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Merged
merged 51 commits into from
Sep 15, 2022
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DOC Rework plot_grid_search_text_feature_extraction.py example #23740

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29f2006
Rename file
Jun 23, 2022
9fe3d7d
Update references to new file name
Jun 23, 2022
497178a
First step to improve notebook style
Jun 23, 2022
8765fc6
Tune ComplementNB instead of SGDClassifier
Jun 23, 2022
ce1f9a9
Add score accuracy on test set
Jun 23, 2022
1c2a102
Add reference to grid search in text classification example
Jun 23, 2022
4f08c16
Add reference to text classification example
Jun 23, 2022
58ed079
Improve references to the twenty_newsgroup description
Jun 23, 2022
e62f74e
Add plotly to CI
Jun 27, 2022
1b12759
Add parallel coordinate plot and interpretation
Jun 27, 2022
a0157a6
Update plotly version
Jun 27, 2022
fc4667b
Add plotly to conda dependencies
Jun 27, 2022
24db4a1
Add plotly to build name doc
Jun 27, 2022
0e48c59
Update enviroments and lock files
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Solve conflicts
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999c7c3
Fix plotly figure
Jun 28, 2022
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Apply suggestions from code review
ArturoAmorQ Jun 28, 2022
02975f1
Move config of the default renderer of plotly to conf.py
Jun 29, 2022
01910dd
Change grid search for randomized search
Jun 29, 2022
675315e
Split code cells for easier reading
Jun 29, 2022
72452af
Wording tweak
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59d501d
Reset pandas index
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ec8e544
improve narrative
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3add472
Add plotly scatterplot and related narrative
Jun 29, 2022
6842945
Add author
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Add interpretation to scatterplot
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Merge branch 'main' of https://github.com/scikit-learn/scikit-learn i…
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Merge branch 'main' of https://github.com/scikit-learn/scikit-learn i…
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Remove max_features and improve narrative
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Add simil to GridSearchCV
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Move ngram_range mapping for consistency
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ArturoAmorQ Jul 20, 2022
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Merge branch 'main' of https://github.com/scikit-learn/scikit-learn i…
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Add plotly as requirement with minimum associated version
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Sep 14, 2022
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Merge branch 'main' of https://github.com/scikit-learn/scikit-learn i…
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Update README.rst
glemaitre Sep 15, 2022
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3 changes: 2 additions & 1 deletion README.rst
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Expand Up @@ -42,6 +42,7 @@
.. |PandasMinVersion| replace:: 1.0.5
.. |SeabornMinVersion| replace:: 0.9.0
.. |PytestMinVersion| replace:: 5.0.1
.. |PlotlyMinVersion| replace:: 5.9.0

.. 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 @@ -83,7 +84,7 @@ 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|.
|SeabornMinVersion| and plotly >= |PlotlyMinVersion|.

User installation
~~~~~~~~~~~~~~~~~
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1 change: 1 addition & 0 deletions build_tools/github/doc_environment.yml
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Expand Up @@ -25,6 +25,7 @@ dependencies:
- sphinx-gallery
- numpydoc
- sphinx-prompt
- plotly
- pip
- pip:
