Merge branch 'main' into submodulev3

Author: adam2392

.circleci/config.yml

@@ -11,7 +11,7 @@ jobs:
           command: |
             source build_tools/shared.sh
             # Include pytest compatibility with mypy
-            pip install pytest ruff $(get_dep mypy min) $(get_dep black min) cython-lint
+            pip install pytest $(get_dep ruff min) $(get_dep mypy min) $(get_dep black min) cython-lint
       - run:
           name: linting
           command: ./build_tools/linting.sh

.github/workflows/artifact-redirector.yml

@@ -15,7 +15,7 @@ jobs:
     name: Run CircleCI artifacts redirector
     steps:
       - name: GitHub Action step
-        uses: larsoner/circleci-artifacts-redirector-action@master
+        uses: scientific-python/circleci-artifacts-redirector-action@v1
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           api-token: ${{ secrets.CIRCLECI_TOKEN }}

.github/workflows/cuda-gpu-ci.yml

@@ -2,8 +2,8 @@ name: CUDA GPU
 on:
   workflow_dispatch:
     inputs:
-      pr_id:
-        description: Test the contents of this Pull Request
+      commit_hash:
+        description: Commit hash to test
         required: true
 
 permissions: read-all
@@ -19,12 +19,13 @@ jobs:
           # XXX: The 3.12.4 release of Python on GitHub Actions is corrupted:
           # https://github.com/actions/setup-python/issues/886
           python-version: '3.12.3'
-      - name: Checkout main repository
-        uses: actions/checkout@v4
-      - run: |
-          git fetch origin +refs/pull/${{ inputs.pr_id }}/head:pr-${{ inputs.pr_id }}
-          git checkout pr-${{ inputs.pr_id }}
-          echo "Checked out commit $(git rev-parse HEAD)"
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.commit_hash }}
+      - name: PRs associated with commit
+        run: |
+          echo "This commit belongs to PR(s):"
+          git ls-remote origin 'pull/*/head' | grep -F -f <(git rev-parse HEAD) | awk -F'/' '{print $3}'
       - name: Cache conda environment
         id: cache-conda
         uses: actions/cache@v4

.github/workflows/lint.yml

@@ -33,7 +33,7 @@ jobs:
         run: |
           source build_tools/shared.sh
           # Include pytest compatibility with mypy
-          pip install pytest ruff $(get_dep mypy min) $(get_dep black min) cython-lint
+          pip install pytest $(get_dep ruff min) $(get_dep mypy min) $(get_dep black min) cython-lint
           # we save the versions of the linters to be used in the error message later.
           python -c "from importlib.metadata import version; print(f\"ruff={version('ruff')}\")" >> /tmp/versions.txt
           python -c "from importlib.metadata import version; print(f\"mypy={version('mypy')}\")" >> /tmp/versions.txt

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

@@ -68,7 +68,7 @@ jobs:
         env:
           GH_TOKEN: ${{ github.token }}
         run: |
-          gh workflow run .github/workflows/cuda-gpu-ci.yml -f pr_id=${{steps.cpr.outputs.pull-request-number}}
+          gh workflow run .github/workflows/cuda-gpu-ci.yml -f commit_hash=`git rev-parse HEAD`
 
       - name: Check Pull Request
         if: steps.cpr.outputs.pull-request-number != ''

.github/workflows/wheels.yml

@@ -86,6 +86,13 @@ jobs:
             python: 312
             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
           - os: macos-12
@@ -154,7 +161,8 @@ jobs:
 
       - name: Build and test wheels
         env:
-          CIBW_PRERELEASE_PYTHONS: ${{ matrix.prerelease }}
+          CIBW_PRERELEASE_PYTHONS: ${{ matrix.prerelease_pythons }}
+          CIBW_FREE_THREADED_SUPPORT: ${{ matrix.free_threaded_support }}
           CIBW_ENVIRONMENT: SKLEARN_SKIP_NETWORK_TESTS=1
             SKLEARN_BUILD_PARALLEL=3
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
@@ -167,7 +175,8 @@ jobs:
           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_TEST_WINDOWS: bash build_tools/github/build_minimal_windows_image.sh ${{ matrix.python }}
-          CIBW_TEST_REQUIRES: pytest pandas
+          CIBW_TEST_REQUIRES: pytest
+          CIBW_BEFORE_TEST: bash {project}/build_tools/wheels/cibw_before_test.sh
           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 }}
           CIBW_BUILD_VERBOSITY: 1
@@ -249,6 +258,6 @@ jobs:
           # Secret variables need to be mapped to environment variables explicitly
           SCIKIT_LEARN_NIGHTLY_UPLOAD_TOKEN: ${{ secrets.SCIKIT_LEARN_NIGHTLY_UPLOAD_TOKEN }}
           SCIKIT_LEARN_STAGING_UPLOAD_TOKEN: ${{ secrets.SCIKIT_LEARN_STAGING_UPLOAD_TOKEN }}
-          ARTIFACTS_PATH: dist/artifact
+          ARTIFACTS_PATH: dist
         # Force a replacement if the remote file already exists
         run: bash build_tools/github/upload_anaconda.sh

