8000 DOC Add example comparing permutation importance and SHAP by lucyleeow · Pull Request #18139 · scikit-learn/scikit-learn · GitHub
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DOC Add example comparing permutation importance and SHAP #18139

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lucyleeow Jul 28, 2020
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lucyleeow Aug 4, 2020
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lucyleeow Aug 7, 2020
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lucyleeow Aug 9, 2020
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lucyleeow Aug 10, 2020
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lucyleeow Aug 11, 2020
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lucyleeow Aug 11, 2020
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lucyleeow Aug 11, 2020
ce78252
add to min dep
lucyleeow Aug 11, 2020
6c2ac89
Merge branch 'master' into doc_shap_fpi
lucyleeow Aug 11, 2020
f5e0934
circular import
lucyleeow Aug 11, 2020
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lucyleeow Aug 11, 2020
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lucyleeow Aug 11, 2020
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lucyleeow Aug 11, 2020
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lucyleeow Aug 12, 2020
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lucyleeow Aug 13, 2020
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merge main, update ver
Oct 9, 2021
810e3da
Update examples/inspection/plot_permutation_importance_SHAP.py
lucyleeow Oct 9, 2021
9b8e728
Update examples/inspection/plot_permutation_importance_SHAP.py
lucyleeow Oct 9, 2021
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Update examples/inspection/plot_permutation_importance_SHAP.py
lucyleeow Oct 9, 2021
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suggestions
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Merge branch 'doc_shap_fpi' of https://github.com/lucyleeow/scikit-le…
Oct 9, 2021
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black
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use arxiv directive
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Merge branch 'main' into doc_shap_fpi
Oct 9, 2021
7970080
add shap version
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try version
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fix version?
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Merge branch 'main' into doc_shap_fpi
Oct 19, 2021
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Merge branch 'main' into doc_shap_fpi
jjerphan Nov 20, 2021
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try doc py 3.9
Nov 24, 2021
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Merge branch 'doc_shap_fpi' of github.com:lucyleeow/scikit-learn into…
Nov 24, 2021
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merge main
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merge main
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Merge remote-tracking branch 'origin/main' into pr/lucyleeow/18139
glemaitre Dec 2, 2021
bb4a8b7
Update examples/inspection/plot_permutation_importance_SHAP.py
lucyleeow Dec 7, 2021
449b814
Update examples/inspection/plot_permutation_importance_SHAP.py
lucyleeow Dec 7, 2021
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Update examples/inspection/plot_permutation_importance_SHAP.py
lucyleeow Dec 7, 2021
735df58
Update examples/inspection/plot_permutation_importance_SHAP.py
lucyleeow Dec 7, 2021
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Update examples/inspection/plot_permutation_importance_SHAP.py
lucyleeow Dec 7, 2021
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merge main
Dec 7, 2021
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Dec 8, 2021
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use new shap api
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Merge branch 'main' into doc_shap_fpi
ogrisel Mar 9, 2022
604c2b1
Use mambaforge as possible to avoid re-installing the numpy dependenc…
ogrisel Mar 9, 2022
a00bacc
Bump-up dependency on scikit-image to be able to install it from cond…
ogrisel Mar 9, 2022
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scikit-image 0.15.0 is not supported by Python 3.8
ogrisel Mar 9, 2022
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Fix plotting functions
ogrisel Mar 9, 2022
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Typo in scikit-image version number
ogrisel Mar 9, 2022
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1 change: 1 addition & 0 deletions .binder/requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,5 @@ scikit-image
pandas
sphinx-gallery
scikit-learn
shap
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How stable are the APIs of shap that we rely on here? should we pin this dependency?

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Small follow-up: do you know if APIs of shap are stable enough, @lucyleeow?

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It should be


2 changes: 2 additions & 0 deletions .circleci/config.yml
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Expand Up @@ -20,6 +20,7 @@ jobs:
- NUMPYDOC_VERSION: 'min'
- SPHINX_PROMPT_VERSION: 'min'
- SPHINXEXT_OPENGRAPH_VERSION: 'min'
- SHAP_VERSION: 'min'
steps:
- checkout
- run: ./build_tools/circle/checkout_merge_commit.sh
Expand Down Expand Up @@ -67,6 +68,7 @@ jobs:
- NUMPYDOC_VERSION: 'latest'
- SPHINX_PROMPT_VERSION: 'latest'
- SPHINXEXT_OPENGRAPH_VERSION: 'latest'
- SHAP_VERSION: 'latest'
steps:
- checkout
- run: ./build_tools/circle/checkout_merge_commit.sh
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13 changes: 9 additions & 4 deletions README.rst
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Expand Up @@ -38,10 +38,11 @@
.. |JoblibMinVersion| replace:: 1.0.0
.. |ThreadpoolctlMinVersion| replace:: 2.0.0
.. |MatplotlibMinVersion| replace:: 3.1.2
.. |Scikit-ImageMinVersion| replace:: 0.14.5
.. |Scikit-ImageMinVersion| replace:: 0.16.2
.. |PandasMinVersion| replace:: 1.0.5
.. |SeabornMinVersion| replace:: 0.9.0
.. |PytestMinVersion| replace:: 5.0.1
.. |SHAPMinVersion| replace::0.35.0