- sphinxext-opengraph
15 changes: 9 additions & 6 deletions build_tools/github/doc_linux-64_conda.lock
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@@ -1,6 +1,6 @@
# Generated by conda-lock.
# platform: linux-64
# input_hash: eb6f446eaacd58fbff84b6520503d14519011e67e0f6ce3d39a9a2922fb781cb
# input_hash: 51824060cd657aa08f97c645d9c3c1efd6eec66aedaf8949d8d7cb5d9d8e69e6
@EXPLICIT
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Expand Down Expand Up @@ -83,7 +83,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-h9b69904_4.tar.b
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https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.37-h753d276_4.tar.bz2#6b611734b73d639c084ac4be2fcd996a
https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.39.2-h753d276_1.tar.bz2#90136dc0a305db4e1df24945d431457b
https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.39.3-h753d276_0.tar.bz2#ccb2457c73609f2622b8a4b3e42e5d8b
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https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.13-h7f98852_1004.tar.bz2#b3653fdc58d03face9724f602218a904
Expand Down Expand Up @@ -112,7 +112,7 @@ https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_openb
https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.4.0-h0e0dad5_3.tar.bz2#5627d42c13a9b117ae1701c6e195624f
https://conda.anaconda.org/conda-forge/linux-64/libxkbcommon-1.0.3-he3ba5ed_0.tar.bz2#f9dbabc7e01c459ed7a1d1d64b206e9b
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https://conda.anaconda.org/conda-forge/linux-64/xcb-util-0.4.0-h166bdaf_0.tar.bz2#384e7fcb3cd162ba3e4aed4b687df566
https://conda.anaconda.org/conda-forge/linux-64/xcb-util-keysyms-0.4.0-h166bdaf_0.tar.bz2#637054603bb7594302e3bf83f0a99879
https://conda.anaconda.org/conda-forge/linux-64/xcb-util-renderutil-0.3.9-h166bdaf_0.tar.bz2#732e22f1741bccea861f5668cf7342a7
Expand Down Expand Up @@ -175,10 +175,12 @@ https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.0-pyhd8
https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jsmath-1.0.1-py_0.tar.bz2#67cd9d9c0382d37479b4d306c369a2d4
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https://conda.anaconda.org/conda-forge/noarch/tenacity-8.0.1-pyhd8ed1ab_0.tar.bz2#8b29b2c12cb21dbd057755e5fd22d005
https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.1.0-pyh8a188c0_0.tar.bz2#a2995ee828f65687ac5b1e71a2ab1e0c
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https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2#5844808ffab9ebdb694585b50ba02a96
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https://conda.anaconda.org/conda-forge/noarch/wheel-0.37.1-pyhd8ed1ab_0.tar.bz2#1ca02aaf78d9c70d9a81a3bed5752022
https://conda.anaconda.org/conda-forge/noarch/zipp-3.8.1-pyhd8ed1ab_0.tar.bz2#a3508a0c850745b875de88aea4c40cc5
https://conda.anaconda.org/conda-forge/noarch/babel-2.10.3-pyhd8ed1ab_0.tar.bz2#72f1c6d03109d7a70087bc1d029a8eda
Expand All @@ -198,6 +200,7 @@ https://conda.anaconda.org/conda-forge/noarch/packaging-21.3-pyhd8ed1ab_0.tar.bz
https://conda.anaconda.org/conda-forge/noarch/partd-1.3.0-pyhd8ed1ab_0.tar.bz2#af8c82d121e63082926062d61d9abb54
https://conda.anaconda.org/conda-forge/linux-64/pillow-9.2.0-py39hd5dbb17_2.tar.bz2#3b74a959f6a8008f5901de60b3572c09
https://conda.anaconda.org/conda-forge/noarch/pip-22.2.2-pyhd8ed1ab_0.tar.bz2#0b43abe4d3ee93e82742d37def53a836
https://conda.anaconda.org/conda-forge/noarch/plotly-5.10.0-pyhd8ed1ab_0.tar.bz2#e95502aa0f8e3db05d198214472575de
https://conda.anaconda.org/conda-forge/linux-64/pluggy-1.0.0-py39hf3d152e_3.tar.bz2#c375c89340e563053f3656c7f134d265
https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.2-py39hb9d737c_0.tar.bz2#1e7ffe59e21862559e06b981817e5058
https://conda.anaconda.org/conda-forge/linux-64/pulseaudio-14.0-h7f54b18_8.tar.bz2#f9dbcfbb942ec9a3c0249cb71da5c7d1
Expand Down Expand Up @@ -231,14 +234,14 @@ https://conda.anaconda.org/conda-forge/noarch/tifffile-2022.8.12-pyhd8ed1ab_0.ta
https://conda.anaconda.org/conda-forge/linux-64/pyqt-5.15.7-py39h18e9c17_0.tar.bz2#5ed8f83afff3b64fa91f7a6af8d7ff04
https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-2.5.0-pyhd8ed1ab_0.tar.bz2#1fdd1f3baccf0deb647385c677a1a48e
