Merge pull request #18 from MolecularAI/misc_fixes

Init 3.1.0
MolecularAI · Jul 9, 2024 · 37d6efc · 37d6efc
2 parents 0db1cd2 + 7e8647d
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diff --git a/README.md b/README.md
@@ -336,3 +336,132 @@ build_best(buildconfig, "target/best.pkl")
 # Build (Train) and save the model on the merged train+test data.
 build_merged(buildconfig, "target/merged.pkl")
 ```
+
+
+## Adding descriptors to QSARtuna
+
+
+Add the descriptor code to the optunaz.descriptor.py file like so:
+
+```python
+@dataclass
+class YourNewDescriptor(RdkitDescriptor):
+    """YOUR DESCRIPTION GOES HERE"""
+
+    @apischema.type_name("YourNewDescriptorParams")
+    @dataclass
+    class Parameters:
+        # Any parameters to pass to your descriptor here
+        exampleOfAParameter: Annotated[
+            int,
+            schema(
+                min=1,
+                title="exampleOfAParameter",
+                description="This is an example int parameter.",
+            ),
+        ] = field(
+            default=1,
+        )
+
+    name: Literal["YourNewDescriptor"]
+    parameters: Parameters
+
+    def calculate_from_smi(self, smi: str):
+        # Insert your code to calculate from SMILES here
+        fp = code_to_calculate_fp(smi)
+        return fp
+```
+
+Then add the descriptor to the list here:
+
+```python
+AnyUnscaledDescriptor = Union[
+    Avalon,
+    ECFP,
+    ECFP_counts,
+    PathFP,
+    AmorProtDescriptors,
+    MACCS_keys,
+    PrecomputedDescriptorFromFile,
+    UnscaledMAPC,
+    UnscaledPhyschemDescriptors,
+    UnscaledJazzyDescriptors,
+    UnscaledZScalesDescriptors,
+    YourNewDescriptor, #Ensure your new descriptor added here
+]
+```
+
+and here:
+
+```python
+CompositeCompatibleDescriptor = Union[
+    AnyUnscaledDescriptor,
+    ScaledDescriptor,
+    MAPC,
+    PhyschemDescriptors,
+    JazzyDescriptors,
+    ZScalesDescriptors,
+    YourNewDescriptor, #Ensure your new descriptor added here
+]
+```
+
+Then you can use YourNewDescriptor inside your Notebook:
+```python
+from qptuna.descriptors import YourNewDescriptor
+
+config = OptimizationConfig(
+    data=Dataset(
+        input_column="canonical",
+        response_column="molwt",
+        training_dataset_file="tests/data/DRD2/subset-50/train.csv",
+    ),
+    descriptors=[YourNewDescriptor.new()],
+    algorithms=[
+        SVR.new(),
+    ],
+    settings=OptimizationConfig.Settings(
+        mode=ModelMode.REGRESSION,
+        cross_validation=3,
+        n_trials=100,
+        direction=OptimizationDirection.MAXIMIZATION,
+    ),
+)
+```
+
+or in a new config:
+
+```json
+{
+  "task": "optimization",
+  "data": {
+    "training_dataset_file": "tests/data/DRD2/subset-50/train.csv",
+    "input_column": "canonical",
+    "response_column": "molwt"
+  },
+  "settings": {
+    "mode": "regression",
+    "cross_validation": 5,
+    "direction": "maximize",
+    "n_trials": 100,
+    "n_startup_trials": 30
+  },
+  "descriptors": [
+    {
+      "name": "YourNewDescriptor",
+      "parameters": {
+        "exampleOfAParameter": 3
+      }
+    }
+  ],
+  "algorithms": [
+    {
+      "name": "RandomForestRegressor",
+      "parameters": {
+        "max_depth": {"low": 2, "high": 32},
+        "n_estimators": {"low": 10, "high": 250},
+        "max_features": ["auto"]
+      }
+    }
+  ]
+}
+```
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diff --git a/docs/sphinx-builddir/doctrees/optunaz.config.doctree b/docs/sphinx-builddir/doctrees/optunaz.config.doctree
diff --git a/docs/sphinx-builddir/doctrees/optunaz.doctree b/docs/sphinx-builddir/doctrees/optunaz.doctree
diff --git a/docs/sphinx-builddir/doctrees/optunaz.utils.doctree b/docs/sphinx-builddir/doctrees/optunaz.utils.doctree
diff --git a/docs/sphinx-builddir/doctrees/optunaz.utils.enums.doctree b/docs/sphinx-builddir/doctrees/optunaz.utils.enums.doctree
diff --git a/docs/sphinx-builddir/doctrees/optunaz.utils.preprocessing.doctree b/docs/sphinx-builddir/doctrees/optunaz.utils.preprocessing.doctree
diff --git a/docs/sphinx-builddir/doctrees/splitters.doctree b/docs/sphinx-builddir/doctrees/splitters.doctree
diff --git a/docs/sphinx-builddir/doctrees/transform.doctree b/docs/sphinx-builddir/doctrees/transform.doctree
diff --git a/docs/sphinx-builddir/html/.buildinfo b/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: 74e083516866086104039ea37495342c
+config: ce10f6da50cb5fb9c54e3d7b69f125b1
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/sphinx-builddir/html/README.html b/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 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ and QPTUNA) &mdash; QSARtuna 3.1.0 documentation</title>
+  <title>QSARtuna 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ and QPTUNA) &mdash; QSARtuna 3.1.1 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" />
@@ -60,6 +60,7 @@