.. image:: https://raw.githubusercontent.com/scikit-learn/scikit-learn/main/doc/logos/scikit-learn-logo.png
:target: https://scikit-learn.org/
Expand Down Expand Up @@ -81,9 +82,13 @@ scikit-learn 1.1 and later require Python 3.8 or newer.
Scikit-learn plotting capabilities (i.e., functions start with ``plot_`` and
classes end with "Display") require Matplotlib (>= |MatplotlibMinVersion|).
For running the examples Matplotlib >= |MatplotlibMinVersion| is required.
A few examples require scikit-image >= |Scikit-ImageMinVersion|, a few examples
require pandas >= |PandasMinVersion|, some examples require seaborn >=
|SeabornMinVersion|.

Some examples require independently:

- scikit-image >= |Scikit-ImageMinVersion|
- pandas >= |PandasMinVersion|
- seaborn >= |SeabornMinVersion|
- SHAP >= |SHAPMinVersion|

User installation
~~~~~~~~~~~~~~~~~
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27 changes: 18 additions & 9 deletions build_tools/circle/build_doc.sh
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Expand Up @@ -143,12 +143,13 @@ if [[ `type -t deactivate` ]]; then
deactivate
fi

MINICONDA_PATH=$HOME/miniconda
# Install dependencies with miniconda
# Install dependencies with mambaforge. Note that the mambaforge installer
# automatically configures the conda-forge channel by default.
MAMBAFORGE_PATH=$HOME/mambaforge
wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
-O miniconda.sh
chmod +x miniconda.sh && ./miniconda.sh -b -p $MINICONDA_PATH
export PATH="/usr/lib/ccache:$MINICONDA_PATH/bin:$PATH"
-O mambaforge.sh
chmod +x mambaforge.sh && ./mambaforge.sh -b -p $MAMBAFORGE_PATH
export PATH="/usr/lib/ccache:$MAMBAFORGE_PATH/bin:$PATH"

ccache -M 512M
export CCACHE_COMPRESS=1
Expand All @@ -173,20 +174,28 @@ mamba create -n $CONDA_ENV_NAME --yes --quiet \
"$(get_dep matplotlib $MATPLOTLIB_VERSION)" \
"$(get_dep sphinx $SPHINX_VERSION)" \
"$(get_dep pandas $PANDAS_VERSION)" \
"$(get_dep shap $SHAP_VERSION)" \
"$(get_dep scikit-image $SCIKIT_IMAGE_VERSION)" \
"$(get_dep sphinx-gallery $SPHINX_GALLERY_VERSION)" \
"$(get_dep numpydoc $NUMPYDOC_VERSION)" \
"$(get_dep sphinx-prompt $SPHINX_PROMPT_VERSION)" \
joblib memory_profiler packaging seaborn pillow pytest coverage \
compilers

source activate testenv
pip install "$(get_dep scikit-image $SCIKIT_IMAGE_VERSION)"
pip install "$(get_dep sphinx-gallery $SPHINX_GALLERY_VERSION)"
pip install "$(get_dep numpydoc $NUMPYDOC_VERSION)"
pip install "$(get_dep sphinx-prompt $SPHINX_PROMPT_VERSION)"

# sphinxext-opengraph not in conda-forge for now, use pip instead:
pip install "$(get_dep sphinxext-opengraph $SPHINXEXT_OPENGRAPH_VERSION)"

# Set parallelism to 3 to overlap IO bound tasks with CPU bound tasks on CI
# workers with 2 cores when building the compiled extensions of scikit-learn.
export SKLEARN_BUILD_PARALLEL=3

# Note: installing scikit-learn from source in develop mode should hopefully
# override the scikit-learn potentially already installed as a dependency of
# shap.
python setup.py develop
python -c "import sklearn; sklearn.show_versions()"

export OMP_NUM_THREADS=1

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