From 4392a2a36dd49b8ad2444b1eb720876b5ea92805 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Fri, 17 Mar 2023 08:18:15 +0100 Subject: [PATCH 01/19] DOC Use JupyterLite sphinx-gallery integration in examples --- build_tools/circle/doc_environment.yml | 3 + build_tools/circle/doc_linux-64_conda.lock | 81 ++++++++++++++----- .../update_environments_and_lock_files.py | 2 +- doc/conf.py | 51 +++++++----- 4 files changed, 100 insertions(+), 37 deletions(-) diff --git a/build_tools/circle/doc_environment.yml b/build_tools/circle/doc_environment.yml index 0c441a5266906..3a79871e94519 100644 --- a/build_tools/circle/doc_environment.yml +++ b/build_tools/circle/doc_environment.yml @@ -29,3 +29,6 @@ dependencies: - pooch - sphinxext-opengraph - pip + - pip: + - jupyterlite-sphinx + - jupyterlite-pyodide-kernel diff --git a/build_tools/circle/doc_linux-64_conda.lock b/build_tools/circle/doc_linux-64_conda.lock index 1b44a49ab03ac..35e160833adac 100644 --- a/build_tools/circle/doc_linux-64_conda.lock +++ b/build_tools/circle/doc_linux-64_conda.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: e94308f010347872a13f1dc0dcc6b19de98bc55b7a0f75b0102c299b78e8b31d +# input_hash: 3c2790bb03feda8fbbf9b5fb06111fce0af10f7a587b5e4c251fa43e0492f7b2 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -58,12 +58,13 @@ https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.21-pthreads_h78a https://conda.anaconda.org/conda-forge/linux-64/libopus-1.3.1-h7f98852_1.tar.bz2#15345e56d527b330e1cacbdf58676e8f https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-11.3.0-h239ccf8_19.tar.bz2#d17fd55aed84ab6592c5419b6600501c https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.7-h27087fc_0.conda#f204c8ba400ec475452737094fb81d52 +https://conda.anaconda.org/conda-forge/linux-64/libudev1-253-h0b41bf4_0.conda#6c2addbd9aa4ee47c76d50c9f0df8cd6 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar.bz2#772d69f030955d9646d3d0eaf21d859d https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.0-h0b41bf4_0.conda#0d4a7508d8c6c65314f2b9c1f56ad408 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2#f3f9de449d32ca9b9c66a22863c96f41 https://conda.anaconda.org/conda-forge/linux-64/libzopfli-1.0.3-h9c3ff4c_0.tar.bz2#c66fe2d123249af7651ebde8984c51c2 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0 -https://conda.anaconda.org/conda-forge/linux-64/mpg123-1.31.3-hcb278e6_0.conda#141a126675b6d1a4eabb111a4a353898 +https://conda.anaconda.org/conda-forge/linux-64/mpg123-1.31.2-hcb278e6_0.conda#08efb1e1813f1a151b7a945b972a049b https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4acfc691e64342b9dae57cf2adc63238 https://conda.anaconda.org/conda-forge/linux-64/nspr-4.35-h27087fc_0.conda#da0ec11a6454ae19bff5b02ed881a2b1 https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.0-h0b41bf4_0.conda#2d833be81a21128e317325a01326d36f @@ -82,14 +83,14 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae https://conda.anaconda.org/conda-forge/linux-64/zfp-1.0.0-h27087fc_3.tar.bz2#0428af0510c3fafedf1c66b43102a34b -https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.0.7-h0b41bf4_0.conda#49e8329110001f04923fe7e864990b0c +https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.0.6-h166bdaf_0.tar.bz2#8650e4fb44c4a618e5ab3e1e19607e32 https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-11.3.0-hab1b70f_19.tar.bz2#89ac16d36e66ccb9ca5d34c9217e5799 https://conda.anaconda.org/conda-forge/linux-64/jack-1.9.22-h11f4161_0.conda#504fa9e712b99494a9cf4630e3ca7d78 https://conda.anaconda.org/conda-forge/linux-64/libavif-0.11.1-h5cdd6b5_0.tar.bz2#2040f9067e8852606208cafa66c3563f https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-16_linux64_openblas.tar.bz2#d9b7a8639171f6c6fa0a983edabcfe2b https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.0.9-h166bdaf_8.tar.bz2#4ae4d7795d33e02bd20f6b23d91caf82 https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.0.9-h166bdaf_8.tar.bz2#04bac51ba35ea023dc48af73c1c88c25 -https://conda.anaconda.org/conda-forge/linux-64/libcap-2.67-he9d0100_0.conda#d05556c80caffff164d17bdea0105a1a +https://conda.anaconda.org/conda-forge/linux-64/libcap-2.66-ha37c62d_0.tar.bz2#2d7665abd0997f1a6d4b7596bc27b657 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-h28343ad_4.tar.bz2#4a049fc560e00e43151dc51368915fdd https://conda.anaconda.org/conda-forge/linux-64/libflac-1.4.2-h27087fc_0.tar.bz2#7daf72d8e2a8e848e11d63ed6d1026e0 @@ -100,11 +101,12 @@ https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar. https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-hf14f497_3.tar.bz2#d85acad4b47dff4e3def14a769a97906 https://conda.anaconda.org/conda-forge/linux-64/libvorbis-1.3.7-h9c3ff4c_0.tar.bz2#309dec04b70a3cc0f1e84a4013683bc0 https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.13-h7f98852_1004.tar.bz2#b3653fdc58d03face9724f602218a904 -https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.10.3-hca2bb57_4.conda#bb808b654bdc3c783deaf107a2ffb503 -https://conda.anaconda.org/conda-forge/linux-64/mysql-common-8.0.32-ha901b37_1.conda#2c18a7a26ec0d0c23a917f37a65fc9a2 +https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.10.3-hca2bb57_3.conda#29474f139e5017090f218ef6b3753efd +https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-15.0.7-h0cdce71_0.conda#589c9a3575a050b583241c3d688ad9aa +https://conda.anaconda.org/conda-forge/linux-64/mysql-common-8.0.32-ha901b37_0.conda#6a39818710235826181e104aada40c75 https://conda.anaconda.org/conda-forge/linux-64/openblas-0.3.21-pthreads_h320a7e8_3.tar.bz2#29155b9196b9d78022f11d86733e25a7 https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.40-hc3806b6_0.tar.bz2#69e2c796349cd9b273890bee0febfe1b -https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.1.2-h0f457ee_0.tar.bz2#db2ebbe2943aae81ed051a6a9af8e0fa https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8c42eb62e9fc961af70bdd6a26e168 https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.3-hd9c2040_1000.tar.bz2#9e856f78d5c80d5a78f61e72d1d473a3 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295 @@ -125,10 +127,8 @@ https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_openb https://conda.anaconda.org/conda-forge/linux-64/libllvm15-15.0.7-hadd5161_1.conda#17d91085ccf5934ce652cb448d0cb65a https://conda.anaconda.org/conda-forge/linux-64/libsndfile-1.2.0-hb75c966_0.conda#c648d19cd9c8625898d5d370414de7c7 https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.5.0-hddfeb54_5.conda#d2343e6594c2a4a654a475a6131ef20d -https://conda.anaconda.org/conda-forge/linux-64/libudev1-253-h0b41bf4_1.conda#bb38b19a41bb94e8a19dbfb062d499c7 https://conda.anaconda.org/conda-forge/linux-64/libxkbcommon-1.5.0-h79f4944_1.conda#04a39cdd663f295653fc143851830563 -https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-16.0.0-h417c0b6_0.conda#8ac4c157172ea816f5c9a0dc33df69d8 -https://conda.anaconda.org/conda-forge/linux-64/mysql-libs-8.0.32-hd7da12d_1.conda#a69fa6f218cfed8e2d61753eeacaf034 +https://conda.anaconda.org/conda-forge/linux-64/mysql-libs-8.0.32-hd7da12d_0.conda#b05d7ea8b76f1172d5fe4f30e03277ea https://conda.anaconda.org/conda-forge/linux-64/nss-3.89-he45b914_0.conda#2745719a58eeaab6657256a3f142f099 https://conda.anaconda.org/conda-forge/linux-64/python-3.9.16-h2782a2a_0_cpython.conda#95c9b7c96a7fd7342e0c9d0a917b8f78 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-0.4.0-h166bdaf_0.tar.bz2#384e7fcb3cd162ba3e4aed4b687df566 @@ -165,10 +165,10 @@ https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.4-py39hf939315_1. https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.15-haa2dc70_1.conda#980d8aca0bc23ca73fa8caa3e7c84c28 https://conda.anaconda.org/conda-forge/linux-64/libclang13-15.0.7-default_h3e3d535_1.conda#a3a0f7a6f0885f5e1e0ec691566afb77 https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h36d4200_3.conda#c9f4416a34bc91e0eb029f912c68f81f -https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.88.1-hdc1c0ab_1.conda#3d1189864d1c0ed2a5919cb067b5903d +https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.88.1-hdc1c0ab_0.conda#81eaeb3b35163c8e90e57532bc93754d https://conda.anaconda.org/conda-forge/linux-64/liblapacke-3.9.0-16_linux64_openblas.tar.bz2#823ceb5567e1a595deb643fcd17aed5a https://conda.anaconda.org/conda-forge/linux-64/libpq-15.2-hb675445_0.conda#4654b17eccaba55b8581d6b9c77f53cc -https://conda.anaconda.org/conda-forge/linux-64/libsystemd0-253-h8c4010b_1.conda#9176b1e2cb8beca37a7510b0e801e38f +https://conda.anaconda.org/conda-forge/linux-64/libsystemd0-252-h2a991cd_0.tar.bz2#3c5ae9f61f663b3d5e1bf7f7da0c85f5 https://conda.anaconda.org/conda-forge/noarch/locket-1.0.0-pyhd8ed1ab_0.tar.bz2#91e27ef3d05cc772ce627e51cff111c4 https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.2-py39h72bdee0_0.conda#35514f5320206df9f4661c138c02e1c1 https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyh9f0ad1d_0.tar.bz2#2ba8498c1018c1e9c61eb99b973dfe19 @@ -219,7 +219,7 @@ https://conda.anaconda.org/conda-forge/linux-64/cytoolz-0.12.0-py39hb9d737c_1.ta https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.39.2-py39h72bdee0_0.conda#f87853cd6f76c4b8014b41fa522e5bda https://conda.anaconda.org/conda-forge/linux-64/fortran-compiler-1.5.2-hdb1a99f_0.conda#265323e1bd53709aeb739c9b1794b398 https://conda.anaconda.org/conda-forge/linux-64/glib-2.74.1-h6239696_1.tar.bz2#f3220a9e9d3abcbfca43419a219df7e4 -https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-6.1.0-pyha770c72_0.conda#30b3127c385ca2ed5ef87f3d53d466bc +https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-6.0.0-pyha770c72_0.conda#691644becbcdca9f73243450b1c63e62 https://conda.anaconda.org/conda-forge/noarch/importlib_resources-5.12.0-pyhd8ed1ab_0.conda#e5fd2260a231ee63b6969f4801082f2b https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.2-pyhd8ed1ab_1.tar.bz2#c8490ed5c70966d232fdd389d0dbed37 https://conda.anaconda.org/conda-forge/noarch/joblib-1.2.0-pyhd8ed1ab_0.tar.bz2#7583652522d71ad78ba536bba06940eb @@ -229,7 +229,7 @@ https://conda.anaconda.org/conda-forge/noarch/partd-1.3.0-pyhd8ed1ab_0.tar.bz2#a https://conda.anaconda.org/conda-forge/linux-64/pillow-9.4.0-py39h7207d5c_2.conda#58d50d33cf1abe2055d2a1c90c7179a5 https://conda.anaconda.org/conda-forge/noarch/pip-23.0.1-pyhd8ed1ab_0.conda#8025ca83b8ba5430b640b83917c2a6f7 https://conda.anaconda.org/conda-forge/noarch/plotly-5.13.1-pyhd8ed1ab_0.conda#761501a3de96c5855d840f4287a65e77 -https://conda.anaconda.org/conda-forge/linux-64/pulseaudio-client-16.1-h5195f5e_3.conda#caeb3302ef1dc8b342b20c710a86f8a9 +https://conda.anaconda.org/conda-forge/linux-64/pulseaudio-16.1-ha8d29e2_1.conda#dbfc2a8d63a43a11acf4c704e1ef9d0c https://conda.anaconda.org/conda-forge/noarch/pygments-2.14.0-pyhd8ed1ab_0.conda#c78cd16b11cd6a295484bd6c8f24bea1 https://conda.anaconda.org/conda-forge/noarch/pytest-7.2.2-pyhd8ed1ab_0.conda#60958b19354e0ec295b43f6ab5cfab86 https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2#dd999d1cc9f79e67dbb855c8924c7984 @@ -248,21 +248,19 @@ https://conda.anaconda.org/conda-forge/noarch/imageio-2.26.0-pyh24c5eb1_0.conda# https://conda.anaconda.org/conda-forge/noarch/importlib-resources-5.12.0-pyhd8ed1ab_0.conda#3544c818f0720c89eb16ae6940ab440b https://conda.anaconda.org/conda-forge/linux-64/pandas-1.5.3-py39h2ad29b5_0.conda#3ea96adbbc2a66fa45178102a9cfbecc https://conda.anaconda.org/conda-forge/noarch/platformdirs-3.1.1-pyhd8ed1ab_0.conda#1d1a27f637808c76dd83e3f469aa6f7e -https://conda.anaconda.org/conda-forge/linux-64/pulseaudio-daemon-16.1-ha8d29e2_3.conda#34d9d75ca896f5919c372a34e25f23ea https://conda.anaconda.org/conda-forge/linux-64/pyqt5-sip-12.11.0-py39h227be39_3.conda#9e381db00691e26bcf670c3586397be1 https://conda.anaconda.org/conda-forge/noarch/pytest-forked-1.6.0-pyhd8ed1ab_0.conda#a46947638b6e005b63d2d6271da529b0 https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.22.0-h4243ec0_2.conda#0d0c6604c8ac4ad5e51efa7bb58da05c https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.7.1-py39he190548_0.conda#f2a931db797bb58bd335f4a857b4c898 -https://conda.anaconda.org/conda-forge/linux-64/pulseaudio-16.1-hcb278e6_3.conda#8b452ab959166d91949af4c2d28f81db https://conda.anaconda.org/conda-forge/noarch/pyopenssl-23.0.0-pyhd8ed1ab_0.conda#d41957700e83bbb925928764cb7f8878 https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-2.5.0-pyhd8ed1ab_0.tar.bz2#1fdd1f3baccf0deb647385c677a1a48e -https://conda.anaconda.org/conda-forge/noarch/tifffile-2023.3.21-pyhd8ed1ab_0.conda#46b79291d783ae327ffcaa342e8d7571 +https://conda.anaconda.org/conda-forge/noarch/tifffile-2023.3.15-pyhd8ed1ab_0.conda#da45d6cc28eac10485aef68c9b0a1e5a https://conda.anaconda.org/conda-forge/linux-64/qt-main-5.15.8-h67dfc38_7.conda#f140acdc15a0196eef664f120c396266 https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.15-pyhd8ed1ab_0.conda#27db656619a55d727eaf5a6ece3d2fd6 https://conda.anaconda.org/conda-forge/linux-64/pyqt-5.15.7-py39h5c7b992_3.conda#19e30314fe824605750da905febb8ee6 https://conda.anaconda.org/conda-forge/noarch/requests-2.28.2-pyhd8ed1ab_0.conda#11d178fc55199482ee48d6812ea83983 https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.7.1-py39hf3d152e_0.conda#682772fa385911fb5efffbce21b269c5 -https://conda.anaconda.org/conda-forge/noarch/pooch-1.7.0-pyha770c72_2.conda#2794d1b53ad3ddb1e61f27d1151ccfc7 +https://conda.anaconda.org/conda-forge/noarch/pooch-1.7.0-pyhd8ed1ab_0.conda#eb2e0fc33ad0d04b51f9280360c13c1e https://conda.anaconda.org/conda-forge/noarch/sphinx-6.0.0-pyhd8ed1ab_2.conda#ac1d3b55da1669ee3a56973054fd7efb https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.5.0-pyhd8ed1ab_0.tar.bz2#3c275d7168a6a135329f4acb364c229a https://conda.anaconda.org/conda-forge/linux-64/scipy-1.10.1-py39h7360e5f_0.conda#7584d1bc5499d25eccfd24a7f656e3ee @@ -275,3 +273,50 @@ https://conda.anaconda.org/conda-forge/linux-64/scikit-image-0.19.3-py39h4661b88 https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.12.2-pyhd8ed1ab_0.conda#cf88f3a1c11536bc3c10c14ad00ccc42 https://conda.anaconda.org/conda-forge/linux-64/statsmodels-0.13.5-py39h2ae25f5_2.tar.bz2#598b14b778a8f3e06a3579649f0e3c00 https://conda.anaconda.org/conda-forge/noarch/seaborn-0.12.2-hd8ed1ab_0.conda#50847a47c07812f88581081c620f5160 +# pip defusedxml @ https://files.pythonhosted.org/packages/07/6c/aa3f2f849e01cb6a001cd8554a88d4c77c5c1a31c95bdf1cf9301e6d9ef4/defusedxml-0.7.1-py2.py3-none-any.whl#sha256=a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61 +# pip fastjsonschema @ https://files.pythonhosted.org/packages/eb/e7/84b1571b866b8abd604f8b72234d16f01bd5944014ef9929b5cb0da198c1/fastjsonschema-2.16.3-py3-none-any.whl#sha256=04fbecc94300436f628517b05741b7ea009506ce8f946d40996567c669318490 +# pip fqdn @ https://files.pythonhosted.org/packages/cf/58/8acf1b3e91c58313ce5cb67df61001fc9dcd21be4fadb76c1a2d540e09ed/fqdn-1.5.1-py3-none-any.whl#sha256=3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014 +# pip json5 @ https://files.pythonhosted.org/packages/1b/9d/46b35ba70bce2261492016edfbb1bca173e0681c486442880f2b0536d491/json5-0.9.11-py2.py3-none-any.whl#sha256=1aa54b80b5e507dfe31d12b7743a642e2ffa6f70bf73b8e3d7d1d5fba83d99bd +# pip jsonpointer @ https://files.pythonhosted.org/packages/a3/be/8dc9d31b50e38172c8020c40f497ce8debdb721545ddb9fcb7cca89ea9e6/jsonpointer-2.3-py2.py3-none-any.whl#sha256=51801e558539b4e9cd268638c078c6c5746c9ac96bc38152d443400e4f3793e9 +# pip jupyterlab-pygments @ https://files.pythonhosted.org/packages/c0/7e/c3d1df3ae9b41686e664051daedbd70eea2e1d2bd9d9c33e7e1455bc9f96/jupyterlab_pygments-0.2.2-py2.py3-none-any.whl#sha256=2405800db07c9f770863bcf8049a529c3dd4d3e28536638bd7c1c01d2748309f +# pip mistune @ 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https://files.pythonhosted.org/packages/22/a6/858897256d0deac81a172289110f31629fc4cee19b6f01283303e18c8db3/ptyprocess-0.7.0-py2.py3-none-any.whl#sha256=4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35 +# pip pyrsistent @ https://files.pythonhosted.org/packages/64/de/375aa14daaee107f987da76ca32f7a907fea00fa8b8afb67dc09bec0de91/pyrsistent-0.19.3-py3-none-any.whl#sha256=ccf0d6bd208f8111179f0c26fdf84ed7c3891982f2edaeae7422575f47e66b64 +# pip python-json-logger @ https://files.pythonhosted.org/packages/35/a6/145655273568ee78a581e734cf35beb9e33a370b29c5d3c8fee3744de29f/python_json_logger-2.0.7-py3-none-any.whl#sha256=f380b826a991ebbe3de4d897aeec42760035ac760345e57b812938dc8b35e2bd +# pip rfc3986-validator @ https://files.pythonhosted.org/packages/9e/51/17023c0f8f1869d8806b979a2bffa3f861f26a3f1a66b094288323fba52f/rfc3986_validator-0.1.1-py2.py3-none-any.whl#sha256=2f235c432ef459970b4306369336b9d5dbdda31b510ca1e327636e01f528bfa9 +# pip send2trash @ https://files.pythonhosted.org/packages/47/26/3435896d757335ea53dce5abf8d658ca80757a7a06258451b358f10232be/Send2Trash-1.8.0-py3-none-any.whl#sha256=f20eaadfdb517eaca5ce077640cb261c7d2698385a6a0f072a4a5447fd49fa08 +# pip sniffio @ https://files.pythonhosted.org/packages/c3/a0/5dba8ed157b0136607c7f2151db695885606968d1fae123dc3391e0cfdbf/sniffio-1.3.0-py3-none-any.whl#sha256=eecefdce1e5bbfb7ad2eeaabf7c1eeb404d7757c379bd1f7e5cce9d8bf425384 +# pip soupsieve @ https://files.pythonhosted.org/packages/d2/70/2c92d7bc961ba43b7b21032b7622144de5f97dec14b62226533f6940798e/soupsieve-2.4-py3-none-any.whl#sha256=49e5368c2cda80ee7e84da9dbe3e110b70a4575f196efb74e51b94549d921955 +# pip traitlets @ https://files.pythonhosted.org/packages/77/75/c28e9ef7abec2b7e9ff35aea3e0be6c1aceaf7873c26c95ae1f0d594de71/traitlets-5.9.0-py3-none-any.whl#sha256=9e6ec080259b9a5940c797d58b613b5e31441c2257b87c2e795c5228ae80d2d8 +# pip uri-template @ https://files.pythonhosted.org/packages/c0/db/d4f9c75b43541f7235daf4d13eb43f4491f9d5f5df45ce41daeed3a903f6/uri_template-1.2.0-py3-none-any.whl#sha256=f1699c77b73b925cf4937eae31ab282a86dc885c333f2e942513f08f691fc7db +# pip webcolors @ https://files.pythonhosted.org/packages/af/a9/71beaebcacd7dd848af470740dbe7f39aa6bd23a60b8162f8c050090eed4/webcolors-1.12-py3-none-any.whl#sha256=d98743d81d498a2d3eaf165196e65481f0d2ea85281463d856b1e51b09f62dce +# pip webencodings @ https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl#sha256=a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78 +# pip websocket-client @ https://files.pythonhosted.org/packages/6d/9a/6c793729c9d48fcca155ce55e4dfafacffb7fb52a62e3ae2198846c31af6/websocket_client-1.5.1-py3-none-any.whl#sha256=cdf5877568b7e83aa7cf2244ab56a3213de587bbe0ce9d8b9600fc77b455d89e +# pip anyio @ https://files.pythonhosted.org/packages/77/2b/b4c0b7a3f3d61adb1a1e0b78f90a94e2b6162a043880704b7437ef297cad/anyio-3.6.2-py3-none-any.whl#sha256=fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3 +# pip