Deploying to gh-pages from @ 7f0e60f 🚀

_modules/index.html

@@ -99,10 +99,12 @@ <h1>All modules for which code is available</h1>
 <li><a href="mtbp3/statlab/kappa.html">mtbp3.statlab.kappa</a></li>
 <li><a href="mtbp3/stdcdisc/lib.html">mtbp3.stdcdisc.lib</a></li>
 <li><a href="mtbp3/stdiso/pdfsummary.html">mtbp3.stdiso.pdfsummary</a></li>
-<li><a href="mtbp3/util/cdt.html">mtbp3.util.cdt</a></li>
+<li><a href="mtbp3/util.html">mtbp3.util</a></li>
+<ul><li><a href="mtbp3/util/cdt.html">mtbp3.util.cdt</a></li>
 <li><a href="mtbp3/util/cdtg.html">mtbp3.util.cdtg</a></li>
 <li><a href="mtbp3/util/lsr.html">mtbp3.util.lsr</a></li>
-</ul></ul>
+<li><a href="mtbp3/util/util.html">mtbp3.util.util</a></li>
+</ul></ul></ul>
 
            </div>
           </div>

_modules/mtbp3.html

@@ -103,6 +103,7 @@ <h1>Source code for mtbp3</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">importlib.metadata</span> <span class="kn">import</span> <span class="n">version</span>
 <span class="n">__version__</span> <span class="o">=</span> <span class="n">version</span><span class="p">(</span><span class="n">__package__</span><span class="p">)</span>
 
+
 <span class="kn">import</span> <span class="nn">os</span>
 
 <span class="n">_ROOT</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="vm">__file__</span><span class="p">))</span>
@@ -111,7 +112,6 @@ <h1>Source code for mtbp3</h1><div class="highlight"><pre>
 <span class="k">def</span> <span class="nf">get_data</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
     <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">_ROOT</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">,</span> <span class="n">path</span><span class="p">)</span></div>
 
-
 </pre></div>
 
            </div>

_modules/mtbp3/health/ectd.html

@@ -110,8 +110,8 @@ <h1>Source code for mtbp3.health.ectd</h1><div class="highlight"><pre>
 
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 <span class="kn">import</span> <span class="nn">os</span>
-<span class="kn">from</span> <span class="nn">mtbp3.util.cdt</span> <span class="kn">import</span> <span class="n">ListTree</span>
 <span class="kn">import</span> <span class="nn">mtbp3</span>
+<span class="kn">from</span> <span class="nn">mtbp3</span> <span class="kn">import</span> <span class="n">util</span>
 
 <div class="viewcode-block" id="ctoc_by_fda">
 <a class="viewcode-back" href="../../../autoapi/mtbp3/health/ectd/index.html#mtbp3.health.ectd.ctoc_by_fda">[docs]</a>
@@ -123,6 +123,7 @@ <h1>Source code for mtbp3.health.ectd</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">ctoc_version</span> <span class="o">=</span> <span class="n">ctoc_version</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">get_data</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;supp_ectd/fda_ectd</span><span class="si">{</span><span class="n">ectd_version</span><span class="si">}</span><span class="s1">_ctocv</span><span class="si">{</span><span class="n">ctoc_version</span><span class="si">}</span><span class="s1">.txt&#39;</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">ctoc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__load_list</span><span class="p">()</span>
+        <span class="nb">print</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">__load_list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="c1">#file_path = f&#39;./mtbp3/data/supp_ectd/fda_ectd{self.ectd_version}_ctocv{ctoc_version}.txt&#39;</span>
@@ -143,7 +144,7 @@ <h1>Source code for mtbp3.health.ectd</h1><div class="highlight"><pre>
             <span class="n">module</span> <span class="o">=</span> <span class="mi">1</span>
 
         <span class="n">filtered_ctoc</span> <span class="o">=</span> <span class="p">[</span><span class="n">item</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ctoc</span> <span class="k">if</span> <span class="n">item</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">module</span><span class="p">))]</span>
-        <span class="n">tree</span> <span class="o">=</span> <span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">filtered_ctoc</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
+        <span class="n">tree</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">filtered_ctoc</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">tree</span><span class="o">.</span><span class="n">list_tree</span><span class="p">(</span><span class="n">to_right</span><span class="o">=</span><span class="n">to_right</span><span class="p">)</span></div>
 
