Adding docs to gh_pages for 3834213

CDDLeiden · Jul 2, 2024 · 1038eec · 1038eec
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diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -132,6 +132,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="qsprpred/data_CLI.html">qsprpred.data_CLI</a></li>
 <li><a href="qsprpred/extra/data/descriptors/fingerprints.html">qsprpred.extra.data.descriptors.fingerprints</a></li>
 <li><a href="qsprpred/extra/data/descriptors/sets.html">qsprpred.extra.data.descriptors.sets</a></li>
+<li><a href="qsprpred/extra/data/descriptors/tests.html">qsprpred.extra.data.descriptors.tests</a></li>
 <li><a href="qsprpred/extra/data/sampling/splits.html">qsprpred.extra.data.sampling.splits</a></li>
 <li><a href="qsprpred/extra/data/sampling/tests.html">qsprpred.extra.data.sampling.tests</a></li>
 <li><a href="qsprpred/extra/data/tables/pcm.html">qsprpred.extra.data.tables.pcm</a></li>

diff --git a/docs/_modules/qsprpred/extra/data/descriptors/sets.html b/docs/_modules/qsprpred/extra/data/descriptors/sets.html
@@ -105,7 +105,9 @@ <h1>Source code for qsprpred.extra.data.descriptors.sets</h1><div class="highlig
 <span class="sd">- `ProDec`: Protein descriptors from the ProDec package.</span>
 
 <span class="sd">&quot;&quot;&quot;</span>
+<span class="kn">import</span> <span class="nn">logging</span>
 <span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">zipfile</span>
 <span class="kn">from</span> <span class="nn">abc</span> <span class="kn">import</span> <span class="n">abstractmethod</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Any</span>
 

diff --git a/docs/_modules/qsprpred/extra/data/descriptors/tests.html b/docs/_modules/qsprpred/extra/data/descriptors/tests.html
diff --git a/docs/_modules/qsprpred/extra/data/utils/testing/path_mixins.html b/docs/_modules/qsprpred/extra/data/utils/testing/path_mixins.html
@@ -162,14 +162,14 @@ <h1>Source code for qsprpred.extra.data.utils.testing.path_mixins</h1><div class
             <span class="n">PaDEL</span><span class="p">(),</span>
             <span class="n">ExtendedValenceSignature</span><span class="p">(</span><span class="mi">1</span><span class="p">),</span>
         <span class="p">]</span>
-        <span class="k">if</span> <span class="n">platform</span><span class="o">.</span><span class="n">system</span><span class="p">()</span> <span class="o">!=</span> <span class="s2">&quot;Darwin&quot;</span><span class="p">:</span>
-            <span class="n">ret</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Mold2</span><span class="p">())</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="c1"># not supported on macOS</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
-                <span class="s2">&quot;Mold2 is not supported on macOS. &quot;</span>
-                <span class="s2">&quot;Skipping Mold2 descriptor set in tests.&quot;</span>
-            <span class="p">)</span>
+        <span class="c1"># if platform.system() != &quot;Darwin&quot;:</span>
+        <span class="c1">#     ret.append(Mold2())</span>
+        <span class="c1"># else:</span>
+        <span class="c1">#     # not supported on macOS</span>
+        <span class="c1">#     logger.warning(</span>
+        <span class="c1">#         &quot;Mold2 is not supported on macOS. &quot;</span>
+        <span class="c1">#         &quot;Skipping Mold2 descriptor set in tests.&quot;</span>
+        <span class="c1">#     )</span>
         <span class="k">return</span> <span class="n">ret</span></div>
 
 <div class="viewcode-block" id="DataSetsMixInExtras.getAllProteinDescriptors"><a class="viewcode-back" href="../../../../../../api/qsprpred.extra.data.utils.testing.html#qsprpred.extra.data.utils.testing.path_mixins.DataSetsMixInExtras.getAllProteinDescriptors">[docs]</a>    <span class="nd">@classmethod</span>

diff --git a/docs/_modules/qsprpred/extra/models/tests.html b/docs/_modules/qsprpred/extra/models/tests.html
@@ -129,7 +129,8 @@ <h1>Source code for qsprpred.extra.models.tests</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="TestPCM.setUp"><a class="viewcode-back" href="../../../../api/qsprpred.extra.models.html#qsprpred.extra.models.tests.TestPCM.setUp">[docs]</a>    <span class="k">def</span> <span class="nf">setUp</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">setUp</span><span class="p">()</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">setUpPaths</span><span class="p">()</span></div>
+        <span class="bp">self</span><span class="o">.</span><span class="n">setUpPaths</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">nCPU</span> <span class="o">=</span> <span class="mi">1</span></div>
 