argon2-cffi-bindings @ https://files.pythonhosted.org/packages/ec/f7/378254e6dd7ae6f31fe40c8649eea7d4832a42243acaf0f1fff9083b2bed/argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=b746dba803a79238e925d9046a63aa26bf86ab2a2fe74ce6b009a1c3f5c8f2ae +# pip arrow @ https://files.pythonhosted.org/packages/67/67/4bca5a595e2f89bff271724ddb1098e6c9e16f7f3d018d120255e3c30313/arrow-1.2.3-py3-none-any.whl#sha256=5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2 +# pip beautifulsoup4 @ https://files.pythonhosted.org/packages/c6/ee/16d6f808f5668317d7c23f942091fbc694bcded6aa39678e5167f61b2ba0/beautifulsoup4-4.11.2-py3-none-any.whl#sha256=0e79446b10b3ecb499c1556f7e228a53e64a2bfcebd455f370d8927cb5b59e39 +# pip bleach @ https://files.pythonhosted.org/packages/ac/e2/dfcab68c9b2e7800c8f06b85c76e5f978d05b195a958daa9b1dda54a1db6/bleach-6.0.0-py3-none-any.whl#sha256=33c16e3353dbd13028ab4799a0f89a83f113405c766e9c122df8a06f5b85b3f4 +# pip doit @ https://files.pythonhosted.org/packages/44/83/a2960d2c975836daa629a73995134fd86520c101412578c57da3d2aa71ee/doit-0.36.0-py3-none-any.whl#sha256=ebc285f6666871b5300091c26eafdff3de968a6bd60ea35dd1e3fc6f2e32479a +# pip jupyter-core @ https://files.pythonhosted.org/packages/41/1e/92a67f333b9335f04ce409799c030dcfb291712658b9d9d13997f7c91e5a/jupyter_core-5.3.0-py3-none-any.whl#sha256=d4201af84559bc8c70cead287e1ab94aeef3c512848dde077b7684b54d67730d +# pip pyzmq @ https://files.pythonhosted.org/packages/98/d3/477f58095f58c8d5c3a7ee30dc9fbe905380d4efbe92fbb0988aff40a090/pyzmq-25.0.1-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=c635d1c40d341835066931a018e378428dfbe0347ed4bb45a6b57f7d8c34196e +# pip rfc3339-validator @ https://files.pythonhosted.org/packages/7b/44/4e421b96b67b2daff264473f7465db72fbdf36a07e05494f50300cc7b0c6/rfc3339_validator-0.1.4-py2.py3-none-any.whl#sha256=24f6ec1eda14ef823da9e36ec7113124b39c04d50a4d3d3a3c2859577e7791fa +# pip terminado @ https://files.pythonhosted.org/packages/84/a7/c7628d79651b8c8c775d27b374315a825141b5783512e82026fb210dd639/terminado-0.17.1-py3-none-any.whl#sha256=8650d44334eba354dd591129ca3124a6ba42c3d5b70df5051b6921d506fdaeae +# pip tinycss2 @ https://files.pythonhosted.org/packages/da/99/fd23634d6962c2791fb8cb6ccae1f05dcbfc39bce36bba8b1c9a8d92eae8/tinycss2-1.2.1-py3-none-any.whl#sha256=2b80a96d41e7c3914b8cda8bc7f705a4d9c49275616e886103dd839dfc847847 +# pip argon2-cffi @ https://files.pythonhosted.org/packages/a8/07/946d5a9431bae05a776a59746ec385fbb79b526738d25e4202d3e0bbf7f4/argon2_cffi-21.3.0-py3-none-any.whl#sha256=8c976986f2c5c0e5000919e6de187906cfd81fb1c72bf9d88c01177e77da7f80 +# pip isoduration @ https://files.pythonhosted.org/packages/7b/55/e5326141505c5d5e34c5e0935d2908a74e4561eca44108fbfb9c13d2911a/isoduration-20.11.0-py3-none-any.whl#sha256=b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042 +# pip jupyter-client @ https://files.pythonhosted.org/packages/78/11/562517956f801607c4f7855ebf8c545e9a9f62ef936f0da1bdec9cd1a7aa/jupyter_client-8.0.3-py3-none-any.whl#sha256=be48ac6bd659cbbddb7a674cf06b3b8afbf53f228253cf58bde604c03bd487b0 +# pip jupyter-server-terminals @ https://files.pythonhosted.org/packages/ea/7f/36db12bdb90f5237766dcbf59892198daab7260acbcf03fc75e2a2a82672/jupyter_server_terminals-0.4.4-py3-none-any.whl#sha256=75779164661cec02a8758a5311e18bb8eb70c4e86c6b699403100f1585a12a36 +# pip jupyterlite-core @ https://files.pythonhosted.org/packages/04/00/983ee59afa6976412c684f5accfbe2e0e742e29aec6cde8852a96418b772/jupyterlite_core-0.1.0b19-py3-none-any.whl#sha256=06f6e8809ef7bee3a22297ea376853482eb8b6f8888bb539382e30cb0c10b7f1 +# pip jsonschema @ https://files.pythonhosted.org/packages/c1/97/c698bd9350f307daad79dd740806e1a59becd693bd11443a0f531e3229b3/jsonschema-4.17.3-py3-none-any.whl#sha256=a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6 +# pip jupyterlite-pyodide-kernel @ https://files.pythonhosted.org/packages/81/ff/9cd69da9e968d529597258c32dee39ac580a8973877c8ca5dd7bd7d349e7/jupyterlite_pyodide_kernel-0.0.5-py3-none-any.whl#sha256=296979b1d8dc5ec7d70cf9742abae7266ec1581638984f34bb1517109615ab42 +# pip jupyter-events @ https://files.pythonhosted.org/packages/ee/14/e11a93c1b47a69432ee7898f1b55f1da27f2f93b009a34dbdafb9b903f81/jupyter_events-0.6.3-py3-none-any.whl#sha256=57a2749f87ba387cd1bfd9b22a0875b889237dbf2edc2121ebb22bde47036c17 +# pip nbformat @ https://files.pythonhosted.org/packages/21/ad/020fed74bfde983a3b70cc95843d6adbe59171aa9a3da5aab403aa722a17/nbformat-5.7.3-py3-none-any.whl#sha256=22a98a6516ca216002b0a34591af5bcb8072ca6c63910baffc901cfa07fefbf0 +# pip nbclient @ https://files.pythonhosted.org/packages/15/49/ea7a0c7e649c54883d76f5119a3e0be592d82a7df1a9b87124fa6663d9c7/nbclient-0.7.2-py3-none-any.whl#sha256=d97ac6257de2794f5397609df754fcbca1a603e94e924eb9b99787c031ae2e7c +# pip nbconvert @ https://files.pythonhosted.org/packages/3f/53/1e99001bc154bd2d243564275e2b7a0e492b48ae032b1377f35cc9defa16/nbconvert-7.2.10-py3-none-any.whl#sha256=e41118f81698d3d59b3c7c2887937446048f741aba6c367c1c1a77810b3e2d08 +# pip jupyter-server @ https://files.pythonhosted.org/packages/1d/dd/77a250131fcc97d4a4fa76cda07e23e6b66028aca723f36d114b635127e9/jupyter_server-2.5.0-py3-none-any.whl#sha256=e6bc1e9e96d7c55b9ce9699ff6cb9a910581fe7349e27c40389acb67632e24c0 +# pip jupyterlab-server @ https://files.pythonhosted.org/packages/99/21/ece3884094b4fe49da97f0090ff4f4a694a9f47f87556bd21b7c4e865e45/jupyterlab_server-2.20.0-py3-none-any.whl#sha256=0203f96913187a9e7a6c8cef3556b499d2be67f014ad4ce9b76c8dcdcadb2367 +# pip jupyterlite-sphinx @ https://files.pythonhosted.org/packages/34/a9/a050b891d5d06a3fe73f1e16992a846a6f6ba21660ac053f5064cbf98bae/jupyterlite_sphinx-0.8.0-py3-none-any.whl#sha256=4a20fcb585ef036d3ed1c62cd6270351f810bc9586d3638f55e6a98665b3373d diff --git a/build_tools/update_environments_and_lock_files.py b/build_tools/update_environments_and_lock_files.py index ec375078bfab8..4480c3ba69fb0 100644 --- a/build_tools/update_environments_and_lock_files.py +++ b/build_tools/update_environments_and_lock_files.py @@ -301,8 +301,8 @@ def remove_from(alist, to_remove): "plotly", "pooch", "sphinxext-opengraph", - "pip", ], + "pip_dependencies": ["jupyterlite-sphinx", "jupyterlite-pyodide-kernel"], "package_constraints": { "python": "3.9", # XXX: sphinx > 6.0 does not correctly generate searchindex.js diff --git a/doc/conf.py b/doc/conf.py index 52b084b331c8c..39679492f75f8 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -60,6 +60,7 @@ "doi_role", "allow_nan_estimators", "matplotlib.sphinxext.plot_directive", + "jupyterlite_sphinx", ] # Produce `plot::` directives for examples that contain `import matplotlib` or @@ -248,9 +249,9 @@ -1 ] latest_highlights = latest_highlights.with_suffix("").name -html_context[ - "release_highlights" -] = f"auto_examples/release_highlights/{latest_highlights}" +html_context["release_highlights"] = ( + f"auto_examples/release_highlights/{latest_highlights}" +) # get version from highlight name assuming highlights have the form # plot_release_highlights_0_22_0 @@ -568,9 +569,11 @@ def setup(app): # The following is used by sphinx.ext.linkcode to provide links to github linkcode_resolve = make_linkcode_resolve( "sklearn", - "https://github.com/scikit-learn/" - "scikit-learn/blob/{revision}/" - "{package}/{path}#L{lineno}", + ( + "https://github.com/scikit-learn/" + "scikit-learn/blob/{revision}/" + "{package}/{path}#L{lineno}" + ), ) warnings.filterwarnings( @@ -616,20 +619,32 @@ def setup(app): # ignore links to specific pdf pages because linkcheck does not handle them # ('utf-8' codec can't decode byte error) r"http://www.utstat.toronto.edu/~rsalakhu/sta4273/notes/Lecture2.pdf#page=.*", - "https://www.fordfoundation.org/media/2976/" - "roads-and-bridges-the-unseen-labor-behind-our-digital-infrastructure.pdf#page=.*", + ( + "https://www.fordfoundation.org/media/2976/" + "roads-and-bridges-the-unseen-labor-behind-our-digital-infrastructure.pdf#page=.