 
@@ -215,9 +216,9 @@ <h1>Source code for mtbp3.health.ectd</h1><div class="highlight"><pre>
                         <span class="n">out_colored</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">first_part</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">colored_second_part</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
                     <span class="k">else</span><span class="p">:</span>
                         <span class="n">out_colored</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">)</span>
-                <span class="n">out_tree</span> <span class="o">=</span> <span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">out_colored</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
+                <span class="n">out_tree</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">out_colored</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
             <span class="k">else</span><span class="p">:</span>
-                <span class="n">out_tree</span> <span class="o">=</span> <span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">out</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
+                <span class="n">out_tree</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">out</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
             <span class="k">return</span> <span class="n">out_tree</span><span class="o">.</span><span class="n">list_tree</span><span class="p">(</span><span class="n">to_right</span><span class="o">=</span><span class="n">to_right</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Invalid value for outfmt. Supported values are &#39;simple&#39; and &#39;tree&#39;.&quot;</span><span class="p">)</span></div>

_modules/mtbp3/health/emt.html

@@ -93,7 +93,7 @@
            <div itemprop="articleBody">
 
   <h1>Source code for mtbp3.health.emt</h1><div class="highlight"><pre>
-<span></span><span class="c1">#  Copyright (C) 2023 Y Hsu &lt;[email protected]&gt;</span>
+<span></span><span class="c1">#  Copyright (C) 2023-2024 Y Hsu &lt;[email protected]&gt;</span>
 <span class="c1">#</span>
 <span class="c1">#  This program is free software: you can redistribute it and/or modify</span>
 <span class="c1">#  it under the terms of the GNU General Public license as published by</span>
@@ -114,8 +114,8 @@ <h1>Source code for mtbp3.health.emt</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">re</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
-<span class="kn">from</span> <span class="nn">mtbp3.util.lsr</span> <span class="kn">import</span> <span class="n">LsrTree</span>
 <span class="kn">import</span> <span class="nn">mtbp3</span>
+<span class="kn">from</span> <span class="nn">mtbp3</span> <span class="kn">import</span> <span class="n">util</span>
 
 <div class="viewcode-block" id="Emt">
 <a class="viewcode-back" href="../../../autoapi/mtbp3/health/index.html#mtbp3.health.emt.Emt">[docs]</a>
@@ -127,7 +127,7 @@ <h1>Source code for mtbp3.health.emt</h1><div class="highlight"><pre>
 
 <span class="sd">    Attributes:</span>
 <span class="sd">        folder_name (str): The folder name associated with the Emt.</span>
-<span class="sd">        lsr (LsrTree): An instance of the LsrTree class for listing files.</span>
+<span class="sd">        lsrt (LsrTree): An instance of the LsrTree class for listing files.</span>
 <span class="sd">        month (str): The month of the version published.</span>
 <span class="sd">        year (str): The year of the version published.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -229,8 +229,8 @@ <h1>Source code for mtbp3.health.emt</h1><div class="highlight"><pre>
 <span class="sd">        Returns:</span>
 <span class="sd">            list: A list of missing file names.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">lsr</span> <span class="o">=</span> <span class="n">LsrTree</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span><span class="p">,</span> <span class="n">outfmt</span><span class="o">=</span><span class="s2">&quot;list&quot;</span><span class="p">)</span>
-        <span class="n">lsr_files</span> <span class="o">=</span> <span class="n">lsr</span><span class="o">.</span><span class="n">list_files</span><span class="p">()</span>
+        <span class="n">lsrt</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">lsr</span><span class="o">.</span><span class="n">LsrTree</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span><span class="p">,</span> <span class="n">outfmt</span><span class="o">=</span><span class="s2">&quot;list&quot;</span><span class="p">)</span>
+        <span class="n">lsr_files</span> <span class="o">=</span> <span class="n">lsrt</span><span class="o">.</span><span class="n">list_files</span><span class="p">()</span>
         <span class="n">support_doc_files</span><span class="p">,</span> <span class="n">med_ascii_files</span><span class="p">,</span> <span class="n">seq_ascii_files</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">expected_file_lists</span><span class="p">()</span>
 