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="#run-from-python-jupyter-notebook">Run from Python/Jupyter Notebook</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#adding-descriptors-to-qsartuna">Adding descriptors to QSARtuna</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/preprocess_data.html">Jupyter Notebook: Preprocessing Data for QSARtuna</a></li>
@@ -427,6 +428,125 @@ <h2>Run from Python/Jupyter Notebook<a class="headerlink" href="#run-from-python
 </pre></div>
 </div>
 </section>
+<section id="adding-descriptors-to-qsartuna">
+<h2>Adding descriptors to QSARtuna<a class="headerlink" href="#adding-descriptors-to-qsartuna" title="Permalink to this heading"></a></h2>
+<p>Add the descriptor code to the optunaz.descriptor.py file like so:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="nd">@dataclass</span>
+<span class="k">class</span> <span class="nc">YourNewDescriptor</span><span class="p">(</span><span class="n">RdkitDescriptor</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;YOUR DESCRIPTION GOES HERE&quot;&quot;&quot;</span>
+
+    <span class="nd">@apischema</span><span class="o">.</span><span class="n">type_name</span><span class="p">(</span><span class="s2">&quot;YourNewDescriptorParams&quot;</span><span class="p">)</span>
+    <span class="nd">@dataclass</span>
+    <span class="k">class</span> <span class="nc">Parameters</span><span class="p">:</span>
+        <span class="c1"># Any parameters to pass to your descriptor here</span>
+        <span class="n">exampleOfAParameter</span><span class="p">:</span> <span class="n">Annotated</span><span class="p">[</span>
+            <span class="nb">int</span><span class="p">,</span>
+            <span class="n">schema</span><span class="p">(</span>
+                <span class="nb">min</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+                <span class="n">title</span><span class="o">=</span><span class="s2">&quot;exampleOfAParameter&quot;</span><span class="p">,</span>
+                <span class="n">description</span><span class="o">=</span><span class="s2">&quot;This is an example int parameter.&quot;</span><span class="p">,</span>
+            <span class="p">),</span>
+        <span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span>
+            <span class="n">default</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+        <span class="p">)</span>
+
+    <span class="n">name</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s2">&quot;YourNewDescriptor&quot;</span><span class="p">]</span>
+    <span class="n">parameters</span><span class="p">:</span> <span class="n">Parameters</span>
+
+    <span class="k">def</span> <span class="nf">calculate_from_smi</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">smi</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+        <span class="c1"># Insert your code to calculate from SMILES here</span>
+        <span class="n">fp</span> <span class="o">=</span> <span class="n">code_to_calculate_fp</span><span class="p">(</span><span class="n">smi</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">fp</span>
+</pre></div>
+</div>
+<p>Then add the descriptor to the list here:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">AnyUnscaledDescriptor</span> <span class="o">=</span> <span class="n">Union</span><span class="p">[</span>
+    <span class="n">Avalon</span><span class="p">,</span>
+    <span class="n">ECFP</span><span class="p">,</span>
+    <span class="n">ECFP_counts</span><span class="p">,</span>
+    <span class="n">PathFP</span><span class="p">,</span>
+    <span class="n">AmorProtDescriptors</span><span class="p">,</span>
+    <span class="n">MACCS_keys</span><span class="p">,</span>
+    <span class="n">PrecomputedDescriptorFromFile</span><span class="p">,</span>
+    <span class="n">UnscaledMAPC</span><span class="p">,</span>
+    <span class="n">UnscaledPhyschemDescriptors</span><span class="p">,</span>
+    <span class="n">UnscaledJazzyDescriptors</span><span class="p">,</span>
+    <span class="n">UnscaledZScalesDescriptors</span><span class="p">,</span>
+    <span class="n">YourNewDescriptor</span><span class="p">,</span> <span class="c1">#Ensure your new descriptor added here</span>
+<span class="p">]</span>
+</pre></div>
+</div>
+<p>and here:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">CompositeCompatibleDescriptor</span> <span class="o">=</span> <span class="n">Union</span><span class="p">[</span>
+    <span class="n">AnyUnscaledDescriptor</span><span class="p">,</span>
+    <span class="n">ScaledDescriptor</span><span class="p">,</span>
+    <span class="n">MAPC</span><span class="p">,</span>
+    <span class="n">PhyschemDescriptors</span><span class="p">,</span>
+    <span class="n">JazzyDescriptors</span><span class="p">,</span>
+    <span class="n">ZScalesDescriptors</span><span class="p">,</span>
