</span><span class="op">[</span><span class="str">f"{self.helpar_name}_stiffness"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">data</span><span class="op">=</span><span class="nam">avg_stiffness</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">columns</span><span class="op">=</span><span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">_stiffness</span><span class="fst">"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">dataset</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -348,7 +348,7 @@ <h2>
             <a class="nav" href="z_9de9475b0a6fab52_basepair_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html b/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
index d5b55353..9a22d13a 100644
--- a/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
+++ b/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_957b841f7413f0a1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -240,7 +240,7 @@ <h2>
     <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                    <span class="nam">j</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                    <span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                    <span class="str">f"{stiff_df[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">stiff_df</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -257,7 +257,7 @@ <h2>
     <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="str">f"Stiffness Constants for Base Pair Step '{basepairname}'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Stiffness Constants for Base Pair Step '</span><span class="op">{</span><span class="nam">basepairname</span><span class="op">}</span><span class="fst">'</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -381,7 +381,7 @@ <h2>
             <a class="nav" href="z_957b841f7413f0a1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cda7f8e8576a7189_test_stiffness_py.html b/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
index 5969820d..d235d16f 100644
--- a/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
+++ b/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -130,7 +130,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 16:20 +0000
+            created at 2025-01-21 16:21 +0000
         </p>
     </div>
 </footer>
diff --git a/flake8/biobb_dna.dna.dna_averages.report.html b/flake8/biobb_dna.dna.dna_averages.report.html
new file mode 100644
index 00000000..49419b66
--- /dev/null
+++ b/flake8/biobb_dna.dna.dna_averages.report.html
@@ -0,0 +1,83 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>flake8 violations: biobb_dna/dna/dna_averages.py</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+<script>
+function bindHandler(link) {
+   var code = link.getAttribute('data-code');
+   var key = location.pathname + '#' + code;
+
+   var ul = link.parentNode.querySelector('.details');
+   if (sessionStorage[key] != 'open') {
+      ul.style.display = 'none';
+   }
+   link.addEventListener('click', function (event) {
+      if (!ul.style.display || ul.style.display == 'none') {
+         ul.style.display = 'block';
+         sessionStorage[key] = 'open';
+      } else {
+         ul.style.display = 'none';
+         sessionStorage[key] = 'closed';
+      }
+   });
+}
+
+window.addEventListener('DOMContentLoaded', function () {
+   var links = document.querySelectorAll('#index > li > a');
+   for (var i = 0; i < links.length; i++) {
+      bindHandler(links[i]);
+   }
+});
+</script>
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <p id="srclink">
+            <a title="View full annotated source"
+               href="biobb_dna.dna.dna_averages.source.html">
+               <img src="file.svg" alt="&#x2261;">
+            </a></p>
+         <h1>
+            <a href="index.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/dna/dna_averages.py
+            </a>
+         </h1>
+
+         <ul id="index">
+         
+         <li>
+            <a data-code="E225">
+               <span class="count sev-2">
+                  3
+               </span>
+               <strong>E225:</strong> missing whitespace around operator
+               
+            </a>
+            <ul class="details">
+            <li>
+               
+               <a href="biobb_dna.dna.dna_averages.source.html#l190">
+                  <tt><i>190</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;Sequence Base Pair &quot;</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span></tt>
+               </a>
+            </li><li>
+               
+               <a href="biobb_dna.dna.dna_averages.source.html#l194">
+                  <tt><i>194</i>             <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2"> &quot;</span></tt>
+               </a>
+            </li><li>
+               
+               <a href="biobb_dna.dna.dna_averages.source.html#l202">
+                  <tt><i>202</i>                 <span class="sa">f</span><span class="s2">&quot;Base Pair </span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">:</span> <span class="n">xlabels</span><span class="p">,</span></tt>
+               </a>
+            </li>
+            </ul>
+         </li>
+         
+         </ul>
+      </div>
+   </body>
+</html>
\ No newline at end of file
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+<!DOCTYPE html>
+<html>
+   <head>
+      <title>biobb_dna/dna/dna_averages.py - flake8 annotated source</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <h1>
+            <a href="biobb_dna.dna.dna_averages.report.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/dna/dna_averages.py source
+            </a>
+         </h1>
+
+         <div id="doc">
+            <div id="l1"
+               class="code sev- "><tt><i>1</i> <span class="ch">#!/usr/bin/env python3</span></tt>
+            </div>
+            <div id="l2"
+               class="code sev- "><tt><i>2</i> &nbsp;</tt>
+            </div>
+            <div id="l3"
+               class="code sev- "><tt><i>3</i> <span class="sd">&quot;&quot;&quot;Module containing the HelParAverages class and the command line interface.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l4"
+               class="code sev- "><tt><i>4</i> &nbsp;</tt>
+            </div>
+            <div id="l5"
+               class="code sev- "><tt><i>5</i> <span class="kn">import</span><span class="w"> </span><span class="nn">argparse</span></tt>
+            </div>
+            <div id="l6"
+               class="code sev- "><tt><i>6</i> <span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span></tt>
+            </div>
+            <div id="l7"
+               class="code sev- "><tt><i>7</i> <span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Optional</span></tt>
+            </div>
+            <div id="l8"
+               class="code sev- "><tt><i>8</i> &nbsp;</tt>
+            </div>
+            <div id="l9"
+               class="code sev- "><tt><i>9</i> <span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span></tt>
+            </div>
+            <div id="l10"
+               class="code sev- "><tt><i>10</i> <span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span></tt>
+            </div>
+            <div id="l11"
+               class="code sev- "><tt><i>11</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_common.configuration</span><span class="w"> </span><span class="kn">import</span> <span class="n">settings</span></tt>
+            </div>
+            <div id="l12"
+               class="code sev- "><tt><i>12</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_common.generic.biobb_object</span><span class="w"> </span><span class="kn">import</span> <span class="n">BiobbObject</span></tt>
+            </div>
+            <div id="l13"
+               class="code sev- "><tt><i>13</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_common.tools.file_utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">launchlogger</span></tt>
+            </div>
+            <div id="l14"
+               class="code sev- "><tt><i>14</i> &nbsp;</tt>
+            </div>
+            <div id="l15"
+               class="code sev- "><tt><i>15</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_dna.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">constants</span></tt>
+            </div>
+            <div id="l16"
+               class="code sev- "><tt><i>16</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_dna.utils.common</span><span class="w"> </span><span class="kn">import</span> <span class="n">_from_string_to_list</span></tt>
+            </div>
+            <div id="l17"
+               class="code sev- "><tt><i>17</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_dna.utils.loader</span><span class="w"> </span><span class="kn">import</span> <span class="n">read_series</span></tt>
+            </div>
+            <div id="l18"
+               class="code sev- "><tt><i>18</i> &nbsp;</tt>
+            </div>
+            <div id="l19"
+               class="code sev- "><tt><i>19</i> &nbsp;</tt>
+            </div>
+            <div id="l20"
+               class="code sev- "><tt><i>20</i> <span class="k">class</span><span class="w"> </span><span class="nc">HelParAverages</span><span class="p">(</span><span class="n">BiobbObject</span><span class="p">):</span></tt>
+            </div>
+            <div id="l21"
+               class="code sev- "><tt><i>21</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l22"
+               class="code sev- "><tt><i>22</i> <span class="sd">    | biobb_dna HelParAverages</span></tt>
+            </div>
+            <div id="l23"
+               class="code sev- "><tt><i>23</i> <span class="sd">    | Load .ser file for a given helical parameter and read each column corresponding to a base calculating average over each one.</span></tt>
+            </div>
+            <div id="l24"
+               class="code sev- "><tt><i>24</i> <span class="sd">    | Calculate average values for each base pair and save them in a .csv file.</span></tt>
+            </div>
+            <div id="l25"
+               class="code sev- "><tt><i>25</i> &nbsp;</tt>
+            </div>
+            <div id="l26"
+               class="code sev- "><tt><i>26</i> <span class="sd">    Args:</span></tt>
+            </div>
+            <div id="l27"
+               class="code sev- "><tt><i>27</i> <span class="sd">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l28"
+               class="code sev- "><tt><i>28</i> <span class="sd">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/shift_avg.csv&gt;`_. Accepted formats: csv (edam:format_3752).</span></tt>
+            </div>
+            <div id="l29"
+               class="code sev- "><tt><i>29</i> <span class="sd">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/shift_avg.jpg&gt;`_. Accepted formats: jpg (edam:format_3579).</span></tt>
+            </div>
+            <div id="l30"
+               class="code sev- "><tt><i>30</i> <span class="sd">        properties (dict):</span></tt>
+            </div>
+            <div id="l31"
+               class="code sev- "><tt><i>31</i> <span class="sd">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span></tt>
+            </div>
+            <div id="l32"
+               class="code sev- "><tt><i>32</i> <span class="sd">            * **helpar_name** (*str*) - (Optional) helical parameter name.</span></tt>
+            </div>
+            <div id="l33"
+               class="code sev- "><tt><i>33</i> <span class="sd">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span></tt>
+            </div>
+            <div id="l34"
+               class="code sev- "><tt><i>34</i> <span class="sd">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span></tt>
+            </div>
+            <div id="l35"
+               class="code sev- "><tt><i>35</i> <span class="sd">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span></tt>
+            </div>
+            <div id="l36"
+               class="code sev- "><tt><i>36</i> <span class="sd">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span></tt>
+            </div>
+            <div id="l37"
+               class="code sev- "><tt><i>37</i> <span class="sd">            * **sandbox_path** (*str*) - (&quot;./&quot;) [WF property] Parent path to the sandbox directory.</span></tt>
+            </div>
+            <div id="l38"
+               class="code sev- "><tt><i>38</i> <span class="sd">    Examples:</span></tt>
+            </div>
+            <div id="l39"
+               class="code sev- "><tt><i>39</i> <span class="sd">        This is a use example of how to use the building block from Python::</span></tt>
+            </div>
+            <div id="l40"
+               class="code sev- "><tt><i>40</i> &nbsp;</tt>
+            </div>
+            <div id="l41"
+               class="code sev- "><tt><i>41</i> <span class="sd">            from biobb_dna.dna.dna_averages import dna_averages</span></tt>
+            </div>
+            <div id="l42"
+               class="code sev- "><tt><i>42</i> &nbsp;</tt>
+            </div>
+            <div id="l43"
+               class="code sev- "><tt><i>43</i> <span class="sd">            prop = {</span></tt>
+            </div>
+            <div id="l44"
+               class="code sev- "><tt><i>44</i> <span class="sd">                &#39;helpar_name&#39;: &#39;twist&#39;,</span></tt>
+            </div>
+            <div id="l45"
+               class="code sev- "><tt><i>45</i> <span class="sd">                &#39;seqpos&#39;: [1,2],</span></tt>
+            </div>
+            <div id="l46"
+               class="code sev- "><tt><i>46</i> <span class="sd">                &#39;sequence&#39;: &#39;GCAT&#39;</span></tt>
+            </div>
+            <div id="l47"
+               class="code sev- "><tt><i>47</i> <span class="sd">            }</span></tt>
+            </div>
+            <div id="l48"
+               class="code sev- "><tt><i>48</i> <span class="sd">            dna_averages(</span></tt>
+            </div>
+            <div id="l49"
+               class="code sev- "><tt><i>49</i> <span class="sd">                input_ser_path=&#39;/path/to/twist.ser&#39;,</span></tt>
+            </div>
+            <div id="l50"
+               class="code sev- "><tt><i>50</i> <span class="sd">                output_csv_path=&#39;/path/to/table/output.csv&#39;,</span></tt>
+            </div>
+            <div id="l51"
+               class="code sev- "><tt><i>51</i> <span class="sd">                output_jpg_path=&#39;/path/to/table/output.jpg&#39;,</span></tt>
+            </div>
+            <div id="l52"
+               class="code sev- "><tt><i>52</i> <span class="sd">                properties=prop)</span></tt>
+            </div>
+            <div id="l53"
+               class="code sev- "><tt><i>53</i> &nbsp;</tt>
+            </div>
+            <div id="l54"
+               class="code sev- "><tt><i>54</i> <span class="sd">    Info:</span></tt>
+            </div>
+            <div id="l55"
+               class="code sev- "><tt><i>55</i> <span class="sd">        * wrapped_software:</span></tt>
+            </div>
+            <div id="l56"
+               class="code sev- "><tt><i>56</i> <span class="sd">            * name: In house</span></tt>
+            </div>
+            <div id="l57"
+               class="code sev- "><tt><i>57</i> <span class="sd">            * license: Apache-2.0</span></tt>
+            </div>
+            <div id="l58"
+               class="code sev- "><tt><i>58</i> <span class="sd">        * ontology:</span></tt>
+            </div>
+            <div id="l59"
+               class="code sev- "><tt><i>59</i> <span class="sd">            * name: EDAM</span></tt>
+            </div>
+            <div id="l60"
+               class="code sev- "><tt><i>60</i> <span class="sd">            * schema: http://edamontology.org/EDAM.owl</span></tt>
+            </div>
+            <div id="l61"
+               class="code sev- "><tt><i>61</i> &nbsp;</tt>
+            </div>
+            <div id="l62"
+               class="code sev- "><tt><i>62</i> <span class="sd">    &quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l63"
+               class="code sev- "><tt><i>63</i> &nbsp;</tt>
+            </div>
+            <div id="l64"
+               class="code sev- "><tt><i>64</i>     <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span></tt>
+            </div>
+            <div id="l65"
+               class="code sev- "><tt><i>65</i>         <span class="bp">self</span><span class="p">,</span></tt>
+            </div>
+            <div id="l66"
+               class="code sev- "><tt><i>66</i>         <span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l67"
+               class="code sev- "><tt><i>67</i>         <span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l68"
+               class="code sev- "><tt><i>68</i>         <span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l69"
+               class="code sev- "><tt><i>69</i>         <span class="n">properties</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l70"
+               class="code sev- "><tt><i>70</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l71"
+               class="code sev- "><tt><i>71</i>     <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l72"
+               class="code sev- "><tt><i>72</i>         <span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span> <span class="ow">or</span> <span class="p">{}</span></tt>
+            </div>
+            <div id="l73"
+               class="code sev- "><tt><i>73</i> &nbsp;</tt>
+            </div>
+            <div id="l74"
+               class="code sev- "><tt><i>74</i>         <span class="c1"># Call parent class constructor</span></tt>
+            </div>
+            <div id="l75"
+               class="code sev- "><tt><i>75</i>         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l76"
+               class="code sev- "><tt><i>76</i>         <span class="bp">self</span><span class="o">.</span><span class="n">locals_var_dict</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l77"
+               class="code sev- "><tt><i>77</i> &nbsp;</tt>
+            </div>
+            <div id="l78"
+               class="code sev- "><tt><i>78</i>         <span class="c1"># Input/Output files</span></tt>
+            </div>
+            <div id="l79"
+               class="code sev- "><tt><i>79</i>         <span class="bp">self</span><span class="o">.</span><span class="n">io_dict</span> <span class="o">=</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l80"
+               class="code sev- "><tt><i>80</i>             <span class="s2">&quot;in&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l81"
+               class="code sev- "><tt><i>81</i>                 <span class="s2">&quot;input_ser_path&quot;</span><span class="p">:</span> <span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l82"
+               class="code sev- "><tt><i>82</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l83"
+               class="code sev- "><tt><i>83</i>             <span class="s2">&quot;out&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l84"
+               class="code sev- "><tt><i>84</i>                 <span class="s2">&quot;output_csv_path&quot;</span><span class="p">:</span> <span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l85"
+               class="code sev- "><tt><i>85</i>                 <span class="s2">&quot;output_jpg_path&quot;</span><span class="p">:</span> <span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l86"
+               class="code sev- "><tt><i>86</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l87"
+               class="code sev- "><tt><i>87</i>         <span class="p">}</span></tt>
+            </div>
+            <div id="l88"
+               class="code sev- "><tt><i>88</i> &nbsp;</tt>
+            </div>
+            <div id="l89"
+               class="code sev- "><tt><i>89</i>         <span class="c1"># Properties specific for BB</span></tt>
+            </div>
+            <div id="l90"
+               class="code sev- "><tt><i>90</i>         <span class="bp">self</span><span class="o">.</span><span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span></tt>
+            </div>
+            <div id="l91"
+               class="code sev- "><tt><i>91</i>         <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;sequence&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l92"
+               class="code sev- "><tt><i>92</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stride</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;stride&quot;</span><span class="p">,</span> <span class="mi">1000</span><span class="p">)</span></tt>
+            </div>
+            <div id="l93"
+               class="code sev- "><tt><i>93</i>         <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l94"
+               class="code sev- "><tt><i>94</i>             <span class="nb">int</span><span class="p">(</span><span class="n">elem</span><span class="p">)</span> <span class="k">for</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">_from_string_to_list</span><span class="p">(</span><span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;seqpos&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span></tt>
+            </div>
+            <div id="l95"
+               class="code sev- "><tt><i>95</i>         <span class="p">]</span></tt>
+            </div>
+            <div id="l96"
+               class="code sev- "><tt><i>96</i>         <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;helpar_name&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l97"
+               class="code sev- "><tt><i>97</i> &nbsp;</tt>
+            </div>
+            <div id="l98"
+               class="code sev- "><tt><i>98</i>         <span class="c1"># Check the properties</span></tt>
+            </div>
+            <div id="l99"
+               class="code sev- "><tt><i>99</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_properties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l100"
+               class="code sev- "><tt><i>100</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">()</span></tt>
+            </div>
+            <div id="l101"
+               class="code sev- "><tt><i>101</i> &nbsp;</tt>
+            </div>
+            <div id="l102"
+               class="code sev- "><tt><i>102</i>     <span class="nd">@launchlogger</span></tt>
+            </div>
+            <div id="l103"
+               class="code sev- "><tt><i>103</i>     <span class="k">def</span><span class="w"> </span><span class="nf">launch</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l104"
+               class="code sev- "><tt><i>104</i> <span class="w">        </span><span class="sd">&quot;&quot;&quot;Execute the :class:`HelParAverages &lt;dna.averages.HelParAverages&gt;` object.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l105"
+               class="code sev- "><tt><i>105</i> &nbsp;</tt>
+            </div>
+            <div id="l106"
+               class="code sev- "><tt><i>106</i>         <span class="c1"># Setup Biobb</span></tt>
+            </div>
+            <div id="l107"
+               class="code sev- "><tt><i>107</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_restart</span><span class="p">():</span></tt>
+            </div>
+            <div id="l108"
+               class="code sev- "><tt><i>108</i>             <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l109"
+               class="code sev- "><tt><i>109</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stage_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l110"
+               class="code sev- "><tt><i>110</i> &nbsp;</tt>
+            </div>
+            <div id="l111"
+               class="code sev- "><tt><i>111</i>         <span class="c1"># check sequence</span></tt>
+            </div>
+            <div id="l112"
+               class="code sev- "><tt><i>112</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span></tt>
+            </div>
+            <div id="l113"
+               class="code sev- "><tt><i>113</i>             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;sequence is null or too short!&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l114"
+               class="code sev- "><tt><i>114</i> &nbsp;</tt>
