Merge pull request #35 from MolecularAI/3.1.4_prep

3.1.4
MolecularAI · Oct 3, 2024 · 1b0c945 · 1b0c945
2 parents b509ff4 + 00f6609
commit 1b0c945
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diff --git a/README.md b/README.md
@@ -48,11 +48,11 @@ Create conda environment with Jupyter and Install QSARtuna there:
 ```shell
 module purge
 module load Miniconda3
-conda create --name my_env_with_qsartuna python=3.10.10 jupyter pip
+conda create --name my_env_with_qsartuna python=3.11 jupyter pip # any python ^3.10
 conda activate my_env_with_qsartuna
 module purge  # Just in case.
 which python  # Check. Should output path that contains "my_env_with_qsartuna".
-python -m pip install https://github.com/MolecularAI/QSARtuna/releases/download/3.1.1/qsartuna-3.1.1.tar.gz
+python -m pip install https://github.com/MolecularAI/QSARtuna/releases/download/3.1.4/qsartuna-3.1.4.tar.gz
 ```
 
 ## Running from Python/Jupyter Notebook
@@ -121,7 +121,7 @@ QSARtuna can be deployed directly from the CLI
 
 To run commands QSARtuna uses the following syntax:
 ```shell
-qsartuna-<optimize|build|predict|schemagen> <command>
+qsartuna-<optimize|build|predict|schemagen|automl|metadata|convert> <command>
 ```
 
 We can run three-step-process from command line with the following command:
@@ -438,12 +438,12 @@ required named arguments:
 
 ```
 
-An example of how to run this in SCP would be:
+An example of how to run this would be:
 
 ```shell
 qsartuna-automl  --input-data "tests/data/automl/*"  --email <email>.com  --user_name <user_name> \
  --input-smiles-csv-column canonical  --input-activity-csv-column molwt --input-task-csv-column one_taskid  \
- --input-initial-template examples/auto^C/config.initial.template  \
+ --input-initial-template examples/automl/config.initial.template  \
  --input-retrain-template examples/automl/config.retrain.template  \
  --input-slurm-template examples/slurm-scripts/automl.template  \
  --n-cores 1 -vvv --slurm-al-pool tests/data/DRD2/subset-50/train.csv  \
@@ -585,13 +585,15 @@ or in a new config:
 
 ## Adding machine learning algorithms to QSARtuna
 
+NB: CustomClassificationModel and CustomRegressionModel algorithm options are now available to allow customised algorithms within QSARtuna (see tutorial for details). This new feature is experimental and should be used with caution
+
 1.) (Optional) consider adding .py algorithm code to the `optunaz/algorithms/` directory, so this can be imported later
 
