Add docstrings to comparator modules

kkrismer · Jun 16, 2021 · b1fb99f · b1fb99f
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diff --git a/docs/_modules/seqgra/comparator/curvetablecomparator.html b/docs/_modules/seqgra/comparator/curvetablecomparator.html
@@ -184,7 +184,10 @@
 
   <h1>Source code for seqgra.comparator.curvetablecomparator</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">MIT - CSAIL - Gifford Lab - seqgra</span>
+<span class="sd">Curve Table Comparator for PR and ROC curve information</span>
+
+<span class="sd">Classes:</span>
+<span class="sd">    - :class:`~seqgra.comparator.curvetablecomparator.CurveTableComparator`: collects PR and ROC curve information in text file</span>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">List</span><span class="p">,</span> <span class="n">Optional</span>
 <span class="kn">import</span> <span class="nn">os</span>

diff --git a/docs/_modules/seqgra/comparator/fietablecomparator.html b/docs/_modules/seqgra/comparator/fietablecomparator.html
@@ -184,7 +184,10 @@
 
   <h1>Source code for seqgra.comparator.fietablecomparator</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">MIT - CSAIL - Gifford Lab - seqgra</span>
+<span class="sd">Feature Importance Evaluator Table Comparator for feature importance measures</span>
+
+<span class="sd">Classes:</span>
+<span class="sd">    - :class:`~seqgra.comparator.fietablecomparator.FIETableComparator`: collects feature importance evaluator information in text file</span>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">List</span><span class="p">,</span> <span class="n">Optional</span>
 <span class="kn">import</span> <span class="nn">os</span>

diff --git a/docs/_modules/seqgra/comparator/prcomparator.html b/docs/_modules/seqgra/comparator/prcomparator.html
@@ -184,11 +184,10 @@
 
   <h1>Source code for seqgra.comparator.prcomparator</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">MIT - CSAIL - Gifford Lab - seqgra</span>
+<span class="sd">Creates PR curves of different models</span>
 
-<span class="sd">ROC comparator: creates ROC curves of different models</span>
-
-<span class="sd">@author: Konstantin Krismer</span>
+<span class="sd">Classes:</span>
+<span class="sd">    - :class:`~seqgra.comparator.prcomparator.PRComparator`: creates PR curves from various grammars and architectures</span>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">List</span><span class="p">,</span> <span class="n">Optional</span>
 <span class="kn">import</span> <span class="nn">os</span>

diff --git a/docs/_modules/seqgra/comparator/roccomparator.html b/docs/_modules/seqgra/comparator/roccomparator.html
@@ -184,11 +184,10 @@
 
   <h1>Source code for seqgra.comparator.roccomparator</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">MIT - CSAIL - Gifford Lab - seqgra</span>
+<span class="sd">Creates ROC curves of different models</span>
 
-<span class="sd">ROC comparator: creates ROC curves of different models</span>
-
-<span class="sd">@author: Konstantin Krismer</span>
+<span class="sd">Classes:</span>
+<span class="sd">    - :class:`~seqgra.comparator.roccomparator.ROCComparator`: creates ROC curves from various grammars and architectures</span>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">List</span><span class="p">,</span> <span class="n">Optional</span>
 <span class="kn">import</span> <span class="nn">os</span>

diff --git a/docs/_modules/seqgra/comparator/tablecomparator.html b/docs/_modules/seqgra/comparator/tablecomparator.html
@@ -184,7 +184,10 @@
 
   <h1>Source code for seqgra.comparator.tablecomparator</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">MIT - CSAIL - Gifford Lab - seqgra</span>
+<span class="sd">Table Comparator for grammar and model information</span>
+
+<span class="sd">Classes:</span>
+<span class="sd">    - :class:`~seqgra.comparator.tablecomparator.TableComparator`: collects grammar and model information in text file</span>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">List</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Tuple</span>
 <span class="kn">import</span> <span class="nn">os</span>

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/seqgra.comparator.curvetablecomparator.html b/docs/seqgra.comparator.curvetablecomparator.html
@@ -214,7 +214,13 @@
 