+            </div>
+            <div id="l115"
+               class="code sev- "><tt><i>115</i>         <span class="c1"># get helical parameter from filename if not specified</span></tt>
+            </div>
+            <div id="l116"
+               class="code sev- "><tt><i>116</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l117"
+               class="code sev- "><tt><i>117</i>             <span class="k">for</span> <span class="n">hp</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="p">:</span></tt>
+            </div>
+            <div id="l118"
+               class="code sev- "><tt><i>118</i>                 <span class="n">ser_name</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_ser_path&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span></tt>
+            </div>
+            <div id="l119"
+               class="code sev- "><tt><i>119</i>                 <span class="k">if</span> <span class="n">hp</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">ser_name</span><span class="p">:</span></tt>
+            </div>
+            <div id="l120"
+               class="code sev- "><tt><i>120</i>                     <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="o">=</span> <span class="n">hp</span></tt>
+            </div>
+            <div id="l121"
+               class="code sev- "><tt><i>121</i>             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l122"
+               class="code sev- "><tt><i>122</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l123"
+               class="code sev- "><tt><i>123</i>                     <span class="s2">&quot;Helical parameter name can&#39;t be inferred from file, &quot;</span></tt>
+            </div>
+            <div id="l124"
+               class="code sev- "><tt><i>124</i>                     <span class="s2">&quot;so it must be specified!&quot;</span></tt>
+            </div>
+            <div id="l125"
+               class="code sev- "><tt><i>125</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l126"
+               class="code sev- "><tt><i>126</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l127"
+               class="code sev- "><tt><i>127</i>             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="p">:</span></tt>
+            </div>
+            <div id="l128"
+               class="code sev- "><tt><i>128</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l129"
+               class="code sev- "><tt><i>129</i>                     <span class="s2">&quot;Helical parameter name is invalid! &quot;</span></tt>
+            </div>
+            <div id="l130"
+               class="code sev- "><tt><i>130</i>                     <span class="sa">f</span><span class="s2">&quot;Options: </span><span class="si">{</span><span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l131"
+               class="code sev- "><tt><i>131</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l132"
+               class="code sev- "><tt><i>132</i> &nbsp;</tt>
+            </div>
+            <div id="l133"
+               class="code sev- "><tt><i>133</i>         <span class="c1"># get base length and unit from helical parameter name</span></tt>
+            </div>
+            <div id="l134"
+               class="code sev- "><tt><i>134</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_basepairs</span><span class="p">:</span></tt>
+            </div>
+            <div id="l135"
+               class="code sev- "><tt><i>135</i>             <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span> <span class="o">=</span> <span class="mi">1</span></tt>
+            </div>
+            <div id="l136"
+               class="code sev- "><tt><i>136</i>         <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_singlebases</span><span class="p">:</span></tt>
+            </div>
+            <div id="l137"
+               class="code sev- "><tt><i>137</i>             <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span> <span class="o">=</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l138"
+               class="code sev- "><tt><i>138</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span><span class="p">:</span></tt>
+            </div>
+            <div id="l139"
+               class="code sev- "><tt><i>139</i>             <span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span> <span class="o">=</span> <span class="s2">&quot;Degrees&quot;</span></tt>
+            </div>
+            <div id="l140"
+               class="code sev- "><tt><i>140</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l141"
+               class="code sev- "><tt><i>141</i>             <span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span> <span class="o">=</span> <span class="s2">&quot;Angstroms&quot;</span></tt>
+            </div>
+            <div id="l142"
+               class="code sev- "><tt><i>142</i> &nbsp;</tt>
+            </div>
+            <div id="l143"
+               class="code sev- "><tt><i>143</i>         <span class="c1"># check seqpos</span></tt>
+            </div>
+            <div id="l144"
+               class="code sev- "><tt><i>144</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l145"
+               class="code sev- "><tt><i>145</i>             <span class="k">if</span> <span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l146"
+               class="code sev- "><tt><i>146</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l147"
+               class="code sev- "><tt><i>147</i>                     <span class="sa">f</span><span class="s2">&quot;seqpos values must be between 1 and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">2</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l148"
+               class="code sev- "><tt><i>148</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l149"
+               class="code sev- "><tt><i>149</i>             <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l150"
+               class="code sev- "><tt><i>150</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;seqpos must be a list of at least two integers&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l151"
+               class="code sev- "><tt><i>151</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l152"
+               class="code sev- "><tt><i>152</i>             <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="kc">None</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l153"
+               class="code sev- "><tt><i>153</i> &nbsp;</tt>
+            </div>
+            <div id="l154"
+               class="code sev- "><tt><i>154</i>         <span class="c1"># read input .ser file</span></tt>
+            </div>
+            <div id="l155"
+               class="code sev- "><tt><i>155</i>         <span class="n">ser_data</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l156"
+               class="code sev- "><tt><i>156</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_ser_path&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l157"
+               class="code sev- "><tt><i>157</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l158"
+               class="code sev- "><tt><i>158</i>         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l159"
+               class="code sev- "><tt><i>159</i>             <span class="n">ser_data</span> <span class="o">=</span> <span class="n">ser_data</span><span class="p">[</span><span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l160"
+               class="code sev- "><tt><i>160</i>             <span class="c1"># discard first and last base(pairs) from sequence</span></tt>
+            </div>
+            <div id="l161"
+               class="code sev- "><tt><i>161</i>             <span class="n">sequence</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span></tt>
+            </div>
+            <div id="l162"
+               class="code sev- "><tt><i>162</i>             <span class="n">xlabels</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l163"
+               class="code sev- "><tt><i>163</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l164"
+               class="code sev- "><tt><i>164</i>                 <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">)</span></tt>
+            </div>
+            <div id="l165"
+               class="code sev- "><tt><i>165</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l166"
+               class="code sev- "><tt><i>166</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l167"
+               class="code sev- "><tt><i>167</i>             <span class="n">sequence</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span></tt>
+            </div>
+            <div id="l168"
+               class="code sev- "><tt><i>168</i>             <span class="n">xlabels</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">]</span></tt>
+            </div>
+            <div id="l169"
+               class="code sev- "><tt><i>169</i> &nbsp;</tt>
+            </div>
+            <div id="l170"
+               class="code sev- "><tt><i>170</i>         <span class="c1"># rename duplicated subunits</span></tt>
+            </div>
+            <div id="l171"
+               class="code sev- "><tt><i>171</i>         <span class="k">while</span> <span class="nb">any</span><span class="p">(</span><span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span><span class="o">.</span><span class="n">duplicated</span><span class="p">()):</span></tt>
+            </div>
+            <div id="l172"
+               class="code sev- "><tt><i>172</i>             <span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l173"
+               class="code sev- "><tt><i>173</i>                 <span class="n">name</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">duplicated</span> <span class="k">else</span> <span class="n">name</span> <span class="o">+</span> <span class="s2">&quot;_dup&quot;</span></tt>
+            </div>
+            <div id="l174"
+               class="code sev- "><tt><i>174</i>                 <span class="k">for</span> <span class="n">duplicated</span><span class="p">,</span> <span class="n">name</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span></tt>
+            </div>
+            <div id="l175"
+               class="code sev- "><tt><i>175</i>                     <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span><span class="o">.</span><span class="n">duplicated</span><span class="p">(),</span> <span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span></tt>
+            </div>
+            <div id="l176"
+               class="code sev- "><tt><i>176</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l177"
+               class="code sev- "><tt><i>177</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l178"
+               class="code sev- "><tt><i>178</i> &nbsp;</tt>
+            </div>
+            <div id="l179"
+               class="code sev- "><tt><i>179</i>         <span class="c1"># write output files for all selected bases</span></tt>
+            </div>
+            <div id="l180"
+               class="code sev- "><tt><i>180</i>         <span class="n">means</span> <span class="o">=</span> <span class="n">ser_data</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:</span> <span class="nb">len</span><span class="p">(</span><span class="n">xlabels</span><span class="p">)]</span></tt>
+            </div>
+            <div id="l181"
+               class="code sev- "><tt><i>181</i>         <span class="n">stds</span> <span class="o">=</span> <span class="n">ser_data</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:</span> <span class="nb">len</span><span class="p">(</span><span class="n">xlabels</span><span class="p">)]</span></tt>
+            </div>
+            <div id="l182"
+               class="code sev- "><tt><i>182</i> &nbsp;</tt>
+            </div>
+            <div id="l183"
+               class="code sev- "><tt><i>183</i>         <span class="c1"># save plot</span></tt>
+            </div>
+            <div id="l184"
+               class="code sev- "><tt><i>184</i>         <span class="n">fig</span><span class="p">,</span> <span class="n">axs</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">tight_layout</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l185"
+               class="code sev- "><tt><i>185</i>         <span class="n">axs</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span></tt>
+            </div>
+            <div id="l186"
+               class="code sev- "><tt><i>186</i>             <span class="n">means</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">means</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(),</span> <span class="n">yerr</span><span class="o">=</span><span class="n">stds</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(),</span> <span class="n">marker</span><span class="o">=</span><span class="s2">&quot;o&quot;</span><span class="p">,</span> <span class="n">capsize</span><span class="o">=</span><span class="mi">5</span></tt>
+            </div>
+            <div id="l187"
+               class="code sev- "><tt><i>187</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l188"
+               class="code sev- "><tt><i>188</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_xticks</span><span class="p">(</span><span class="n">means</span><span class="o">.</span><span class="n">index</span><span class="p">)</span></tt>
+            </div>
+            <div id="l189"
+               class="code sev- "><tt><i>189</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_xticklabels</span><span class="p">(</span><span class="n">xlabels</span><span class="p">,</span> <span class="n">rotation</span><span class="o">=</span><span class="mi">90</span><span class="p">)</span></tt>
+            </div>
+            <div id="l190"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        E225
+                     </span>
+                     Missing whitespace around operator</li>
+               
+               </ul><tt><i>190</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;Sequence Base Pair &quot;</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l191"
+               class="code sev- "><tt><i>191</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2"> (</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span><span class="si">}</span><span class="s2">)&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l192"
+               class="code sev- "><tt><i>192</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span></tt>
+            </div>
+            <div id="l193"
+               class="code sev- "><tt><i>193</i>             <span class="s2">&quot;Base Pair &quot;</span></tt>
+            </div>
+            <div id="l194"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        E225
+                     </span>
+                     Missing whitespace around operator</li>
+               
+               </ul><tt><i>194</i>             <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2"> &quot;</span></tt>
+            </div>
+            <div id="l195"
+               class="code sev- "><tt><i>195</i>             <span class="sa">f</span><span class="s2">&quot;Helical Parameter: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l196"
+               class="code sev- "><tt><i>196</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l197"
+               class="code sev- "><tt><i>197</i>         <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_jpg_path&quot;</span><span class="p">],</span> <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;jpg&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l198"
+               class="code sev- "><tt><i>198</i> &nbsp;</tt>
+            </div>
+            <div id="l199"
+               class="code sev- "><tt><i>199</i>         <span class="c1"># save table</span></tt>
+            </div>
+            <div id="l200"
+               class="code sev- "><tt><i>200</i>         <span class="n">dataset</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span></tt>
+            </div>
+            <div id="l201"
+               class="code sev- "><tt><i>201</i>             <span class="p">{</span></tt>
+            </div>
+            <div id="l202"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        E225
+                     </span>
+                     Missing whitespace around operator</li>
+               
+               </ul><tt><i>202</i>                 <span class="sa">f</span><span class="s2">&quot;Base Pair </span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">:</span> <span class="n">xlabels</span><span class="p">,</span></tt>
+            </div>
+            <div id="l203"
+               class="code sev- "><tt><i>203</i>                 <span class="s2">&quot;mean&quot;</span><span class="p">:</span> <span class="n">means</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(),</span></tt>
+            </div>
+            <div id="l204"
+               class="code sev- "><tt><i>204</i>                 <span class="s2">&quot;std&quot;</span><span class="p">:</span> <span class="n">stds</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(),</span></tt>
+            </div>
+            <div id="l205"
+               class="code sev- "><tt><i>205</i>             <span class="p">}</span></tt>
+            </div>
+            <div id="l206"
+               class="code sev- "><tt><i>206</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l207"
+               class="code sev- "><tt><i>207</i>         <span class="n">dataset</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_csv_path&quot;</span><span class="p">],</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></tt>
+            </div>
+            <div id="l208"
+               class="code sev- "><tt><i>208</i> &nbsp;</tt>
+            </div>
+            <div id="l209"
+               class="code sev- "><tt><i>209</i>         <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l210"
+               class="code sev- "><tt><i>210</i> &nbsp;</tt>
+            </div>
+            <div id="l211"
+               class="code sev- "><tt><i>211</i>         <span class="c1"># Copy files to host</span></tt>
+            </div>
+            <div id="l212"
+               class="code sev- "><tt><i>212</i>         <span class="bp">self</span><span class="o">.</span><span class="n">copy_to_host</span><span class="p">()</span></tt>
+            </div>
+            <div id="l213"
+               class="code sev- "><tt><i>213</i> &nbsp;</tt>
+            </div>
+            <div id="l214"
+               class="code sev- "><tt><i>214</i>         <span class="c1"># Remove temporary file(s)</span></tt>
+            </div>
+            <div id="l215"
+               class="code sev- "><tt><i>215</i>         <span class="bp">self</span><span class="o">.</span><span class="n">tmp_files</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">)])</span></tt>
+            </div>
+            <div id="l216"
+               class="code sev- "><tt><i>216</i>         <span class="bp">self</span><span class="o">.</span><span class="n">remove_tmp_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l217"
+               class="code sev- "><tt><i>217</i> &nbsp;</tt>
+            </div>
+            <div id="l218"
+               class="code sev- "><tt><i>218</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">(</span><span class="n">output_files_created</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">raise_exception</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></tt>
+            </div>
+            <div id="l219"
+               class="code sev- "><tt><i>219</i> &nbsp;</tt>
+            </div>
+            <div id="l220"
+               class="code sev- "><tt><i>220</i>         <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l221"
+               class="code sev- "><tt><i>221</i> &nbsp;</tt>
+            </div>
+            <div id="l222"
+               class="code sev- "><tt><i>222</i> &nbsp;</tt>
+            </div>
+            <div id="l223"
+               class="code sev- "><tt><i>223</i> <span class="k">def</span><span class="w"> </span><span class="nf">dna_averages</span><span class="p">(</span></tt>
+            </div>
+            <div id="l224"
+               class="code sev- "><tt><i>224</i>     <span class="n">input_ser_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l225"
+               class="code sev- "><tt><i>225</i>     <span class="n">output_csv_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l226"
+               class="code sev- "><tt><i>226</i>     <span class="n">output_jpg_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l227"
+               class="code sev- "><tt><i>227</i>     <span class="n">properties</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l228"
+               class="code sev- "><tt><i>228</i>     <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l229"
+               class="code sev- "><tt><i>229</i> <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l230"
+               class="code sev- "><tt><i>230</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Create :class:`HelParAverages &lt;dna.dna_averages.HelParAverages&gt;` class and</span></tt>
+            </div>
+            <div id="l231"
+               class="code sev- "><tt><i>231</i> <span class="sd">    execute the :meth:`launch() &lt;dna.dna_averages.HelParAverages.launch&gt;` method.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l232"
+               class="code sev- "><tt><i>232</i> &nbsp;</tt>
+            </div>
+            <div id="l233"
+               class="code sev- "><tt><i>233</i>     <span class="k">return</span> <span class="n">HelParAverages</span><span class="p">(</span></tt>
+            </div>
+            <div id="l234"
+               class="code sev- "><tt><i>234</i>         <span class="n">input_ser_path</span><span class="o">=</span><span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l235"
+               class="code sev- "><tt><i>235</i>         <span class="n">output_csv_path</span><span class="o">=</span><span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l236"
+               class="code sev- "><tt><i>236</i>         <span class="n">output_jpg_path</span><span class="o">=</span><span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l237"
+               class="code sev- "><tt><i>237</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l238"
+               class="code sev- "><tt><i>238</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l239"
+               class="code sev- "><tt><i>239</i>     <span class="p">)</span><span class="o">.</span><span class="n">launch</span><span class="p">()</span></tt>
+            </div>
+            <div id="l240"
+               class="code sev- "><tt><i>240</i> &nbsp;</tt>
+            </div>
+            <div id="l241"
+               class="code sev- "><tt><i>241</i> &nbsp;</tt>
+            </div>
+            <div id="l242"
+               class="code sev- "><tt><i>242</i> <span class="k">def</span><span class="w"> </span><span class="nf">main</span><span class="p">():</span></tt>
+            </div>
+            <div id="l243"
+               class="code sev- "><tt><i>243</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Command line execution of this building block. Please check the command line documentation.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l244"
+               class="code sev- "><tt><i>244</i>     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span></tt>
+            </div>
+            <div id="l245"
+               class="code sev- "><tt><i>245</i>         <span class="n">description</span><span class="o">=</span><span class="s2">&quot;Load helical parameter file and calculate average values for each base pair.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l246"
+               class="code sev- "><tt><i>246</i>         <span class="n">formatter_class</span><span class="o">=</span><span class="k">lambda</span> <span class="n">prog</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">RawTextHelpFormatter</span><span class="p">(</span><span class="n">prog</span><span class="p">,</span> <span class="n">width</span><span class="o">=</span><span class="mi">99999</span><span class="p">),</span></tt>
+            </div>