         <span class="n">missing_files</span> <span class="o">=</span> <span class="p">[]</span>
@@ -269,8 +269,8 @@ <h1>Source code for mtbp3.health.emt</h1><div class="highlight"><pre>
 <span class="sd">        Returns:</span>
 <span class="sd">            list: A list of file names.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">lsr</span> <span class="o">=</span> <span class="n">LsrTree</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span><span class="p">,</span> <span class="n">outfmt</span><span class="o">=</span><span class="s2">&quot;tree&quot;</span><span class="p">,</span> <span class="n">with_counts</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-        <span class="n">lsr_files</span> <span class="o">=</span> <span class="n">lsr</span><span class="o">.</span><span class="n">list_files</span><span class="p">()</span>
+        <span class="n">lsrt</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">lsr</span><span class="o">.</span><span class="n">LsrTree</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span><span class="p">,</span> <span class="n">outfmt</span><span class="o">=</span><span class="s2">&quot;tree&quot;</span><span class="p">,</span> <span class="n">with_counts</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="n">lsr_files</span> <span class="o">=</span> <span class="n">lsrt</span><span class="o">.</span><span class="n">list_files</span><span class="p">()</span>
         <span class="k">return</span> <span class="n">lsr_files</span></div>
 
 
@@ -936,7 +936,7 @@ <h1>Source code for mtbp3.health.emt</h1><div class="highlight"><pre>
             <span class="n">list1</span> <span class="o">=</span> <span class="n">pt_df</span><span class="p">[</span><span class="s1">&#39;fmq_class&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
             <span class="n">lists</span> <span class="o">=</span> <span class="n">pt_df</span><span class="p">[</span><span class="s1">&#39;fmq_class_soc&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
             <span class="n">list2</span> <span class="o">=</span> <span class="n">pt_df</span><span class="p">[</span><span class="s1">&#39;fmq_class_soc_pt&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
-            <span class="n">tree</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;FMQ/&#39;</span><span class="p">]</span><span class="o">+</span><span class="n">list0</span><span class="o">+</span><span class="n">list1</span><span class="o">+</span><span class="n">lists</span><span class="o">+</span><span class="n">list2</span><span class="p">)</span>
+            <span class="n">tree</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">lsr</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;FMQ/&#39;</span><span class="p">]</span><span class="o">+</span><span class="n">list0</span><span class="o">+</span><span class="n">list1</span><span class="o">+</span><span class="n">lists</span><span class="o">+</span><span class="n">list2</span><span class="p">)</span>
             <span class="k">return</span> <span class="n">tree</span><span class="o">.</span><span class="n">list_tree</span><span class="p">(</span><span class="n">to_right</span><span class="o">=</span><span class="n">to_right</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">pt_df</span> <span class="o">=</span> <span class="n">pt_df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;fmq&#39;</span><span class="p">,</span> <span class="s1">&#39;classification&#39;</span><span class="p">])</span>
@@ -953,7 +953,7 @@ <h1>Source code for mtbp3.health.emt</h1><div class="highlight"><pre>
 
             <span class="n">list1</span> <span class="o">=</span> <span class="n">pt_df</span><span class="p">[</span><span class="s1">&#39;fmq_class&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
             <span class="n">list2</span> <span class="o">=</span> <span class="n">pt_df</span><span class="p">[</span><span class="s1">&#39;fmq_class_pt&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
-            <span class="n">tree</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;FMQ/&#39;</span><span class="p">]</span><span class="o">+</span><span class="n">list0</span><span class="o">+</span><span class="n">list1</span><span class="o">+</span><span class="n">list2</span><span class="p">)</span>
+            <span class="n">tree</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">lsr</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;FMQ/&#39;</span><span class="p">]</span><span class="o">+</span><span class="n">list0</span><span class="o">+</span><span class="n">list1</span><span class="o">+</span><span class="n">list2</span><span class="p">)</span>
             <span class="k">return</span> <span class="n">tree</span><span class="o">.</span><span class="n">list_tree</span><span class="p">(</span><span class="n">to_right</span><span class="o">=</span><span class="n">to_right</span><span class="p">)</span></div>
 </div>