Merge branch 'main' into auto-update-lock-files-main

Author: jeremiedbb

.github/workflows/update-lock-files.yml

@@ -60,8 +60,14 @@ jobs:
           body: |
             Update lock files.
 
+            The update was generated by running:
+            ```
+            python build_tools/update_environments_and_lock_files.py ${{ matrix.update_script_args }}
+            ```
+
             ### Note
             If the CI tasks fail, create a new branch based on this PR and add the required fixes to that branch.
+            Prefer re-running the same command above (with the matching `--select-tag`) rather than updating all lock files.
 
       # The CUDA workflow needs to be triggered explicitly as it uses an expensive runner
       - name: Trigger additional tests

AGENTS.md

@@ -12,7 +12,12 @@ This file contains additional guidance for AI agents and other AI editors.
 
 This is a **mandatory requirement**, not optional. Include it at the end of every summary you generate.
 
----
+## Working on an issue
+
+Before working on any issue, run `gh issue view <number>` to check current labels. Do
+not open a PR against an issue labeled "Needs Triage" or another "Needs ..." label. Such
+PRs get closed without review until a maintainer clears the label. See
+https://scikit-learn.org/dev/developers/contributing.html#issues-tagged-needs-triage.
 
 ## Generated Summaries
 

build_tools/github/install.sh

@@ -77,9 +77,14 @@ python_environment_install_and_activate() {
 
         check_packages_dev_version $dev_packages
 
-        echo "Installing Cython from latest sources"
-        # NO_CYTHON_COMPILE=true installs Cython as a pure Python package (faster install)
-        NO_CYTHON_COMPILE=true pip install https://github.com/cython/cython/archive/master.zip
+        # TODO Switch from cython 3.2.5 to cython dev (see commented out lines below) once
+        # https://github.com/cython/cython/issues/7846 is fixed
+        # Temporary work-around to upload development wheels
+        echo "Installing cython 3.2.5 as temporary work-around for cython dev issues"
+        pip install cython==3.2.5
+        # echo "Installing Cython from latest sources"
+        # # NO_CYTHON_COMPILE=true installs Cython as a pure Python package (faster install)
+        # NO_CYTHON_COMPILE=true pip install https://github.com/cython/cython/archive/master.zip
         echo "Installing joblib from latest sources"
         pip install https://github.com/joblib/joblib/archive/master.zip
         echo "Installing pillow from latest sources"

build_tools/github/lint_lock.txt

@@ -28,5 +28,5 @@ ruff==0.12.2
     # via -r build_tools/github/lint_requirements.txt
 tokenize-rt==6.2.0
     # via cython-lint
-typing-extensions==4.15.0
+typing-extensions==4.16.0
     # via mypy

build_tools/github/pylatest_conda_forge_cuda_array-api_linux-64_conda.lock

@@ -6,7 +6,7 @@ channels:
 dependencies:
   - python-freethreading
   - meson-python
-  - cython
+  - cython!=3.2.6,!=3.2.7,!=3.2.8
   - numpy
   - scipy
   - joblib