+    <span class="n">YourNewDescriptor</span><span class="p">,</span> <span class="c1">#Ensure your new descriptor added here</span>
+<span class="p">]</span>
+</pre></div>
+</div>
+<p>Then you can use YourNewDescriptor inside your Notebook:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">qptuna.descriptors</span> <span class="kn">import</span> <span class="n">YourNewDescriptor</span>
+
+<span class="n">config</span> <span class="o">=</span> <span class="n">OptimizationConfig</span><span class="p">(</span>
+    <span class="n">data</span><span class="o">=</span><span class="n">Dataset</span><span class="p">(</span>
+        <span class="n">input_column</span><span class="o">=</span><span class="s2">&quot;canonical&quot;</span><span class="p">,</span>
+        <span class="n">response_column</span><span class="o">=</span><span class="s2">&quot;molwt&quot;</span><span class="p">,</span>
+        <span class="n">training_dataset_file</span><span class="o">=</span><span class="s2">&quot;tests/data/DRD2/subset-50/train.csv&quot;</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="n">descriptors</span><span class="o">=</span><span class="p">[</span><span class="n">YourNewDescriptor</span><span class="o">.</span><span class="n">new</span><span class="p">()],</span>
+    <span class="n">algorithms</span><span class="o">=</span><span class="p">[</span>
+        <span class="n">SVR</span><span class="o">.</span><span class="n">new</span><span class="p">(),</span>
+    <span class="p">],</span>
+    <span class="n">settings</span><span class="o">=</span><span class="n">OptimizationConfig</span><span class="o">.</span><span class="n">Settings</span><span class="p">(</span>
+        <span class="n">mode</span><span class="o">=</span><span class="n">ModelMode</span><span class="o">.</span><span class="n">REGRESSION</span><span class="p">,</span>
+        <span class="n">cross_validation</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span>
+        <span class="n">n_trials</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span>
+        <span class="n">direction</span><span class="o">=</span><span class="n">OptimizationDirection</span><span class="o">.</span><span class="n">MAXIMIZATION</span><span class="p">,</span>
+    <span class="p">),</span>
+<span class="p">)</span>
+</pre></div>
+</div>
+<p>or in a new config:</p>
+<div class="highlight-json notranslate"><div class="highlight"><pre><span></span><span class="p">{</span>
+<span class="w">  </span><span class="nt">&quot;task&quot;</span><span class="p">:</span><span class="w"> </span><span class="s2">&quot;optimization&quot;</span><span class="p">,</span>
+<span class="w">  </span><span class="nt">&quot;data&quot;</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="nt">&quot;training_dataset_file&quot;</span><span class="p">:</span><span class="w"> </span><span class="s2">&quot;tests/data/DRD2/subset-50/train.csv&quot;</span><span class="p">,</span>
+<span class="w">    </span><span class="nt">&quot;input_column&quot;</span><span class="p">:</span><span class="w"> </span><span class="s2">&quot;canonical&quot;</span><span class="p">,</span>
+<span class="w">    </span><span class="nt">&quot;response_column&quot;</span><span class="p">:</span><span class="w"> </span><span class="s2">&quot;molwt&quot;</span>
+<span class="w">  </span><span class="p">},</span>
+<span class="w">  </span><span class="nt">&quot;settings&quot;</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="nt">&quot;mode&quot;</span><span class="p">:</span><span class="w"> </span><span class="s2">&quot;regression&quot;</span><span class="p">,</span>
+<span class="w">    </span><span class="nt">&quot;cross_validation&quot;</span><span class="p">:</span><span class="w"> </span><span class="mi">5</span><span class="p">,</span>
+<span class="w">    </span><span class="nt">&quot;direction&quot;</span><span class="p">:</span><span class="w"> </span><span class="s2">&quot;maximize&quot;</span><span class="p">,</span>
+<span class="w">    </span><span class="nt">&quot;n_trials&quot;</span><span class="p">:</span><span class="w"> </span><span class="mi">100</span><span class="p">,</span>
+<span class="w">    </span><span class="nt">&quot;n_startup_trials&quot;</span><span class="p">:</span><span class="w"> </span><span class="mi">30</span>
+<span class="w">  </span><span class="p">},</span>
+<span class="w">  </span><span class="nt">&quot;descriptors&quot;</span><span class="p">:</span><span class="w"> </span><span class="p">[</span>
+<span class="w">    </span><span class="p">{</span>
+<span class="w">      </span><span class="nt">&quot;name&quot;</span><span class="p">:</span><span class="w"> </span><span class="s2">&quot;YourNewDescriptor&quot;</span><span class="p">,</span>
+<span class="w">      </span><span class="nt">&quot;parameters&quot;</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
