Merge branch 'main' into submodulev3

Author: adam2392

.github/workflows/cuda-ci.yml

@@ -16,7 +16,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.20.0
+        uses: pypa/cibuildwheel@v2.21.1
         env:
           CIBW_BUILD: cp312-manylinux_x86_64
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014

.github/workflows/publish_pypi.yml

@@ -39,13 +39,13 @@ jobs:
       run: |
         python build_tools/github/check_wheels.py
     - name: Publish package to TestPyPI
-      uses: pypa/gh-action-pypi-publish@8a08d616893759ef8e1aa1f2785787c0b97e20d6 # v1.10.0
+      uses: pypa/gh-action-pypi-publish@897895f1e160c830e369f9779632ebc134688e1b # v1.10.2
       with:
         repository-url: https://test.pypi.org/legacy/
         print-hash: true
       if: ${{ github.event.inputs.pypi_repo == 'testpypi' }}
     - name: Publish package to PyPI
-      uses: pypa/gh-action-pypi-publish@8a08d616893759ef8e1aa1f2785787c0b97e20d6 # v1.10.0
+      uses: pypa/gh-action-pypi-publish@897895f1e160c830e369f9779632ebc134688e1b # v1.10.2
       if: ${{ github.event.inputs.pypi_repo == 'pypi' }}
       with:
         print-hash: true

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

@@ -6,6 +6,7 @@ on:
 
 permissions:
   contents: write
+  statuses: write
 
 jobs:
   update-lock-files:
@@ -23,12 +24,30 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          pr_info=$(gh pr view ${{ github.event.issue.number }} --repo ${{ github.repository }} --json headRefName,headRepository,headRepositoryOwner)
+          pr_info=$(gh pr view ${{ github.event.issue.number }} --repo ${{ github.repository }} --json headRefName,headRefOid,headRepository,headRepositoryOwner)
           pr_head_ref=$(echo "$pr_info" | jq -r '.headRefName')
+          pr_head_sha=$(echo "$pr_info" | jq -r '.headRefOid')
           pr_head_repository=$(echo "$pr_info" | jq -r '.headRepositoryOwner.login + "/" + .headRepository.name')
           echo "pr_head_ref=$pr_head_ref" >> $GITHUB_OUTPUT
+          echo "pr_head_sha=$pr_head_sha" >> $GITHUB_OUTPUT
           echo "pr_head_repository=$pr_head_repository" >> $GITHUB_OUTPUT
 
+      # Set the status of the latest commit in the PR to indicate that the update is in progress
+      # https://docs.github.com/en/rest/commits/statuses?apiVersion=2022-11-28#create-a-commit-status
+      - name: Set pending status
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh api \
+            --method POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            /repos/${{ github.repository }}/statuses/${{ steps.pr-head-info.outputs.pr_head_sha }} \
+            -f "state=pending" \
+            -f "target_url=https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}" \
+            -f "description=Updating lock files..." \
+            -f "context=update-lock-files-pr"
+
       - name: Check out the PR branch
         uses: actions/checkout@v4
         with:
@@ -57,3 +76,18 @@ jobs:
           conda install -c conda-forge "$(get_dep conda-lock min)" -y
 
           python build_tools/on_pr_comment_update_environments_and_lock_files.py
+
+      - name: Set completion status
+        if: ${{ always() }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh api \
+            --method POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            /repos/${{ github.repository }}/statuses/${{ steps.pr-head-info.outputs.pr_head_sha }} \
+            -f "state=${{ job.status == 'success' && 'success' || 'error' }}" \
+            -f "target_url=https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}" \
+            -f "description=Lock files ${{ job.status == 'success' && 'updated' || 'failed to update' }}." \
+            -f "context=update-lock-files-pr"

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

@@ -6,10 +6,6 @@ on:
   schedule:
     - cron: '0 5 * * 1'
 
-# In order to add the "CUDA CI" label we need to have write permissions for PRs
-permissions:
-  pull-requests: write
-
 jobs:
   update_lock_files:
     if: github.repository == 'scikit-learn/scikit-learn'
@@ -46,7 +42,7 @@ jobs:
 
       - name: Create Pull Request
         id: cpr
-        uses: peter-evans/create-pull-request@v6
+        uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ secrets.BOT_GITHUB_TOKEN }}
           push-to-fork: scikit-learn-bot/scikit-learn
@@ -66,7 +62,7 @@ jobs:
       - name: Trigger additional tests
         if: steps.cpr.outputs.pull-request-number != '' && matrix.name == 'array-api'
         env:
-          GH_TOKEN: ${{ github.token }}
+          GH_TOKEN: ${{ secrets.BOT_GITHUB_TOKEN }}
         run: |
           gh pr edit ${{steps.cpr.outputs.pull-request-number}} --add-label "CUDA CI"
 

.github/workflows/wheels.yml

@@ -65,6 +65,11 @@ jobs:
           - os: windows-latest
             python: 312
             platform_id: win_amd64
+          - os: windows-latest
+            python: 313
+            platform_id: win_amd64
+            # TODO: remove next line when Python 3.13 is released
+            prerelease_pythons: True
 
