Skip to content

Commit

Permalink
Update tests and docs
Browse files Browse the repository at this point in the history
  • Loading branch information
lewismervin1 committed Jul 2, 2024
1 parent c059a9e commit 92520ac
Show file tree
Hide file tree
Showing 39 changed files with 16,434 additions and 11,371 deletions.
Binary file modified docs/sphinx-builddir/doctrees/environment.pickle
Binary file not shown.
Binary file modified docs/sphinx-builddir/doctrees/index.doctree
Binary file not shown.
2,276 changes: 1,125 additions & 1,151 deletions docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QSARtuna_Tutorial.ipynb

Large diffs are not rendered by default.

Binary file not shown.
2 changes: 0 additions & 2 deletions docs/sphinx-builddir/html/_sources/index.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,4 @@ Development
-----------
* `Test report <_static/pytest/pytest/index.html>`_
* `Test coverage <_static/pytest/coverage/index.html>`_
* `Source code (GitHub) <https://github.com/AZU-RDIT/optuna_az/>`_
* `Issues (Jira) <https://jira.rd.astrazeneca.net/browse/OPTUNA/>`_
* `Public release (3.1.0) <https://github.com/MolecularAI/QSARtuna/>`_
2 changes: 0 additions & 2 deletions docs/sphinx-builddir/html/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -218,8 +218,6 @@ <h2>Development<a class="headerlink" href="#development" title="Permalink to thi
<ul class="simple">
<li><p><a class="reference external" href="_static/pytest/pytest/index.html">Test report</a></p></li>
<li><p><a class="reference external" href="_static/pytest/coverage/index.html">Test coverage</a></p></li>
<li><p><a class="reference external" href="https://github.com/AZU-RDIT/optuna_az/">Source code (GitHub)</a></p></li>
<li><p><a class="reference external" href="https://jira.rd.astrazeneca.net/browse/OPTUNA/">Issues (Jira)</a></p></li>
<li><p><a class="reference external" href="https://github.com/MolecularAI/QSARtuna/">Public release (3.1.0)</a></p></li>
</ul>
</section>
Expand Down
2,191 changes: 1,089 additions & 1,102 deletions docs/sphinx-builddir/html/notebooks/QSARtuna_Tutorial.html

Large diffs are not rendered by default.

2,276 changes: 1,125 additions & 1,151 deletions docs/sphinx-builddir/html/notebooks/QSARtuna_Tutorial.ipynb

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion docs/sphinx-builddir/html/searchindex.js

Large diffs are not rendered by default.