+<span class="w">        </span><span class="nt">&quot;exampleOfAParameter&quot;</span><span class="p">:</span><span class="w"> </span><span class="mi">3</span>
+<span class="w">      </span><span class="p">}</span>
+<span class="w">    </span><span class="p">}</span>
+<span class="w">  </span><span class="p">],</span>
+<span class="w">  </span><span class="nt">&quot;algorithms&quot;</span><span class="p">:</span><span class="w"> </span><span class="p">[</span>
+<span class="w">    </span><span class="p">{</span>
+<span class="w">      </span><span class="nt">&quot;name&quot;</span><span class="p">:</span><span class="w"> </span><span class="s2">&quot;RandomForestRegressor&quot;</span><span class="p">,</span>
+<span class="w">      </span><span class="nt">&quot;parameters&quot;</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
+<span class="w">        </span><span class="nt">&quot;max_depth&quot;</span><span class="p">:</span><span class="w"> </span><span class="p">{</span><span class="nt">&quot;low&quot;</span><span class="p">:</span><span class="w"> </span><span class="mi">2</span><span class="p">,</span><span class="w"> </span><span class="nt">&quot;high&quot;</span><span class="p">:</span><span class="w"> </span><span class="mi">32</span><span class="p">},</span>
+<span class="w">        </span><span class="nt">&quot;n_estimators&quot;</span><span class="p">:</span><span class="w"> </span><span class="p">{</span><span class="nt">&quot;low&quot;</span><span class="p">:</span><span class="w"> </span><span class="mi">10</span><span class="p">,</span><span class="w"> </span><span class="nt">&quot;high&quot;</span><span class="p">:</span><span class="w"> </span><span class="mi">250</span><span class="p">},</span>
+<span class="w">        </span><span class="nt">&quot;max_features&quot;</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="s2">&quot;auto&quot;</span><span class="p">]</span>
+<span class="w">      </span><span class="p">}</span>
+<span class="w">    </span><span class="p">}</span>
+<span class="w">  </span><span class="p">]</span>
+<span class="p">}</span>
+</pre></div>
+</div>
+</section>
 </section>
 
 

diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_148_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_148_0.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_153_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_153_0.png
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diff --git a/docs/sphinx-builddir/html/_images/notebooks_preprocess_data_18_0.png b/docs/sphinx-builddir/html/_images/notebooks_preprocess_data_18_0.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_preprocess_data_32_0.png b/docs/sphinx-builddir/html/_images/notebooks_preprocess_data_32_0.png
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diff --git a/docs/sphinx-builddir/html/_images/notebooks_preprocess_data_50_1.png b/docs/sphinx-builddir/html/_images/notebooks_preprocess_data_50_1.png
diff --git a/...images/notebooks_preprocess_data_67_1.png → ...images/notebooks_preprocess_data_67_0.png b/...images/notebooks_preprocess_data_67_1.png → ...images/notebooks_preprocess_data_67_0.png
diff --git a/docs/sphinx-builddir/html/_modules/index.html b/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 3.1.0 documentation</title>
+  <title>Overview: module code &mdash; QSARtuna 3.1.1 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" />

diff --git a/docs/sphinx-builddir/html/_modules/optunaz/builder.html b/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 3.1.0 documentation</title>
+  <title>optunaz.builder &mdash; QSARtuna 3.1.1 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" />

diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config.html b/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 3.1.0 documentation</title>
+  <title>optunaz.config &mdash; QSARtuna 3.1.1 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" />

diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html b/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 3.1.0 documentation</title>
+  <title>optunaz.config.build_from_opt &mdash; QSARtuna 3.1.1 documentation</title>
       <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
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diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html b/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 3.1.0 documentation</title>
+  <title>optunaz.config.buildconfig &mdash; QSARtuna 3.1.1 documentation</title>
       <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
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diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html b/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 3.1.0 documentation</title>
+  <title>optunaz.config.optconfig &mdash; QSARtuna 3.1.1 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" />