https://conda.anaconda.org/conda-forge/linux-64/scikit-image-0.19.3-py39h1832856_1.tar.bz2#472bb5b9d9eb26ac697902da265ee551
https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.11.2-pyhd8ed1ab_0.tar.bz2#fe2303dc8f1febeb82d927ce8ad153ed
https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.12.0-pyhd8ed1ab_0.tar.bz2#05ee2fb22c1eca4309c06d11aff049f3
https://conda.anaconda.org/conda-forge/linux-64/statsmodels-0.13.2-py39hd257fcd_0.tar.bz2#bd7cdadf70e34a19333c3aacc40206e8
https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.11-pyhd8ed1ab_0.tar.bz2#0738978569b10669bdef41c671252dd1
https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.5.3-py39hf3d152e_2.tar.bz2#98bf9bdfbac2ac73bbd1dc12a61519eb
https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_1.tar.bz2#089382ee0e2dc2eae33a04cc3c2bddb0
https://conda.anaconda.org/conda-forge/noarch/seaborn-0.11.2-hd8ed1ab_0.tar.bz2#e56b6a19f4b717eca7c68ad78196b075
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https://conda.anaconda.org/conda-forge/noarch/sphinx-5.1.1-pyhd8ed1ab_1.tar.bz2#cd1129e88f6278787212624e1b7a8001
https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.4.0-pyhd8ed1ab_1.tar.bz2#0aac89c61a466b0f9c4fd0ec44d81f1d
https://conda.anaconda.org/conda-forge/noarch/sphinx-gallery-0.11.1-pyhd8ed1ab_0.tar.bz2#729254314a5d178eefca50acbc2687b8
https://conda.anaconda.org/conda-forge/noarch/sphinx-prompt-1.4.0-pyhd8ed1ab_0.tar.bz2#88ee91e8679603f2a5bd036d52919cc2
# pip sphinxext-opengraph @ https://files.pythonhosted.org/packages/58/ed/59df64b8400caf736f38bd3725ab9b1d9e50874f629980973aea090c1a8b/sphinxext_opengraph-0.6.3-py3-none-any.whl#sha256=bf76017c105856b07edea6caf4942b6ae9bb168585dccfd6dbdb6e4161f6b03a
# pip sphinxext-opengraph @ https://files.pythonhosted.org/packages/58/ed/59df64b8400caf736f38bd3725ab9b1d9e50874f629980973aea090c1a8b/sphinxext_opengraph-0.6.3-py3-none-any.whl#md5=None
1 change: 1 addition & 0 deletions build_tools/github/doc_min_dependencies_environment.yml
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Expand Up @@ -25,6 +25,7 @@ dependencies:
- sphinx-gallery=0.7.0 # min
- numpydoc=1.2.0 # min
- sphinx-prompt=1.3.0 # min
- plotly=5.9.0 # min
- pip
- pip:
- sphinxext-opengraph==0.4.2 # min
15 changes: 9 additions & 6 deletions build_tools/github/doc_min_dependencies_linux-64_conda.lock
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# Generated by conda-lock.
# platform: linux-64
# input_hash: d7c5b73a8e5033accbbf23734674ee617f6e77fbc98fe96e654c88b245458829
# input_hash: 53d568af487a4ac9a260bfa1bcd5263594b6a4aef53e17e7ccf17e2e2165ab96
@EXPLICIT
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https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.6.15-ha878542_0.tar.bz2#c320890f77fd1d617fa876e0982002c2
Expand Down Expand Up @@ -45,7 +45,7 @@ https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-7.5.0-h56
https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-7.5.0-hd0bb8aa_20.tar.bz2#dbe78fc5fb9c339f8e55426559e12f7b
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Expand All @@ -61,7 +61,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libglib-2.66.3-hbe7bbb4_0.tar.bz
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Expand Down Expand Up @@ -102,9 +102,11 @@ https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.0-pyhd8
https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jsmath-1.0.1-py_0.tar.bz2#67cd9d9c0382d37479b4d306c369a2d4
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https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.5-pyhd8ed1ab_2.tar.bz2#9ff55a0901cf952f05c654394de76bf7
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https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.1.0-pyh8a188c0_0.tar.bz2#a2995ee828f65687ac5b1e71a2ab1e0c
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https://conda.anaconda.org/conda-forge/noarch/wheel-0.37.1-pyhd8ed1ab_0.tar.bz2#1ca02aaf78d9c70d9a81a3bed5752022
https://conda.anaconda.org/conda-forge/noarch/babel-2.10.3-pyhd8ed1ab_0.tar.bz2#72f1c6d03109d7a70087bc1d029a8eda
https://conda.anaconda.org/conda-forge/linux-64/cffi-1.14.4-py38ha312104_0.tar.bz2#8f82b87522fbb1d4b24e8b5e2b1d0501
Expand All @@ -120,6 +122,7 @@ https://conda.anaconda.org/conda-forge/linux-64/numpy-1.17.3-py38h95a1406_0.tar.