+            <div id="l247"
+               class="code sev- "><tt><i>247</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l248"
+               class="code sev- "><tt><i>248</i>     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">&quot;--config&quot;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Configuration file&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l249"
+               class="code sev- "><tt><i>249</i> &nbsp;</tt>
+            </div>
+            <div id="l250"
+               class="code sev- "><tt><i>250</i>     <span class="n">required_args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s2">&quot;required arguments&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l251"
+               class="code sev- "><tt><i>251</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l252"
+               class="code sev- "><tt><i>252</i>         <span class="s2">&quot;--input_ser_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l253"
+               class="code sev- "><tt><i>253</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l254"
+               class="code sev- "><tt><i>254</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Helical parameter input ser file path. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l255"
+               class="code sev- "><tt><i>255</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l256"
+               class="code sev- "><tt><i>256</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l257"
+               class="code sev- "><tt><i>257</i>         <span class="s2">&quot;--output_csv_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l258"
+               class="code sev- "><tt><i>258</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l259"
+               class="code sev- "><tt><i>259</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output csv file. Accepted formats: csv.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l260"
+               class="code sev- "><tt><i>260</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l261"
+               class="code sev- "><tt><i>261</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l262"
+               class="code sev- "><tt><i>262</i>         <span class="s2">&quot;--output_jpg_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l263"
+               class="code sev- "><tt><i>263</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l264"
+               class="code sev- "><tt><i>264</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output jpg file. Accepted formats: jpg.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l265"
+               class="code sev- "><tt><i>265</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l266"
+               class="code sev- "><tt><i>266</i> &nbsp;</tt>
+            </div>
+            <div id="l267"
+               class="code sev- "><tt><i>267</i>     <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></tt>
+            </div>
+            <div id="l268"
+               class="code sev- "><tt><i>268</i>     <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="ow">or</span> <span class="s2">&quot;</span><span class="si">{}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l269"
+               class="code sev- "><tt><i>269</i>     <span class="n">properties</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">ConfReader</span><span class="p">(</span><span class="n">config</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">config</span><span class="p">)</span><span class="o">.</span><span class="n">get_prop_dic</span><span class="p">()</span></tt>
+            </div>
+            <div id="l270"
+               class="code sev- "><tt><i>270</i> &nbsp;</tt>
+            </div>
+            <div id="l271"
+               class="code sev- "><tt><i>271</i>     <span class="n">dna_averages</span><span class="p">(</span></tt>
+            </div>
+            <div id="l272"
+               class="code sev- "><tt><i>272</i>         <span class="n">input_ser_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l273"
+               class="code sev- "><tt><i>273</i>         <span class="n">output_csv_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l274"
+               class="code sev- "><tt><i>274</i>         <span class="n">output_jpg_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l275"
+               class="code sev- "><tt><i>275</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l276"
+               class="code sev- "><tt><i>276</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l277"
+               class="code sev- "><tt><i>277</i> &nbsp;</tt>
+            </div>
+            <div id="l278"
+               class="code sev- "><tt><i>278</i> &nbsp;</tt>
+            </div>
+            <div id="l279"
+               class="code sev- "><tt><i>279</i> <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span></tt>
+            </div>
+            <div id="l280"
+               class="code sev- "><tt><i>280</i>     <span class="n">main</span><span class="p">()</span></tt>
+            </div>
+            
+         </div>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/biobb_dna.dna.dna_timeseries.report.html b/flake8/biobb_dna.dna.dna_timeseries.report.html
new file mode 100644
index 00000000..9c998414
--- /dev/null
+++ b/flake8/biobb_dna.dna.dna_timeseries.report.html
@@ -0,0 +1,73 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>flake8 violations: biobb_dna/dna/dna_timeseries.py</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+<script>
+function bindHandler(link) {
+   var code = link.getAttribute('data-code');
+   var key = location.pathname + '#' + code;
+
+   var ul = link.parentNode.querySelector('.details');
+   if (sessionStorage[key] != 'open') {
+      ul.style.display = 'none';
+   }
+   link.addEventListener('click', function (event) {
+      if (!ul.style.display || ul.style.display == 'none') {
+         ul.style.display = 'block';
+         sessionStorage[key] = 'open';
+      } else {
+         ul.style.display = 'none';
+         sessionStorage[key] = 'closed';
+      }
+   });
+}
+
+window.addEventListener('DOMContentLoaded', function () {
+   var links = document.querySelectorAll('#index > li > a');
+   for (var i = 0; i < links.length; i++) {
+      bindHandler(links[i]);
+   }
+});
+</script>
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <p id="srclink">
+            <a title="View full annotated source"
+               href="biobb_dna.dna.dna_timeseries.source.html">
+               <img src="file.svg" alt="&#x2261;">
+            </a></p>
+         <h1>
+            <a href="index.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/dna/dna_timeseries.py
+            </a>
+         </h1>
+
+         <ul id="index">
+         
+         <li>
+            <a data-code="E225">
+               <span class="count sev-2">
+                  1
+               </span>
+               <strong>E225:</strong> missing whitespace around operator
+               
+            </a>
+            <ul class="details">
+            <li>
+               
+               <a href="biobb_dna.dna.dna_timeseries.source.html#l235">
+                  <tt><i>235</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">)&quot;</span></tt>
+               </a>
+            </li>
+            </ul>
+         </li>
+         
+         </ul>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/biobb_dna.dna.dna_timeseries.source.html b/flake8/biobb_dna.dna.dna_timeseries.source.html
new file mode 100644
index 00000000..66a429ea
--- /dev/null
+++ b/flake8/biobb_dna.dna.dna_timeseries.source.html
@@ -0,0 +1,1037 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>biobb_dna/dna/dna_timeseries.py - flake8 annotated source</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <h1>
+            <a href="biobb_dna.dna.dna_timeseries.report.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/dna/dna_timeseries.py source
+            </a>
+         </h1>
+
+         <div id="doc">
+            <div id="l1"
+               class="code sev- "><tt><i>1</i> <span class="ch">#!/usr/bin/env python3</span></tt>
+            </div>
+            <div id="l2"
+               class="code sev- "><tt><i>2</i> &nbsp;</tt>
+            </div>
+            <div id="l3"
+               class="code sev- "><tt><i>3</i> <span class="sd">&quot;&quot;&quot;Module containing the HelParTimeSeries class and the command line interface.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l4"
+               class="code sev- "><tt><i>4</i> &nbsp;</tt>
+            </div>
+            <div id="l5"
+               class="code sev- "><tt><i>5</i> <span class="kn">import</span><span class="w"> </span><span class="nn">argparse</span></tt>
+            </div>
+            <div id="l6"
+               class="code sev- "><tt><i>6</i> <span class="kn">import</span><span class="w"> </span><span class="nn">re</span></tt>
+            </div>
+            <div id="l7"
+               class="code sev- "><tt><i>7</i> <span class="kn">import</span><span class="w"> </span><span class="nn">zipfile</span></tt>
+            </div>
+            <div id="l8"
+               class="code sev- "><tt><i>8</i> <span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span></tt>
+            </div>
+            <div id="l9"
+               class="code sev- "><tt><i>9</i> <span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Optional</span></tt>
+            </div>
+            <div id="l10"
+               class="code sev- "><tt><i>10</i> &nbsp;</tt>
+            </div>
+            <div id="l11"
+               class="code sev- "><tt><i>11</i> <span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span></tt>
+            </div>
+            <div id="l12"
+               class="code sev- "><tt><i>12</i> <span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span></tt>
+            </div>
+            <div id="l13"
+               class="code sev- "><tt><i>13</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_common.configuration</span><span class="w"> </span><span class="kn">import</span> <span class="n">settings</span></tt>
+            </div>
+            <div id="l14"
+               class="code sev- "><tt><i>14</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_common.generic.biobb_object</span><span class="w"> </span><span class="kn">import</span> <span class="n">BiobbObject</span></tt>
+            </div>
+            <div id="l15"
+               class="code sev- "><tt><i>15</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_common.tools</span><span class="w"> </span><span class="kn">import</span> <span class="n">file_utils</span> <span class="k">as</span> <span class="n">fu</span></tt>
+            </div>
+            <div id="l16"
+               class="code sev- "><tt><i>16</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_common.tools.file_utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">launchlogger</span></tt>
+            </div>
+            <div id="l17"
+               class="code sev- "><tt><i>17</i> &nbsp;</tt>
+            </div>
+            <div id="l18"
+               class="code sev- "><tt><i>18</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_dna.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">constants</span></tt>
+            </div>
+            <div id="l19"
+               class="code sev- "><tt><i>19</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_dna.utils.common</span><span class="w"> </span><span class="kn">import</span> <span class="n">_from_string_to_list</span></tt>
+            </div>
+            <div id="l20"
+               class="code sev- "><tt><i>20</i> <span class="kn">from</span><span class="w"> </span><span class="nn">biobb_dna.utils.loader</span><span class="w"> </span><span class="kn">import</span> <span class="n">read_series</span></tt>
+            </div>
+            <div id="l21"
+               class="code sev- "><tt><i>21</i> &nbsp;</tt>
+            </div>
+            <div id="l22"
+               class="code sev- "><tt><i>22</i> &nbsp;</tt>
+            </div>
+            <div id="l23"
+               class="code sev- "><tt><i>23</i> <span class="k">class</span><span class="w"> </span><span class="nc">HelParTimeSeries</span><span class="p">(</span><span class="n">BiobbObject</span><span class="p">):</span></tt>
+            </div>
+            <div id="l24"
+               class="code sev- "><tt><i>24</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l25"
+               class="code sev- "><tt><i>25</i> <span class="sd">    | biobb_dna HelParTimeSeries</span></tt>
+            </div>
+            <div id="l26"
+               class="code sev- "><tt><i>26</i> <span class="sd">    | Created time series and histogram plots for each base pair from a helical parameter series file.</span></tt>
+            </div>
+            <div id="l27"
+               class="code sev- "><tt><i>27</i> <span class="sd">    | The helical parameter series file is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair.</span></tt>
+            </div>
+            <div id="l28"
+               class="code sev- "><tt><i>28</i> &nbsp;</tt>
+            </div>
+            <div id="l29"
+               class="code sev- "><tt><i>29</i> <span class="sd">    Args:</span></tt>
+            </div>
+            <div id="l30"
+               class="code sev- "><tt><i>30</i> <span class="sd">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l31"
+               class="code sev- "><tt><i>31</i> <span class="sd">        output_zip_path (str): Path to output .zip files where data is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/timeseries_output.zip&gt;`_. Accepted formats: zip (edam:format_3987).</span></tt>
+            </div>
+            <div id="l32"
+               class="code sev- "><tt><i>32</i> <span class="sd">        properties (dict):</span></tt>
+            </div>
+            <div id="l33"
+               class="code sev- "><tt><i>33</i> <span class="sd">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *usecols* option).</span></tt>
+            </div>
+            <div id="l34"
+               class="code sev- "><tt><i>34</i> <span class="sd">            * **bins** (*int*) - (None) Bins for histogram. Parameter has same options as matplotlib.pyplot.hist.</span></tt>
+            </div>
+            <div id="l35"
+               class="code sev- "><tt><i>35</i> <span class="sd">            * **helpar_name** (*str*) - (None) Helical parameter name. It must match the name of the helical parameter in the .ser input file. Values: majd, majw, mind, minw, inclin, tip, xdisp, ydisp, shear, stretch, stagger, buckle, propel, opening, rise, roll, twist, shift, slide, tilt, alphaC, alphaW, betaC, betaW, gammaC, gammaW, deltaC, deltaW, epsilC, epsilW, zetaC, zetaW, chiC, chiW, phaseC, phaseW.</span></tt>
+            </div>
+            <div id="l36"
+               class="code sev- "><tt><i>36</i> <span class="sd">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span></tt>
+            </div>
+            <div id="l37"
+               class="code sev- "><tt><i>37</i> <span class="sd">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 1) to analyze.  If not specified it will analyse the complete sequence.</span></tt>
+            </div>
+            <div id="l38"
+               class="code sev- "><tt><i>38</i> <span class="sd">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span></tt>
+            </div>
+            <div id="l39"
+               class="code sev- "><tt><i>39</i> <span class="sd">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span></tt>
+            </div>
+            <div id="l40"
+               class="code sev- "><tt><i>40</i> <span class="sd">            * **sandbox_path** (*str*) - (&quot;./&quot;) [WF property] Parent path to the sandbox directory.</span></tt>
+            </div>
+            <div id="l41"
+               class="code sev- "><tt><i>41</i> &nbsp;</tt>
+            </div>
+            <div id="l42"
+               class="code sev- "><tt><i>42</i> <span class="sd">    Examples:</span></tt>
+            </div>
+            <div id="l43"
+               class="code sev- "><tt><i>43</i> <span class="sd">        This is a use example of how to use the building block from Python::</span></tt>
+            </div>
+            <div id="l44"
+               class="code sev- "><tt><i>44</i> &nbsp;</tt>
+            </div>
+            <div id="l45"
+               class="code sev- "><tt><i>45</i> <span class="sd">            from biobb_dna.dna.dna_timeseries import dna_timeseries</span></tt>
+            </div>
+            <div id="l46"
+               class="code sev- "><tt><i>46</i> &nbsp;</tt>
+            </div>
+            <div id="l47"
+               class="code sev- "><tt><i>47</i> <span class="sd">            prop = {</span></tt>
+            </div>
+            <div id="l48"
+               class="code sev- "><tt><i>48</i> <span class="sd">                &#39;helpar_name&#39;: &#39;twist&#39;,</span></tt>
+            </div>
+            <div id="l49"
+               class="code sev- "><tt><i>49</i> <span class="sd">                &#39;seqpos&#39;: [1,2,3,4,5],</span></tt>
+            </div>
+            <div id="l50"
+               class="code sev- "><tt><i>50</i> <span class="sd">                &#39;sequence&#39;: &#39;GCAACGTGCTATGGAAGC&#39;,</span></tt>
+            </div>
+            <div id="l51"
+               class="code sev- "><tt><i>51</i> <span class="sd">            }</span></tt>
+            </div>
+            <div id="l52"
+               class="code sev- "><tt><i>52</i> <span class="sd">            dna_timeseries(</span></tt>
+            </div>
+            <div id="l53"
+               class="code sev- "><tt><i>53</i> <span class="sd">                input_ser_path=&#39;/path/to/twist.ser&#39;,</span></tt>
+            </div>
+            <div id="l54"
+               class="code sev- "><tt><i>54</i> <span class="sd">                output_zip_path=&#39;/path/to/output/file.zip&#39;</span></tt>
+            </div>
+            <div id="l55"
+               class="code sev- "><tt><i>55</i> <span class="sd">                properties=prop)</span></tt>
+            </div>
+            <div id="l56"
+               class="code sev- "><tt><i>56</i> <span class="sd">    Info:</span></tt>
+            </div>
+            <div id="l57"
+               class="code sev- "><tt><i>57</i> <span class="sd">        * wrapped_software:</span></tt>
+            </div>
+            <div id="l58"
+               class="code sev- "><tt><i>58</i> <span class="sd">            * name: In house</span></tt>
+            </div>
+            <div id="l59"
+               class="code sev- "><tt><i>59</i> <span class="sd">            * license: Apache-2.0</span></tt>
+            </div>
+            <div id="l60"
+               class="code sev- "><tt><i>60</i> <span class="sd">        * ontology:</span></tt>
+            </div>
+            <div id="l61"
+               class="code sev- "><tt><i>61</i> <span class="sd">            * name: EDAM</span></tt>
+            </div>
+            <div id="l62"
+               class="code sev- "><tt><i>62</i> <span class="sd">            * schema: http://edamontology.org/EDAM.owl</span></tt>
+            </div>
+            <div id="l63"
+               class="code sev- "><tt><i>63</i> &nbsp;</tt>
+            </div>
+            <div id="l64"
+               class="code sev- "><tt><i>64</i> <span class="sd">    &quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l65"
+               class="code sev- "><tt><i>65</i> &nbsp;</tt>
+            </div>
+            <div id="l66"
+               class="code sev- "><tt><i>66</i>     <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span></tt>
+            </div>
+            <div id="l67"
+               class="code sev- "><tt><i>67</i>         <span class="bp">self</span><span class="p">,</span> <span class="n">input_ser_path</span><span class="p">,</span> <span class="n">output_zip_path</span><span class="p">,</span> <span class="n">properties</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span></tt>
+            </div>
+            <div id="l68"
+               class="code sev- "><tt><i>68</i>     <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l69"
+               class="code sev- "><tt><i>69</i>         <span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span> <span class="ow">or</span> <span class="p">{}</span></tt>
+            </div>
+            <div id="l70"
+               class="code sev- "><tt><i>70</i> &nbsp;</tt>
+            </div>
+            <div id="l71"
+               class="code sev- "><tt><i>71</i>         <span class="c1"># Call parent class constructor</span></tt>
+            </div>
+            <div id="l72"
+               class="code sev- "><tt><i>72</i>         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l73"
+               class="code sev- "><tt><i>73</i>         <span class="bp">self</span><span class="o">.</span><span class="n">locals_var_dict</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l74"
+               class="code sev- "><tt><i>74</i> &nbsp;</tt>
+            </div>
+            <div id="l75"
+               class="code sev- "><tt><i>75</i>         <span class="c1"># Input/Output files</span></tt>
+            </div>
+            <div id="l76"
+               class="code sev- "><tt><i>76</i>         <span class="bp">self</span><span class="o">.</span><span class="n">io_dict</span> <span class="o">=</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l77"
+               class="code sev- "><tt><i>77</i>             <span class="s2">&quot;in&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l78"
+               class="code sev- "><tt><i>78</i>                 <span class="s2">&quot;input_ser_path&quot;</span><span class="p">:</span> <span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l79"
+               class="code sev- "><tt><i>79</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l80"
+               class="code sev- "><tt><i>80</i>             <span class="s2">&quot;out&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;output_zip_path&quot;</span><span class="p">:</span> <span class="n">output_zip_path</span><span class="p">},</span></tt>
+            </div>
+            <div id="l81"
+               class="code sev- "><tt><i>81</i>         <span class="p">}</span></tt>
+            </div>
+            <div id="l82"
+               class="code sev- "><tt><i>82</i> &nbsp;</tt>
+            </div>
+            <div id="l83"
+               class="code sev- "><tt><i>83</i>         <span class="bp">self</span><span class="o">.</span><span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span></tt>
+            </div>
+            <div id="l84"
+               class="code sev- "><tt><i>84</i>         <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;sequence&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l85"
+               class="code sev- "><tt><i>85</i>         <span class="bp">self</span><span class="o">.</span><span class="n">bins</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;bins&quot;</span><span class="p">,</span> <span class="s2">&quot;auto&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l86"
+               class="code sev- "><tt><i>86</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stride</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;stride&quot;</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span></tt>
+            </div>
+            <div id="l87"
+               class="code sev- "><tt><i>87</i>         <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l88"
+               class="code sev- "><tt><i>88</i>             <span class="nb">int</span><span class="p">(</span><span class="n">elem</span><span class="p">)</span> <span class="k">for</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">_from_string_to_list</span><span class="p">(</span><span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;seqpos&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span></tt>
+            </div>
+            <div id="l89"
+               class="code sev- "><tt><i>89</i>         <span class="p">]</span></tt>
+            </div>
+            <div id="l90"
+               class="code sev- "><tt><i>90</i>         <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;helpar_name&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l91"