 2.) Add the algorithm to `optunaz.config.optconfig.py`. For example, create a class among the existing algorithms like so:
 
 ```python
 @dataclass
-class YourAglrotihm(Algorithm):
+class YourAlgorithm(Algorithm):
     """Your description goes here
     """
 
@@ -787,3 +789,44 @@ or in a new config:
     }
   ]
 }
+
+
+## Converting models to QSARtuna models
+
+QSARtuna has a CLI helper to convert models to QSARtuna models
+
+We can perform this with the following command:
+
+```shell
+  qsartuna-convert \
+  --input-model-file {project_folder}/sklearn_model.pkl\
+  --input-model-mode regression \
+  --output-model-path {project_folder}/qsartuna.pkl \
+```
+
+The convert CLI tool accepts the following command line arguments:
+
+```
+shell
+qsartuna-convert -h
+usage: qsartuna-convert [-h] --input-model-file INPUT_MODEL_FILE --input-model-mode INPUT_MODEL_MODE --output-model-path OUTPUT_MODEL_PATH [--input-json-descriptor-file INPUT_JSON_DESCRIPTOR_FILE] [--wrap-for-uncertainty]
+
+Convert an existing sklearn(-like) model into a QSARtuna model
+
+options:
+  -h, --help            show this help message and exit
+  --input-json-descriptor-file INPUT_JSON_DESCRIPTOR_FILE
+                        Name of input JSON file with descriptor configuration. Defaults to PrecomputedDescriptorFromFile
+  --wrap-for-uncertainty
+                        Whether to wrap regression in MAPIE or classification in VennAbers Calibrated Classifiers for uncertainty support
+
+required named arguments:
+  --input-model-file INPUT_MODEL_FILE
+                        Model file name.
+  --input-model-mode INPUT_MODEL_MODE
+                        Classification or regression mode for the existing model.
+  --output-model-path OUTPUT_MODEL_PATH
+                        Path where to write the converted model.
+```
+
+Advanced options for the QSARtuna convert CLI tool are covered in the QSARtuna Notebook tutorial
diff --git a/docs/sphinx-builddir/doctrees/README.doctree b/docs/sphinx-builddir/doctrees/README.doctree
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/nbsphinx/notebooks/QSARtuna_Tutorial.ipynb b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QSARtuna_Tutorial.ipynb
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_101_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_101_0.png
diff --git a/...inx/notebooks_QSARtuna_Tutorial_123_1.png → ...inx/notebooks_QSARtuna_Tutorial_123_0.png b/...inx/notebooks_QSARtuna_Tutorial_123_1.png → ...inx/notebooks_QSARtuna_Tutorial_123_0.png
diff --git a/...inx/notebooks_QSARtuna_Tutorial_125_1.png → ...inx/notebooks_QSARtuna_Tutorial_125_0.png b/...inx/notebooks_QSARtuna_Tutorial_125_1.png → ...inx/notebooks_QSARtuna_Tutorial_125_0.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_148_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_148_0.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_153_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_153_0.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_160_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_160_0.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_162_2.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_162_2.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_170_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_170_0.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_172_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_172_0.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_174_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_174_0.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_176_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_176_0.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_279_1.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_279_1.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_67_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_67_0.png
diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_71_0.png b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks_QSARtuna_Tutorial_71_0.png
diff --git a/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.doctree b/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.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.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/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: cd8105a3e394e54ace4ef41b1def0634
+config: aef108bc3193b5297b76666fcb5f2b5d
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/sphinx-builddir/html/README.html b/docs/sphinx-builddir/html/README.html
diff --git a/.../sphinx-builddir/html/_images/math/3f70390a18466402130c5506d33246d065501df2.png b/.../sphinx-builddir/html/_images/math/3f70390a18466402130c5506d33246d065501df2.png
diff --git a/.../sphinx-builddir/html/_images/math/70bac2a2847dd0c54f3ae16fce06d3ee57f8e9b6.png b/.../sphinx-builddir/html/_images/math/70bac2a2847dd0c54f3ae16fce06d3ee57f8e9b6.png
diff --git a/.../sphinx-builddir/html/_images/math/70d78bd3db115d769a17bff8db1f61f47ba66ad3.png b/.../sphinx-builddir/html/_images/math/70d78bd3db115d769a17bff8db1f61f47ba66ad3.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_101_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_101_0.png
diff --git a/...ges/notebooks_QSARtuna_Tutorial_123_1.png → ...ges/notebooks_QSARtuna_Tutorial_123_0.png b/...ges/notebooks_QSARtuna_Tutorial_123_1.png → ...ges/notebooks_QSARtuna_Tutorial_123_0.png
diff --git a/...ges/notebooks_QSARtuna_Tutorial_125_1.png → ...ges/notebooks_QSARtuna_Tutorial_125_0.png b/...ges/notebooks_QSARtuna_Tutorial_125_1.png → ...ges/notebooks_QSARtuna_Tutorial_125_0.png
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
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_160_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_160_0.png
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diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_170_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_170_0.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_172_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_172_0.png
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diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_176_0.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_176_0.png