*" + ), # links falsely flagged as broken - "https://www.researchgate.net/publication/" - "233096619_A_Dendrite_Method_for_Cluster_Analysis", - "https://www.researchgate.net/publication/221114584_Random_Fourier_Approximations_" - "for_Skewed_Multiplicative_Histogram_Kernels", - "https://www.researchgate.net/publication/4974606_" - "Hedonic_housing_prices_and_the_demand_for_clean_air", - "https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_" - "Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations", + ( + "https://www.researchgate.net/publication/" + "233096619_A_Dendrite_Method_for_Cluster_Analysis" + ), + ( + "https://www.researchgate.net/publication/221114584_Random_Fourier_Approximations_" + "for_Skewed_Multiplicative_Histogram_Kernels" + ), + ( + "https://www.researchgate.net/publication/4974606_" + "Hedonic_housing_prices_and_the_demand_for_clean_air" + ), + ( + "https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_" + "Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations" + ), "https://doi.org/10.13140/RG.2.2.35280.02565", - "https://www.microsoft.com/en-us/research/uploads/prod/2006/01/" - "Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf", + ( + "https://www.microsoft.com/en-us/research/uploads/prod/2006/01/" + "Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf" + ), "https://www.microsoft.com/en-us/research/wp-content/uploads/2016/02/tr-99-87.pdf", "https://microsoft.com/", "https://www.jstor.org/stable/2984099", From 3cbc62365d1e5de49e6ffbb0c604f2076a28d013 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Fri, 17 Mar 2023 08:37:06 +0100 Subject: [PATCH 02/19] Use same black as in CI --- doc/conf.py | 50 ++++++++++++++++++-------------------------------- 1 file changed, 18 insertions(+), 32 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 39679492f75f8..a6806c2003e5e 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -249,9 +249,9 @@ -1 ] latest_highlights = latest_highlights.with_suffix("").name -html_context["release_highlights"] = ( - f"auto_examples/release_highlights/{latest_highlights}" -) +html_context[ + "release_highlights" +] = f"auto_examples/release_highlights/{latest_highlights}" # get version from highlight name assuming highlights have the form # plot_release_highlights_0_22_0 @@ -569,11 +569,9 @@ def setup(app): # The following is used by sphinx.ext.linkcode to provide links to github linkcode_resolve = make_linkcode_resolve( "sklearn", - ( - "https://github.com/scikit-learn/" - "scikit-learn/blob/{revision}/" - "{package}/{path}#L{lineno}" - ), + "https://github.com/scikit-learn/" + "scikit-learn/blob/{revision}/" + "{package}/{path}#L{lineno}", ) warnings.filterwarnings( @@ -619,32 +617,20 @@ def setup(app): # ignore links to specific pdf pages because linkcheck does not handle them # ('utf-8' codec can't decode byte error) r"http://www.utstat.toronto.edu/~rsalakhu/sta4273/notes/Lecture2.pdf#page=.*", - ( - "https://www.fordfoundation.org/media/2976/" - "roads-and-bridges-the-unseen-labor-behind-our-digital-infrastructure.pdf#page=.*" - ), + "https://www.fordfoundation.org/media/2976/" + "roads-and-bridges-the-unseen-labor-behind-our-digital-infrastructure.pdf#page=.*", # links falsely flagged as broken - ( - "https://www.researchgate.net/publication/" - "233096619_A_Dendrite_Method_for_Cluster_Analysis" - ), - ( - "https://www.researchgate.net/publication/221114584_Random_Fourier_Approximations_" - "for_Skewed_Multiplicative_Histogram_Kernels" - ), - ( - "https://www.researchgate.net/publication/4974606_" - "Hedonic_housing_prices_and_the_demand_for_clean_air" - ), - ( - "https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_" - "Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations" - ), + "https://www.researchgate.net/publication/" + "233096619_A_Dendrite_Method_for_Cluster_Analysis", + "https://www.researchgate.net/publication/221114584_Random_Fourier_Approximations_" + "for_Skewed_Multiplicative_Histogram_Kernels", + "https://www.researchgate.net/publication/4974606_" + "Hedonic_housing_prices_and_the_demand_for_clean_air", + "https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_" + "Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations", "https://doi.org/10.13140/RG.2.2.35280.02565", - ( - "https://www.microsoft.com/en-us/research/uploads/prod/2006/01/" - "Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf" - ), + "https://www.microsoft.com/en-us/research/uploads/prod/2006/01/" + "Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf", "https://www.microsoft.com/en-us/research/wp-content/uploads/2016/02/tr-99-87.pdf", "https://microsoft.com/", "https://www.jstor.org/stable/2984099", From e54709616c063659b84a9aed789714e50f2bc26a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Fri, 17 Mar 2023 08:59:09 +0100 Subject: [PATCH 03/19] Fix doc-min-dependencies --- doc/conf.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index a6806c2003e5e..181626654b5f4 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -60,9 +60,20 @@ "doi_role", "allow_nan_estimators", "matplotlib.sphinxext.plot_directive", - "jupyterlite_sphinx", ] +try: + import jupyterlite_sphinx # noqa: F401 + + extensions.append("jupyterlite_sphinx") +except ImportError: + # In some cases we don't want to require jupyterlite_sphinx to be installed, + # e.g. the doc-min-dependencies build + warnings.warn( + "jupyterlite_sphinx is not installed, you need to install it " + "if you want JupyterLite links to appear in each example" + ) + # Produce `plot::` directives for examples that contain `import matplotlib` or # `from matplotlib import`. numpydoc_use_plots = True From acc8d5b0b96b8baba4d8af4d42fbbc4d078282b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Fri, 17 Mar 2023 10:25:42 +0100 Subject: [PATCH 04/19] Remove %matplotlib inline cell --- doc/conf.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/conf.py b/doc/conf.py index 181626654b5f4..c2ba54d16e435 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -436,6 +436,11 @@ def __call__(self, filename): "inspect_global_variables": False, "remove_config_comments": True, "plot_gallery": "True", + # Remove %matplotlib inline cell which does not work in JupyterLite if you + # have not imported matplotlib before. TODO it can be removed when + # https://github.com/sphinx-gallery/sphinx-gallery/pull/1099 is in a + # released version + "first_notebook_cell": None, } From 34299b10bcbd341d7a02d4e2042816d2c936e3f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Mon, 20 Mar 2023 17:02:40 +0100 Subject: [PATCH 05/19] Add jupyterlite_contents to .gitignore --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 89600846100a8..f4601a15655a5 100644 --- a/.gitignore +++ b/.gitignore @@ -99,3 +99,6 @@ sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.pxd sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.pyx sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.pxd sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.pyx + +# Default JupyterLite content +jupyterlite_contents From 62cabcdf733c47348a0d35233fee325917050550 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Tue, 21 Mar 2023 14:10:42 +0100 Subject: [PATCH 06/19] Install sphinx-gallery development version --- build_tools/circle/build_doc.sh | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/build_tools/circle/build_doc.sh b/build_tools/circle/build_doc.sh index 9f6733373ca20..f0e891f921275 100755 --- a/build_tools/circle/build_doc.sh +++ b/build_tools/circle/build_doc.sh @@ -177,6 +177,10 @@ mamba install "$(get_dep conda-lock min)" -y conda-lock install --log-level WARNING --name $CONDA_ENV_NAME $LOCK_FILE source activate $CONDA_ENV_NAME +# TODO remove once all features we need are in a sphinx-gallery release, e.g. +# https://github.com/sphinx-gallery/sphinx-gallery/pull/1105 +pip install git+https://github.com/sphinx-gallery/sphinx-gallery + show_installed_libraries # Set parallelism to 3 to overlap IO bound tasks with CPU bound tasks on CI From 359f8ba15b7e4e8dd5b206e9c5efcbf04d30ad5f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Wed, 29 Mar 2023 12:12:32 +0200 Subject: [PATCH 07/19] Modify JupyterLite notebooks based on their content --- doc/conf.py | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/doc/conf.py b/doc/conf.py index c2ba54d16e435..c5deb506112cd 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -28,6 +28,8 @@ from github_link import make_linkcode_resolve import sphinx_gallery from sphinx_gallery.sorting import ExampleTitleSortKey +from sphinx_gallery.notebook import add_markdown_cell, add_code_cell +from sphinx_gallery.notebook import add_markdown_cell, add_code_cell try: # Configure plotly to integrate its output into the HTML pages generated by @@ -415,6 +417,66 @@ def __call__(self, filename): return -version_float +def notebook_modification_function(notebook_content, notebook_filename): + notebook_content_str = str(notebook_content) + warning_template = "\n".join( + [ + "
", + "", + "# JupyterLite warning", + "", + "{message}", + "
", + ] + ) + + if "import plotly" in notebook_content_str: + message_class = "danger" + message = ( + "This notebook is not expected to work inside JupyterLite for now." + " There seems to be some issues with Plotly, see " + "[this]('https://github.com/jupyterlite/jupyterlite/pull/950') " + "for more details." + ) + else: + message_class = "warning" + message = ( + "JupyterLite integration in sphinx-gallery is beta " + "and it may break in unexpected ways" + ) + + markdown = warning_template.format(message_class=message_class, message=message) + + dummy_notebook_content = {"cells": []} + add_markdown_cell(dummy_notebook_content, markdown) + + code_lines = [] + + if "seaborn" in notebook_content_str: + code_lines.append("%pip install seaborn") + if "plotly.express" in notebook_content_str: + code_lines.extend(["%pip install plotly", "import pandas"]) + if "skimage" in notebook_content_str: + code_lines.append("%pip install scikit-image") + if "fetch_" in notebook_content_str: + code_lines.extend( + [ + "%pip install pyodide-http", + "import pyodide_http", + "pyodide_http.patch_all()", + ] + ) + + if code_lines: + code_lines = ["# JupyterLite-specific code"] + code_lines + code = "\n".join(code_lines) + add_code_cell(dummy_notebook_content, code) + + notebook_content["cells"] = ( + dummy_notebook_content["cells"] + notebook_content["cells"] + ) + + sphinx_gallery_conf = { "doc_module": "sklearn", "backreferences_dir": os.path.join("modules", "generated"), @@ -432,6 +494,7 @@ def __call__(self, filename): "dependencies": "./binder/requirements.txt", "use_jupyter_lab": True, }, + "jupyterlite": {"notebook_modification_function": notebook_modification_function}, # avoid generating too many cross links "inspect_global_variables": False, "remove_config_comments": True, From 366b1ab40a622f60b474b3047ca43303fcfc7018 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Wed, 29 Mar 2023 12:18:57 +0200 Subject: [PATCH 08/19] lint --- doc/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index c5deb506112cd..7a50e0bccd1e6 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -29,7 +29,6 @@ import sphinx_gallery from sphinx_gallery.sorting import ExampleTitleSortKey from sphinx_gallery.notebook import add_markdown_cell, add_code_cell -from sphinx_gallery.notebook import add_markdown_cell, add_code_cell try: # Configure plotly to integrate its output into the HTML pages generated by From a80e6dffc637292440d881d908308d916fd0d1b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Wed, 29 Mar 2023 13:51:56 +0200 Subject: [PATCH 09/19] Update doc lock file after rebase --- build_tools/circle/doc_linux-64_conda.lock | 90 +++++++++++----------- 1 file changed, 47 insertions(+), 43 deletions(-) diff --git a/build_tools/circle/doc_linux-64_conda.lock b/build_tools/circle/doc_linux-64_conda.lock index 35e160833adac..e8c69c37dd16c 100644 --- a/build_tools/circle/doc_linux-64_conda.lock +++ b/build_tools/circle/doc_linux-64_conda.