+               class="code sev- "><tt><i>91</i> &nbsp;</tt>
+            </div>
+            <div id="l92"
+               class="code sev- "><tt><i>92</i>         <span class="c1"># get helical parameter from filename if not specified</span></tt>
+            </div>
+            <div id="l93"
+               class="code sev- "><tt><i>93</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l94"
+               class="code sev- "><tt><i>94</i>             <span class="k">for</span> <span class="n">hp</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="p">:</span></tt>
+            </div>
+            <div id="l95"
+               class="code sev- "><tt><i>95</i>                 <span class="k">if</span> <span class="n">hp</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">Path</span><span class="p">(</span><span class="n">input_ser_path</span><span class="p">)</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span></tt>
+            </div>
+            <div id="l96"
+               class="code sev- "><tt><i>96</i>                     <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="o">=</span> <span class="n">hp</span></tt>
+            </div>
+            <div id="l97"
+               class="code sev- "><tt><i>97</i>             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l98"
+               class="code sev- "><tt><i>98</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l99"
+               class="code sev- "><tt><i>99</i>                     <span class="s2">&quot;Helical parameter name can&#39;t be inferred from file, &quot;</span></tt>
+            </div>
+            <div id="l100"
+               class="code sev- "><tt><i>100</i>                     <span class="s2">&quot;so it must be specified!&quot;</span></tt>
+            </div>
+            <div id="l101"
+               class="code sev- "><tt><i>101</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l102"
+               class="code sev- "><tt><i>102</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l103"
+               class="code sev- "><tt><i>103</i>             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="p">:</span></tt>
+            </div>
+            <div id="l104"
+               class="code sev- "><tt><i>104</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l105"
+               class="code sev- "><tt><i>105</i>                     <span class="s2">&quot;Helical parameter name is invalid! &quot;</span></tt>
+            </div>
+            <div id="l106"
+               class="code sev- "><tt><i>106</i>                     <span class="sa">f</span><span class="s2">&quot;Options: </span><span class="si">{</span><span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l107"
+               class="code sev- "><tt><i>107</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l108"
+               class="code sev- "><tt><i>108</i> &nbsp;</tt>
+            </div>
+            <div id="l109"
+               class="code sev- "><tt><i>109</i>         <span class="c1"># get base length from helical parameter name</span></tt>
+            </div>
+            <div id="l110"
+               class="code sev- "><tt><i>110</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_singlebases</span><span class="p">:</span></tt>
+            </div>
+            <div id="l111"
+               class="code sev- "><tt><i>111</i>             <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span> <span class="o">=</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l112"
+               class="code sev- "><tt><i>112</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l113"
+               class="code sev- "><tt><i>113</i>             <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span> <span class="o">=</span> <span class="mi">1</span></tt>
+            </div>
+            <div id="l114"
+               class="code sev- "><tt><i>114</i>         <span class="c1"># get unit from helical parameter name</span></tt>
+            </div>
+            <div id="l115"
+               class="code sev- "><tt><i>115</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span><span class="p">:</span></tt>
+            </div>
+            <div id="l116"
+               class="code sev- "><tt><i>116</i>             <span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span> <span class="o">=</span> <span class="s2">&quot;Degrees&quot;</span></tt>
+            </div>
+            <div id="l117"
+               class="code sev- "><tt><i>117</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l118"
+               class="code sev- "><tt><i>118</i>             <span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span> <span class="o">=</span> <span class="s2">&quot;Angstroms&quot;</span></tt>
+            </div>
+            <div id="l119"
+               class="code sev- "><tt><i>119</i> &nbsp;</tt>
+            </div>
+            <div id="l120"
+               class="code sev- "><tt><i>120</i>         <span class="c1"># Check the properties</span></tt>
+            </div>
+            <div id="l121"
+               class="code sev- "><tt><i>121</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_properties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l122"
+               class="code sev- "><tt><i>122</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">()</span></tt>
+            </div>
+            <div id="l123"
+               class="code sev- "><tt><i>123</i> &nbsp;</tt>
+            </div>
+            <div id="l124"
+               class="code sev- "><tt><i>124</i>     <span class="nd">@launchlogger</span></tt>
+            </div>
+            <div id="l125"
+               class="code sev- "><tt><i>125</i>     <span class="k">def</span><span class="w"> </span><span class="nf">launch</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l126"
+               class="code sev- "><tt><i>126</i> <span class="w">        </span><span class="sd">&quot;&quot;&quot;Execute the :class:`HelParTimeSeries &lt;dna.dna_timeseries.HelParTimeSeries&gt;` object.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l127"
+               class="code sev- "><tt><i>127</i> &nbsp;</tt>
+            </div>
+            <div id="l128"
+               class="code sev- "><tt><i>128</i>         <span class="c1"># Setup Biobb</span></tt>
+            </div>
+            <div id="l129"
+               class="code sev- "><tt><i>129</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_restart</span><span class="p">():</span></tt>
+            </div>
+            <div id="l130"
+               class="code sev- "><tt><i>130</i>             <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l131"
+               class="code sev- "><tt><i>131</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stage_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l132"
+               class="code sev- "><tt><i>132</i> &nbsp;</tt>
+            </div>
+            <div id="l133"
+               class="code sev- "><tt><i>133</i>         <span class="c1"># check sequence</span></tt>
+            </div>
+            <div id="l134"
+               class="code sev- "><tt><i>134</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span></tt>
+            </div>
+            <div id="l135"
+               class="code sev- "><tt><i>135</i>             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;sequence is null or too short!&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l136"
+               class="code sev- "><tt><i>136</i> &nbsp;</tt>
+            </div>
+            <div id="l137"
+               class="code sev- "><tt><i>137</i>         <span class="c1"># calculate cols with 0 index</span></tt>
+            </div>
+            <div id="l138"
+               class="code sev- "><tt><i>138</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l139"
+               class="code sev- "><tt><i>139</i>             <span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">]</span></tt>
+            </div>
+            <div id="l140"
+               class="code sev- "><tt><i>140</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l141"
+               class="code sev- "><tt><i>141</i>             <span class="n">cols</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)))</span></tt>
+            </div>
+            <div id="l142"
+               class="code sev- "><tt><i>142</i> &nbsp;</tt>
+            </div>
+            <div id="l143"
+               class="code sev- "><tt><i>143</i>         <span class="c1"># sort cols in ascending order</span></tt>
+            </div>
+            <div id="l144"
+               class="code sev- "><tt><i>144</i>         <span class="n">cols</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span></tt>
+            </div>
+            <div id="l145"
+               class="code sev- "><tt><i>145</i> &nbsp;</tt>
+            </div>
+            <div id="l146"
+               class="code sev- "><tt><i>146</i>         <span class="c1"># check seqpos for base pairs</span></tt>
+            </div>
+            <div id="l147"
+               class="code sev- "><tt><i>147</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_basepairs</span><span class="p">:</span></tt>
+            </div>
+            <div id="l148"
+               class="code sev- "><tt><i>148</i>             <span class="k">if</span> <span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">):</span></tt>
+            </div>
+            <div id="l149"
+               class="code sev- "><tt><i>149</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l150"
+               class="code sev- "><tt><i>150</i>                     <span class="sa">f</span><span class="s2">&quot;seqpos values must be between 1 and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">1</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l151"
+               class="code sev- "><tt><i>151</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l152"
+               class="code sev- "><tt><i>152</i>             <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l153"
+               class="code sev- "><tt><i>153</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;seqpos must be a list of at least two integers&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l154"
+               class="code sev- "><tt><i>154</i>         <span class="c1"># check seqpos for non base pairs</span></tt>
+            </div>
+            <div id="l155"
+               class="code sev- "><tt><i>155</i>         <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_basepairs</span><span class="p">:</span></tt>
+            </div>
+            <div id="l156"
+               class="code sev- "><tt><i>156</i>             <span class="k">if</span> <span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">):</span></tt>
+            </div>
+            <div id="l157"
+               class="code sev- "><tt><i>157</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l158"
+               class="code sev- "><tt><i>158</i>                     <span class="sa">f</span><span class="s2">&quot;seqpos values must be between 1 and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l159"
+               class="code sev- "><tt><i>159</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l160"
+               class="code sev- "><tt><i>160</i>             <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l161"
+               class="code sev- "><tt><i>161</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;seqpos must be a list of at least two integers&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l162"
+               class="code sev- "><tt><i>162</i> &nbsp;</tt>
+            </div>
+            <div id="l163"
+               class="code sev- "><tt><i>163</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_basepairs</span><span class="p">:</span></tt>
+            </div>
+            <div id="l164"
+               class="code sev- "><tt><i>164</i>             <span class="c1"># remove first and last base pairs from cols if they match 0 and len(sequence)</span></tt>
+            </div>
+            <div id="l165"
+               class="code sev- "><tt><i>165</i>             <span class="k">if</span> <span class="nb">min</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span></tt>
+            </div>
+            <div id="l166"
+               class="code sev- "><tt><i>166</i>                 <span class="n">cols</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span></tt>
+            </div>
+            <div id="l167"
+               class="code sev- "><tt><i>167</i>             <span class="k">if</span> <span class="nb">max</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span></tt>
+            </div>
+            <div id="l168"
+               class="code sev- "><tt><i>168</i>                 <span class="n">cols</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span></tt>
+            </div>
+            <div id="l169"
+               class="code sev- "><tt><i>169</i> &nbsp;</tt>
+            </div>
+            <div id="l170"
+               class="code sev- "><tt><i>170</i>             <span class="c1"># discard first and last base(pairs) from sequence</span></tt>
+            </div>
+            <div id="l171"
+               class="code sev- "><tt><i>171</i>             <span class="n">sequence</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span></tt>
+            </div>
+            <div id="l172"
+               class="code sev- "><tt><i>172</i>             <span class="c1"># create indices list</span></tt>
+            </div>
+            <div id="l173"
+               class="code sev- "><tt><i>173</i>             <span class="n">indices</span> <span class="o">=</span> <span class="n">cols</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l174"
+               class="code sev- "><tt><i>174</i>             <span class="c1"># create subunits list from cols</span></tt>
+            </div>
+            <div id="l175"
+               class="code sev- "><tt><i>175</i>             <span class="n">subunits</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">]</span></tt>
+            </div>
+            <div id="l176"
+               class="code sev- "><tt><i>176</i>             <span class="c1"># clean subunits (leave only basepairs)</span></tt>
+            </div>
+            <div id="l177"
+               class="code sev- "><tt><i>177</i>             <span class="n">pattern</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;\d+_[A-Za-z]</span><span class="si">{2}</span><span class="s2">&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l178"
+               class="code sev- "><tt><i>178</i>             <span class="c1"># get removed items</span></tt>
+            </div>
+            <div id="l179"
+               class="code sev- "><tt><i>179</i>             <span class="n">removed_items</span> <span class="o">=</span> <span class="p">[</span><span class="n">s</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">subunits</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">pattern</span><span class="o">.</span><span class="n">fullmatch</span><span class="p">(</span><span class="n">s</span><span class="p">)]</span></tt>
+            </div>
+            <div id="l180"
+               class="code sev- "><tt><i>180</i>             <span class="c1"># get indices of removed items (in integer format and starting from 0)</span></tt>
+            </div>
+            <div id="l181"
+               class="code sev- "><tt><i>181</i>             <span class="n">removed_numbers</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l182"
+               class="code sev- "><tt><i>182</i>                 <span class="nb">int</span><span class="p">(</span><span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">())</span></tt>
+            </div>
+            <div id="l183"
+               class="code sev- "><tt><i>183</i>                 <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">removed_items</span></tt>
+            </div>
+            <div id="l184"
+               class="code sev- "><tt><i>184</i>                 <span class="k">if</span> <span class="p">(</span><span class="n">match</span> <span class="o">:=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;\d+&quot;</span><span class="p">,</span> <span class="n">item</span><span class="p">))</span></tt>
+            </div>
+            <div id="l185"
+               class="code sev- "><tt><i>185</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l186"
+               class="code sev- "><tt><i>186</i>             <span class="n">removed_numbers</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">removed_numbers</span><span class="p">))</span></tt>
+            </div>
+            <div id="l187"
+               class="code sev- "><tt><i>187</i>             <span class="n">removed_numbers</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">removed_numbers</span><span class="p">]</span></tt>
+            </div>
+            <div id="l188"
+               class="code sev- "><tt><i>188</i>             <span class="c1"># remove non basepairs from subunits and indices</span></tt>
+            </div>
+            <div id="l189"
+               class="code sev- "><tt><i>189</i>             <span class="n">subunits</span> <span class="o">=</span> <span class="p">[</span><span class="n">s</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">subunits</span> <span class="k">if</span> <span class="n">pattern</span><span class="o">.</span><span class="n">fullmatch</span><span class="p">(</span><span class="n">s</span><span class="p">)]</span></tt>
+            </div>
+            <div id="l190"
+               class="code sev- "><tt><i>190</i>             <span class="n">indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">indices</span> <span class="k">if</span> <span class="n">i</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">removed_numbers</span><span class="p">]</span></tt>
+            </div>
+            <div id="l191"
+               class="code sev- "><tt><i>191</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l192"
+               class="code sev- "><tt><i>192</i>             <span class="n">sequence</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span></tt>
+            </div>
+            <div id="l193"
+               class="code sev- "><tt><i>193</i>             <span class="c1"># create indices list</span></tt>
+            </div>
+            <div id="l194"
+               class="code sev- "><tt><i>194</i>             <span class="n">indices</span> <span class="o">=</span> <span class="n">cols</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l195"
+               class="code sev- "><tt><i>195</i>             <span class="c1"># trick for getting the index column from the .ser file</span></tt>
+            </div>
+            <div id="l196"
+               class="code sev- "><tt><i>196</i>             <span class="n">indices</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span></tt>
+            </div>
+            <div id="l197"
+               class="code sev- "><tt><i>197</i>             <span class="c1"># create subunits list from cols</span></tt>
+            </div>
+            <div id="l198"
+               class="code sev- "><tt><i>198</i>             <span class="n">subunits</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">]</span></tt>
+            </div>
+            <div id="l199"
+               class="code sev- "><tt><i>199</i> &nbsp;</tt>
+            </div>
+            <div id="l200"
+               class="code sev- "><tt><i>200</i>         <span class="c1"># read input .ser file</span></tt>
+            </div>
+            <div id="l201"
+               class="code sev- "><tt><i>201</i>         <span class="n">ser_data</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l202"
+               class="code sev- "><tt><i>202</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_ser_path&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="n">indices</span></tt>
+            </div>
+            <div id="l203"
+               class="code sev- "><tt><i>203</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l204"
+               class="code sev- "><tt><i>204</i> &nbsp;</tt>
+            </div>
+            <div id="l205"
+               class="code sev- "><tt><i>205</i>         <span class="c1"># get columns for selected bases</span></tt>
+            </div>
+            <div id="l206"
+               class="code sev- "><tt><i>206</i>         <span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">subunits</span></tt>
+            </div>
+            <div id="l207"
+               class="code sev- "><tt><i>207</i> &nbsp;</tt>
+            </div>
+            <div id="l208"
+               class="code sev- "><tt><i>208</i>         <span class="c1"># write output files for all selected bases (one per column)</span></tt>
+            </div>
+            <div id="l209"
+               class="code sev- "><tt><i>209</i>         <span class="n">zf</span> <span class="o">=</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_zip_path&quot;</span><span class="p">]),</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l210"
+               class="code sev- "><tt><i>210</i>         <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span></tt>
+            </div>
+            <div id="l211"
+               class="code sev- "><tt><i>211</i>             <span class="c1"># unstack columns to prevent errors from repeated base pairs</span></tt>
+            </div>
+            <div id="l212"
+               class="code sev- "><tt><i>212</i>             <span class="n">column_data</span> <span class="o">=</span> <span class="n">ser_data</span><span class="p">[[</span><span class="n">col</span><span class="p">]]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l213"
+               class="code sev- "><tt><i>213</i>             <span class="n">column_data</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">col</span></tt>
+            </div>
+            <div id="l214"
+               class="code sev- "><tt><i>214</i>             <span class="n">fu</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Computing base number </span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">...&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l215"
+               class="code sev- "><tt><i>215</i> &nbsp;</tt>
+            </div>
+            <div id="l216"
+               class="code sev- "><tt><i>216</i>             <span class="c1"># column series</span></tt>
+            </div>
+            <div id="l217"
+               class="code sev- "><tt><i>217</i>             <span class="n">series_colfn</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;series_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l218"
+               class="code sev- "><tt><i>218</i>             <span class="n">column_data</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span></tt>
+            </div>
+            <div id="l219"
+               class="code sev- "><tt><i>219</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span></tt>
+            </div>
+            <div id="l220"
+               class="code sev- "><tt><i>220</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l221"
+               class="code sev- "><tt><i>221</i>             <span class="c1"># save table</span></tt>
+            </div>
+            <div id="l222"
+               class="code sev- "><tt><i>222</i>             <span class="n">zf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span></tt>
+            </div>
+            <div id="l223"
+               class="code sev- "><tt><i>223</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l224"
+               class="code sev- "><tt><i>224</i>                 <span class="n">arcname</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l225"
+               class="code sev- "><tt><i>225</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l226"
+               class="code sev- "><tt><i>226</i> &nbsp;</tt>
+            </div>
+            <div id="l227"
+               class="code sev- "><tt><i>227</i>             <span class="n">fig</span><span class="p">,</span> <span class="n">axs</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">tight_layout</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l228"