Makefile

@@ -1,55 +1,30 @@
 # simple makefile to simplify repetitive build env management tasks under posix
 
-# caution: testing won't work on windows, see README
-
 PYTHON ?= python
-CYTHON ?= cython
-PYTEST ?= pytest
 
-# skip doctests on 32bit python
-BITS := $(shell python -c 'import struct; print(8 * struct.calcsize("P"))')
+all:
+	@echo "Please use 'make <target>' where <target> is one of"
+	@echo "  dev                  build scikit-learn with Meson"
+	@echo "  clean                clean scikit-learn Meson build. Very rarely needed,"
+	@echo "                       one use case is when switching back to setuptools"
+	@echo "  dev-setuptools       build scikit-learn with setuptools (deprecated)"
+	@echo "  clean-setuptools     clean scikit-learn setuptools build (deprecated)"
 
-all: clean inplace test
+.PHONY: all
 
-clean:
-	$(PYTHON) setup.py clean
-	rm -rf dist
-
-in: inplace # just a shortcut
-inplace:
-	$(PYTHON) setup.py build_ext -i
+dev: dev-meson
 
 dev-meson:
 	pip install --verbose --no-build-isolation --editable . --check-build-dependencies --config-settings editable-verbose=true
 
+clean: clean-meson
+
 clean-meson:
 	pip uninstall -y scikit-learn
 
-test-code: in
-	$(PYTEST) --showlocals -v sklearn --durations=20
-test-sphinxext:
-	$(PYTEST) --showlocals -v doc/sphinxext/
-test-doc:
-ifeq ($(BITS),64)
-	$(PYTEST) $(shell find doc -name '*.rst' | sort)
-endif
-test-code-parallel: in
-	$(PYTEST) -n auto --showlocals -v sklearn --durations=20
-
-test-coverage:
-	rm -rf coverage .coverage
-	$(PYTEST) sklearn --showlocals -v --cov=sklearn --cov-report=html:coverage
-test-coverage-parallel:
-	rm -rf coverage .coverage .coverage.*
-	$(PYTEST) sklearn -n auto --showlocals -v --cov=sklearn --cov-report=html:coverage
-
-test: test-code test-sphinxext test-doc
-
-cython:
-	python setup.py build_src
-
-doc: inplace
-	$(MAKE) -C doc html
-
-doc-noplot: inplace
-	$(MAKE) -C doc html-noplot
+dev-setuptools:
+	$(PYTHON) setup.py build_ext -i
+
+clean-setuptools:
+	$(PYTHON) setup.py clean
+	rm -rf dist

asv_benchmarks/asv.conf.json

@@ -23,11 +23,7 @@
     //
     // "install_command": ["python -mpip install {wheel_file}"],
     // "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
-    // "build_command": [
-    //     "python setup.py build",
-    //     "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"
-    // ],
-
+    // "build_command": ["python -m build --wheel -o {build_cache_dir} {build_dir}"],
     // List of branches to benchmark. If not provided, defaults to "master
     // (for git) or "default" (for mercurial).
     "branches": ["main"],

azure-pipelines.yml

@@ -35,7 +35,7 @@ jobs:
     - bash: |
         source build_tools/shared.sh
         # Include pytest compatibility with mypy
-        pip install pytest ruff $(get_dep mypy min) $(get_dep black min) cython-lint
+        pip install pytest $(get_dep ruff min) $(get_dep mypy min) $(get_dep black min) cython-lint
       displayName: Install linters
     - bash: |
         ./build_tools/linting.sh