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 3c2790bb03feda8fbbf9b5fb06111fce0af10f7a587b5e4c251fa43e0492f7b2 +# input_hash: bc7ade520415ccca1eb8f425ca67039c65ba96ea4ba63d41d1a7c9aa9e14a478 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -15,7 +15,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19. https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-devel_linux-64-11.3.0-h210ce93_19.tar.bz2#8aee006c0662f551f3acef9a7077a5b9 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2#1030b1f38c129f2634eae026f704fe60 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.9-3_cp39.conda#0dd193187d54e585cac7eab942a8847e -https://conda.anaconda.org/conda-forge/noarch/tzdata-2022g-h191b570_0.conda#51fc4fcfb19f5d95ffc8c339db5068e8 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.2.0-h69a702a_19.tar.bz2#cd7a806282c16e1f2d39a7e80d3a3e0d https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373 @@ -23,7 +23,7 @@ https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_15. https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.39-he00db2b_1.conda#3d726e8b51a1f5bfd66892a2b7d9db2d https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab https://conda.anaconda.org/conda-forge/linux-64/binutils-2.39-hdd6e379_1.conda#1276c18b0a562739185dbf5bd14b57b2 -https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.39-h5fc0e48_11.tar.bz2#b7d26ab37be17ea4c366a97138684bcb +https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.39-h5fc0e48_12.conda#4395b0d4f6e3553bc3b804a9a3cdb234 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_kmp_llvm.tar.bz2#562b26ba2e19059551a811e72ab7f793 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535 https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.8-h166bdaf_0.tar.bz2#be733e69048951df1e4b4b7bb8c7666f @@ -47,7 +47,7 @@ https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76 https://conda.anaconda.org/conda-forge/linux-64/libaec-1.0.6-hcb278e6_1.conda#0f683578378cddb223e7fd24f785ab2a https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.0.9-h166bdaf_8.tar.bz2#9194c9bf9428035a05352d031462eae4 https://conda.anaconda.org/conda-forge/linux-64/libdb-6.2.32-h9c3ff4c_0.tar.bz2#3f3258d8f841fbac63b36b75bdac1afd -https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.17-h0b41bf4_0.conda#5cc781fd91968b11a8a7fdbee0982676 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2#b62b52da46c39ee2bc3c162ac7f1804d @@ -58,13 +58,12 @@ https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.21-pthreads_h78a https://conda.anaconda.org/conda-forge/linux-64/libopus-1.3.1-h7f98852_1.tar.bz2#15345e56d527b330e1cacbdf58676e8f https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-11.3.0-h239ccf8_19.tar.bz2#d17fd55aed84ab6592c5419b6600501c https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.7-h27087fc_0.conda#f204c8ba400ec475452737094fb81d52 -https://conda.anaconda.org/conda-forge/linux-64/libudev1-253-h0b41bf4_0.conda#6c2addbd9aa4ee47c76d50c9f0df8cd6 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar.bz2#772d69f030955d9646d3d0eaf21d859d https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.0-h0b41bf4_0.conda#0d4a7508d8c6c65314f2b9c1f56ad408 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2#f3f9de449d32ca9b9c66a22863c96f41 https://conda.anaconda.org/conda-forge/linux-64/libzopfli-1.0.3-h9c3ff4c_0.tar.bz2#c66fe2d123249af7651ebde8984c51c2 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0 -https://conda.anaconda.org/conda-forge/linux-64/mpg123-1.31.2-hcb278e6_0.conda#08efb1e1813f1a151b7a945b972a049b +https://conda.anaconda.org/conda-forge/linux-64/mpg123-1.31.3-hcb278e6_0.conda#141a126675b6d1a4eabb111a4a353898 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4acfc691e64342b9dae57cf2adc63238 https://conda.anaconda.org/conda-forge/linux-64/nspr-4.35-h27087fc_0.conda#da0ec11a6454ae19bff5b02ed881a2b1 https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.0-h0b41bf4_0.conda#2d833be81a21128e317325a01326d36f @@ -83,14 +82,14 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae 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https://files.pythonhosted.org/packages/81/ff/9cd69da9e968d529597258c32dee39ac580a8973877c8ca5dd7bd7d349e7/jupyterlite_pyodide_kernel-0.0.5-py3-none-any.whl#sha256=296979b1d8dc5ec7d70cf9742abae7266ec1581638984f34bb1517109615ab42 # pip jupyter-events @ https://files.pythonhosted.org/packages/ee/14/e11a93c1b47a69432ee7898f1b55f1da27f2f93b009a34dbdafb9b903f81/jupyter_events-0.6.3-py3-none-any.whl#sha256=57a2749f87ba387cd1bfd9b22a0875b889237dbf2edc2121ebb22bde47036c17 -# pip nbformat @ https://files.pythonhosted.org/packages/21/ad/020fed74bfde983a3b70cc95843d6adbe59171aa9a3da5aab403aa722a17/nbformat-5.7.3-py3-none-any.whl#sha256=22a98a6516ca216002b0a34591af5bcb8072ca6c63910baffc901cfa07fefbf0 +# pip nbformat @ https://files.pythonhosted.org/packages/1d/f6/38f4694b5035306a8c2685e9e6ea7bf46ea344c03422d7131442ac9677c1/nbformat-5.8.0-py3-none-any.whl#sha256=d910082bd3e0bffcf07eabf3683ed7dda0727a326c446eeb2922abe102e65162 # pip nbclient @ https://files.pythonhosted.org/packages/15/49/ea7a0c7e649c54883d76f5119a3e0be592d82a7df1a9b87124fa6663d9c7/nbclient-0.7.2-py3-none-any.whl#sha256=d97ac6257de2794f5397609df754fcbca1a603e94e924eb9b99787c031ae2e7c # pip nbconvert @ https://files.pythonhosted.org/packages/3f/53/1e99001bc154bd2d243564275e2b7a0e492b48ae032b1377f35cc9defa16/nbconvert-7.2.10-py3-none-any.whl#sha256=e41118f81698d3d59b3c7c2887937446048f741aba6c367c1c1a77810b3e2d08 # pip jupyter-server @ https://files.pythonhosted.org/packages/1d/dd/77a250131fcc97d4a4fa76cda07e23e6b66028aca723f36d114b635127e9/jupyter_server-2.5.0-py3-none-any.whl#sha256=e6bc1e9e96d7c55b9ce9699ff6cb9a910581fe7349e27c40389acb67632e24c0 -# pip jupyterlab-server @ https://files.pythonhosted.org/packages/99/21/ece3884094b4fe49da97f0090ff4f4a694a9f47f87556bd21b7c4e865e45/jupyterlab_server-2.20.0-py3-none-any.whl#sha256=0203f96913187a9e7a6c8cef3556b499d2be67f014ad4ce9b76c8dcdcadb2367 +# pip jupyterlab-server @ https://files.pythonhosted.org/packages/a0/e3/1af3f5be602852d7abe46b80b86d915e907fca6a308e44e6b6e848b92f00/jupyterlab_server-2.21.0-py3-none-any.whl#sha256=ff1e7a81deb2dcb433215d469000988590fd5a5733574aa2698d643a6c9b3ace # pip jupyterlite-sphinx @ https://files.pythonhosted.org/packages/34/a9/a050b891d5d06a3fe73f1e16992a846a6f6ba21660ac053f5064cbf98bae/jupyterlite_sphinx-0.8.0-py3-none-any.whl#sha256=4a20fcb585ef036d3ed1c62cd6270351f810bc9586d3638f55e6a98665b3373d From a4bc914b19c4e938f5a47651c44578ac62975d4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Wed, 29 Mar 2023 14:11:30 +0200 Subject: [PATCH 10/19] Update lock file with conda-lock development version --- build_tools/circle/doc_linux-64_conda.lock | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/build_tools/circle/doc_linux-64_conda.lock b/build_tools/circle/doc_linux-64_conda.lock index e8c69c37dd16c..d993bb0210c59 100644 --- a/build_tools/circle/doc_linux-64_conda.lock +++ b/build_tools/circle/doc_linux-64_conda.