QSARtuna docs init

docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QPTUNA_Tutorial.ipynb → docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QSARtuna_Tutorial.ipynb

@@ -2478,17 +2478,17 @@
       "  warnings.warn(\n",
       "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
       "  warnings.warn(\n",
-      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
+      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
       "  warnings.warn(\n",
-      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
+      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
       "  warnings.warn(\n",
-      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
+      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
       "  warnings.warn(\n",
-      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
+      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
       "  warnings.warn(\n",
-      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
+      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
       "  warnings.warn(\n",
-      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
+      "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
       "  warnings.warn(\n",
       "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n",
       "  warnings.warn(\n",

docs/sphinx-builddir/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ebf8cec33d6e4660415dab029412735a
+config: 0b6a7dd1525e6ee19a49f01ec81f57f7
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/sphinx-builddir/html/README.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>QSARtuna: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ) &mdash; QSARtuna 2.7.11 documentation</title>
+  <title>QSARtuna 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ) &mdash; QSARtuna 3.0.0.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/autodoc_pydantic.css" type="text/css" />
@@ -22,7 +22,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Preprocessing data for QSARtuna" href="notebooks/preprocess_data.html" />
-    <link rel="prev" title="Welcome to QSARtuna Documentation!" href="index.html" />
+    <link rel="prev" title="Welcome to QSARtuna Documentation!" href="index.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -83,7 +83,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">QSARtuna: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ)</li>
+      <li class="breadcrumb-item active">QSARtuna 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ)</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/README.md.txt" rel="nofollow"> View page source</a>
       </li>
@@ -118,7 +118,7 @@
 }
 </style>
 <section id="qsartuna-qsar-using-optimization-for-hyperparameter-tuning-formerly-optuna-az">
-<h1>QSARtuna: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ)<a class="headerlink" href="#qsartuna-qsar-using-optimization-for-hyperparameter-tuning-formerly-optuna-az" title="Permalink to this heading"></a></h1>
+<h1>QSARtuna 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ)<a class="headerlink" href="#qsartuna-qsar-using-optimization-for-hyperparameter-tuning-formerly-optuna-az" title="Permalink to this heading"></a></h1>
 <p>Build predictive models for CompChem with hyperparameters optimized by <a class="reference external" href="https://optuna.org/">Optuna</a>.</p>
 <p>Developed with Uncertainty Quantification and model explainability in mind.</p>
 <section id="background">
@@ -129,9 +129,9 @@ <h2>Background<a class="headerlink" href="#background" title="Permalink to this
 for the given data.</p>
 <p>The search itself
 is done using <a class="reference external" href="https://optuna.org/">Optuna</a>.</p>
-<p>Devloped models employ
+<p>Developed models employ
 the latest state-of-the-art
-uncertinaty estimation and
+uncertainty estimation and
 explainability python packages</p>
 <section id="the-three-step-process">
 <h3>The three-step process<a class="headerlink" href="#the-three-step-process" title="Permalink to this heading"></a></h3>
@@ -354,7 +354,7 @@ <h2>Run from Python/Jupyter Notebook<a class="headerlink" href="#run-from-python
 conda<span class="w"> </span>activate<span class="w"> </span>my_env_with_qsartuna
 module<span class="w"> </span>purge<span class="w">  </span><span class="c1"># Just in case.</span>
 which<span class="w"> </span>python<span class="w">  </span><span class="c1"># Check. Should output path that contains &quot;my_env_with_qsartuna&quot;.</span>
-python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>http://pages.scp.astrazeneca.net/mai/qsartuna/releases/QSARtuna_latest.tar.gz
+python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>
 </pre></div>
 </div>
 <p>Then you can use QSARtuna inside your Notebook:</p>
@@ -436,7 +436,7 @@ <h2>Run from Python/Jupyter Notebook<a class="headerlink" href="#run-from-python
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, AstraZeneca.</p>
+    <p>&#169; Copyright 2024, AstraZeneca.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/sphinx-builddir/html/_modules/index.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; QSARtuna 2.7.11 documentation</title>
+  <title>Overview: module code &mdash; QSARtuna 3.0.0.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/autodoc_pydantic.css" type="text/css" />
@@ -120,7 +120,7 @@ <h1>All modules for which code is available</h1>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, AstraZeneca.</p>
+    <p>&#169; Copyright 2024, AstraZeneca.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/sphinx-builddir/html/_modules/optunaz/builder.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>optunaz.builder &mdash; QSARtuna 2.7.11 documentation</title>
+  <title>optunaz.builder &mdash; QSARtuna 3.0.0.1 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/autodoc_pydantic.css" type="text/css" />
@@ -132,7 +132,7 @@ <h1>Source code for optunaz.builder</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, AstraZeneca.</p>