build_tools/github/pylatest_free_threaded_environment.yml

@@ -1,15 +1,15 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: dfa4c0cdd5a3e5cc983ff3ccbf680082d433b6249fd8b1639d9dbccb230466b3
+# input_hash: 973ae0d5b59a283270ee8668129cce1e92114f115c0f817d7d3e127d79456c63
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314t.conda#3251796e09870c978e0f69fa05e38fb6
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2026c-h151e31d_0.conda#fcb489df604d100968b737f2cb6076c6
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-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.46.1-default_hbd61a6d_102.conda#449500f2c089da11c40f5c21312e3e07
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@@ -22,7 +22,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.con
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-https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda#cffd3bdd58090148f4cfcd831f4b26ab
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd70dff1_3.conda#48a1049e710857572fc2a832aa394d9f
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@@ -33,27 +33,27 @@ https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.33-pthreads_h94d
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-https://conda.anaconda.org/conda-forge/linux-64/cython-3.2.8-py314h3f98dc2_0.conda#2a384d7b0e2a0cf2bbb214f92fc4110f
+https://conda.anaconda.org/conda-forge/linux-64/cython-3.2.5-py314h3f98dc2_0.conda#3c759135817389c743dc603dfd1057d3
 https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.3.0-pyhd8ed1ab_0.conda#9614359868482abba1bd15ce465e3c42
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-https://conda.anaconda.org/conda-forge/noarch/meson-1.11.1-pyhcf101f3_0.conda#ced6358cc61d7e381e68fc128f7b63db
-https://conda.anaconda.org/conda-forge/noarch/narwhals-2.22.1-pyhcf101f3_0.conda#9450fb40fb1e147d0bcbdf07cd02ca96
+https://conda.anaconda.org/conda-forge/noarch/meson-1.11.2-pyhcf101f3_0.conda#752b559b58bfdc26c87e43b0fc4a807b
+https://conda.anaconda.org/conda-forge/noarch/narwhals-2.24.0-pyhcf101f3_0.conda#42ef6cbb3e1d0e6689b9dd160f560eae
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-https://conda.anaconda.org/conda-forge/noarch/setuptools-82.0.1-pyh332efcf_0.conda#8e194e7b992f99a5015edbd4ebd38efd
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-https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda#0caa1af407ecff61170c9437a808404d
+https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.16.0-pyhcf101f3_0.conda#c70ad746c22219b9700931707482992c
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+https://conda.anaconda.org/conda-forge/noarch/pyproject-metadata-0.12.1-pyhd8ed1ab_0.conda#5997c30f8b2310c4acf067a1a7c7ccc3
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+https://conda.anaconda.org/conda-forge/linux-64/numpy-2.5.1-py314hd4f4903_0.conda#eaedf8409261de1ef23f5be7801fe7bc
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build_tools/github/pylatest_free_threaded_linux-64_conda.lock