+               class="code sev- "><tt><i>228</i>             <span class="n">reduced_data</span> <span class="o">=</span> <span class="n">column_data</span><span class="o">.</span><span class="n">iloc</span><span class="p">[::</span> <span class="bp">self</span><span class="o">.</span><span class="n">stride</span><span class="p">]</span></tt>
+            </div>
+            <div id="l229"
+               class="code sev- "><tt><i>229</i>             <span class="n">axs</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">reduced_data</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">reduced_data</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">())</span></tt>
+            </div>
+            <div id="l230"
+               class="code sev- "><tt><i>230</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;Time (Snapshots)&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l231"
+               class="code sev- "><tt><i>231</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2"> (</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span><span class="si">}</span><span class="s2">)&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l232"
+               class="code sev- "><tt><i>232</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span></tt>
+            </div>
+            <div id="l233"
+               class="code sev- "><tt><i>233</i>                 <span class="sa">f</span><span class="s2">&quot;Helical Parameter vs Time: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2"> &quot;</span></tt>
+            </div>
+            <div id="l234"
+               class="code sev- "><tt><i>234</i>                 <span class="s2">&quot;(base pair &quot;</span></tt>
+            </div>
+            <div id="l235"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        E225
+                     </span>
+                     Missing whitespace around operator</li>
+               
+               </ul><tt><i>235</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">)&quot;</span></tt>
+            </div>
+            <div id="l236"
+               class="code sev- "><tt><i>236</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l237"
+               class="code sev- "><tt><i>237</i>             <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span></tt>
+            </div>
+            <div id="l238"
+               class="code sev- "><tt><i>238</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l239"
+               class="code sev- "><tt><i>239</i>                 <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l240"
+               class="code sev- "><tt><i>240</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l241"
+               class="code sev- "><tt><i>241</i>             <span class="c1"># save plot</span></tt>
+            </div>
+            <div id="l242"
+               class="code sev- "><tt><i>242</i>             <span class="n">zf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span></tt>
+            </div>
+            <div id="l243"
+               class="code sev- "><tt><i>243</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l244"
+               class="code sev- "><tt><i>244</i>                 <span class="n">arcname</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l245"
+               class="code sev- "><tt><i>245</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l246"
+               class="code sev- "><tt><i>246</i>             <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l247"
+               class="code sev- "><tt><i>247</i> &nbsp;</tt>
+            </div>
+            <div id="l248"
+               class="code sev- "><tt><i>248</i>             <span class="c1"># columns histogram</span></tt>
+            </div>
+            <div id="l249"
+               class="code sev- "><tt><i>249</i>             <span class="n">hist_colfn</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;hist_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l250"
+               class="code sev- "><tt><i>250</i>             <span class="n">fig</span><span class="p">,</span> <span class="n">axs</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">tight_layout</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l251"
+               class="code sev- "><tt><i>251</i>             <span class="n">ybins</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">axs</span><span class="o">.</span><span class="n">hist</span><span class="p">(</span><span class="n">column_data</span><span class="p">,</span> <span class="n">bins</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">bins</span><span class="p">)</span></tt>
+            </div>
+            <div id="l252"
+               class="code sev- "><tt><i>252</i>             <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="p">:</span> <span class="n">x</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="s2">&quot;density&quot;</span><span class="p">:</span> <span class="n">ybins</span><span class="p">})</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span></tt>
+            </div>
+            <div id="l253"
+               class="code sev- "><tt><i>253</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l254"
+               class="code sev- "><tt><i>254</i>                 <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span></tt>
+            </div>
+            <div id="l255"
+               class="code sev- "><tt><i>255</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l256"
+               class="code sev- "><tt><i>256</i>             <span class="c1"># save table</span></tt>
+            </div>
+            <div id="l257"
+               class="code sev- "><tt><i>257</i>             <span class="n">zf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span></tt>
+            </div>
+            <div id="l258"
+               class="code sev- "><tt><i>258</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l259"
+               class="code sev- "><tt><i>259</i>                 <span class="n">arcname</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l260"
+               class="code sev- "><tt><i>260</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l261"
+               class="code sev- "><tt><i>261</i> &nbsp;</tt>
+            </div>
+            <div id="l262"
+               class="code sev- "><tt><i>262</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;Density&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l263"
+               class="code sev- "><tt><i>263</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2"> (</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span><span class="si">}</span><span class="s2">)&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l264"
+               class="code sev- "><tt><i>264</i>             <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span></tt>
+            </div>
+            <div id="l265"
+               class="code sev- "><tt><i>265</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l266"
+               class="code sev- "><tt><i>266</i>                 <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l267"
+               class="code sev- "><tt><i>267</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l268"
+               class="code sev- "><tt><i>268</i>             <span class="c1"># save plot</span></tt>
+            </div>
+            <div id="l269"
+               class="code sev- "><tt><i>269</i>             <span class="n">zf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span></tt>
+            </div>
+            <div id="l270"
+               class="code sev- "><tt><i>270</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l271"
+               class="code sev- "><tt><i>271</i>                 <span class="n">arcname</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l272"
+               class="code sev- "><tt><i>272</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l273"
+               class="code sev- "><tt><i>273</i>             <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l274"
+               class="code sev- "><tt><i>274</i>         <span class="n">zf</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l275"
+               class="code sev- "><tt><i>275</i> &nbsp;</tt>
+            </div>
+            <div id="l276"
+               class="code sev- "><tt><i>276</i>         <span class="c1"># Copy files to host</span></tt>
+            </div>
+            <div id="l277"
+               class="code sev- "><tt><i>277</i>         <span class="bp">self</span><span class="o">.</span><span class="n">copy_to_host</span><span class="p">()</span></tt>
+            </div>
+            <div id="l278"
+               class="code sev- "><tt><i>278</i> &nbsp;</tt>
+            </div>
+            <div id="l279"
+               class="code sev- "><tt><i>279</i>         <span class="c1"># Remove temporary file(s)</span></tt>
+            </div>
+            <div id="l280"
+               class="code sev- "><tt><i>280</i>         <span class="bp">self</span><span class="o">.</span><span class="n">tmp_files</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">)])</span></tt>
+            </div>
+            <div id="l281"
+               class="code sev- "><tt><i>281</i>         <span class="bp">self</span><span class="o">.</span><span class="n">remove_tmp_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l282"
+               class="code sev- "><tt><i>282</i> &nbsp;</tt>
+            </div>
+            <div id="l283"
+               class="code sev- "><tt><i>283</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">(</span><span class="n">output_files_created</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">raise_exception</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></tt>
+            </div>
+            <div id="l284"
+               class="code sev- "><tt><i>284</i> &nbsp;</tt>
+            </div>
+            <div id="l285"
+               class="code sev- "><tt><i>285</i>         <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l286"
+               class="code sev- "><tt><i>286</i> &nbsp;</tt>
+            </div>
+            <div id="l287"
+               class="code sev- "><tt><i>287</i> &nbsp;</tt>
+            </div>
+            <div id="l288"
+               class="code sev- "><tt><i>288</i> <span class="k">def</span><span class="w"> </span><span class="nf">dna_timeseries</span><span class="p">(</span></tt>
+            </div>
+            <div id="l289"
+               class="code sev- "><tt><i>289</i>     <span class="n">input_ser_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l290"
+               class="code sev- "><tt><i>290</i>     <span class="n">output_zip_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l291"
+               class="code sev- "><tt><i>291</i>     <span class="n">properties</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l292"
+               class="code sev- "><tt><i>292</i>     <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l293"
+               class="code sev- "><tt><i>293</i> <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l294"
+               class="code sev- "><tt><i>294</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Create :class:`HelParTimeSeries &lt;dna.dna_timeseries.HelParTimeSeries&gt;` class and</span></tt>
+            </div>
+            <div id="l295"
+               class="code sev- "><tt><i>295</i> <span class="sd">    execute the :meth:`launch() &lt;dna.dna_timeseries.HelParTimeSeries.launch&gt;` method.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l296"
+               class="code sev- "><tt><i>296</i> &nbsp;</tt>
+            </div>
+            <div id="l297"
+               class="code sev- "><tt><i>297</i>     <span class="k">return</span> <span class="n">HelParTimeSeries</span><span class="p">(</span></tt>
+            </div>
+            <div id="l298"
+               class="code sev- "><tt><i>298</i>         <span class="n">input_ser_path</span><span class="o">=</span><span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l299"
+               class="code sev- "><tt><i>299</i>         <span class="n">output_zip_path</span><span class="o">=</span><span class="n">output_zip_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l300"
+               class="code sev- "><tt><i>300</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l301"
+               class="code sev- "><tt><i>301</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l302"
+               class="code sev- "><tt><i>302</i>     <span class="p">)</span><span class="o">.</span><span class="n">launch</span><span class="p">()</span></tt>
+            </div>
+            <div id="l303"
+               class="code sev- "><tt><i>303</i> &nbsp;</tt>
+            </div>
+            <div id="l304"
+               class="code sev- "><tt><i>304</i> &nbsp;</tt>
+            </div>
+            <div id="l305"
+               class="code sev- "><tt><i>305</i> <span class="k">def</span><span class="w"> </span><span class="nf">main</span><span class="p">():</span></tt>
+            </div>
+            <div id="l306"
+               class="code sev- "><tt><i>306</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Command line execution of this building block. Please check the command line documentation.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l307"
+               class="code sev- "><tt><i>307</i>     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span></tt>
+            </div>
+            <div id="l308"
+               class="code sev- "><tt><i>308</i>         <span class="n">description</span><span class="o">=</span><span class="s2">&quot;Created time series and histogram plots for each base pair from a helical parameter series file.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l309"
+               class="code sev- "><tt><i>309</i>         <span class="n">formatter_class</span><span class="o">=</span><span class="k">lambda</span> <span class="n">prog</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">RawTextHelpFormatter</span><span class="p">(</span><span class="n">prog</span><span class="p">,</span> <span class="n">width</span><span class="o">=</span><span class="mi">99999</span><span class="p">),</span></tt>
+            </div>
+            <div id="l310"
+               class="code sev- "><tt><i>310</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l311"
+               class="code sev- "><tt><i>311</i>     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">&quot;--config&quot;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Configuration file&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l312"
+               class="code sev- "><tt><i>312</i> &nbsp;</tt>
+            </div>
+            <div id="l313"
+               class="code sev- "><tt><i>313</i>     <span class="n">required_args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s2">&quot;required arguments&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l314"
+               class="code sev- "><tt><i>314</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l315"
+               class="code sev- "><tt><i>315</i>         <span class="s2">&quot;--input_ser_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l316"
+               class="code sev- "><tt><i>316</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l317"
+               class="code sev- "><tt><i>317</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Helical parameter input ser file path. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l318"
+               class="code sev- "><tt><i>318</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l319"
+               class="code sev- "><tt><i>319</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l320"
+               class="code sev- "><tt><i>320</i>         <span class="s2">&quot;--output_zip_path&quot;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output directory.&quot;</span></tt>
+            </div>
+            <div id="l321"
+               class="code sev- "><tt><i>321</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l322"
+               class="code sev- "><tt><i>322</i> &nbsp;</tt>
+            </div>
+            <div id="l323"
+               class="code sev- "><tt><i>323</i>     <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></tt>
+            </div>
+            <div id="l324"
+               class="code sev- "><tt><i>324</i>     <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="ow">or</span> <span class="s2">&quot;</span><span class="si">{}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l325"
+               class="code sev- "><tt><i>325</i>     <span class="n">properties</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">ConfReader</span><span class="p">(</span><span class="n">config</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">config</span><span class="p">)</span><span class="o">.</span><span class="n">get_prop_dic</span><span class="p">()</span></tt>
+            </div>
+            <div id="l326"
+               class="code sev- "><tt><i>326</i> &nbsp;</tt>
+            </div>
+            <div id="l327"
+               class="code sev- "><tt><i>327</i>     <span class="n">dna_timeseries</span><span class="p">(</span></tt>
+            </div>
+            <div id="l328"
+               class="code sev- "><tt><i>328</i>         <span class="n">input_ser_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l329"
+               class="code sev- "><tt><i>329</i>         <span class="n">output_zip_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_zip_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l330"
+               class="code sev- "><tt><i>330</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l331"
+               class="code sev- "><tt><i>331</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l332"
+               class="code sev- "><tt><i>332</i> &nbsp;</tt>
+            </div>
+            <div id="l333"
+               class="code sev- "><tt><i>333</i> &nbsp;</tt>
+            </div>
+            <div id="l334"
+               class="code sev- "><tt><i>334</i> <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span></tt>
+            </div>
+            <div id="l335"
+               class="code sev- "><tt><i>335</i>     <span class="n">main</span><span class="p">()</span></tt>
+            </div>
+            
+         </div>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/flake8badge.svg b/flake8/flake8badge.svg
index 58d58174..55710d42 100644
--- a/flake8/flake8badge.svg
+++ b/flake8/flake8badge.svg
@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="128" height="20" role="img" aria-label="Flake8: 0 C, 0 W, 0 I"><title>Flake8: 0 C, 0 W, 0 I</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="128" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="47" height="20" fill="#555"/><rect x="47" width="81" height="20" fill="#4c1"/><rect width="128" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="245" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="370">Flake8</text><text x="245" y="140" transform="scale(.1)" fill="#fff" textLength="370">Flake8</text><text aria-hidden="true" x="865" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="710">0 C, 0 W, 0 I</text><text x="865" y="140" transform="scale(.1)" fill="#fff" textLength="710">0 C, 0 W, 0 I</text></g></svg>
\ No newline at end of file
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="128" height="20" role="img" aria-label="Flake8: 0 C, 4 W, 0 I"><title>Flake8: 0 C, 4 W, 0 I</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="128" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="47" height="20" fill="#555"/><rect x="47" width="81" height="20" fill="#fe7d37"/><rect width="128" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="245" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="370">Flake8</text><text x="245" y="140" transform="scale(.1)" fill="#fff" textLength="370">Flake8</text><text aria-hidden="true" x="865" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="710">0 C, 4 W, 0 I</text><text x="865" y="140" transform="scale(.1)" fill="#fff" textLength="710">0 C, 4 W, 0 I</text></g></svg>
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diff --git a/flake8/flake8stats.txt b/flake8/flake8stats.txt
index e69de29b..485dc39c 100644
--- a/flake8/flake8stats.txt
+++ b/flake8/flake8stats.txt
@@ -0,0 +1 @@
+4     E225 missing whitespace around operator
diff --git a/flake8/index.html b/flake8/index.html
index 72ffb954..f85061bd 100644
--- a/flake8/index.html
+++ b/flake8/index.html
@@ -6,22 +6,30 @@
       <link rel="stylesheet" href="styles.css">
    </head>
    <body>
-      <div id="masthead" class="sev-4"></div>
+      <div id="masthead" class="sev-2"></div>
       <div id="page">
           <h1>flake8 violations</h1>
-         <p id="versions">Generated on 2025-01-21 16:19
+         <p id="versions">Generated on 2025-01-21 16:20
             with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.12.1, pyflakes: 3.2.0
          </p>
          <ul id="index">
          
          <li>
-            <div id="all-good">
-               <span class="count sev-4">
-                  <span class="tick">&#x2713;</span>
+            <a href="biobb_dna.dna.dna_averages.report.html">
+               <span class="count sev-2">
+                  3
                </span>
-               <h2>All good!</h2>
-               <p>No flake8 errors found in 46 files scanned.</p>
-            </div>
+               biobb_dna/dna/dna_averages.py
+            </a>
+         </li>
+         
+         <li>
+            <a href="biobb_dna.dna.dna_timeseries.report.html">
+               <span class="count sev-2">
+                  1
+               </span>
+               biobb_dna/dna/dna_timeseries.py
+            </a>
          </li>
          
          </ul>
diff --git a/junit/junit.xml b/junit/junit.xml
index f281ff09..0ae1d8d9 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="19" time="27.919" timestamp="2025-01-21T16:19:56.927906+00:00" hostname="biobb-runners"><testcase classname="biobb_dna.test.unitests.test_backbone.test_bipopulations.TestBIPopulations" name="test_bipopulations" time="0.519" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_canonical_alpha_gamma.TestCanonicalAlphaGamma" name="test_canonicalag" time="0.470" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_puckering.TestPuckering" name="test_puckering" time="0.574" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterHelparCorrelation" name="test_helparcorrelation" time="0.613" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterSequenceCorrelation" name="test_sequencecorrelation" time="0.380" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterBasepairCorrelation" name="test_basepaircorrelation" time="0.988" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraHelparCorrelation" name="test_helparcorrelation" time="0.282" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraSequenceCorrelation" name="test_sequencecorrelation" time="0.370" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraBasepairCorrelation" name="test_basepaircorrelation" time="0.853" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal.TestCanal" name="test_canal" time="7.311" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal_unzip.TestCanalUnzip" name="test_canal_unzip" time="0.087" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canion.TestCanal" name="test_canion" time="0.357" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_curves.TestCurves" name="test_curves" time="6.822" /><testcase classname="biobb_dna.test.unitests.test_dna.test_averages.TestAverages" name="test_helparaverages" time="0.231" /><testcase classname="biobb_dna.test.unitests.test_dna.test_bimodality.TestBimodality" name="test_helparbimodality" time="0.505" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries.TestTimeSeries" name="test_helpartimeseries" time="4.729" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries_unzip.TestCanalUnzip" name="test_dna_timeseries_unzip" time="0.082" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestAvgStiffness" name="test_averagestiffness" time="0.245" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestBasePairStiffness" name="test_basepairstiffness" time="0.259" /></testsuite></testsuites>
\ No newline at end of file