   <div class="section" id="module-seqgra.comparator.curvetablecomparator">
 <span id="seqgra-comparator-curvetablecomparator-module"></span><h1>seqgra.comparator.curvetablecomparator module<a class="headerlink" href="#module-seqgra.comparator.curvetablecomparator" title="Permalink to this headline">¶</a></h1>
-<p>MIT - CSAIL - Gifford Lab - seqgra</p>
+<p>Curve Table Comparator for PR and ROC curve information</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="#seqgra.comparator.curvetablecomparator.CurveTableComparator" title="seqgra.comparator.curvetablecomparator.CurveTableComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">CurveTableComparator</span></code></a>: collects PR and ROC curve information in text file</p></li>
+</ul>
+</dd>
+</dl>
 <dl class="py class">
 <dt class="sig sig-object py" id="seqgra.comparator.curvetablecomparator.CurveTableComparator">
 <em class="property"><span class="pre">class</span> </em><span class="sig-name descname"><span class="pre">CurveTableComparator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analysis_id</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_labels</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/seqgra/comparator/curvetablecomparator.html#CurveTableComparator"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#seqgra.comparator.curvetablecomparator.CurveTableComparator" title="Permalink to this definition">¶</a></dt>

diff --git a/docs/seqgra.comparator.fietablecomparator.html b/docs/seqgra.comparator.fietablecomparator.html
@@ -214,7 +214,13 @@
 
   <div class="section" id="module-seqgra.comparator.fietablecomparator">
 <span id="seqgra-comparator-fietablecomparator-module"></span><h1>seqgra.comparator.fietablecomparator module<a class="headerlink" href="#module-seqgra.comparator.fietablecomparator" title="Permalink to this headline">¶</a></h1>
-<p>MIT - CSAIL - Gifford Lab - seqgra</p>
+<p>Feature Importance Evaluator Table Comparator for feature importance measures</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="#seqgra.comparator.fietablecomparator.FIETableComparator" title="seqgra.comparator.fietablecomparator.FIETableComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">FIETableComparator</span></code></a>: collects feature importance evaluator information in text file</p></li>
+</ul>
+</dd>
+</dl>
 <dl class="py class">
 <dt class="sig sig-object py" id="seqgra.comparator.fietablecomparator.FIETableComparator">
 <em class="property"><span class="pre">class</span> </em><span class="sig-name descname"><span class="pre">FIETableComparator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analysis_id</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_labels</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/seqgra/comparator/fietablecomparator.html#FIETableComparator"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#seqgra.comparator.fietablecomparator.FIETableComparator" title="Permalink to this definition">¶</a></dt>

diff --git a/docs/seqgra.comparator.prcomparator.html b/docs/seqgra.comparator.prcomparator.html
@@ -214,9 +214,13 @@
 
   <div class="section" id="module-seqgra.comparator.prcomparator">
 <span id="seqgra-comparator-prcomparator-module"></span><h1>seqgra.comparator.prcomparator module<a class="headerlink" href="#module-seqgra.comparator.prcomparator" title="Permalink to this headline">¶</a></h1>
-<p>MIT - CSAIL - Gifford Lab - seqgra</p>
-<p>ROC comparator: creates ROC curves of different models</p>
-<p>&#64;author: Konstantin Krismer</p>
+<p>Creates PR curves of different models</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="#seqgra.comparator.prcomparator.PRComparator" title="seqgra.comparator.prcomparator.PRComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">PRComparator</span></code></a>: creates PR curves from various grammars and architectures</p></li>
+</ul>
+</dd>
+</dl>
 <dl class="py class">
 <dt class="sig sig-object py" id="seqgra.comparator.prcomparator.PRComparator">
 <em class="property"><span class="pre">class</span> </em><span class="sig-name descname"><span class="pre">PRComparator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analysis_id</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_labels</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/seqgra/comparator/prcomparator.html#PRComparator"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#seqgra.comparator.prcomparator.PRComparator" title="Permalink to this definition">¶</a></dt>

diff --git a/docs/seqgra.comparator.roccomparator.html b/docs/seqgra.comparator.roccomparator.html
@@ -214,9 +214,13 @@
 