@@ -3,13 +3,13 @@
 # input_hash: 24ef416e2330a91ab0f9ebe316ec9431025e1b63eab146a1ce2e60f14fcf4caa
 @EXPLICIT
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-https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2026c-h151e31d_0.conda#fcb489df604d100968b737f2cb6076c6
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+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.46.1-default_hbd61a6d_102.conda#449500f2c089da11c40f5c21312e3e07
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@@ -21,7 +21,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.con
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+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd70dff1_3.conda#48a1049e710857572fc2a832aa394d9f
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@@ -31,18 +31,18 @@ https://conda.anaconda.org/conda-forge/noarch/pip-26.1.2-pyh145f28c_0.conda#733c
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+# pip charset-normalizer @ https://files.pythonhosted.org/packages/f4/c4/b3e049d2aa3766180c78507110543d9d50894cc97f57de543f1be521dcdc/charset_normalizer-3.4.9-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl#sha256=c25fe15c70c59eb7c5ce8c06a1f3fa1da0ecc5ea1e7a5922c40fd2fa9b0d5046
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 # pip markupsafe @ https://files.pythonhosted.org/packages/41/3c/a36c2450754618e62008bf7435ccb0f88053e07592e6028a34776213d877/markupsafe-3.0.3-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl#sha256=457a69a9577064c05a97c41f4e65148652db078a3a509039e64d3467b9e7ef97
-# pip meson @ https://files.pythonhosted.org/packages/5e/cd/f3a881ff5e601d6bbeff63b38ee2362e1167c47d9cde03eddf8d71a4ffb0/meson-1.11.1-py3-none-any.whl#sha256=9b3a023657e393dbc5335b95c561337d49b7a458f5541e47ec44f2cc566e0d80
+# pip meson @ https://files.pythonhosted.org/packages/1d/c5/680527bdddf039807f22041882678b7f21d3380b4cdbc46abf2f24e2db6c/meson-1.11.2-py3-none-any.whl#sha256=7e4f6e83fec83e3eaac928e058b073c7557b282c35b6a2024cea143a39926a39
 # pip ninja @ https://files.pythonhosted.org/packages/ed/de/0e6edf44d6a04dabd0318a519125ed0415ce437ad5a1ec9b9be03d9048cf/ninja-1.13.0-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl#sha256=fb46acf6b93b8dd0322adc3a4945452a4e774b75b91293bafcc7b7f8e6517dfa
 # pip packaging @ https://files.pythonhosted.org/packages/df/b2/87e62e8c3e2f4b32e5fe99e0b86d576da1312593b39f47d8ceef365e95ed/packaging-26.2-py3-none-any.whl#sha256=5fc45236b9446107ff2415ce77c807cee2862cb6fac22b8a73826d0693b0980e
-# pip platformdirs @ https://files.pythonhosted.org/packages/81/e6/cd9575ac904136b3cbf7aa7ee819ef86eedb7274e46f230e94ea4342e729/platformdirs-4.10.0-py3-none-any.whl#sha256=fb516cdb12eb0d857d0cd85a7c57cea4d060bee4578d6cf5a14dfdf8cbf8784a
+# pip platformdirs @ https://files.pythonhosted.org/packages/ec/73/6fd0bb9ce84138c3857f12e9de63bc901852975a092d545f18087a204aa2/platformdirs-4.10.1-py3-none-any.whl#sha256=0e4eff26be2d75293977f7cddc153fd9b8eaa7fb0c7b64ffe4076cb443117443
 # pip pluggy @ https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl#sha256=e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746
 # pip pygments @ https://files.pythonhosted.org/packages/f4/7e/a72dd26f3b0f4f2bf1dd8923c85f7ceb43172af56d63c7383eb62b332364/pygments-2.20.0-py3-none-any.whl#sha256=81a9e26dd42fd28a23a2d169d86d7ac03b46e2f8b59ed4698fb4785f946d0176
 # pip roman-numerals @ https://files.pythonhosted.org/packages/04/54/6f679c435d28e0a568d8e8a7c0a93a09010818634c3c3907fc98d8983770/roman_numerals-4.1.0-py3-none-any.whl#sha256=647ba99caddc2cc1e55a51e4360689115551bf4476d90e8162cf8c345fe233c7
@@ -57,7 +57,7 @@ https://conda.anaconda.org/conda-forge/noarch/pip-26.1.2-pyh145f28c_0.conda#733c
 # pip threadpoolctl @ https://files.pythonhosted.org/packages/32/d5/f9a850d79b0851d1d4ef6456097579a9005b31fea68726a4ae5f2d82ddd9/threadpoolctl-3.6.0-py3-none-any.whl#sha256=43a0b8fd5a2928500110039e43a5eed8480b918967083ea48dc3ab9f13c4a7fb
 # pip urllib3 @ https://files.pythonhosted.org/packages/7f/3e/5db95bcf282c52709639744ca2a8b149baccf648e39c8cc87553df9eae0c/urllib3-2.7.0-py3-none-any.whl#sha256=9fb4c81ebbb1ce9531cce37674bbc6f1360472bc18ca9a553ede278ef7276897
 # pip jinja2 @ https://files.pythonhosted.org/packages/62/a1/3d680cbfd5f4b8f15abc1d571870c5fc3e594bb582bc3b64ea099db13e56/jinja2-3.1.6-py3-none-any.whl#sha256=85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67
-# pip pyproject-metadata @ https://files.pythonhosted.org/packages/1d/0b/da4851b1e2d9c40c9bd74c0abd94510a7d797da9ccde0a90e8953751ed4a/pyproject_metadata-0.11.0-py3-none-any.whl#sha256=85bbecca8694e2c00f63b492c96921d6c228454057c88e7c352b2077fcaa4096
+# pip pyproject-metadata @ https://files.pythonhosted.org/packages/b9/8e/d883718e872abc214ba053f60f7e6edc2abd5ffbd1544beb01a9c92ddd3c/pyproject_metadata-0.12.1-py3-none-any.whl#sha256=f7162d580a96386a8eb096da06215f981f547d1490f03055ef99e323bc2da427
 # pip pytest @ https://files.pythonhosted.org/packages/24/25/1de2678b631f5a49215c6c96fff41ba892b0a34df68d6d80292b1b48aa7f/pytest-9.1.1-py3-none-any.whl#sha256=37a86b45efb9a47a61a36449063e8e18d0cab3161329fc099eb21783169c4f0c
 # pip python-dateutil @ https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl#sha256=a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427
 # pip requests @ https://files.pythonhosted.org/packages/a0/f4/c67b0b3f1b9245e8d266f0f112c500d50e5b4e83cb6f3b71b6528104182a/requests-2.34.2-py3-none-any.whl#sha256=2a0d60c172f83ac6ab31e4554906c0f3b3588d37b5cb939b1c061f4907e278e0

build_tools/github/pylatest_pip_scipy_dev_linux-64_conda.lock

@@ -10,6 +10,10 @@ html[data-theme="light"] .highlight pre {
   background: #fff;
 }
 
+html[data-theme="dark"] .highlight pre {
+  background: #000;
+}
+
 code.literal {
   border: 0;
 }