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="19" time="69.403" timestamp="2025-01-21T16:20:35.323447+00:00" hostname="github-actions.vm.mmb.pcb.ub.es"><testcase classname="biobb_dna.test.unitests.test_backbone.test_bipopulations.TestBIPopulations" name="test_bipopulations" time="1.440" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_canonical_alpha_gamma.TestCanonicalAlphaGamma" name="test_canonicalag" time="1.350" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_puckering.TestPuckering" name="test_puckering" time="1.617" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterHelparCorrelation" name="test_helparcorrelation" time="0.721" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterSequenceCorrelation" name="test_sequencecorrelation" time="0.955" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterBasepairCorrelation" name="test_basepaircorrelation" time="2.240" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraHelparCorrelation" name="test_helparcorrelation" time="0.710" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraSequenceCorrelation" name="test_sequencecorrelation" time="0.951" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraBasepairCorrelation" name="test_basepaircorrelation" time="2.284" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal.TestCanal" name="test_canal" time="17.279" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal_unzip.TestCanalUnzip" name="test_canal_unzip" time="0.208" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canion.TestCanal" name="test_canion" time="1.264" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_curves.TestCurves" name="test_curves" time="15.322" /><testcase classname="biobb_dna.test.unitests.test_dna.test_averages.TestAverages" name="test_helparaverages" time="0.679" /><testcase classname="biobb_dna.test.unitests.test_dna.test_bimodality.TestBimodality" name="test_helparbimodality" time="1.101" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries.TestTimeSeries" name="test_helpartimeseries" time="11.861" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries_unzip.TestCanalUnzip" name="test_dna_timeseries_unzip" time="0.178" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestAvgStiffness" name="test_averagestiffness" time="0.614" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestBasePairStiffness" name="test_basepairstiffness" time="0.651" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index 5532737b..12ffd4b7 100644
--- a/junit/report.html
+++ b/junit/report.html
@@ -7,7 +7,7 @@
   </head>
   <body>
     <h1 id="title">report.html</h1>
-    <p>Report generated on 21-Jan-2025 at 16:20:24 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 21-Jan-2025 at 16:21:44 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
         v4.1.1</p>
     <div id="environment-header">
       <h2>Environment</h2>
@@ -61,7 +61,7 @@ <h2>Environment</h2>
         <h2>Summary</h2>
         <div class="additional-summary prefix">
         </div>
-        <p class="run-count">19 tests took 00:00:26.</p>
+        <p class="run-count">19 tests took 00:01:01.</p>
         <p class="filter">(Un)check the boxes to filter the results.</p>
         <div class="summary__reload">
           <div class="summary__reload__button hidden" onclick="location.reload()">
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.11.11&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-204-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.4&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&#34;, &#34;duration&#34;: &#34;519 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;519 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nseqpos::::::::\n[]\n2025-01-21 16:19:58,859 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.bipopulations Version: 5.0.1\n2025-01-21 16:19:58,860 [MainThread  ] [INFO ]  /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e directory successfully created\n2025-01-21 16:19:58,861 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e\n2025-01-21 16:19:58,862 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e\n2025-01-21 16:19:58,862 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e\n2025-01-21 16:19:58,863 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e\n2025-01-21 16:19:59,284 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e&amp;#x27;]\n2025-01-21 16:19:59,284 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_12/bipopulations/bipop.csv\nChecking if empty file: /tmp/biobb/unitests_12/bipopulations/bipop.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_12/bipopulations/bipop.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/bipop_ref.jpg\n     IMAGE_A HASH: ff8981818181c9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8981818180c9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 1 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_12/bipopulations/bipopulations_log.out:file_utils.py:409 Module: biobb_dna.backbone.bipopulations Version: 5.0.1\nINFO     /tmp/biobb/unitests_12/bipopulations/bipopulations_log.out:file_utils.py:82 /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e directory successfully created\nINFO     /tmp/biobb/unitests_12/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e\nINFO     /tmp/biobb/unitests_12/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e\nINFO     /tmp/biobb/unitests_12/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e\nINFO     /tmp/biobb/unitests_12/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e\nINFO     /tmp/biobb/unitests_12/bipopulations/bipopulations_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_12/bipopulations/sandbox_15853096-7a51-44b8-bd41-cba225d92d5e&amp;#x27;]\nINFO     /tmp/biobb/unitests_12/bipopulations/bipopulations_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;, &#34;duration&#34;: &#34;470 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;470 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:19:59,388 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.canonicalag Version: 5.0.1\n2025-01-21 16:19:59,388 [MainThread  ] [INFO ]  /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2 directory successfully created\n2025-01-21 16:19:59,389 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2\n2025-01-21 16:19:59,390 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2\n2025-01-21 16:19:59,391 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2\n2025-01-21 16:19:59,392 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2\n2025-01-21 16:19:59,774 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_13/canonicalag/canonag.csv\nChecking if empty file: /tmp/biobb/unitests_13/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_13/canonicalag/canonag.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/canonag_ref.jpg\n     IMAGE_A HASH: ff8081818180f9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8081818180f9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/canonicalag/canonicalag_log.out:file_utils.py:409 Module: biobb_dna.backbone.canonicalag Version: 5.0.1\nINFO     /tmp/biobb/unitests_13/canonicalag/canonicalag_log.out:file_utils.py:82 /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2 directory successfully created\nINFO     /tmp/biobb/unitests_13/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2\nINFO     /tmp/biobb/unitests_13/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2\nINFO     /tmp/biobb/unitests_13/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2\nINFO     /tmp/biobb/unitests_13/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2\nINFO     /tmp/biobb/unitests_13/canonicalag/canonicalag_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_13/canonicalag/sandbox_d28f2c55-9437-4149-862c-d405a1379fe2&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;, &#34;duration&#34;: &#34;574 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;574 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:19:59,860 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.puckering Version: 5.0.1\n2025-01-21 16:19:59,860 [MainThread  ] [INFO ]  /tmp/biobb/unitests_13/puckering/sandbox_641279b5-1855-44c8-8e03-e4cc091e8ba9 directory successfully created\n2025-01-21 16:19:59,861 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_13/puckering/sandbox_641279b5-1855-44c8-8e03-e4cc091e8ba9\n2025-01-21 16:19:59,862 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_13/puckering/sandbox_641279b5-1855-44c8-8e03-e4cc091e8ba9\n2025-01-21 16:20:00,351 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/puckering/sandbox_641279b5-1855-44c8-8e03-e4cc091e8ba9&amp;#x27;]\n2025-01-21 16:20:00,351 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_13/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_13/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_13/puckering/puckering.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/puckering_ref.jpg\n     IMAGE_A HASH: eb8181808081ffff SIZE: 64 bits\n     IMAGE_B HASH: eb8181808081ffff SIZE: 64 bits\n     TOLERANCE: 20%, ABS TOLERANCE: 12.8 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/puckering/puckering_log.out:file_utils.py:409 Module: biobb_dna.backbone.puckering Version: 5.0.1\nINFO     /tmp/biobb/unitests_13/puckering/puckering_log.out:file_utils.py:82 /tmp/biobb/unitests_13/puckering/sandbox_641279b5-1855-44c8-8e03-e4cc091e8ba9 directory successfully created\nINFO     /tmp/biobb/unitests_13/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_13/puckering/sandbox_641279b5-1855-44c8-8e03-e4cc091e8ba9\nINFO     /tmp/biobb/unitests_13/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_13/puckering/sandbox_641279b5-1855-44c8-8e03-e4cc091e8ba9\nINFO     /tmp/biobb/unitests_13/puckering/puckering_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_13/puckering/sandbox_641279b5-1855-44c8-8e03-e4cc091e8ba9&amp;#x27;]\nINFO     /tmp/biobb/unitests_13/puckering/puckering_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;613 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;613 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:00,759 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.1\n2025-01-21 16:20:00,759 [MainThread  ] [INFO ]  /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89 directory successfully created\n2025-01-21 16:20:00,760 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\n2025-01-21 16:20:00,760 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\n2025-01-21 16:20:00,760 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\n2025-01-21 16:20:00,761 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\n2025-01-21 16:20:00,761 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\n2025-01-21 16:20:00,761 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\n2025-01-21 16:20:00,967 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89&amp;#x27;]\n2025-01-21 16:20:00,968 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_13/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_13/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_13/interhpcorr/inter_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_hpcorr_ref.jpg\n     IMAGE_A HASH: ff83868890a1c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83868890a1c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89 directory successfully created\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_13/interhpcorr/sandbox_4ff241eb-b7ae-45f9-a6e7-71cf7a8a5e89&amp;#x27;]\nINFO     /tmp/biobb/unitests_13/interhpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;380 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;380 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:01,049 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.1\n2025-01-21 16:20:01,049 [MainThread  ] [INFO ]  /tmp/biobb/unitests_13/interseqcorr/sandbox_f6b88bc7-a462-4983-97a7-19d49c0040b6 directory successfully created\n2025-01-21 16:20:01,050 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_13/interseqcorr/sandbox_f6b88bc7-a462-4983-97a7-19d49c0040b6\n2025-01-21 16:20:01,345 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/interseqcorr/sandbox_f6b88bc7-a462-4983-97a7-19d49c0040b6&amp;#x27;]\n2025-01-21 16:20:01,346 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_13/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_13/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_13/interseqcorr/inter_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_seqcorr_roll.jpg\n     IMAGE_A HASH: ff8080889080c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff8080889080c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/interseqcorr/interseqcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_13/interseqcorr/interseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_13/interseqcorr/sandbox_f6b88bc7-a462-4983-97a7-19d49c0040b6 directory successfully created\nINFO     /tmp/biobb/unitests_13/interseqcorr/interseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_13/interseqcorr/sandbox_f6b88bc7-a462-4983-97a7-19d49c0040b6\nINFO     /tmp/biobb/unitests_13/interseqcorr/interseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_13/interseqcorr/sandbox_f6b88bc7-a462-4983-97a7-19d49c0040b6&amp;#x27;]\nINFO     /tmp/biobb/unitests_13/interseqcorr/interseqcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;988 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;988 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:01,432 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.1\n2025-01-21 16:20:01,433 [MainThread  ] [INFO ]  /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81 directory successfully created\n2025-01-21 16:20:01,433 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\n2025-01-21 16:20:01,434 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\n2025-01-21 16:20:01,435 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\n2025-01-21 16:20:01,436 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\n2025-01-21 16:20:01,437 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\n2025-01-21 16:20:01,437 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\n2025-01-21 16:20:02,329 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81&amp;#x27;]\n2025-01-21 16:20:02,329 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_13/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_13/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_13/interbpcorr/inter_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_bpcorr_ref.jpg\n     IMAGE_A HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     IMAGE_B HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81 directory successfully created\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_13/interbpcorr/sandbox_e7022ec2-9780-48d8-8d64-eb12e3db7e81&amp;#x27;]\nINFO     /tmp/biobb/unitests_13/interbpcorr/interbpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;282 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;282 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:02,422 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.1\n2025-01-21 16:20:02,422 [MainThread  ] [INFO ]  /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d directory successfully created\n2025-01-21 16:20:02,423 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\n2025-01-21 16:20:02,423 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\n2025-01-21 16:20:02,423 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\n2025-01-21 16:20:02,423 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\n2025-01-21 16:20:02,424 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\n2025-01-21 16:20:02,424 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\n2025-01-21 16:20:02,623 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d&amp;#x27;]\n2025-01-21 16:20:02,624 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_13/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_13/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_13/intrahpcorr/intra_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_hpcorr_ref.jpg\n     IMAGE_A HASH: fb81848890a0e0ff SIZE: 64 bits\n     IMAGE_B HASH: fb81848890a0e0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d directory successfully created\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_13/intrahpcorr/sandbox_e814df77-bba4-4698-bd49-cbad2bfa669d&amp;#x27;]\nINFO     /tmp/biobb/unitests_13/intrahpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_13\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;370 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;370 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:02,706 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.1\n2025-01-21 16:20:02,706 [MainThread  ] [INFO ]  /tmp/biobb/unitests_13/intraseqcorr/sandbox_2b11ad32-2d1e-44e0-9811-f2ae6054edb9 directory successfully created\n2025-01-21 16:20:02,707 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_13/intraseqcorr/sandbox_2b11ad32-2d1e-44e0-9811-f2ae6054edb9\n2025-01-21 16:20:02,992 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_13/intraseqcorr/sandbox_2b11ad32-2d1e-44e0-9811-f2ae6054edb9&amp;#x27;]\n2025-01-21 16:20:02,992 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_13/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_13/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_13/intraseqcorr/intra_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.jpg\n     IMAGE_A HASH: ff83848890a0c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83848890a0c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_13/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_13/intraseqcorr/intraseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_13/intraseqcorr/sandbox_2b11ad32-2d1e-44e0-9811-f2ae6054edb9 directory successfully created\nINFO     /tmp/biobb/unitests_13/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_13/intraseqcorr/sandbox_2b11ad32-2d1e-44e0-9811-f2ae6054edb9\nINFO     /tmp/biobb/unitests_13/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_13/intraseqcorr/sandbox_2b11ad32-2d1e-44e0-9811-f2ae6054edb9&amp;#x27;]\nINFO     /tmp/biobb/unitests_13/intraseqcorr/intraseqcorr_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;853 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;853 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:03,077 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.1\n2025-01-21 16:20:03,078 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7 directory successfully created\n2025-01-21 16:20:03,078 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\n2025-01-21 16:20:03,079 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\n2025-01-21 16:20:03,080 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\n2025-01-21 16:20:03,081 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\n2025-01-21 16:20:03,081 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\n2025-01-21 16:20:03,082 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\n2025-01-21 16:20:03,843 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7&amp;#x27;]\n2025-01-21 16:20:03,843 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_14/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_14/intrabpcorr/intra_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_bpcorr_ref.jpg\n     IMAGE_A HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     IMAGE_B HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7 directory successfully created\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/intrabpcorr/sandbox_48394129-4524-42aa-84bc-62da421081c7&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/intrabpcorr/intrabpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:03,932 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.1\n2025-01-21 16:20:03,932 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/biobb_canal/sandbox_5e9dc292-98d8-44ad-88a5-424593317e57 directory successfully created\n2025-01-21 16:20:03,943 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_14/biobb_canal/sandbox_5e9dc292-98d8-44ad-88a5-424593317e57\n2025-01-21 16:20:03,943 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2025-01-21 16:20:03,943 [MainThread  ] [INFO ]  Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\n2025-01-21 16:20:11,033 [MainThread  ] [INFO ]  Executing: Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd...\n2025-01-21 16:20:11,033 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 16:20:11,194 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/biobb_canal/sandbox_5e9dc292-98d8-44ad-88a5-424593317e57&amp;#x27;]\n2025-01-21 16:20:11,195 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/biobb_canal/biobb_canal_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/biobb_canal/biobb_canal_log.out:file_utils.py:82 /tmp/biobb/unitests_14/biobb_canal/sandbox_5e9dc292-98d8-44ad-88a5-424593317e57 directory successfully created\nINFO     /tmp/biobb/unitests_14/biobb_canal/biobb_canal_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_14/biobb_canal/sandbox_5e9dc292-98d8-44ad-88a5-424593317e57\nINFO     /tmp/biobb/unitests_14/biobb_canal/biobb_canal_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_14/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:63 Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\nINFO     /tmp/biobb/unitests_14/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:36 Executing: Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd...\nINFO     /tmp/biobb/unitests_14/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_14/biobb_canal/biobb_canal_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/biobb_canal/sandbox_5e9dc292-98d8-44ad-88a5-424593317e57&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/biobb_canal/biobb_canal_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;, &#34;duration&#34;: &#34;87 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;87 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:11,251 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.1\n2025-01-21 16:20:11,251 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/canal_unzip/sandbox_b6884c72-b8b9-49bb-a857-73f990286f18 directory successfully created\n2025-01-21 16:20:11,284 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_14/canal_unzip/sandbox_b6884c72-b8b9-49bb-a857-73f990286f18\n2025-01-21 16:20:11,287 [MainThread  ] [INFO ]  canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_14/canal_unzip/sandbox_b6884c72-b8b9-49bb-a857-73f990286f18/canal_unzip_output.ser.\n2025-01-21 16:20:11,292 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/canal_unzip/sandbox_b6884c72-b8b9-49bb-a857-73f990286f18&amp;#x27;]\n2025-01-21 16:20:11,292 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/canal_unzip/canal_unzip_output.ser\nChecking if empty file: /tmp/biobb/unitests_14/canal_unzip/canal_unzip_output.txt\nComparing: \n        File_A: /tmp/biobb/unitests_14/canal_unzip/canal_unzip_output.ser\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.ser\n        File_A hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_14/canal_unzip/canal_unzip_output.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.txt\n        File_A hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n        File_B hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/canal_unzip/canal_unzip_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/canal_unzip/canal_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_14/canal_unzip/sandbox_b6884c72-b8b9-49bb-a857-73f990286f18 directory successfully created\nINFO     /tmp/biobb/unitests_14/canal_unzip/canal_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_14/canal_unzip/sandbox_b6884c72-b8b9-49bb-a857-73f990286f18\nINFO     /tmp/biobb/unitests_14/canal_unzip/canal_unzip_log.out:file_utils.py:409 canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_14/canal_unzip/sandbox_b6884c72-b8b9-49bb-a857-73f990286f18/canal_unzip_output.ser.