diff --git a/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_279_1.png b/docs/sphinx-builddir/html/_images/notebooks_QSARtuna_Tutorial_279_1.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
@@ -84,7 +84,8 @@ <h1>All modules for which code is available</h1>
 <ul><li><a href="optunaz/config/build_from_opt.html">optunaz.config.build_from_opt</a></li>
 <li><a href="optunaz/config/buildconfig.html">optunaz.config.buildconfig</a></li>
 <li><a href="optunaz/config/optconfig.html">optunaz.config.optconfig</a></li>
-</ul><li><a href="optunaz/datareader.html">optunaz.datareader</a></li>
+</ul><li><a href="optunaz/convert.html">optunaz.convert</a></li>
+<li><a href="optunaz/datareader.html">optunaz.datareader</a></li>
 <li><a href="optunaz/descriptors.html">optunaz.descriptors</a></li>
 <li><a href="optunaz/evaluate.html">optunaz.evaluate</a></li>
 <li><a href="optunaz/explainability.html">optunaz.explainability</a></li>

diff --git a/docs/sphinx-builddir/html/_modules/optunaz/automl.html b/docs/sphinx-builddir/html/_modules/optunaz/automl.html
@@ -89,6 +89,7 @@ <h1>Source code for optunaz.automl</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 <span class="kn">import</span> <span class="nn">time</span>
 <span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">logging.config</span>
 <span class="kn">import</span> <span class="nn">argparse</span>
 <span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">datetime</span><span class="p">,</span> <span class="n">timedelta</span>
 <span class="kn">import</span> <span class="nn">dataclasses</span>
@@ -626,7 +627,13 @@ <h1>Source code for optunaz.automl</h1><div class="highlight"><pre>
             <span class="k">elif</span> <span class="nb">any</span><span class="p">(</span>
                 <span class="p">[</span>
                     <span class="n">err</span> <span class="ow">in</span> <span class="n">slurm_log</span>
-                    <span class="k">for</span> <span class="n">err</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;DUE TO MEMORY&quot;</span><span class="p">,</span> <span class="s2">&quot;Bus error&quot;</span><span class="p">,</span> <span class="s2">&quot;Unable to allocate&quot;</span><span class="p">]</span>
+                    <span class="k">for</span> <span class="n">err</span> <span class="ow">in</span> <span class="p">[</span>
+                        <span class="s2">&quot;DUE TO MEMORY&quot;</span><span class="p">,</span>
+                        <span class="s2">&quot;Bus error&quot;</span><span class="p">,</span>
+                        <span class="s2">&quot;Unable to allocate&quot;</span><span class="p">,</span>
+                        <span class="s2">&quot;oom_kill&quot;</span><span class="p">,</span>
+                        <span class="s2">&quot;OOM Killed&quot;</span><span class="p">,</span>
+                    <span class="p">]</span>
                 <span class="p">]</span>
             <span class="p">):</span>
                 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">slurm_name</span><span class="si">}</span><span class="s2"> memory was reached&quot;</span><span class="p">)</span>
@@ -641,6 +648,9 @@ <h1>Source code for optunaz.automl</h1><div class="highlight"><pre>
             <span class="k">elif</span> <span class="s2">&quot;Adjust any of the aforementioned parameters&quot;</span> <span class="ow">in</span> <span class="n">slurm_log</span><span class="p">:</span>
                 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">slurm_name</span><span class="si">}</span><span class="s2"> had splitting error&quot;</span><span class="p">)</span>
                 <span class="k">raise</span> <span class="n">SlurmJobSkip</span>
+            <span class="k">elif</span> <span class="s2">&quot;qptuna.predict.UncertaintyError&quot;</span> <span class="ow">in</span> <span class="n">slurm_log</span><span class="p">:</span>
+                <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">slurm_name</span><span class="si">}</span><span class="s2"> does not support uncertainty estimation&quot;</span><span class="p">)</span>
+                <span class="k">raise</span> <span class="n">SlurmJobSkip</span>
         <span class="k">except</span> <span class="ne">FileNotFoundError</span><span class="p">:</span>
             <span class="k">raise</span> <span class="n">SlurmNoLog</span></div>
 
@@ -993,14 +1003,14 @@ <h1>Source code for optunaz.automl</h1><div class="highlight"><pre>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-v&#39;</span><span class="p">,</span> <span class="s1">&#39;--verbose&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;count&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
 
     <span class="c1"># SLURM global variables</span>
-    <span class="n">requiredNamed</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-job-prefix&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-req-cores&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">12</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-req-mem&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="c1"># By default, None = dynamic mem resource allocation</span>
     <span class="n">requiredNamed</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-req-partition&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
     <span class="n">requiredNamed</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-al-pool&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
     <span class="n">requiredNamed</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-al-smiles-csv-column&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 
     <span class="c1"># dispatcher variables</span>
+    <span class="n">requiredNamed</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-job-prefix&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-failure-cores-increment&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">4</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-failure-mem-increment&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">20</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--slurm-failure-mins-increment&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">720</span><span class="p">)</span>