   <div class="section" id="module-seqgra.comparator.roccomparator">
 <span id="seqgra-comparator-roccomparator-module"></span><h1>seqgra.comparator.roccomparator module<a class="headerlink" href="#module-seqgra.comparator.roccomparator" title="Permalink to this headline">¶</a></h1>
-<p>MIT - CSAIL - Gifford Lab - seqgra</p>
-<p>ROC comparator: creates ROC curves of different models</p>
-<p>&#64;author: Konstantin Krismer</p>
+<p>Creates ROC curves of different models</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="#seqgra.comparator.roccomparator.ROCComparator" title="seqgra.comparator.roccomparator.ROCComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">ROCComparator</span></code></a>: creates ROC curves from various grammars and architectures</p></li>
+</ul>
+</dd>
+</dl>
 <dl class="py class">
 <dt class="sig sig-object py" id="seqgra.comparator.roccomparator.ROCComparator">
 <em class="property"><span class="pre">class</span> </em><span class="sig-name descname"><span class="pre">ROCComparator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analysis_id</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_labels</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/seqgra/comparator/roccomparator.html#ROCComparator"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#seqgra.comparator.roccomparator.ROCComparator" title="Permalink to this definition">¶</a></dt>

diff --git a/docs/seqgra.comparator.tablecomparator.html b/docs/seqgra.comparator.tablecomparator.html
@@ -214,7 +214,13 @@
 
   <div class="section" id="module-seqgra.comparator.tablecomparator">
 <span id="seqgra-comparator-tablecomparator-module"></span><h1>seqgra.comparator.tablecomparator module<a class="headerlink" href="#module-seqgra.comparator.tablecomparator" title="Permalink to this headline">¶</a></h1>
-<p>MIT - CSAIL - Gifford Lab - seqgra</p>
+<p>Table Comparator for grammar and model information</p>
+<dl class="simple">
+<dt>Classes:</dt><dd><ul class="simple">
+<li><p><a class="reference internal" href="#seqgra.comparator.tablecomparator.TableComparator" title="seqgra.comparator.tablecomparator.TableComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">TableComparator</span></code></a>: collects grammar and model information in text file</p></li>
+</ul>
+</dd>
+</dl>
 <dl class="py class">
 <dt class="sig sig-object py" id="seqgra.comparator.tablecomparator.TableComparator">
 <em class="property"><span class="pre">class</span> </em><span class="sig-name descname"><span class="pre">TableComparator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analysis_id</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_labels</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/seqgra/comparator/tablecomparator.html#TableComparator"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#seqgra.comparator.tablecomparator.TableComparator" title="Permalink to this definition">¶</a></dt>

diff --git a/seqgra/comparator/curvetablecomparator.py b/seqgra/comparator/curvetablecomparator.py
@@ -1,5 +1,8 @@
 """
-MIT - CSAIL - Gifford Lab - seqgra
+Curve Table Comparator for PR and ROC curve information
+
+Classes:
+    - :class:`~seqgra.comparator.curvetablecomparator.CurveTableComparator`: collects PR and ROC curve information in text file
 """
 from typing import List, Optional
 import os

diff --git a/seqgra/comparator/fietablecomparator.py b/seqgra/comparator/fietablecomparator.py
@@ -1,5 +1,8 @@
 """
-MIT - CSAIL - Gifford Lab - seqgra
+Feature Importance Evaluator Table Comparator for feature importance measures
+
+Classes:
+    - :class:`~seqgra.comparator.fietablecomparator.FIETableComparator`: collects feature importance evaluator information in text file
 """
 from typing import List, Optional
 import os

diff --git a/seqgra/comparator/prcomparator.py b/seqgra/comparator/prcomparator.py
@@ -1,9 +1,8 @@
 """
-MIT - CSAIL - Gifford Lab - seqgra
+Creates PR curves of different models
 
-ROC comparator: creates ROC curves of different models
-
-@author: Konstantin Krismer
+Classes:
+    - :class:`~seqgra.comparator.prcomparator.PRComparator`: creates PR curves from various grammars and architectures
 """
 from typing import List, Optional
 import os

diff --git a/seqgra/comparator/roccomparator.py b/seqgra/comparator/roccomparator.py
@@ -1,9 +1,8 @@
 """
-MIT - CSAIL - Gifford Lab - seqgra
+Creates ROC curves of different models
 
-ROC comparator: creates ROC curves of different models
-
-@author: Konstantin Krismer
+Classes:
+    - :class:`~seqgra.comparator.roccomparator.ROCComparator`: creates ROC curves from various grammars and architectures
 """
 from typing import List, Optional
 import os

diff --git a/seqgra/comparator/tablecomparator.py b/seqgra/comparator/tablecomparator.py
@@ -1,5 +1,8 @@
 """
-MIT - CSAIL - Gifford Lab - seqgra
+Table Comparator for grammar and model information
+
+Classes:
+    - :class:`~seqgra.comparator.tablecomparator.TableComparator`: collects grammar and model information in text file
 """
 from typing import List, Optional, Tuple
 import os