 <div class="viewcode-block" id="TestPCM.getModel"><a class="viewcode-back" href="../../../../api/qsprpred.extra.models.html#qsprpred.extra.models.tests.TestPCM.getModel">[docs]</a>    <span class="k">def</span> <span class="nf">getModel</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
@@ -194,10 +195,10 @@ <h1>Source code for qsprpred.extra.models.tests</h1><div class="highlight"><pre>
                 <span class="n">random_state</span><span class="p">,</span>
             <span class="p">)</span>
             <span class="k">for</span> <span class="n">alg</span><span class="p">,</span> <span class="n">alg_name</span> <span class="ow">in</span> <span class="p">((</span><span class="n">XGBClassifier</span><span class="p">,</span> <span class="s2">&quot;XGBC&quot;</span><span class="p">),)</span>
-            <span class="k">for</span> <span class="n">random_state</span> <span class="ow">in</span> <span class="p">([</span><span class="kc">None</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">42</span><span class="p">],</span> <span class="p">[</span><span class="mi">42</span><span class="p">,</span> <span class="mi">42</span><span class="p">])</span>
+            <span class="k">for</span> <span class="n">random_state</span> <span class="ow">in</span> <span class="p">([</span><span class="kc">None</span><span class="p">],</span> <span class="p">[</span><span class="mi">21</span><span class="p">,</span> <span class="mi">42</span><span class="p">],</span> <span class="p">[</span><span class="mi">42</span><span class="p">,</span> <span class="mi">42</span><span class="p">])</span>
         <span class="p">]</span>
     <span class="p">)</span>
-    <span class="k">def</span> <span class="nf">testRegressionBasicFitPCM</span><span class="p">(</span>
+    <span class="k">def</span> <span class="nf">testFittingPCM</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">_</span><span class="p">,</span>
         <span class="n">props</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">TargetProperty</span> <span class="o">|</span> <span class="nb">dict</span><span class="p">],</span>

diff --git a/docs/_modules/qsprpred/models/model.html b/docs/_modules/qsprpred/models/model.html
@@ -275,7 +275,7 @@ <h1>Source code for qsprpred.models.model</h1><div class="highlight"><pre>
                     <span class="sa">f</span><span class="s2">&quot;Estimator will be reloaded with the new parameters &quot;</span>
                     <span class="sa">f</span><span class="s2">&quot;and will have to be re-fitted if fitted previously.&quot;</span>
                 <span class="p">)</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">parameters</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">estimator</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">loadEstimator</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">)</span>
             <span class="k">if</span> <span class="n">random_state</span><span class="p">:</span>
                 <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
@@ -284,7 +284,8 @@ <h1>Source code for qsprpred.models.model</h1><div class="highlight"><pre>
                 <span class="p">)</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">initRandomState</span><span class="p">(</span><span class="n">random_state</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">parameters</span>
+            <span class="c1"># make a deep copy of the params to make sure no problems happen downstream</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
             <span class="c1"># initialize an estimator instance with the given parameters</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">alg</span> <span class="o">=</span> <span class="n">alg</span>
             <span class="c1"># initialize random state</span>

diff --git a/docs/_modules/qsprpred/models/tests.html b/docs/_modules/qsprpred/models/tests.html
@@ -464,6 +464,7 @@ <h1>Source code for qsprpred.models.tests</h1><div class="highlight"><pre>
                 <span class="s2">&quot;th&quot;</span><span class="p">:</span> <span class="p">[</span><span class="mf">6.5</span><span class="p">]</span>
             <span class="p">}],</span>
             <span class="n">preparation_settings</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">getDefaultPrep</span><span class="p">(),</span>
+            <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">,</span>
         <span class="p">)</span>
         <span class="c1"># test classifier</span>
         <span class="c1"># initialize model for training from class</span>
@@ -480,6 +481,7 @@ <h1>Source code for qsprpred.models.tests</h1><div class="highlight"><pre>
             <span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;RFC_</span><span class="si">{</span><span class="n">TargetTasks</span><span class="o">.</span><span class="n">SINGLECLASS</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
             <span class="n">alg</span><span class="o">=</span><span class="n">RandomForestClassifier</span><span class="p">,</span>
             <span class="n">parameters</span><span class="o">=</span><span class="n">parameters</span><span class="p">,</span>
+            <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">,</span>
         <span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">fitTest</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">dataset</span><span class="p">)</span>
         <span class="n">summary</span> <span class="o">=</span> <span class="n">create_metrics_summary</span><span class="p">(</span><span class="n">model</span><span class="p">)</span>

diff --git a/docs/_modules/qsprpred/utils/testing/check_mixins.html b/docs/_modules/qsprpred/utils/testing/check_mixins.html
@@ -457,14 +457,14 @@ <h1>Source code for qsprpred.utils.testing.check_mixins</h1><div class="highligh
                 <span class="p">)</span>
 
         <span class="c1"># define check for comparing predictions with expected result</span>
-        <span class="k">def</span> <span class="nf">check_predictions</span><span class="p">(</span><span class="n">predictions</span><span class="p">,</span> <span class="n">expected_result</span><span class="p">,</span> <span class="n">expect_equal_result</span><span class="p">):</span>
+        <span class="k">def</span> <span class="nf">check_predictions</span><span class="p">(</span><span class="n">preds</span><span class="p">,</span> <span class="n">expected</span><span class="p">,</span> <span class="n">expect_equal</span><span class="p">):</span>
             <span class="c1"># check if predictions are almost equal to expected result (rtol=1e-5)</span>
-            <span class="n">check_outcome</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertTrue</span> <span class="k">if</span> <span class="n">expect_equal_result</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertFalse</span>
-            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">expected_result</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
-                <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">expected_result</span><span class="p">)):</span>
-                    <span class="n">check_outcome</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">predictions</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">expected_result</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
+            <span class="n">check_outcome</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertTrue</span> <span class="k">if</span> <span class="n">expect_equal</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertFalse</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">expected</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+                <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">expected</span><span class="p">)):</span>
+                    <span class="n">check_outcome</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">preds</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">expected</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
             <span class="k">else</span><span class="p">:</span>
-                <span class="n">check_outcome</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">predictions</span><span class="p">,</span> <span class="n">expected_result</span><span class="p">))</span>
+                <span class="n">check_outcome</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">preds</span><span class="p">,</span> <span class="n">expected</span><span class="p">))</span>
 
         <span class="c1"># Check if the predictMols function gives the same result as the</span>
         <span class="c1"># predict/predictProba function</span>