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: bc7ade520415ccca1eb8f425ca67039c65ba96ea4ba63d41d1a7c9aa9e14a478 +# input_hash: 3c2790bb03feda8fbbf9b5fb06111fce0af10f7a587b5e4c251fa43e0492f7b2 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -289,7 +289,6 @@ https://conda.anaconda.org/conda-forge/noarch/seaborn-0.12.2-hd8ed1ab_0.conda#50 # pip ptyprocess @ https://files.pythonhosted.org/packages/22/a6/858897256d0deac81a172289110f31629fc4cee19b6f01283303e18c8db3/ptyprocess-0.7.0-py2.py3-none-any.whl#sha256=4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35 # pip pyrsistent @ https://files.pythonhosted.org/packages/64/de/375aa14daaee107f987da76ca32f7a907fea00fa8b8afb67dc09bec0de91/pyrsistent-0.19.3-py3-none-any.whl#sha256=ccf0d6bd208f8111179f0c26fdf84ed7c3891982f2edaeae7422575f47e66b64 # pip python-json-logger @ https://files.pythonhosted.org/packages/35/a6/145655273568ee78a581e734cf35beb9e33a370b29c5d3c8fee3744de29f/python_json_logger-2.0.7-py3-none-any.whl#sha256=f380b826a991ebbe3de4d897aeec42760035ac760345e57b812938dc8b35e2bd -# pip pywinpty @ https://files.pythonhosted.org/packages/d3/89/2b9113eabacfe3bbebcdf95c24772e2267c7b6b9fed6e35bffba2080a4c1/pywinpty-2.0.10.tar.gz#sha256=cdbb5694cf8c7242c2ecfaca35c545d31fa5d5814c3d67a4e628f803f680ebea # pip rfc3986-validator @ https://files.pythonhosted.org/packages/9e/51/17023c0f8f1869d8806b979a2bffa3f861f26a3f1a66b094288323fba52f/rfc3986_validator-0.1.1-py2.py3-none-any.whl#sha256=2f235c432ef459970b4306369336b9d5dbdda31b510ca1e327636e01f528bfa9 # pip send2trash @ https://files.pythonhosted.org/packages/47/26/3435896d757335ea53dce5abf8d658ca80757a7a06258451b358f10232be/Send2Trash-1.8.0-py3-none-any.whl#sha256=f20eaadfdb517eaca5ce077640cb261c7d2698385a6a0f072a4a5447fd49fa08 # pip sniffio @ https://files.pythonhosted.org/packages/c3/a0/5dba8ed157b0136607c7f2151db695885606968d1fae123dc3391e0cfdbf/sniffio-1.3.0-py3-none-any.whl#sha256=eecefdce1e5bbfb7ad2eeaabf7c1eeb404d7757c379bd1f7e5cce9d8bf425384 From 0af4a771230f7b6c46f2e4120ca81fffdd1729a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Thu, 13 Apr 2023 16:46:00 +0200 Subject: [PATCH 11/19] Tweak warning wording --- doc/conf.py | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 7a50e0bccd1e6..b4cab85f0adb2 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -429,20 +429,15 @@ def notebook_modification_function(notebook_content, notebook_filename): ] ) - if "import plotly" in notebook_content_str: - message_class = "danger" - message = ( - "This notebook is not expected to work inside JupyterLite for now." - " There seems to be some issues with Plotly, see " - "[this]('https://github.com/jupyterlite/jupyterlite/pull/950') " - "for more details." - ) - else: - message_class = "warning" - message = ( - "JupyterLite integration in sphinx-gallery is beta " - "and it may break in unexpected ways" - ) + message_class = "warning" + message = ( + "Running the scikit-learn examples in JupyterLite is experimental " + "and you may encounter some unexpected behavior.\n\n" + "The main difference is that imports will take a lot longer than usual, " + "for example the first `import sklearn` can take roughly 20-30s.\n\n" + "If you notice problems, feel free to open an " + "[issue](https://github.com/scikit-learn/scikit-learn/issues/new/choose) about it." + ) markdown = warning_template.format(message_class=message_class, message=message) @@ -465,6 +460,13 @@ def notebook_modification_function(notebook_content, notebook_filename): "pyodide_http.patch_all()", ] ) + if ( + # TODO(1.4) the default fetch_openml parser will be pandas so any + # notebook using fetch_openml will need 'import pandas' + 'parser="pandas"' in notebook_content_str + or "as_frame=True" in notebook_content_str + ): + code_lines.extend("import pandas") if code_lines: code_lines = ["# JupyterLite-specific code"] + code_lines From ea878c7a50fdee6710c72ed063a701854aaaa83c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Fri, 14 Apr 2023 09:34:23 +0200 Subject: [PATCH 12/19] lint --- doc/conf.py | 62 ++++++++++++++++++++++++++++++++--------------------- 1 file changed, 38 insertions(+), 24 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index b4cab85f0adb2..523fd991af985 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -261,9 +261,9 @@ -1 ] latest_highlights = latest_highlights.with_suffix("").name -html_context[ - "release_highlights" -] = f"auto_examples/release_highlights/{latest_highlights}" +html_context["release_highlights"] = ( + f"auto_examples/release_highlights/{latest_highlights}" +) # get version from highlight name assuming highlights have the form # plot_release_highlights_0_22_0 @@ -431,12 +431,12 @@ def notebook_modification_function(notebook_content, notebook_filename): message_class = "warning" message = ( - "Running the scikit-learn examples in JupyterLite is experimental " - "and you may encounter some unexpected behavior.\n\n" - "The main difference is that imports will take a lot longer than usual, " - "for example the first `import sklearn` can take roughly 20-30s.\n\n" - "If you notice problems, feel free to open an " - "[issue](https://github.com/scikit-learn/scikit-learn/issues/new/choose) about it." + "Running the scikit-learn examples in JupyterLite is experimental and you may" + " encounter some unexpected behavior.\n\nThe main difference is that imports" + " will take a lot longer than usual, for example the first `import sklearn` can" + " take roughly 20-30s.\n\nIf you notice problems, feel free to open an" + " [issue](https://github.com/scikit-learn/scikit-learn/issues/new/choose)" + " about it." ) markdown = warning_template.format(message_class=message_class, message=message) @@ -649,9 +649,11 @@ def setup(app): # The following is used by sphinx.ext.linkcode to provide links to github linkcode_resolve = make_linkcode_resolve( "sklearn", - "https://github.com/scikit-learn/" - "scikit-learn/blob/{revision}/" - "{package}/{path}#L{lineno}", + ( + "https://github.com/scikit-learn/" + "scikit-learn/blob/{revision}/" + "{package}/{path}#L{lineno}" + ), ) warnings.filterwarnings( @@ -697,20 +699,32 @@ def setup(app): # ignore links to specific pdf pages because linkcheck does not handle them # ('utf-8' codec can't decode byte error) r"http://www.utstat.toronto.edu/~rsalakhu/sta4273/notes/Lecture2.pdf#page=.*", - "https://www.fordfoundation.org/media/2976/" - "roads-and-bridges-the-unseen-labor-behind-our-digital-infrastructure.pdf#page=.*", + ( + "https://www.fordfoundation.org/media/2976/" + "roads-and-bridges-the-unseen-labor-behind-our-digital-infrastructure.pdf#page=.*" + ), # links falsely flagged as broken - "https://www.researchgate.net/publication/" - "233096619_A_Dendrite_Method_for_Cluster_Analysis", - "https://www.researchgate.net/publication/221114584_Random_Fourier_Approximations_" - "for_Skewed_Multiplicative_Histogram_Kernels", - "https://www.researchgate.net/publication/4974606_" - "Hedonic_housing_prices_and_the_demand_for_clean_air", - "https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_" - "Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations", + ( + "https://www.researchgate.net/publication/" + "233096619_A_Dendrite_Method_for_Cluster_Analysis" + ), + ( + "https://www.researchgate.net/publication/221114584_Random_Fourier_Approximations_" + "for_Skewed_Multiplicative_Histogram_Kernels" + ), + ( + "https://www.researchgate.net/publication/4974606_" + "Hedonic_housing_prices_and_the_demand_for_clean_air" + ), + ( + "https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_" + "Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations" + ), "https://doi.org/10.13140/RG.2.2.35280.02565", - "https://www.microsoft.com/en-us/research/uploads/prod/2006/01/" - "Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf", + ( + "https://www.microsoft.com/en-us/research/uploads/prod/2006/01/" + "Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf" + ), "https://www.microsoft.com/en-us/research/wp-content/uploads/2016/02/tr-99-87.pdf", "https://microsoft.com/", "https://www.jstor.org/stable/2984099", From 5d9216f676b3cd73597e5a69d55a2fceeb5aa3c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Fri, 14 Apr 2023 10:50:43 +0200 Subject: [PATCH 13/19] Lint with the right black version --- doc/conf.py | 50 ++++++++++++++++++-------------------------------- 1 file changed, 18 insertions(+), 32 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 523fd991af985..0114b048c19fa 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -261,9 +261,9 @@ -1 ] latest_highlights = latest_highlights.with_suffix("").name -html_context["release_highlights"] = ( - f"auto_examples/release_highlights/{latest_highlights}" -) +html_context[ + "release_highlights" +] = f"auto_examples/release_highlights/{latest_highlights}" # get version from highlight name assuming highlights have the form # plot_release_highlights_0_22_0 @@ -649,11 +649,9 @@ def setup(app): # The following is used by sphinx.ext.linkcode to provide links to github linkcode_resolve = make_linkcode_resolve( "sklearn", - ( - "https://github.com/scikit-learn/" - "scikit-learn/blob/{revision}/" - "{package}/{path}#L{lineno}" - ), + "https://github.com/scikit-learn/" + "scikit-learn/blob/{revision}/" + "{package}/{path}#L{lineno}", ) warnings.filterwarnings( @@ -699,32 +697,20 @@ def setup(app): # ignore links to specific pdf pages because linkcheck does not handle them # ('utf-8' codec can't decode byte error) r"http://www.utstat.toronto.edu/~rsalakhu/sta4273/notes/Lecture2.pdf#page=.*", - ( - "https://www.fordfoundation.org/media/2976/" - "roads-and-bridges-the-unseen-labor-behind-our-digital-infrastructure.pdf#page=.*" - ), + "https://www.fordfoundation.org/media/2976/" + "roads-and-bridges-the-unseen-labor-behind-our-digital-infrastructure.pdf#page=.