Merge pull request #8 from MolecularAI/3.1.0

Bump 3.1.0
MolecularAI · Jul 2, 2024 · 0a7fd9f · 0a7fd9f
2 parents 87a7ab2 + 7852ba2
commit 0a7fd9f
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Showing 215 changed files with 21,836 additions and 65,143 deletions.
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# QSARtuna 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ and QPTUNA)
+# QSARtuna 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ and QSARtuna)
 
 Build predictive models for CompChem with hyperparameters optimized by [Optuna](https://optuna.org/).
 

diff --git a/docs/Makefile b/docs/Makefile
@@ -33,5 +33,11 @@ html: Makefile
 $(SOURCEDIR)/_static/pytest:
 	cd .. && pytest --cov-report html:docs/$(SOURCEDIR)/_static/pytest/coverage/ --cov-report xml:coverage.xml --html=docs/$(SOURCEDIR)/_static/pytest/pytest/index.html --cov optunaz
 
+scpdocdeploy:
+	rsync -avz $(BUILDDIR)/html/ login.scp.astrazeneca.net:/projects/mai/public_html/qsartuna/ --no-o --no-g --omit-dir-times --no-perms
+	# adding --delete to rsync removes qsartuna/releases!
+	# Alternative:
+	# scp -r $(BUILDDIR)/html login.scp.astrazeneca.net:/projects/mai/public_html/qsartuna/
+
 clean:
 	rm -rf $(BUILDDIR) $(SOURCEDIR)
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diff --git a/docs/sphinx-builddir/doctrees/algorithms.doctree b/docs/sphinx-builddir/doctrees/algorithms.doctree
diff --git a/docs/sphinx-builddir/doctrees/deduplicator.doctree b/docs/sphinx-builddir/doctrees/deduplicator.doctree
diff --git a/docs/sphinx-builddir/doctrees/descriptors.doctree b/docs/sphinx-builddir/doctrees/descriptors.doctree
diff --git a/docs/sphinx-builddir/doctrees/environment.pickle b/docs/sphinx-builddir/doctrees/environment.pickle
diff --git a/docs/sphinx-builddir/doctrees/index.doctree b/docs/sphinx-builddir/doctrees/index.doctree
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QSARtuna_Tutorial.ipynb b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QSARtuna_Tutorial.ipynb
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diff --git a/docs/sphinx-builddir/doctrees/notebooks/preprocess_data.doctree b/docs/sphinx-builddir/doctrees/notebooks/preprocess_data.doctree
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.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: 0b6a7dd1525e6ee19a49f01ec81f57f7
+config: 9b1af61dfe8db8b73ea495bbe6736b6a
 tags: 645f666f9bcd5a90fca523b33c5a78b7
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diff --git a/docs/sphinx-builddir/html/_images/mlflow-inspecting-trials.png b/docs/sphinx-builddir/html/_images/mlflow-inspecting-trials.png
diff --git a/docs/sphinx-builddir/html/_images/mlflow-select-experiment.png b/docs/sphinx-builddir/html/_images/mlflow-select-experiment.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QPTUNA_Tutorial_101_0.png b/docs/sphinx-builddir/html/_images/notebooks_QPTUNA_Tutorial_101_0.png
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diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_23_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_23_0.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_35_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_35_0.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_56_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_56_0.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_67_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_67_0.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_71_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_71_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 3.0.0.1 documentation</title>
+  <title>Overview: module code &mdash; QSARtuna 3.1.0 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" />
@@ -49,6 +49,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../algorithms.html">List of available ML algorithms</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../descriptors.html">List of available molecular descriptors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../splitters.html">List of available evaluation splits</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../transform.html">List of available data transform</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../deduplicator.html">List of available deduplicators</a></li>
 </ul>
 
         </div>

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 3.0.0.1 documentation</title>
+  <title>optunaz.builder &mdash; QSARtuna 3.1.0 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" />
@@ -49,6 +49,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../../algorithms.html">List of available ML algorithms</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../descriptors.html">List of available molecular descriptors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../splitters.html">List of available evaluation splits</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../transform.html">List of available data transform</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../deduplicator.html">List of available deduplicators</a></li>
 </ul>
 
         </div>

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 3.0.0.1 documentation</title>
+  <title>optunaz.config &mdash; QSARtuna 3.1.0 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" />
@@ -49,6 +49,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../../algorithms.html">List of available ML algorithms</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../descriptors.html">List of available molecular descriptors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../splitters.html">List of available evaluation splits</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../transform.html">List of available data transform</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../deduplicator.html">List of available deduplicators</a></li>
 </ul>
 
         </div>