scikit-learn · lesteve · May 9, 2025 · May 9, 2025 · May 9, 2025 · May 9, 2025
diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
@@ -67,17 +67,7 @@ python_environment_install_and_activate() {
     fi
 
     # Install additional packages on top of the lock-file in specific cases
-    if [[ "$DISTRIB" == "conda-free-threaded" ]]; then
-        # TODO: we install scipy with pip. When there is a conda-forge package,
-        # we can update build_tools/update_environments_and_lock_files.py and
-        # remove the line below
-        pip install scipy --only-binary :all:
-        # TODO: we install cython 3.1 alpha from pip. When there is a conda-forge package,
-        # we can update build_tools/update_environments_and_lock_files.py and
-        # remove the line below
-        pip install --pre cython --only-binary :all:
-
-    elif [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then
+    if [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then
         echo "Installing development dependency wheels"
         dev_anaconda_url=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
         dev_packages="numpy scipy pandas Cython"

diff --git a/build_tools/azure/pylatest_free_threaded_environment.yml b/build_tools/azure/pylatest_free_threaded_environment.yml
@@ -6,6 +6,8 @@ channels:
 dependencies:
   - python-freethreading
   - numpy
+  - scipy
+  - cython
   - joblib
   - threadpoolctl
   - pytest

diff --git a/build_tools/azure/pylatest_free_threaded_linux-64_conda.lock b/build_tools/azure/pylatest_free_threaded_linux-64_conda.lock
@@ -1,39 +1,40 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: c7db5547fb9ea583bb70736e98b526e9e435c63cb5f6f3c4f38e0f0925e28535
+# input_hash: b76364b5635e8c36a0fc0777955b5664a336ba94ac96f3ade7aad842ab7e15c5
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-7_cp313t.conda#df81edcc11a1176315e8226acab83eec
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda#4222072737ccff51314b5ece9c7d6f5a
 https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.4.26-hbd8a1cb_0.conda#95db94f75ba080a22eb623590993167b
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h767d61c_2.conda#06d02030237f4d5b3d9a7e7d348fe3c6
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_2.conda#fbe7d535ff9d3a168c148e07358cd5b1
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h767d61c_2.conda#ef504d1acbd74b7cc6849ef8af47dd03
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_2.conda#ea8ac52380885ed41c1baa8f1d6d2b93
 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.0-h5888daf_0.conda#db0bfbe7dd197b68ad5f30333bae6ce0
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_2.conda#a2222a6ada71fb478682efe483ce0f92
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.2.0-hf1ad2bd_2.conda#556a4fdfac7287d349b8f09aba899693
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_2.conda#ddca86c7040dd0e73b2b69bd7833d225
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_2.conda#01de444988ed960031dbe84cf4f9b1fc
 https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_1.conda#a76fd702c93cd2dfd89eff30a5fd45a8
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-h8f9b012_2.conda#a78c856b6dc6bf4ea8daeb9beaaa3fb0
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_2.conda#1cb1c67961f6dd257eae9e9691b341aa
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
 https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.0-h7b32b05_1.conda#de356753cfdbffcde5bb1e86e3aa6cd0
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.2.0-h69a702a_2.conda#fb54c4ea68b460c278d26eea89cfbcc3
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_2.conda#f92e6e0a3c0c0c85561ef61aa59d555d
 https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-h4bc722e_0.conda#aeb98fdeb2e8f25d43ef71fbacbeec80
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.1-hee588c1_2.conda#962d6ac93c30b1dfc54c9cccafd1003e
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_2.conda#c75da67f045c2627f59e6fcb5f4e3a9b
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.2-hee588c1_0.conda#93048463501053a00739215ea3f36324
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_2.conda#9d2072af184b5caa29492bf2344597bb
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/ninja-1.12.1-hff21bea_1.conda#2322531904f27501ee19847b87ba7c64
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.2.0-h69a702a_2.conda#4056c857af1a99ee50589a941059ec55
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-15.1.0-h69a702a_2.conda#a483a87b71e974bb75d1b9413d4436dd
 https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.29-pthreads_h94d23a6_0.conda#0a4d0252248ef9a0f88f2ba8b8a08e12
 https://conda.anaconda.org/conda-forge/linux-64/python-3.13.3-h4724d56_1_cp313t.conda#8193603fe48ace3d8801cfb246f44491
 https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda#962b9857ee8e7018c22f2776ffa0b2d7
 https://conda.anaconda.org/conda-forge/noarch/cpython-3.13.3-py313hd8ed1ab_1.conda#6ba9ba47b91b7758cb963d0f0eaf3422
+https://conda.anaconda.org/conda-forge/noarch/cython-3.1.0-pyh2c78169_100.conda#89943f37072ca254aa4b7de98c6d7f0a
 https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.2-pyhd8ed1ab_1.conda#a16662747cdeb9abbac74d0057cc976e
 https://conda.anaconda.org/conda-forge/noarch/execnet-2.1.1-pyhd8ed1ab_1.conda#a71efeae2c160f6789900ba2631a2c90
 https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_1.conda#6837f3eff7dcea42ecd714ce1ac2b108
@@ -56,3 +57,4 @@ https://conda.anaconda.org/conda-forge/noarch/python-freethreading-3.13.3-h92d6c
 https://conda.anaconda.org/conda-forge/noarch/meson-python-0.18.0-pyh70fd9c4_0.conda#576c04b9d9f8e45285fb4d9452c26133
 https://conda.anaconda.org/conda-forge/linux-64/numpy-2.2.5-py313h103f029_0.conda#7dcbd568d6f8a4ffba5ace28915f1230
 https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-3.6.1-pyhd8ed1ab_1.conda#59aad4fb37cabc0bacc73cf344612ddd
+https://conda.anaconda.org/conda-forge/linux-64/scipy-1.15.2-py313h7f7b39c_0.conda#65f0c403e4324062633e648933f20a2e
diff --git a/build_tools/update_environments_and_lock_files.py b/build_tools/update_environments_and_lock_files.py
@@ -271,11 +271,8 @@ def remove_from(alist, to_remove):
         "conda_dependencies": [
             "python-freethreading",
             "numpy",
-            # TODO add cython and scipy when there are conda-forge packages for
-            # them and remove dev version install in
-            # build_tools/azure/install.sh. Note that for now conda-lock does
-            # not deal with free-threaded wheels correctly, see
-            # https://github.com/conda/conda-lock/issues/754.
+            "scipy",
+            "cython",
             "joblib",
             "threadpoolctl",
             "pytest",

diff --git a/sklearn/meson.build b/sklearn/meson.build
@@ -1,7 +1,5 @@
 fs = import('fs')
 
-cython_args = []
-
 # Platform detection
 is_windows = host_machine.system() == 'windows'
 is_mingw = is_windows and cc.get_id() == 'gcc'
@@ -180,6 +178,11 @@ else:
     check: true
     ).stdout().strip()
 
+cython_args = []
+if cython.version().version_compare('>=3.1.0')
+  cython_args += ['-Xfreethreading_compatible=True']
+endif
+
 scikit_learn_cython_args = [
   '-X language_level=3', '-X boundscheck=' + boundscheck, '-X wraparound=False',
   '-X initializedcheck=False', '-X nonecheck=False', '-X cdivision=True',
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,6 +6,8 @@ channels: @@
     dependencies:
       - python-freethreading
       - numpy
+      - scipy
+      - cython
       - joblib
       - threadpoolctl
       - pytest
@@ Expand Down @@