\nINFO     /tmp/biobb/unitests_14/canal_unzip/canal_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/canal_unzip/sandbox_b6884c72-b8b9-49bb-a857-73f990286f18&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/canal_unzip/canal_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;, &#34;duration&#34;: &#34;357 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;357 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:11,341 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.1\n2025-01-21 16:20:11,341 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2 directory successfully created\n2025-01-21 16:20:11,604 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2\n2025-01-21 16:20:11,604 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2\n2025-01-21 16:20:11,604 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2\n2025-01-21 16:20:11,605 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2025-01-21 16:20:11,605 [MainThread  ] [INFO ]  Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\n2025-01-21 16:20:11,609 [MainThread  ] [INFO ]  Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\n2025-01-21 16:20:11,609 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 16:20:11,651 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2&amp;#x27;]\n2025-01-21 16:20:11,652 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:file_utils.py:82 /tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2 directory successfully created\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:63 Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:36 Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/biobb_canion/sandbox_314b896f-63cc-4572-ae5a-262711b3eae2&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/biobb_canion/biobb_canion_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:11,699 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.1\n2025-01-21 16:20:11,699 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/biobb_curves/sandbox_ae344278-b8ba-4e3f-bfe8-63fde7dc7e25 directory successfully created\n2025-01-21 16:20:11,760 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_14/biobb_curves/sandbox_ae344278-b8ba-4e3f-bfe8-63fde7dc7e25\n2025-01-21 16:20:11,760 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_14/biobb_curves/sandbox_ae344278-b8ba-4e3f-bfe8-63fde7dc7e25\n2025-01-21 16:20:11,761 [MainThread  ] [INFO ]  Appending provided topology to command\n2025-01-21 16:20:11,762 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2025-01-21 16:20:11,762 [MainThread  ] [INFO ]  Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=.curvesplus/standard,\n  ions=.t.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\n2025-01-21 16:20:18,385 [MainThread  ] [INFO ]  Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\n2025-01-21 16:20:18,386 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 16:20:18,424 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/biobb_curves/sandbox_ae344278-b8ba-4e3f-bfe8-63fde7dc7e25&amp;#x27;]\n2025-01-21 16:20:18,425 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_14/biobb_curves/curves_output.lis\nChecking if empty file: /tmp/biobb/unitests_14/biobb_curves/curves_output.zip\nComparing ignoring lines containing this words: [2]\n     FILE_A: /tmp/biobb/unitests_14/biobb_curves/curves_output.lis\n     FILE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.lis\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_14/biobb_curves/curves_output.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.zip\nComparing: \n        File_A: e4bb0b12-7e37-4716-ba06-458cc5cdd921/curves_output.cdi\n        File_B: 36cf3dfb-6fec-45ef-a2b8-d09f998fe136/curves_output.cdi\n        File_A hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n        File_B hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:file_utils.py:82 /tmp/biobb/unitests_14/biobb_curves/sandbox_ae344278-b8ba-4e3f-bfe8-63fde7dc7e25 directory successfully created\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_14/biobb_curves/sandbox_ae344278-b8ba-4e3f-bfe8-63fde7dc7e25\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_14/biobb_curves/sandbox_ae344278-b8ba-4e3f-bfe8-63fde7dc7e25\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:file_utils.py:409 Appending provided topology to command\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:63 Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=.curvesplus/standard,\n  ions=.t.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:36 Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/biobb_curves/sandbox_ae344278-b8ba-4e3f-bfe8-63fde7dc7e25&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/biobb_curves/biobb_curves_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;, &#34;duration&#34;: &#34;231 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;231 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:18,521 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_averages Version: 5.0.1\n2025-01-21 16:20:18,521 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/dna_averages/sandbox_8139e43c-89c8-4436-b89f-25eeff6e6902 directory successfully created\n2025-01-21 16:20:18,522 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_14/dna_averages/sandbox_8139e43c-89c8-4436-b89f-25eeff6e6902\n2025-01-21 16:20:18,676 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/dna_averages/sandbox_8139e43c-89c8-4436-b89f-25eeff6e6902&amp;#x27;]\n2025-01-21 16:20:18,677 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_14/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_14/dna_averages/avg_out.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/shift_avg.jpg\n     IMAGE_A HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     IMAGE_B HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/dna_averages/dna_averages_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_averages Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/dna_averages/dna_averages_log.out:file_utils.py:82 /tmp/biobb/unitests_14/dna_averages/sandbox_8139e43c-89c8-4436-b89f-25eeff6e6902 directory successfully created\nINFO     /tmp/biobb/unitests_14/dna_averages/dna_averages_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_14/dna_averages/sandbox_8139e43c-89c8-4436-b89f-25eeff6e6902\nINFO     /tmp/biobb/unitests_14/dna_averages/dna_averages_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/dna_averages/sandbox_8139e43c-89c8-4436-b89f-25eeff6e6902&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/dna_averages/dna_averages_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;, &#34;duration&#34;: &#34;505 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;505 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:18,753 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_bimodality Version: 5.0.1\n2025-01-21 16:20:18,754 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/dna_bimodality/sandbox_e0c2f105-ccf5-4f40-8360-cc0f4bfd4f80 directory successfully created\n2025-01-21 16:20:18,754 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_14/dna_bimodality/sandbox_e0c2f105-ccf5-4f40-8360-cc0f4bfd4f80\n2025-01-21 16:20:19,215 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/dna_bimodality/sandbox_e0c2f105-ccf5-4f40-8360-cc0f4bfd4f80&amp;#x27;]\n2025-01-21 16:20:19,215 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_14/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_bimodality Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/dna_bimodality/dna_bimodality_log.out:file_utils.py:82 /tmp/biobb/unitests_14/dna_bimodality/sandbox_e0c2f105-ccf5-4f40-8360-cc0f4bfd4f80 directory successfully created\nINFO     /tmp/biobb/unitests_14/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_14/dna_bimodality/sandbox_e0c2f105-ccf5-4f40-8360-cc0f4bfd4f80\nINFO     /tmp/biobb/unitests_14/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/dna_bimodality/sandbox_e0c2f105-ccf5-4f40-8360-cc0f4bfd4f80&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/dna_bimodality/dna_bimodality_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:19,263 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries Version: 5.0.1\n2025-01-21 16:20:19,263 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/dna_timeseries/sandbox_e23d1cf1-fab0-4059-82b5-a13180453718 directory successfully created\n2025-01-21 16:20:19,264 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_14/dna_timeseries/sandbox_e23d1cf1-fab0-4059-82b5-a13180453718\n2025-01-21 16:20:23,945 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/dna_timeseries/sandbox_e23d1cf1-fab0-4059-82b5-a13180453718&amp;#x27;]\n2025-01-21 16:20:23,945 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/dna_timeseries/dna_timeseries_log.out:file_utils.py:82 /tmp/biobb/unitests_14/dna_timeseries/sandbox_e23d1cf1-fab0-4059-82b5-a13180453718 directory successfully created\nINFO     /tmp/biobb/unitests_14/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_14/dna_timeseries/sandbox_e23d1cf1-fab0-4059-82b5-a13180453718\nINFO     /tmp/biobb/unitests_14/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/dna_timeseries/sandbox_e23d1cf1-fab0-4059-82b5-a13180453718&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/dna_timeseries/dna_timeseries_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;, &#34;duration&#34;: &#34;82 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;82 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:23,993 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.1\n2025-01-21 16:20:23,993 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b directory successfully created\n2025-01-21 16:20:23,994 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b\n2025-01-21 16:20:23,994 [MainThread  ] [INFO ]  hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b/dna_timeseries_unzip.csv.\n2025-01-21 16:20:23,995 [MainThread  ] [INFO ]  hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b/dna_timeseries_unzip.jpg.\n2025-01-21 16:20:23,996 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b&amp;#x27;]\n2025-01-21 16:20:23,996 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip.csv\nChecking if empty file: /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip.jpg\nChecking if empty file: /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip.txt\nComparing: \n        File_A: /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip.csv\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.csv\n        File_A hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.txt\n        File_A hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.jpg\n     IMAGE_A HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     IMAGE_B HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b directory successfully created\nINFO     /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b\nINFO     /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b/dna_timeseries_unzip.csv.\nINFO     /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b/dna_timeseries_unzip.jpg.\nINFO     /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/dna_timeseries_unzip/sandbox_223a7806-a1b3-4e76-868d-5f8563c1b84b&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;, &#34;duration&#34;: &#34;245 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;245 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:24,073 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.average_stiffness Version: 5.0.1\n2025-01-21 16:20:24,074 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/average_stiffness/sandbox_fc83ed01-1a7c-4f4f-90c9-477aaae875fc directory successfully created\n2025-01-21 16:20:24,074 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_14/average_stiffness/sandbox_fc83ed01-1a7c-4f4f-90c9-477aaae875fc\n2025-01-21 16:20:24,242 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_14/average_stiffness/sandbox_fc83ed01-1a7c-4f4f-90c9-477aaae875fc&amp;#x27;]\n2025-01-21 16:20:24,242 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_14/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_14/average_stiffness/avgstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffavg_roll.jpg\n     IMAGE_A HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     IMAGE_B HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/average_stiffness/average_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.average_stiffness Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/average_stiffness/average_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_14/average_stiffness/sandbox_fc83ed01-1a7c-4f4f-90c9-477aaae875fc directory successfully created\nINFO     /tmp/biobb/unitests_14/average_stiffness/average_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_14/average_stiffness/sandbox_fc83ed01-1a7c-4f4f-90c9-477aaae875fc\nINFO     /tmp/biobb/unitests_14/average_stiffness/average_stiffness_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_14/average_stiffness/sandbox_fc83ed01-1a7c-4f4f-90c9-477aaae875fc&amp;#x27;]\nINFO     /tmp/biobb/unitests_14/average_stiffness/average_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;, &#34;duration&#34;: &#34;259 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;259 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:24,321 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.1\n2025-01-21 16:20:24,321 [MainThread  ] [INFO ]  /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1 directory successfully created\n2025-01-21 16:20:24,321 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\n2025-01-21 16:20:24,322 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\n2025-01-21 16:20:24,322 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\n2025-01-21 16:20:24,322 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\n2025-01-21 16:20:24,322 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\n2025-01-21 16:20:24,323 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\n2025-01-21 16:20:24,503 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_14/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_14/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_14/basepair_stiffness/bpstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffbp_ref.jpg\n     IMAGE_A HASH: ff8080909080ffff SIZE: 64 bits\n     IMAGE_B HASH: ff8080909080ffff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_14/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.1\nINFO     /tmp/biobb/unitests_14/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1 directory successfully created\nINFO     /tmp/biobb/unitests_14/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\nINFO     /tmp/biobb/unitests_14/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\nINFO     /tmp/biobb/unitests_14/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\nINFO     /tmp/biobb/unitests_14/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\nINFO     /tmp/biobb/unitests_14/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\nINFO     /tmp/biobb/unitests_14/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_14/basepair_stiffness/sandbox_856158b0-2326-4945-a828-b92fcaf37ba1\nINFO     /tmp/biobb/unitests_14/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_14\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nseqpos::::::::\n[]\n2025-01-21 16:20:42,749 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.bipopulations Version: 5.0.1\n2025-01-21 16:20:42,750 [MainThread  ] [INFO ]  /tmp/biobb/unitests_31/bipopulations/sandbox_a27fee94-658e-473c-9397-fe1f06cf74c4 directory successfully created\n2025-01-21 16:20:42,753 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_31/bipopulations/sandbox_a27fee94-658e-473c-9397-fe1f06cf74c4\n2025-01-21 16:20:42,756 [MainThread  ] [INFO ]  Copy: 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/tmp/biobb/unitests_31/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_31/bipopulations/sandbox_a27fee94-658e-473c-9397-fe1f06cf74c4\nINFO     /tmp/biobb/unitests_31/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_31/bipopulations/sandbox_a27fee94-658e-473c-9397-fe1f06cf74c4\nINFO     /tmp/biobb/unitests_31/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_31/bipopulations/sandbox_a27fee94-658e-473c-9397-fe1f06cf74c4\nINFO     /tmp/biobb/unitests_31/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_31/bipopulations/sandbox_a27fee94-658e-473c-9397-fe1f06cf74c4\nINFO     /tmp/biobb/unitests_31/bipopulations/bipopulations_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_31/bipopulations/sandbox_a27fee94-658e-473c-9397-fe1f06cf74c4&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/bipopulations/bipopulations_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td 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/tmp/biobb/unitests_32/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_32/canonicalag/canonag.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/canonag_ref.jpg\n     IMAGE_A HASH: ff8081818180f9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8081818180f9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_32/canonicalag/canonicalag_log.out:file_utils.py:409 Module: biobb_dna.backbone.canonicalag Version: 5.0.1\nINFO     /tmp/biobb/unitests_32/canonicalag/canonicalag_log.out:file_utils.py:82 /tmp/biobb/unitests_32/canonicalag/sandbox_3ee9f64c-d791-4bb4-ac79-ff51c017544f directory successfully created\nINFO     /tmp/biobb/unitests_32/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_32/canonicalag/sandbox_3ee9f64c-d791-4bb4-ac79-ff51c017544f\nINFO     /tmp/biobb/unitests_32/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_32/canonicalag/sandbox_3ee9f64c-d791-4bb4-ac79-ff51c017544f\nINFO     /tmp/biobb/unitests_32/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_32/canonicalag/sandbox_3ee9f64c-d791-4bb4-ac79-ff51c017544f\nINFO     /tmp/biobb/unitests_32/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_32/canonicalag/sandbox_3ee9f64c-d791-4bb4-ac79-ff51c017544f\nINFO     /tmp/biobb/unitests_32/canonicalag/canonicalag_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_32/canonicalag/sandbox_3ee9f64c-d791-4bb4-ac79-ff51c017544f&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_32\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:45,556 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.puckering Version: 5.0.1\n2025-01-21 16:20:45,557 [MainThread  ] [INFO ]  /tmp/biobb/unitests_32/puckering/sandbox_ef25bafa-dce4-4fe6-8f82-2dda6623bef8 directory successfully created\n2025-01-21 16:20:45,559 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_32/puckering/sandbox_ef25bafa-dce4-4fe6-8f82-2dda6623bef8\n2025-01-21 16:20:45,561 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_32/puckering/sandbox_ef25bafa-dce4-4fe6-8f82-2dda6623bef8\n2025-01-21 16:20:46,991 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_32/puckering/sandbox_ef25bafa-dce4-4fe6-8f82-2dda6623bef8&amp;#x27;]\n2025-01-21 16:20:46,993 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_32/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_32/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_32/puckering/puckering.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/puckering_ref.jpg\n     IMAGE_A HASH: eb8181808081ffff SIZE: 64 bits\n     IMAGE_B HASH: eb8181808081ffff SIZE: 64 bits\n     TOLERANCE: 20%, ABS TOLERANCE: 12.8 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_32/puckering/puckering_log.out:file_utils.py:409 Module: biobb_dna.backbone.puckering Version: 5.0.1\nINFO     /tmp/biobb/unitests_32/puckering/puckering_log.out:file_utils.py:82 /tmp/biobb/unitests_32/puckering/sandbox_ef25bafa-dce4-4fe6-8f82-2dda6623bef8 directory successfully created\nINFO     /tmp/biobb/unitests_32/puckering/puckering_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_32/puckering/sandbox_ef25bafa-dce4-4fe6-8f82-2dda6623bef8\nINFO     /tmp/biobb/unitests_32/puckering/puckering_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_32/puckering/sandbox_ef25bafa-dce4-4fe6-8f82-2dda6623bef8\nINFO     /tmp/biobb/unitests_32/puckering/puckering_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_32/puckering/sandbox_ef25bafa-dce4-4fe6-8f82-2dda6623bef8&amp;#x27;]\nINFO     /tmp/biobb/unitests_32/puckering/puckering_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_32\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;721 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;721 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:47,179 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.1\n2025-01-21 16:20:47,180 [MainThread  ] [INFO ]  /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491 directory successfully created\n2025-01-21 16:20:47,181 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\n2025-01-21 16:20:47,182 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\n2025-01-21 16:20:47,183 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\n2025-01-21 16:20:47,184 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\n2025-01-21 16:20:47,185 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\n2025-01-21 16:20:47,186 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\n2025-01-21 16:20:47,718 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491&amp;#x27;]\n2025-01-21 16:20:47,720 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_32/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_32/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_32/interhpcorr/inter_hpcorr.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_hpcorr_ref.jpg\n     IMAGE_A HASH: ff83868890a1c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83868890a1c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491 directory successfully created\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_32/interhpcorr/sandbox_d421e6bd-740b-4ef8-8741-b68258747491&amp;#x27;]\nINFO     /tmp/biobb/unitests_32/interhpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_32\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;955 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;955 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:47,901 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.1\n2025-01-21 16:20:47,902 [MainThread  ] [INFO ]  /tmp/biobb/unitests_32/interseqcorr/sandbox_faeb7df0-cab1-482a-8382-3c02ef6d13e7 directory successfully created\n2025-01-21 16:20:47,905 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_32/interseqcorr/sandbox_faeb7df0-cab1-482a-8382-3c02ef6d13e7\n2025-01-21 16:20:48,674 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_32/interseqcorr/sandbox_faeb7df0-cab1-482a-8382-3c02ef6d13e7&amp;#x27;]\n2025-01-21 16:20:48,675 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_32/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_32/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_32/interseqcorr/inter_seqcorr.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_seqcorr_roll.jpg\n     IMAGE_A HASH: ff8080889080c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff8080889080c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_32/interseqcorr/interseqcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_32/interseqcorr/interseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_32/interseqcorr/sandbox_faeb7df0-cab1-482a-8382-3c02ef6d13e7 directory successfully created\nINFO     /tmp/biobb/unitests_32/interseqcorr/interseqcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_32/interseqcorr/sandbox_faeb7df0-cab1-482a-8382-3c02ef6d13e7\nINFO     /tmp/biobb/unitests_32/interseqcorr/interseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_32/interseqcorr/sandbox_faeb7df0-cab1-482a-8382-3c02ef6d13e7&amp;#x27;]\nINFO     /tmp/biobb/unitests_32/interseqcorr/interseqcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_32\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:48,860 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.1\n2025-01-21 16:20:48,860 [MainThread  ] [INFO ]  /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7 directory successfully created\n2025-01-21 16:20:48,863 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\n2025-01-21 16:20:48,865 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\n2025-01-21 16:20:48,869 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\n2025-01-21 16:20:48,871 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\n2025-01-21 16:20:48,874 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\n2025-01-21 16:20:48,876 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\n2025-01-21 16:20:50,900 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7&amp;#x27;]\n2025-01-21 16:20:50,902 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_32/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_32/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_32/interbpcorr/inter_bpcorr.