+    <p>&#169; Copyright 2024, AstraZeneca.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/sphinx-builddir/html/_modules/optunaz/config.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>optunaz.config &mdash; QSARtuna 2.7.11 documentation</title>
+  <title>optunaz.config &mdash; QSARtuna 3.0.0.1 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/autodoc_pydantic.css" type="text/css" />
@@ -190,7 +190,7 @@ <h1>Source code for optunaz.config</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, AstraZeneca.</p>
+    <p>&#169; Copyright 2024, AstraZeneca.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>optunaz.config.build_from_opt &mdash; QSARtuna 2.7.11 documentation</title>
+  <title>optunaz.config.build_from_opt &mdash; QSARtuna 3.0.0.1 documentation</title>
       <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/autodoc_pydantic.css" type="text/css" />
@@ -684,7 +684,7 @@ <h1>Source code for optunaz.config.build_from_opt</h1><div class="highlight"><pr
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, AstraZeneca.</p>
+    <p>&#169; Copyright 2024, AstraZeneca.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>optunaz.config.buildconfig &mdash; QSARtuna 2.7.11 documentation</title>
+  <title>optunaz.config.buildconfig &mdash; QSARtuna 3.0.0.1 documentation</title>
       <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/autodoc_pydantic.css" type="text/css" />
@@ -656,7 +656,7 @@ <h1>Source code for optunaz.config.buildconfig</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, AstraZeneca.</p>
+    <p>&#169; Copyright 2024, AstraZeneca.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>optunaz.config.optconfig &mdash; QSARtuna 2.7.11 documentation</title>
+  <title>optunaz.config.optconfig &mdash; QSARtuna 3.0.0.1 documentation</title>
       <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/autodoc_pydantic.css" type="text/css" />
@@ -1918,7 +1918,7 @@ <h1>Source code for optunaz.config.optconfig</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, AstraZeneca.</p>
+    <p>&#169; Copyright 2024, AstraZeneca.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/sphinx-builddir/html/_modules/optunaz/datareader.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>optunaz.datareader &mdash; QSARtuna 2.7.11 documentation</title>
+  <title>optunaz.datareader &mdash; QSARtuna 3.0.0.1 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/autodoc_pydantic.css" type="text/css" />
@@ -677,7 +677,7 @@ <h1>Source code for optunaz.datareader</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, AstraZeneca.</p>
+    <p>&#169; Copyright 2024, AstraZeneca.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/sphinx-builddir/html/_modules/optunaz/descriptors.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>optunaz.descriptors &mdash; QSARtuna 2.7.11 documentation</title>
+  <title>optunaz.descriptors &mdash; QSARtuna 3.0.0.1 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/autodoc_pydantic.css" type="text/css" />
@@ -638,9 +638,9 @@ <h1>Source code for optunaz.descriptors</h1><div class="highlight"><pre>
                 <span class="sa">f</span><span class="s2">&quot;Multiple descriptors found for </span><span class="si">{</span><span class="n">smi</span><span class="si">}</span><span class="s2">, taking the first one.&quot;</span>
             <span class="p">)</span>
         <span class="n">descriptor_iloc</span> <span class="o">=</span> <span class="n">rows</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">response_column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">descriptor_iloc</span><span class="p">)</span> <span class="o">==</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">descriptor_iloc</span><span class="p">])</span>
-        <span class="k">else</span><span class="p">:</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">descriptor_iloc</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)])</span>
+        <span class="k">except</span> <span class="p">(</span><span class="ne">ValueError</span><span class="p">,</span> <span class="ne">AttributeError</span><span class="p">):</span>
             <span class="n">fp</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">fromstring</span><span class="p">(</span><span class="n">descriptor_iloc</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;,&quot;</span><span class="p">)</span>
             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
                 <span class="k">return</span> <span class="kc">None</span>
@@ -975,7 +975,7 @@ <h1>Source code for optunaz.descriptors</h1><div class="highlight"><pre>
             <span class="n">ds</span> <span class="o">=</span> <span class="p">[]</span>
             <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">descriptors</span><span class="p">:</span>
                 <span class="k">try</span><span class="p">:</span>
-                    <span class="c1"># Copmosite descriptors comprising scaled descriptors pass through cache</span>
+                    <span class="c1"># Composite descriptors comprising scaled descriptors pass through cache</span>
                     <span class="n">ds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">d</span><span class="o">.</span><span class="n">calculate_from_smi</span><span class="p">(</span><span class="n">smi</span><span class="p">,</span> <span class="n">cache</span><span class="o">=</span><span class="n">cache</span><span class="p">))</span>
                 <span class="k">except</span> <span class="ne">TypeError</span><span class="p">:</span>
                     <span class="c1"># All other descriptors use the cache directly and do not expect cache as parameter</span>
@@ -1138,7 +1138,7 @@ <h1>Source code for optunaz.descriptors</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, AstraZeneca.</p>
+    <p>&#169; Copyright 2024, AstraZeneca.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a