           # Linux 64 bit manylinux2014
           - os: ubuntu-latest
@@ -86,12 +91,14 @@ jobs:
             python: 312
             platform_id: manylinux_x86_64
             manylinux_image: manylinux2014
+          - os: ubuntu-latest
+            python: 313
+            platform_id: manylinux_x86_64
+            manylinux_image: manylinux2014
           - os: ubuntu-latest
             python: 313t
             platform_id: manylinux_x86_64
             manylinux_image: manylinux2014
-            # TODO: remove next line when Python 3.13 is released
-            prerelease_pythons: True
             free_threaded_support: True
 
           # MacOS x86_64
@@ -107,6 +114,13 @@ jobs:
           - os: macos-12
             python: 312
             platform_id: macosx_x86_64
+          - os: macos-12
+            python: 313
+            platform_id: macosx_x86_64
+          - os: macos-12
+            python: 313t
+            platform_id: macosx_x86_64
+            free_threaded_support: True
 
           # MacOS arm64
           - os: macos-14
@@ -121,6 +135,13 @@ jobs:
           - os: macos-14
             python: 312
             platform_id: macosx_arm64
+          - os: macos-14
+            python: 313
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 313t
+            platform_id: macosx_arm64
+            free_threaded_support: True
 
     steps:
       - name: Checkout scikit-learn
@@ -173,11 +194,17 @@ jobs:
           # toolchain
           CIBW_CONFIG_SETTINGS_WINDOWS: "setup-args=--vsenv"
           CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: bash build_tools/github/repair_windows_wheels.sh {wheel} {dest_dir}
+          CIBW_BEFORE_BUILD: bash {project}/build_tools/wheels/cibw_before_build.sh {project}
           CIBW_BEFORE_TEST_WINDOWS: bash build_tools/github/build_minimal_windows_image.sh ${{ matrix.python }}
           CIBW_BEFORE_TEST: bash {project}/build_tools/wheels/cibw_before_test.sh
+          CIBW_ENVIRONMENT_PASS_LINUX: RUNNER_OS
           CIBW_TEST_REQUIRES: pytest pandas
-          CIBW_TEST_COMMAND: bash {project}/build_tools/wheels/test_wheels.sh
-          CIBW_TEST_COMMAND_WINDOWS: bash {project}/build_tools/github/test_windows_wheels.sh ${{ matrix.python }}
+          # On Windows, we use a custom Docker image and CIBW_TEST_REQUIRES_WINDOWS
+          # does not make sense because it would install dependencies in the host
+          # rather than inside the Docker image
+          CIBW_TEST_REQUIRES_WINDOWS: ""
+          CIBW_TEST_COMMAND: bash {project}/build_tools/wheels/test_wheels.sh {project}
+          CIBW_TEST_COMMAND_WINDOWS: bash {project}/build_tools/github/test_windows_wheels.sh ${{ matrix.python }} {project}
           CIBW_BUILD_VERBOSITY: 1
 
         run: bash build_tools/wheels/build_wheels.sh

.gitignore

@@ -90,3 +90,6 @@ sklearn-env/
 
 # Default JupyterLite content
 jupyterlite_contents
+
+# file recognised by vscode IDEs containing env variables
+.env

SECURITY.md

@@ -4,8 +4,8 @@
 
 | Version       | Supported          |
 | ------------- | ------------------ |
-| 1.5.1         | :white_check_mark: |
-| < 1.5.1       | :x:                |
+| 1.5.2         | :white_check_mark: |
+| < 1.5.2       | :x:                |
 
 ## Reporting a Vulnerability
 

benchmarks/bench_20newsgroups.py

@@ -21,7 +21,7 @@
     "extra_trees": ExtraTreesClassifier(max_features="sqrt", min_samples_split=10),
     "logistic_regression": LogisticRegression(),
     "naive_bayes": MultinomialNB(),
-    "adaboost": AdaBoostClassifier(n_estimators=10, algorithm="SAMME"),
+    "adaboost": AdaBoostClassifier(n_estimators=10),
 }
 
 

build_tools/azure/debian_32bit_lock.txt

@@ -12,7 +12,7 @@ iniconfig==2.0.0
     # via pytest
 joblib==1.4.2
     # via -r build_tools/azure/debian_32bit_requirements.txt
-meson==1.5.1
+meson==1.5.2
     # via meson-python
 meson-python==0.16.0
     # via -r build_tools/azure/debian_32bit_requirements.txt
@@ -27,7 +27,7 @@ pluggy==1.5.0
     # via pytest
 pyproject-metadata==0.8.0
     # via meson-python
-pytest==8.3.2
+pytest==8.3.3
     # via
     #   -r build_tools/azure/debian_32bit_requirements.txt
     #   pytest-cov

build_tools/azure/install.sh

@@ -120,6 +120,9 @@ scikit_learn_install() {
         # brings in openmp so that you end up having the omp.h include inside
         # the conda environment.
         find $CONDA_PREFIX -name omp.h -delete -print
+        # meson 1.5 detects OpenMP installed with brew and OpenMP is installed
+        # with brew in CI runner
+        brew uninstall --ignore-dependencies libomp
     fi
 
     if [[ "$UNAMESTR" == "Linux" ]]; then