https://conda.anaconda.org/conda-forge/noarch/packaging-21.3-pyhd8ed1ab_0.tar.bz2#71f1ab2de48613876becddd496371c85
https://conda.anaconda.org/conda-forge/noarch/partd-1.3.0-pyhd8ed1ab_0.tar.bz2#af8c82d121e63082926062d61d9abb54
https://conda.anaconda.org/conda-forge/linux-64/pillow-9.2.0-py38ha3b2c9c_2.tar.bz2#a077cc2bb9d854074b1cf4607252da7a
https://conda.anaconda.org/conda-forge/noarch/plotly-5.9.0-pyhd8ed1ab_0.tar.bz2#00a668931d448ce0ce42d1b02005d636
https://conda.anaconda.org/conda-forge/linux-64/pluggy-1.0.0-py38h578d9bd_3.tar.bz2#6ce4ce3d4490a56eb33b52c179609193
https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.2-py38h0a891b7_0.tar.bz2#907a39b6d7443f770ed755885694f864
https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2#dd999d1cc9f79e67dbb855c8924c7984
Expand Down Expand Up @@ -148,16 +151,16 @@ https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.0.0-pyhd8ed1ab_0.tar.
https://conda.anaconda.org/conda-forge/noarch/pytest-forked-1.4.0-pyhd8ed1ab_0.tar.bz2#95286e05a617de9ebfe3246cecbfb72f
https://conda.anaconda.org/conda-forge/linux-64/qt-5.12.5-hd8c4c69_1.tar.bz2#0e105d4afe0c3c81c4fbd9937ec4f359
https://conda.anaconda.org/conda-forge/linux-64/scikit-image-0.16.2-py38hb3f55d8_0.tar.bz2#468b398fefac8884cd6e6513af66549b
https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.11.2-pyhd8ed1ab_0.tar.bz2#fe2303dc8f1febeb82d927ce8ad153ed
https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.12.0-pyhd8ed1ab_0.tar.bz2#05ee2fb22c1eca4309c06d11aff049f3
https://conda.anaconda.org/conda-forge/linux-64/pyqt-5.12.3-py38ha8c2ead_3.tar.bz2#242c206b0c30fdc4c18aea16f04c4262
https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-2.5.0-pyhd8ed1ab_0.tar.bz2#1fdd1f3baccf0deb647385c677a1a48e
https://conda.anaconda.org/conda-forge/linux-64/statsmodels-0.12.2-py38h5c078b8_0.tar.bz2#33787719ad03d33cffc4e2e3ea82bc9e
https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.11-pyhd8ed1ab_0.tar.bz2#0738978569b10669bdef41c671252dd1
https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.1.2-py38_1.tar.bz2#c2b9671a19c01716c37fe0a0e18b0aec
https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_1.tar.bz2#089382ee0e2dc2eae33a04cc3c2bddb0
https://conda.anaconda.org/conda-forge/noarch/seaborn-0.11.2-hd8ed1ab_0.tar.bz2#e56b6a19f4b717eca7c68ad78196b075
https://conda.anaconda.org/conda-forge/noarch/seaborn-0.12.0-hd8ed1ab_0.tar.bz2#c22474d96fa1725ae47def82b5668686
https://conda.anaconda.org/conda-forge/noarch/sphinx-4.0.1-pyh6c4a22f_2.tar.bz2#c203dcc46f262853ecbb9552c50d664e
https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.2-pyhd8ed1ab_0.tar.bz2#025ad7ca2c7f65007ab6b6f5d93a56eb
https://conda.anaconda.org/conda-forge/noarch/sphinx-gallery-0.7.0-py_0.tar.bz2#80bad3f857ecc86a4ab73f3e57addd13
https://conda.anaconda.org/conda-forge/noarch/sphinx-prompt-1.3.0-py_0.tar.bz2#9363002e2a134a287af4e32ff0f26cdc
# pip sphinxext-opengraph @ https://files.pythonhosted.org/packages/50/ac/c105ed3e0a00b14b28c0aa630935af858fd8a32affeff19574b16e2c6ae8/sphinxext_opengraph-0.4.2-py3-none-any.whl#sha256=a51f2604f9a5b6c0d25d3a88e694d5c02e20812dc0e482adf96c8628f9109357
# pip sphinxext-opengraph @ https://files.pythonhosted.org/packages/50/ac/c105ed3e0a00b14b28c0aa630935af858fd8a32affeff19574b16e2c6ae8/sphinxext_opengraph-0.4.2-py3-none-any.whl#md5=None
3 changes: 3 additions & 0 deletions build_tools/update_environments_and_lock_files.py
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Expand Up @@ -242,6 +242,7 @@ def remove_from(alist, to_remove):
"sphinx-gallery",
"numpydoc",
"sphinx-prompt",
"plotly",
],
"pip_dependencies": ["sphinxext-opengraph"],
"package_constraints": {
Expand All @@ -257,6 +258,7 @@ def remove_from(alist, to_remove):
"numpydoc": "min",
"sphinx-prompt": "min",
"sphinxext-opengraph": "min",
"plotly": "min",
},
},
{
Expand All @@ -274,6 +276,7 @@ def remove_from(alist, to_remove):
"sphinx-gallery",
"numpydoc",
"sphinx-prompt",
"plotly",
],
"pip_dependencies": ["sphinxext-opengraph"],
"package_constraints": {
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14 changes: 14 additions & 0 deletions doc/conf.py
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Expand Up @@ -29,6 +29,17 @@
import sphinx_gallery
from sphinx_gallery.sorting import ExampleTitleSortKey

try:
# Configure plotly to integrate its output into the HTML pages generated by
# sphinx-gallery.
import plotly.io as pio

pio.renderers.default = "sphinx_gallery"
except ImportError:
# Make it possible to render the doc when not running the examples
# that need plotly.
pass

# -- General configuration ---------------------------------------------------

# Add any Sphinx extension module names here, as strings. They can be
Expand Down Expand Up @@ -257,6 +268,9 @@
"auto_examples/linear_model/plot_bayesian_ridge": (
"auto_examples/linear_model/plot_ard"
),
"examples/model_selection/grid_search_text_feature_extraction.py": (
"examples/model_selection/plot_grid_search_text_feature_extraction.py"
),
}
html_context["redirects"] = redirects
for old_link in redirects:
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2 changes: 1 addition & 1 deletion doc/modules/compose.rst
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Expand Up @@ -163,7 +163,7 @@ You can also provide custom feature names for the input data using
.. topic:: Examples:

* :ref:`sphx_glr_auto_examples_feature_selection_plot_feature_selection_pipeline.py`
* :ref:`sphx_glr_auto_examples_model_selection_grid_search_text_feature_extraction.py`
* :ref:`sphx_glr_auto_examples_model_selection_plot_grid_search_text_feature_extraction.py`
* :ref:`sphx_glr_auto_examples_compose_plot_digits_pipe.py`
* :ref:`sphx_glr_auto_examples_miscellaneous_plot_kernel_approximation.py`
* :ref:`sphx_glr_auto_examples_svm_plot_svm_anova.py`
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2 changes: 1 addition & 1 deletion doc/modules/cross_validation.rst
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Expand Up @@ -295,7 +295,7 @@ section.
* :ref:`sphx_glr_auto_examples_model_selection_plot_roc_crossval.py`,
* :ref:`sphx_glr_auto_examples_feature_selection_plot_rfe_with_cross_validation.py`,
* :ref:`sphx_glr_auto_examples_model_selection_plot_grid_search_digits.py`,
* :ref:`sphx_glr_auto_examples_model_selection_grid_search_text_feature_extraction.py`,
* :ref:`sphx_glr_auto_examples_model_selection_plot_grid_search_text_feature_extraction.py`,
* :ref:`sphx_glr_auto_examples_model_selection_plot_cv_predict.py`,
* :ref:`sphx_glr_auto_examples_model_selection_plot_nested_cross_validation_iris.py`.

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2 changes: 1 addition & 1 deletion doc/modules/feature_extraction.rst
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Expand Up @@ -607,7 +607,7 @@ As usual the best way to adjust the feature extraction parameters
is to use a cross-validated grid search, for instance by pipelining the
feature extractor with a classifier:

* :ref:`sphx_glr_auto_examples_model_selection_grid_search_text_feature_extraction.py`
* :ref:`sphx_glr_auto_examples_model_selection_plot_grid_search_text_feature_extraction.py`


Decoding text files
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2 changes: 1 addition & 1 deletion doc/modules/grid_search.rst
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Expand Up @@ -77,7 +77,7 @@ evaluated and the best combination is retained.
- See :ref:`sphx_glr_auto_examples_model_selection_plot_grid_search_digits.py` for an example of
Grid Search computation on the digits dataset.

- See :ref:`sphx_glr_auto_examples_model_selection_grid_search_text_feature_extraction.py` for an example
- See :ref:`sphx_glr_auto_examples_model_selection_plot_grid_search_text_feature_extraction.py` for an example
of Grid Search coupling parameters from a text documents feature
extractor (n-gram count vectorizer and TF-IDF transformer) with a
classifier (here a linear SVM trained with SGD with either elastic
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