*", # links falsely flagged as broken - ( - "https://www.researchgate.net/publication/" - "233096619_A_Dendrite_Method_for_Cluster_Analysis" - ), - ( - "https://www.researchgate.net/publication/221114584_Random_Fourier_Approximations_" - "for_Skewed_Multiplicative_Histogram_Kernels" - ), - ( - "https://www.researchgate.net/publication/4974606_" - "Hedonic_housing_prices_and_the_demand_for_clean_air" - ), - ( - "https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_" - "Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations" - ), + "https://www.researchgate.net/publication/" + "233096619_A_Dendrite_Method_for_Cluster_Analysis", + "https://www.researchgate.net/publication/221114584_Random_Fourier_Approximations_" + "for_Skewed_Multiplicative_Histogram_Kernels", + "https://www.researchgate.net/publication/4974606_" + "Hedonic_housing_prices_and_the_demand_for_clean_air", + "https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_" + "Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations", "https://doi.org/10.13140/RG.2.2.35280.02565", - ( - "https://www.microsoft.com/en-us/research/uploads/prod/2006/01/" - "Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf" - ), + "https://www.microsoft.com/en-us/research/uploads/prod/2006/01/" + "Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf", "https://www.microsoft.com/en-us/research/wp-content/uploads/2016/02/tr-99-87.pdf", "https://microsoft.com/", "https://www.jstor.org/stable/2984099", From 196822196c8b30df87ff74311caca91bd5fc5f2c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Mon, 17 Apr 2023 10:15:27 +0200 Subject: [PATCH 14/19] Use latest sphinx-gallery release --- build_tools/circle/build_doc.sh | 4 - build_tools/circle/doc_linux-64_conda.lock | 101 ++++++++++----------- 2 files changed, 48 insertions(+), 57 deletions(-) diff --git a/build_tools/circle/build_doc.sh b/build_tools/circle/build_doc.sh index f0e891f921275..9f6733373ca20 100755 --- a/build_tools/circle/build_doc.sh +++ b/build_tools/circle/build_doc.sh @@ -177,10 +177,6 @@ mamba install "$(get_dep conda-lock min)" -y conda-lock install --log-level WARNING --name $CONDA_ENV_NAME $LOCK_FILE source activate $CONDA_ENV_NAME -# TODO remove once all features we need are in a sphinx-gallery release, e.g. -# https://github.com/sphinx-gallery/sphinx-gallery/pull/1105 -pip install git+https://github.com/sphinx-gallery/sphinx-gallery - show_installed_libraries # Set parallelism to 3 to overlap IO bound tasks with CPU bound tasks on CI diff --git a/build_tools/circle/doc_linux-64_conda.lock b/build_tools/circle/doc_linux-64_conda.lock index d993bb0210c59..bea77a9d0c170 100644 --- a/build_tools/circle/doc_linux-64_conda.lock +++ b/build_tools/circle/doc_linux-64_conda.lock @@ -33,22 +33,19 @@ https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2#f26ef8098fab1f719c91eb760d63381a https://conda.anaconda.org/conda-forge/linux-64/charls-2.4.1-hcb278e6_0.conda#445926523a9ecf989f07162643854296 https://conda.anaconda.org/conda-forge/linux-64/dav1d-1.0.0-h166bdaf_1.tar.bz2#e890928299fe7242a108850fc0a5b7fc 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https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-hca18f0e_1.conda#e1232042de76d24539a436d37597eb06 https://conda.anaconda.org/conda-forge/linux-64/gcc-11.3.0-h02d0930_12.conda#4965c0bd382fcf0520d74b4da123b9f9 https://conda.anaconda.org/conda-forge/linux-64/gcc_linux-64-11.3.0-he6f903b_12.conda#b8f5f99cc68dbdd083fc03f9765dea64 @@ -122,12 +118,11 @@ https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-16_linux64_openbl https://conda.anaconda.org/conda-forge/linux-64/libgcrypt-1.10.1-h166bdaf_0.tar.bz2#f967fc95089cd247ceed56eda31de3a9 https://conda.anaconda.org/conda-forge/linux-64/libglib-2.74.1-h606061b_1.tar.bz2#ed5349aa96776e00b34eccecf4a948fe https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_openblas.tar.bz2#955d993f41f9354bf753d29864ea20ad -https://conda.anaconda.org/conda-forge/linux-64/libllvm15-15.0.7-hadd5161_1.conda#17d91085ccf5934ce652cb448d0cb65a 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https://files.pythonhosted.org/packages/cf/58/8acf1b3e91c58313ce5cb67df61001fc9dcd21be4fadb76c1a2d540e09ed/fqdn-1.5.1-py3-none-any.whl#sha256=3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014 @@ -292,7 +287,7 @@ https://conda.anaconda.org/conda-forge/noarch/seaborn-0.12.2-hd8ed1ab_0.conda#50 # pip rfc3986-validator @ https://files.pythonhosted.org/packages/9e/51/17023c0f8f1869d8806b979a2bffa3f861f26a3f1a66b094288323fba52f/rfc3986_validator-0.1.1-py2.py3-none-any.whl#sha256=2f235c432ef459970b4306369336b9d5dbdda31b510ca1e327636e01f528bfa9 # pip send2trash @ https://files.pythonhosted.org/packages/47/26/3435896d757335ea53dce5abf8d658ca80757a7a06258451b358f10232be/Send2Trash-1.8.0-py3-none-any.whl#sha256=f20eaadfdb517eaca5ce077640cb261c7d2698385a6a0f072a4a5447fd49fa08 # pip sniffio @ https://files.pythonhosted.org/packages/c3/a0/5dba8ed157b0136607c7f2151db695885606968d1fae123dc3391e0cfdbf/sniffio-1.3.0-py3-none-any.whl#sha256=eecefdce1e5bbfb7ad2eeaabf7c1eeb404d7757c379bd1f7e5cce9d8bf425384 -# pip soupsieve @ https://files.pythonhosted.org/packages/d2/70/2c92d7bc961ba43b7b21032b7622144de5f97dec14b62226533f6940798e/soupsieve-2.4-py3-none-any.whl#sha256=49e5368c2cda80ee7e84da9dbe3e110b70a4575f196efb74e51b94549d921955 +# pip soupsieve @ https://files.pythonhosted.org/packages/49/37/673d6490efc51ec46d198c75903d99de59baffdd47aea3d071b80a9e4e89/soupsieve-2.4.1-py3-none-any.whl#sha256=1c1bfee6819544a3447586c889157365a27e10d88cde3ad3da0cf0ddf646feb8 # pip traitlets @ https://files.pythonhosted.org/packages/77/75/c28e9ef7abec2b7e9ff35aea3e0be6c1aceaf7873c26c95ae1f0d594de71/traitlets-5.9.0-py3-none-any.whl#sha256=9e6ec080259b9a5940c797d58b613b5e31441c2257b87c2e795c5228ae80d2d8 # pip uri-template @ https://files.pythonhosted.org/packages/c0/db/d4f9c75b43541f7235daf4d13eb43f4491f9d5f5df45ce41daeed3a903f6/uri_template-1.2.0-py3-none-any.whl#sha256=f1699c77b73b925cf4937eae31ab282a86dc885c333f2e942513f08f691fc7db # pip webcolors @ https://files.pythonhosted.org/packages/d5/e1/3e9013159b4cbb71df9bd7611cbf90dc2c621c8aeeb677fc41dad72f2261/webcolors-1.13-py3-none-any.whl#sha256=29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf @@ -301,7 +296,7 @@ https://conda.anaconda.org/conda-forge/noarch/seaborn-0.12.2-hd8ed1ab_0.conda#50 # pip anyio @ https://files.pythonhosted.org/packages/77/2b/b4c0b7a3f3d61adb1a1e0b78f90a94e2b6162a043880704b7437ef297cad/anyio-3.6.2-py3-none-any.whl#sha256=fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3 # pip argon2-cffi-bindings @ https://files.pythonhosted.org/packages/ec/f7/378254e6dd7ae6f31fe40c8649eea7d4832a42243acaf0f1fff9083b2bed/argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=b746dba803a79238e925d9046a63aa26bf86ab2a2fe74ce6b009a1c3f5c8f2ae # pip arrow @ https://files.pythonhosted.org/packages/67/67/4bca5a595e2f89bff271724ddb1098e6c9e16f7f3d018d120255e3c30313/arrow-1.2.3-py3-none-any.whl#sha256=5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2 -# pip beautifulsoup4 @ https://files.pythonhosted.org/packages/ee/a7/06b189a2e280e351adcef25df532af3c59442123187e228b960ab3238687/beautifulsoup4-4.12.0-py3-none-any.whl#sha256=2130a5ad7f513200fae61a17abb5e338ca980fa28c439c0571014bc0217e9591 +# pip beautifulsoup4 @ https://files.pythonhosted.org/packages/57/f4/a69c20ee4f660081a7dedb1ac57f29be9378e04edfcb90c526b923d4bebc/beautifulsoup4-4.12.2-py3-none-any.whl#sha256=bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a # pip bleach @ https://files.pythonhosted.org/packages/ac/e2/dfcab68c9b2e7800c8f06b85c76e5f978d05b195a958daa9b1dda54a1db6/bleach-6.0.0-py3-none-any.whl#sha256=33c16e3353dbd13028ab4799a0f89a83f113405c766e9c122df8a06f5b85b3f4 # pip doit @ https://files.pythonhosted.org/packages/44/83/a2960d2c975836daa629a73995134fd86520c101412578c57da3d2aa71ee/doit-0.36.0-py3-none-any.whl#sha256=ebc285f6666871b5300091c26eafdff3de968a6bd60ea35dd1e3fc6f2e32479a # pip jupyter-core @ https://files.pythonhosted.org/packages/41/1e/92a67f333b9335f04ce409799c030dcfb291712658b9d9d13997f7c91e5a/jupyter_core-5.3.0-py3-none-any.whl#sha256=d4201af84559bc8c70cead287e1ab94aeef3c512848dde077b7684b54d67730d @@ -311,15 +306,15 @@ https://conda.anaconda.org/conda-forge/noarch/seaborn-0.12.2-hd8ed1ab_0.conda#50 # pip tinycss2 @ https://files.pythonhosted.org/packages/da/99/fd23634d6962c2791fb8cb6ccae1f05dcbfc39bce36bba8b1c9a8d92eae8/tinycss2-1.2.1-py3-none-any.whl#sha256=2b80a96d41e7c3914b8cda8bc7f705a4d9c49275616e886103dd839dfc847847 # pip argon2-cffi @ https://files.pythonhosted.org/packages/a8/07/946d5a9431bae05a776a59746ec385fbb79b526738d25e4202d3e0bbf7f4/argon2_cffi-21.3.0-py3-none-any.whl#sha256=8c976986f2c5c0e5000919e6de187906cfd81fb1c72bf9d88c01177e77da7f80 # pip isoduration @ https://files.pythonhosted.org/packages/7b/55/e5326141505c5d5e34c5e0935d2908a74e4561eca44108fbfb9c13d2911a/isoduration-20.11.0-py3-none-any.whl#sha256=b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042 -# pip jupyter-client @ https://files.pythonhosted.org/packages/31/6c/96771d6b3ce94da927f7688be821899f169306f16023dd0af5ef55f71a52/jupyter_client-8.1.0-py3-none-any.whl#sha256=d5b8e739d7816944be50f81121a109788a3d92732ecf1ad1e4dadebc948818fe +# pip jupyter-client @ https://files.pythonhosted.org/packages/07/37/4019d2c41ca333c08dfdfeb84c0fc0368c8defbbd3c8f0c9a530851e5813/jupyter_client-8.2.0-py3-none-any.whl#sha256=b18219aa695d39e2ad570533e0d71fb7881d35a873051054a84ee2a17c4b7389 # pip jupyter-server-terminals @ https://files.pythonhosted.org/packages/ea/7f/36db12bdb90f5237766dcbf59892198daab7260acbcf03fc75e2a2a82672/jupyter_server_terminals-0.4.4-py3-none-any.whl#sha256=75779164661cec02a8758a5311e18bb8eb70c4e86c6b699403100f1585a12a36 -# pip jupyterlite-core @ https://files.pythonhosted.org/packages/2b/4b/1a54a906bdb1c3783d472b0c1a18dbd82356081ef6451defdb9ce0fd4438/jupyterlite_core-0.1.0b22-py3-none-any.whl#sha256=483bd79b99249239e1ac9f2df8399612c9fcc57916e027c78ba85976285870f8 +# pip jupyterlite-core @ https://files.pythonhosted.org/packages/5e/25/dd347708151764152b75f6606c02e2571e1228ba52c28502495b48ac17d8/jupyterlite_core-0.1.0-py3-none-any.whl#sha256=2f17afa282447594cb38f7a1d2619ceface28d8f4747e038790cac22c394e804 # pip jsonschema @ https://files.pythonhosted.org/packages/c1/97/c698bd9350f307daad79dd740806e1a59becd693bd11443a0f531e3229b3/jsonschema-4.17.3-py3-none-any.whl#sha256=a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6 -# pip jupyterlite-pyodide-kernel @ https://files.pythonhosted.org/packages/81/ff/9cd69da9e968d529597258c32dee39ac580a8973877c8ca5dd7bd7d349e7/jupyterlite_pyodide_kernel-0.0.5-py3-none-any.whl#sha256=296979b1d8dc5ec7d70cf9742abae7266ec1581638984f34bb1517109615ab42 +# pip jupyterlite-pyodide-kernel @ https://files.pythonhosted.org/packages/44/e7/51ea279696f6aa85ad3e007590ff43321b098845782a3054885ddf7f05c2/jupyterlite_pyodide_kernel-0.0.6-py3-none-any.whl#sha256=38ee0889f83270e06d893de211bbcd2674d57ba5b3292b2f80c5fbb9eeb5fe71 # pip jupyter-events @ https://files.pythonhosted.org/packages/ee/14/e11a93c1b47a69432ee7898f1b55f1da27f2f93b009a34dbdafb9b903f81/jupyter_events-0.6.3-py3-none-any.whl#sha256=57a2749f87ba387cd1bfd9b22a0875b889237dbf2edc2121ebb22bde47036c17 # pip nbformat @ https://files.pythonhosted.org/packages/1d/f6/38f4694b5035306a8c2685e9e6ea7bf46ea344c03422d7131442ac9677c1/nbformat-5.8.0-py3-none-any.whl#sha256=d910082bd3e0bffcf07eabf3683ed7dda0727a326c446eeb2922abe102e65162 -# pip nbclient @ https://files.pythonhosted.org/packages/15/49/ea7a0c7e649c54883d76f5119a3e0be592d82a7df1a9b87124fa6663d9c7/nbclient-0.7.2-py3-none-any.whl#sha256=d97ac6257de2794f5397609df754fcbca1a603e94e924eb9b99787c031ae2e7c -# pip nbconvert @ https://files.pythonhosted.org/packages/3f/53/1e99001bc154bd2d243564275e2b7a0e492b48ae032b1377f35cc9defa16/nbconvert-7.2.10-py3-none-any.whl#sha256=e41118f81698d3d59b3c7c2887937446048f741aba6c367c1c1a77810b3e2d08 +# pip nbclient @ https://files.pythonhosted.org/packages/b6/d0/d7a60eb2791e76efe8f88c02431e53e08fa4577d4da7c1599703c685ae61/nbclient-0.7.3-py3-none-any.whl#sha256=8fa96f7e36693d5e83408f5e840f113c14a45c279befe609904dbe05dad646d1 +# pip nbconvert @ https://files.pythonhosted.org/packages/35/3a/60a1821e977104c98fa3a6142adb768a10e1c110438b323076fbda2c0087/nbconvert-7.3.1-py3-none-any.whl#sha256=d2e95904666f1ff77d36105b9de4e0801726f93b862d5b28f69e93d99ad3b19c # pip jupyter-server @ https://files.pythonhosted.org/packages/1d/dd/77a250131fcc97d4a4fa76cda07e23e6b66028aca723f36d114b635127e9/jupyter_server-2.5.0-py3-none-any.whl#sha256=e6bc1e9e96d7c55b9ce9699ff6cb9a910581fe7349e27c40389acb67632e24c0 -# pip jupyterlab-server @ https://files.pythonhosted.org/packages/a0/e3/1af3f5be602852d7abe46b80b86d915e907fca6a308e44e6b6e848b92f00/jupyterlab_server-2.21.0-py3-none-any.whl#sha256=ff1e7a81deb2dcb433215d469000988590fd5a5733574aa2698d643a6c9b3ace +# pip jupyterlab-server @ https://files.pythonhosted.org/packages/ad/31/cfb84feb3803c1e0e69dbe6928ab9251b9a1548b9092a5013413c0dd49f8/jupyterlab_server-2.22.1-py3-none-any.whl#sha256=1c8eb55c7cd70a50a51fef42a7b4e26ef2f7fc48728f0290604bd89b1dd156e6 # pip jupyterlite-sphinx @ https://files.pythonhosted.org/packages/34/a9/a050b891d5d06a3fe73f1e16992a846a6f6ba21660ac053f5064cbf98bae/jupyterlite_sphinx-0.8.0-py3-none-any.whl#sha256=4a20fcb585ef036d3ed1c62cd6270351f810bc9586d3638f55e6a98665b3373d From 84914710da84411df633eca5743b79667330dc5e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Mon, 17 Apr 2023 10:18:27 +0200 Subject: [PATCH 15/19] Always import pandas and matplotlib --- doc/conf.py | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 0114b048c19fa..10eee3addf09c 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -449,7 +449,7 @@ def notebook_modification_function(notebook_content, notebook_filename): if "seaborn" in notebook_content_str: code_lines.append("%pip install seaborn") if "plotly.express" in notebook_content_str: - code_lines.extend(["%pip install plotly", "import pandas"]) + code_lines.append("%pip install plotly") if "skimage" in notebook_content_str: code_lines.append("%pip install scikit-image") if "fetch_" in notebook_content_str: @@ -460,13 +460,9 @@ def notebook_modification_function(notebook_content, notebook_filename): "pyodide_http.patch_all()", ] ) - if ( - # TODO(1.4) the default fetch_openml parser will be pandas so any - # notebook using fetch_openml will need 'import pandas' - 'parser="pandas"' in notebook_content_str - or "as_frame=True" in notebook_content_str - ): - code_lines.extend("import pandas") + # always import matplotlib and pandas to avoid Pyodide limitation with + # imports inside functions + code_lines.extend(["import matplotlib", "import pandas"]) if code_lines: code_lines = ["# JupyterLite-specific code"] + code_lines From 59947d32c4133538ea180919a640838aad1be3c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Mon, 17 Apr 2023 10:20:39 +0200 Subject: [PATCH 16/19] tweak --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index 10eee3addf09c..aa1fd51dff777 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -434,7 +434,7 @@ def notebook_modification_function(notebook_content, notebook_filename): "Running the scikit-learn examples in JupyterLite is experimental and you may" " encounter some unexpected behavior.\n\nThe main difference is that imports" " will take a lot longer than usual, for example the first `import sklearn` can" - " take roughly 20-30s.\n\nIf you notice problems, feel free to open an" + " take roughly 10-20s.\n\nIf you notice problems, feel free to open an" " [issue](https://github.com/scikit-learn/scikit-learn/issues/new/choose)" " about it." ) From a606f406c24f0dc50461dd18709b99769f7e7da5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Mon, 17 Apr 2023 19:45:57 +0200 Subject: [PATCH 17/19] OpenML work-around --- doc/conf.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/doc/conf.py b/doc/conf.py index aa1fd51dff777..d8ca80841e223 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -463,6 +463,14 @@ def notebook_modification_function(notebook_content, notebook_filename): # always import matplotlib and pandas to avoid Pyodide limitation with # imports inside functions code_lines.extend(["import matplotlib", "import pandas"]) + # TODO temporary work-around for OpenML CORS headers issue + # https://github.com/openml/OpenML/issues/1135 + code_lines.extend( + [ + "from sklearn.datasets import _openml", + "_openml._OPENML_PREFIX = 'https://api.openml.org/'", + ] + ) if code_lines: code_lines = ["# JupyterLite-specific code"] + code_lines From 2ab5f33bbef93fc25d99c5426fdc65bb97bc8a6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Mon, 17 Apr 2023 21:31:44 +0200 Subject: [PATCH 18/19] Only do the OpenML work-around when necessary --- doc/conf.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index d8ca80841e223..93714dc76bcc8 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -465,12 +465,13 @@ def notebook_modification_function(notebook_content, notebook_filename): code_lines.extend(["import matplotlib", "import pandas"]) # TODO temporary work-around for OpenML CORS headers issue # https://github.com/openml/OpenML/issues/1135 - code_lines.extend( - [ - "from sklearn.datasets import _openml", - "_openml._OPENML_PREFIX = 'https://api.openml.org/'", - ] - ) + if "fetch_openml" in notebook_content_str: + code_lines.extend( + [ + "from sklearn.datasets import _openml", + "_openml._OPENML_PREFIX = 'https://api.openml.org/'", + ] + ) if code_lines: code_lines = ["# JupyterLite-specific code"] + code_lines From 148971c57f4fd281526c6b4c6985372eef79d738 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= Date: Wed, 19 Apr 2023 12:17:42 +0200 Subject: [PATCH 19/19] Remove OpenML work-around --- doc/conf.py | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 93714dc76bcc8..4e7d8c463fb2b 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -463,15 +463,6 @@ def notebook_modification_function(notebook_content, notebook_filename): # always import matplotlib and pandas to avoid Pyodide limitation with # imports inside functions code_lines.extend(["import matplotlib", "import pandas"]) - # TODO temporary work-around for OpenML CORS headers issue - # https://github.com/openml/OpenML/issues/1135 - if "fetch_openml" in notebook_content_str: - code_lines.extend( - [ - "from sklearn.datasets import _openml", - "_openml._OPENML_PREFIX = 'https://api.openml.org/'", - ] - ) if code_lines: code_lines = ["# JupyterLite-specific code"] + code_lines @@ -505,11 +496,6 @@ def notebook_modification_function(notebook_content, notebook_filename): "inspect_global_variables": False, "remove_config_comments": True, "plot_gallery": "True", - # Remove %matplotlib inline cell which does not work in JupyterLite if you - # have not imported matplotlib before. TODO it can be removed when - # https://github.com/sphinx-gallery/sphinx-gallery/pull/1099 is in a - # released version - "first_notebook_cell": None, }