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

Author: jeremiedbb

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
 https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.6.17-hbd8a1cb_0.conda#a9965dd99f683c5f444428f896635716
 https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda#faac990cb7aedc7f3a2224f2c9b0c26c
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de
 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829
-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
 https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda#57736f29cc2b0ec0b6c2952d3f101b6a
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885
 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.1-hecca717_1.conda#b24d3c612f71e7aa74158d92106318b2
@@ -22,7 +22,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.con
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.2-h5347b49_0.conda#01bb81d12c957de066ea7362007df642
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda#fc21868a1a5aacc937e7a18747acb8a5
 https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.3-h35e630c_0.conda#79dd2074b5cd5c5c6b2930514a11e22d
-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
 https://conda.anaconda.org/conda-forge/linux-64/xxhash-0.8.3-hb47aa4a_0.conda#607e13a8caac17f9a664bcab5302ce06
 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_19.conda#42bf7eca1a951735fa06c0e3c0d5c8e6
 https://conda.anaconda.org/conda-forge/linux-64/libhiredis-1.3.0-h5888daf_1.conda#aa342fcf3bc583660dbfdb2eae6be48e
@@ -33,27 +33,27 @@ https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.33-pthreads_h94d
 https://conda.anaconda.org/conda-forge/linux-64/python-3.14.6-hf9ea5aa_0_cp314t.conda#054621389e1cfbef617475720307fa8b
 https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda#962b9857ee8e7018c22f2776ffa0b2d7
 https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.6-py314hd8ed1ab_0.conda#3d0e6c3783fa4fff20f7a4e1db36fe7b
-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
 https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-8_h4a7cf45_openblas.conda#00fc660ab1b2f5ca07e92b4900d10c79
-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
 https://conda.anaconda.org/conda-forge/noarch/packaging-26.2-pyhc364b38_0.conda#4c06a92e74452cfa53623a81592e8934
 https://conda.anaconda.org/conda-forge/noarch/pip-26.1.2-pyh145f28c_0.conda#733cc07ed34162ac50b936464b163366
 https://conda.anaconda.org/conda-forge/noarch/pluggy-1.6.0-pyhf9edf01_1.conda#d7585b6550ad04c8c5e21097ada2888e
 https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0
-https://conda.anaconda.org/conda-forge/noarch/setuptools-82.0.1-pyh332efcf_0.conda#8e194e7b992f99a5015edbd4ebd38efd
+https://conda.anaconda.org/conda-forge/noarch/setuptools-83.0.0-pyh332efcf_0.conda#6bf6acbab2499830180ec88c3aff2fa4
 https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.6.0-pyhecae5ae_0.conda#9d64911b31d57ca443e9f1e36b04385f
 https://conda.anaconda.org/conda-forge/noarch/tomli-2.4.1-pyhcf101f3_0.conda#b5325cf06a000c5b14970462ff5e4d58
-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
 https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda#8e662bd460bda79b1ea39194e3c4c9ab
 https://conda.anaconda.org/conda-forge/noarch/joblib-1.5.3-pyhd8ed1ab_0.conda#615de2a4d97af50c350e5cf160149e77
 https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-8_h0358290_openblas.conda#33a413f1095f8325e5c30fde3b0d2445
 https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-8_h47877c9_openblas.conda#809be8ba8712c77bc7d44c2d99390dc4
-https://conda.anaconda.org/conda-forge/noarch/pyproject-metadata-0.11.0-pyhd8ed1ab_0.conda#cd6dae6c673c8f12fe7267eac3503961
+https://conda.anaconda.org/conda-forge/noarch/pyproject-metadata-0.12.1-pyhd8ed1ab_0.conda#5997c30f8b2310c4acf067a1a7c7ccc3
 https://conda.anaconda.org/conda-forge/noarch/python-freethreading-3.14.6-h92d6c8b_0.conda#2456a886c46342eed65b27481a7da8fb
 https://conda.anaconda.org/conda-forge/noarch/meson-python-0.20.0-pyh7e86bf3_0.conda#f5f0d602a73fb52e59ae9a1aa4a326c2
-https://conda.anaconda.org/conda-forge/linux-64/numpy-2.5.0-py314hd4f4903_0.conda#820f9f5a329f3c3c58c9ccefa7692ab0
+https://conda.anaconda.org/conda-forge/linux-64/numpy-2.5.1-py314hd4f4903_0.conda#eaedf8409261de1ef23f5be7801fe7bc
 https://conda.anaconda.org/conda-forge/noarch/pytest-9.1.1-pyhc364b38_2.conda#64c98a12c4e23eb238bf66bbecafdf3c
 https://conda.anaconda.org/conda-forge/noarch/pytest-run-parallel-0.9.1-pyhd8ed1ab_0.conda#35e2cc981ca9a0e237f7a2f2286556ad
 https://conda.anaconda.org/conda-forge/linux-64/scipy-1.18.0-py314h529d2a9_0.conda#99bee56848517debb3c46eecc889ff00

build_tools/github/pylatest_free_threaded_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;
 }