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_bpcorr_ref.jpg\n     IMAGE_A HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     IMAGE_B HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7 directory successfully created\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_32/interbpcorr/sandbox_8987be24-accc-406d-99c6-339e56a5bfa7&amp;#x27;]\nINFO     /tmp/biobb/unitests_32/interbpcorr/interbpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_32\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;710 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;710 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:51,104 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.1\n2025-01-21 16:20:51,105 [MainThread  ] [INFO ]  /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd directory successfully created\n2025-01-21 16:20:51,106 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\n2025-01-21 16:20:51,107 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\n2025-01-21 16:20:51,108 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\n2025-01-21 16:20:51,109 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\n2025-01-21 16:20:51,110 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\n2025-01-21 16:20:51,111 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\n2025-01-21 16:20:51,631 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd&amp;#x27;]\n2025-01-21 16:20:51,633 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_32/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_32/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_32/intrahpcorr/intra_hpcorr.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_hpcorr_ref.jpg\n     IMAGE_A HASH: fb81848890a0e0ff SIZE: 64 bits\n     IMAGE_B HASH: fb81848890a0e0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd directory successfully created\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_32/intrahpcorr/sandbox_6d7c4880-3a56-49a4-b98e-333be669dfcd&amp;#x27;]\nINFO     /tmp/biobb/unitests_32/intrahpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_32\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;951 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;951 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:51,822 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.1\n2025-01-21 16:20:51,823 [MainThread  ] [INFO ]  /tmp/biobb/unitests_32/intraseqcorr/sandbox_81cda31e-e2fc-4be0-8487-c1919fc2056a directory successfully created\n2025-01-21 16:20:51,825 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_32/intraseqcorr/sandbox_81cda31e-e2fc-4be0-8487-c1919fc2056a\n2025-01-21 16:20:52,588 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_32/intraseqcorr/sandbox_81cda31e-e2fc-4be0-8487-c1919fc2056a&amp;#x27;]\n2025-01-21 16:20:52,589 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_32/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_32/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_32/intraseqcorr/intra_seqcorr.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.jpg\n     IMAGE_A HASH: ff83848890a0c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83848890a0c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_32/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_32/intraseqcorr/intraseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_32/intraseqcorr/sandbox_81cda31e-e2fc-4be0-8487-c1919fc2056a directory successfully created\nINFO     /tmp/biobb/unitests_32/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_32/intraseqcorr/sandbox_81cda31e-e2fc-4be0-8487-c1919fc2056a\nINFO     /tmp/biobb/unitests_32/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_32/intraseqcorr/sandbox_81cda31e-e2fc-4be0-8487-c1919fc2056a&amp;#x27;]\nINFO     /tmp/biobb/unitests_32/intraseqcorr/intraseqcorr_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:52,771 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.1\n2025-01-21 16:20:52,772 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7 directory successfully created\n2025-01-21 16:20:52,774 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\n2025-01-21 16:20:52,776 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\n2025-01-21 16:20:52,778 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\n2025-01-21 16:20:52,780 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\n2025-01-21 16:20:52,782 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\n2025-01-21 16:20:52,783 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\n2025-01-21 16:20:54,853 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7&amp;#x27;]\n2025-01-21 16:20:54,855 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_33/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_33/intrabpcorr/intra_bpcorr.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_bpcorr_ref.jpg\n     IMAGE_A HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     IMAGE_B HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7 directory successfully created\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/intrabpcorr/sandbox_65d9c433-05c3-45c6-8e14-0b8b0de973b7&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/intrabpcorr/intrabpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;, &#34;duration&#34;: &#34;00:00:17&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:17&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:20:55,062 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.1\n2025-01-21 16:20:55,062 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/biobb_canal/sandbox_a4c36660-409e-40cf-ba12-4f1af418f345 directory successfully created\n2025-01-21 16:20:55,092 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_33/biobb_canal/sandbox_a4c36660-409e-40cf-ba12-4f1af418f345\n2025-01-21 16:20:55,093 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2025-01-21 16:20:55,094 [MainThread  ] [INFO ]  Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\n2025-01-21 16:21:11,670 [MainThread  ] [INFO ]  Executing: Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd...\n2025-01-21 16:21:11,670 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 16:21:12,223 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/biobb_canal/sandbox_a4c36660-409e-40cf-ba12-4f1af418f345&amp;#x27;]\n2025-01-21 16:21:12,224 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/biobb_canal/biobb_canal_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/biobb_canal/biobb_canal_log.out:file_utils.py:82 /tmp/biobb/unitests_33/biobb_canal/sandbox_a4c36660-409e-40cf-ba12-4f1af418f345 directory successfully created\nINFO     /tmp/biobb/unitests_33/biobb_canal/biobb_canal_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_33/biobb_canal/sandbox_a4c36660-409e-40cf-ba12-4f1af418f345\nINFO     /tmp/biobb/unitests_33/biobb_canal/biobb_canal_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_33/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:63 Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\nINFO     /tmp/biobb/unitests_33/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:36 Executing: Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd...\nINFO     /tmp/biobb/unitests_33/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_33/biobb_canal/biobb_canal_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/biobb_canal/sandbox_a4c36660-409e-40cf-ba12-4f1af418f345&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/biobb_canal/biobb_canal_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;, &#34;duration&#34;: &#34;208 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;208 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:21:12,340 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.1\n2025-01-21 16:21:12,341 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/canal_unzip/sandbox_6d2947a3-b730-4fb6-8463-840145ce75ad directory successfully created\n2025-01-21 16:21:12,416 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_33/canal_unzip/sandbox_6d2947a3-b730-4fb6-8463-840145ce75ad\n2025-01-21 16:21:12,431 [MainThread  ] [INFO ]  canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_33/canal_unzip/sandbox_6d2947a3-b730-4fb6-8463-840145ce75ad/canal_unzip_output.ser.\n2025-01-21 16:21:12,443 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/canal_unzip/sandbox_6d2947a3-b730-4fb6-8463-840145ce75ad&amp;#x27;]\n2025-01-21 16:21:12,444 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/canal_unzip/canal_unzip_output.ser\nChecking if empty file: /tmp/biobb/unitests_33/canal_unzip/canal_unzip_output.txt\nComparing: \n        File_A: /tmp/biobb/unitests_33/canal_unzip/canal_unzip_output.ser\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.ser\n        File_A hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_33/canal_unzip/canal_unzip_output.txt\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.txt\n        File_A hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n        File_B hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/canal_unzip/canal_unzip_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/canal_unzip/canal_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_33/canal_unzip/sandbox_6d2947a3-b730-4fb6-8463-840145ce75ad directory successfully created\nINFO     /tmp/biobb/unitests_33/canal_unzip/canal_unzip_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_33/canal_unzip/sandbox_6d2947a3-b730-4fb6-8463-840145ce75ad\nINFO     /tmp/biobb/unitests_33/canal_unzip/canal_unzip_log.out:file_utils.py:409 canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_33/canal_unzip/sandbox_6d2947a3-b730-4fb6-8463-840145ce75ad/canal_unzip_output.ser.\nINFO     /tmp/biobb/unitests_33/canal_unzip/canal_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/canal_unzip/sandbox_6d2947a3-b730-4fb6-8463-840145ce75ad&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/canal_unzip/canal_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:21:12,552 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.1\n2025-01-21 16:21:12,553 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98 directory successfully created\n2025-01-21 16:21:13,611 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98\n2025-01-21 16:21:13,613 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98\n2025-01-21 16:21:13,614 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98\n2025-01-21 16:21:13,614 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2025-01-21 16:21:13,615 [MainThread  ] [INFO ]  Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\n2025-01-21 16:21:13,622 [MainThread  ] [INFO ]  Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\n2025-01-21 16:21:13,623 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 16:21:13,711 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98&amp;#x27;]\n2025-01-21 16:21:13,713 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:file_utils.py:82 /tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98 directory successfully created\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:63 Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:36 Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/biobb_canion/sandbox_34ac70c2-8330-47ad-8ea2-656609b2aa98&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/biobb_canion/biobb_canion_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;, &#34;duration&#34;: &#34;00:00:15&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:15&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:21:13,821 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.1\n2025-01-21 16:21:13,821 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/biobb_curves/sandbox_959d071e-e146-48b5-b140-ebf30cc7f776 directory successfully created\n2025-01-21 16:21:13,975 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_33/biobb_curves/sandbox_959d071e-e146-48b5-b140-ebf30cc7f776\n2025-01-21 16:21:13,977 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_33/biobb_curves/sandbox_959d071e-e146-48b5-b140-ebf30cc7f776\n2025-01-21 16:21:13,982 [MainThread  ] [INFO ]  Appending provided topology to command\n2025-01-21 16:21:13,982 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2025-01-21 16:21:13,983 [MainThread  ] [INFO ]  Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=.curvesplus/standard,\n  ions=.t.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\n2025-01-21 16:21:28,805 [MainThread  ] [INFO ]  Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\n2025-01-21 16:21:28,806 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 16:21:28,912 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/biobb_curves/sandbox_959d071e-e146-48b5-b140-ebf30cc7f776&amp;#x27;]\n2025-01-21 16:21:28,913 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_33/biobb_curves/curves_output.lis\nChecking if empty file: /tmp/biobb/unitests_33/biobb_curves/curves_output.zip\nComparing ignoring lines containing this words: [2]\n     FILE_A: /tmp/biobb/unitests_33/biobb_curves/curves_output.lis\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.lis\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_33/biobb_curves/curves_output.zip\nCreating a unique_dir for: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.zip\nComparing: \n        File_A: 7e5f29c8-2be0-40d0-8299-c90014aefb60/curves_output.cdi\n        File_B: c7ab6b4f-13dc-4eb2-8077-17476142c3e5/curves_output.cdi\n        File_A hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n        File_B hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:file_utils.py:82 /tmp/biobb/unitests_33/biobb_curves/sandbox_959d071e-e146-48b5-b140-ebf30cc7f776 directory successfully created\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_33/biobb_curves/sandbox_959d071e-e146-48b5-b140-ebf30cc7f776\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_33/biobb_curves/sandbox_959d071e-e146-48b5-b140-ebf30cc7f776\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:file_utils.py:409 Appending provided topology to command\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:63 Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=.curvesplus/standard,\n  ions=.t.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:36 Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/biobb_curves/sandbox_959d071e-e146-48b5-b140-ebf30cc7f776&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/biobb_curves/biobb_curves_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;, &#34;duration&#34;: &#34;679 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;679 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:21:29,144 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_averages Version: 5.0.1\n2025-01-21 16:21:29,145 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/dna_averages/sandbox_31aa2c86-1dbc-46a3-ac30-ed629689e852 directory successfully created\n2025-01-21 16:21:29,147 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_33/dna_averages/sandbox_31aa2c86-1dbc-46a3-ac30-ed629689e852\n2025-01-21 16:21:29,653 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/dna_averages/sandbox_31aa2c86-1dbc-46a3-ac30-ed629689e852&amp;#x27;]\n2025-01-21 16:21:29,654 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_33/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_33/dna_averages/avg_out.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/shift_avg.jpg\n     IMAGE_A HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     IMAGE_B HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/dna_averages/dna_averages_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_averages Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/dna_averages/dna_averages_log.out:file_utils.py:82 /tmp/biobb/unitests_33/dna_averages/sandbox_31aa2c86-1dbc-46a3-ac30-ed629689e852 directory successfully created\nINFO     /tmp/biobb/unitests_33/dna_averages/dna_averages_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_33/dna_averages/sandbox_31aa2c86-1dbc-46a3-ac30-ed629689e852\nINFO     /tmp/biobb/unitests_33/dna_averages/dna_averages_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/dna_averages/sandbox_31aa2c86-1dbc-46a3-ac30-ed629689e852&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/dna_averages/dna_averages_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:21:29,826 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_bimodality Version: 5.0.1\n2025-01-21 16:21:29,826 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/dna_bimodality/sandbox_00737241-64d5-4308-8bf2-82d9ec4916f9 directory successfully created\n2025-01-21 16:21:29,827 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_33/dna_bimodality/sandbox_00737241-64d5-4308-8bf2-82d9ec4916f9\n2025-01-21 16:21:30,827 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/dna_bimodality/sandbox_00737241-64d5-4308-8bf2-82d9ec4916f9&amp;#x27;]\n2025-01-21 16:21:30,828 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_33/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_bimodality Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/dna_bimodality/dna_bimodality_log.out:file_utils.py:82 /tmp/biobb/unitests_33/dna_bimodality/sandbox_00737241-64d5-4308-8bf2-82d9ec4916f9 directory successfully created\nINFO     /tmp/biobb/unitests_33/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_33/dna_bimodality/sandbox_00737241-64d5-4308-8bf2-82d9ec4916f9\nINFO     /tmp/biobb/unitests_33/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/dna_bimodality/sandbox_00737241-64d5-4308-8bf2-82d9ec4916f9&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/dna_bimodality/dna_bimodality_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;, &#34;duration&#34;: &#34;00:00:12&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:12&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:21:30,933 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries Version: 5.0.1\n2025-01-21 16:21:30,934 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/dna_timeseries/sandbox_5b43a096-27c8-41c8-913e-2c99da98c557 directory successfully created\n2025-01-21 16:21:30,936 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_33/dna_timeseries/sandbox_5b43a096-27c8-41c8-913e-2c99da98c557\n2025-01-21 16:21:42,691 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/dna_timeseries/sandbox_5b43a096-27c8-41c8-913e-2c99da98c557&amp;#x27;]\n2025-01-21 16:21:42,692 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/dna_timeseries/dna_timeseries_log.out:file_utils.py:82 /tmp/biobb/unitests_33/dna_timeseries/sandbox_5b43a096-27c8-41c8-913e-2c99da98c557 directory successfully created\nINFO     /tmp/biobb/unitests_33/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_33/dna_timeseries/sandbox_5b43a096-27c8-41c8-913e-2c99da98c557\nINFO     /tmp/biobb/unitests_33/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/dna_timeseries/sandbox_5b43a096-27c8-41c8-913e-2c99da98c557&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/dna_timeseries/dna_timeseries_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;, &#34;duration&#34;: &#34;178 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;178 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:21:42,796 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.1\n2025-01-21 16:21:42,797 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec directory successfully created\n2025-01-21 16:21:42,799 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec\n2025-01-21 16:21:42,801 [MainThread  ] [INFO ]  hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec/dna_timeseries_unzip.csv.\n2025-01-21 16:21:42,802 [MainThread  ] [INFO ]  hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec/dna_timeseries_unzip.jpg.\n2025-01-21 16:21:42,805 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec&amp;#x27;]\n2025-01-21 16:21:42,806 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip.csv\nChecking if empty file: /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip.jpg\nChecking if empty file: /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip.txt\nComparing: \n        File_A: /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip.csv\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.csv\n        File_A hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip.txt\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.txt\n        File_A hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.jpg\n     IMAGE_A HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     IMAGE_B HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec directory successfully created\nINFO     /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec\nINFO     /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec/dna_timeseries_unzip.csv.\nINFO     /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec/dna_timeseries_unzip.jpg.\nINFO     /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/dna_timeseries_unzip/sandbox_ce8f696e-572e-415f-bf38-91fe11a447ec&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;, &#34;duration&#34;: &#34;614 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;614 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:21:42,977 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.average_stiffness Version: 5.0.1\n2025-01-21 16:21:42,977 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/average_stiffness/sandbox_ec302864-3cae-43e1-bd5f-61be082a1056 directory successfully created\n2025-01-21 16:21:42,979 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_33/average_stiffness/sandbox_ec302864-3cae-43e1-bd5f-61be082a1056\n2025-01-21 16:21:43,424 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_33/average_stiffness/sandbox_ec302864-3cae-43e1-bd5f-61be082a1056&amp;#x27;]\n2025-01-21 16:21:43,425 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_33/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_33/average_stiffness/avgstiff.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffavg_roll.jpg\n     IMAGE_A HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     IMAGE_B HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/average_stiffness/average_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.average_stiffness Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/average_stiffness/average_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_33/average_stiffness/sandbox_ec302864-3cae-43e1-bd5f-61be082a1056 directory successfully created\nINFO     /tmp/biobb/unitests_33/average_stiffness/average_stiffness_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_33/average_stiffness/sandbox_ec302864-3cae-43e1-bd5f-61be082a1056\nINFO     /tmp/biobb/unitests_33/average_stiffness/average_stiffness_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_33/average_stiffness/sandbox_ec302864-3cae-43e1-bd5f-61be082a1056&amp;#x27;]\nINFO     /tmp/biobb/unitests_33/average_stiffness/average_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;, &#34;duration&#34;: &#34;651 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;651 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 16:21:43,596 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.1\n2025-01-21 16:21:43,597 [MainThread  ] [INFO ]  /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953 directory successfully created\n2025-01-21 16:21:43,598 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\n2025-01-21 16:21:43,599 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\n2025-01-21 16:21:43,600 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\n2025-01-21 16:21:43,601 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\n2025-01-21 16:21:43,602 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\n2025-01-21 16:21:43,603 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\n2025-01-21 16:21:44,075 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_33/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_33/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_33/basepair_stiffness/bpstiff.jpg\n     IMAGE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffbp_ref.jpg\n     IMAGE_A HASH: ff8080909080ffff SIZE: 64 bits\n     IMAGE_B HASH: ff8080909080ffff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_33/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.1\nINFO     /tmp/biobb/unitests_33/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953 directory successfully created\nINFO     /tmp/biobb/unitests_33/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\nINFO     /tmp/biobb/unitests_33/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\nINFO     /tmp/biobb/unitests_33/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\nINFO     /tmp/biobb/unitests_33/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\nINFO     /tmp/biobb/unitests_33/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\nINFO     /tmp/biobb/unitests_33/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_33/basepair_stiffness/sandbox_cc2e172f-0e72-428b-91d8-9ac54cdbd953\nINFO     /tmp/biobb/unitests_33/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_33\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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