2 changes: 0 additions & 2 deletions docs/sphinx-source/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,4 @@ Development
-----------
* `Test report <_static/pytest/pytest/index.html>`_
* `Test coverage <_static/pytest/coverage/index.html>`_
* `Source code (GitHub) <https://github.com/AZU-RDIT/optuna_az/>`_
* `Issues (Jira) <https://jira.rd.astrazeneca.net/browse/OPTUNA/>`_
* `Public release (3.1.0) <https://github.com/MolecularAI/QSARtuna/>`_
43 changes: 43 additions & 0 deletions examples/building/calibration_chemprop_build.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,43 @@
{
"task": "building",
"data": {
"input_column": "canonical",
"response_column": "molwt_gt_330",
"training_dataset_file": "tests/data/DRD2/subset-50/train.csv",
"test_dataset_file": "tests/data/DRD2/subset-50/test.csv"
},
"metadata": {
"cross_validation": 5,
"best_trial": null,
"best_value": null,
"n_trials": 15
},
"descriptor":
{ "name": "SmilesFromFile",
"parameters": {
}
}
,
"settings": {
"mode": "classification",
"direction": "maximize"
},
"algorithm": {
"name": "CalibratedClassifierCVWithVA",
"parameters": {
"method": "vennabers",
"n_folds": 2,
"ensemble": "True",
"estimator": {
"name": "ChemPropHyperoptClassifier",
"parameters": {
"ensemble_size": 1,
"epochs": 4,
"features_generator": "none",
"num_iters": 1,
"search_parameter_level": "auto"
}
}
}
}
}
29 changes: 29 additions & 0 deletions examples/optimization/ChemProp_drd2_50_retrain.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
{
"task": "optimization",
"data": {
"input_column": "canonical",
"response_column": "molwt",
"training_dataset_file": "tests/data/DRD2/subset-50/train.csv"
},
"descriptors": [
{
"name": "SmilesFromFile",
"parameters": {
}
}
],
"settings": {
"mode": "regression",
"cross_validation": 2,
"direction": "maximize",
"n_trials": 3
},
"algorithms": [
{
"name": "ChemPropRegressorPretrained",
"parameters": {
"pretrained_model": "tests/data/DRD2/drd2_reg.pkl"
}
}
]
}
29 changes: 29 additions & 0 deletions examples/optimization/ChemProp_drd2_50_retrain_cls_error.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
{
"task": "optimization",
"data": {
"input_column": "canonical",
"response_column": "molwt",
"training_dataset_file": "tests/data/DRD2/subset-50/train.csv"
},
"descriptors": [
{
"name": "SmilesFromFile",
"parameters": {
}
}
],
"settings": {
"mode": "regression",
"cross_validation": 2,
"direction": "maximize",
"n_trials": 3
},
"algorithms": [
{
"name": "ChemPropRegressorPretrained",
"parameters": {
"pretrained_model": "tests/data/DRD2/drd2_cls.pkl"
}
}
]
}
36 changes: 36 additions & 0 deletions examples/optimization/ChemProp_drd2_50_retrain_missingfile.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
{
"task": "optimization",
"data": {
"input_column": "canonical",
"response_column": "molwt",
"training_dataset_file": "tests/data/DRD2/subset-50/train.csv"
},
"descriptors": [
{
"name": "SmilesFromFile",
"parameters": {
}
}
],
"settings": {
"mode": "regression",
"cross_validation": 2,
"direction": "maximize",
"n_trials": 3,
"random_seed": 643
},
"algorithms": [
{
"name": "ChemPropRegressorPretrained",
"parameters": {
"pretrained_model": "missing.pkl"
}
},
{
"name": "ChemPropRegressorPretrained",
"parameters": {
"pretrained_model": "tests/data/DRD2/drd2_reg.pkl"
}
}
]
}
89 changes: 89 additions & 0 deletions examples/optimization/peptide_classification.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,89 @@
{
"task": "optimization",
"data": {
"input_column": "Smiles",
"response_column": "Class",
"training_dataset_file": "tests/data/peptide/toxinpred3/train.csv",
"test_dataset_file": "tests/data/peptide/toxinpred3/test.csv",
"aux_column": "Peptide",
"aux_transform": {
"name": "ZScales",
"parameters": {
}
}
},
"descriptors": [
{
"name": "CompositeDescriptor",
"parameters": {
"descriptors": [
{
"name": "ECFP",
"parameters": {
"radius": 3,
"nBits": 2048
}
},
{
"name": "UnscaledZScalesDescriptors",
"parameters": {
}
},
{
"name": "UnscaledPhyschemDescriptors",
"parameters": {}
}
]
}
}
],
"settings": {
"mode": "classification",
"cross_validation": 5,
"shuffle": true,
"direction": "maximize",
"n_trials": 15,
"random_seed": 2,
"n_jobs": 1
},
"algorithms":
[
{ "name": "RandomForestClassifier",
"parameters": {
"max_depth": {
"low": 10,
"high": 20
},
"n_estimators": {
"low": 10,
"high": 100
},
"max_features": ["sqrt", "log2"]
}
},
{
"name": "KNeighborsClassifier",
"parameters": {
"n_neighbors": {
"low": 1,
"high": 3
},
"weights": ["uniform", "distance"],
"metric": ["minkowski", "euclidean", "manhattan"]
}
},
{ "name": "SVC",
"parameters": {
"C": {
"low": 1e-7,
"high": 1e7
},
"gamma": {
"low": 1e-9,
"high": 1000
}
}
}
]
}

102 changes: 102 additions & 0 deletions examples/optimization/peptide_regression.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,102 @@
{
"task": "optimization",
"data": {
"input_column": "Structure",
"response_column": "Permeability",
"training_dataset_file": "train/data/peptide/permeability/train.csv"
},
"descriptors": [
{
"name": "ECFP",
"parameters": {
"radius": 3,
"nBits": 2048
}
},
{
"name": "SmilesFromFile",
"parameters": {
}
}
],
"settings": {
"mode": "regression",
"cross_validation": 5,
"shuffle": true,
"direction": "maximize",
"n_trials": 15,
"random_seed": 2,
"n_jobs": 1
},
"algorithms": [
{
"name": "RandomForestRegressor",
"parameters": {
"max_depth": {
"low": 10,
"high": 20
},
"n_estimators": {
"low": 10,
"high": 100
},
"max_features": [
"auto",
"sqrt",
"log2"
]
}
},
{
"name": "KNeighborsRegressor",
"parameters": {
"n_neighbors": {
"low": 1,
"high": 3
},
"weights": ["uniform", "distance"],
"metric": ["minkowski", "euclidean", "manhattan"]
}
},
{
"name": "SVR",
"parameters": {
"C": {
"low": 1e-7,
"high": 1e7
},
"gamma": {
"low": 1e-9,
"high": 1000
}
}
},
{
"name": "Ridge",
"parameters": {
"alpha": {
"low": 1,
"high": 2
}
}
},
{
"name": "Lasso",
"parameters": {
"alpha": {
"low": 1,
"high": 2
}
}
},
{
"name": "ChemPropHyperoptRegressor",
"parameters": {
"ensemble_size": 1,
"epochs": 4,
"num_iters": 1
}
}
]
}

Loading

0 comments on commit 92520ac

Please sign in to comment.