[FAKE] GMM IC PR for comment

.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

.codecov.yml

@@ -30,5 +30,4 @@ ignore:
 - "sklearn/_build_utils"
 - "sklearn/__check_build"
 - "sklearn/_min_dependencies.py"
-- "**/setup.py"
 - "**/conftest.py"

.coveragerc

@@ -6,4 +6,3 @@ omit =
     */sklearn/externals/*
     */sklearn/_build_utils/*
     */benchmarks/*
-    **/setup.py

.git-blame-ignore-revs

@@ -31,3 +31,6 @@ d4aad64b1eb2e42e76f49db2ccfbe4b4660d092b
 
 # PR 26649: Add isort and ruff rules
 42173fdb34b5aded79664e045cada719dfbe39dc
+
+# PR #28802: Update black to 24.3.0
+c4c546355667b070edd5c892b206aa4a97af9a0b

.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions as recommended in SPEC8:
+  # https://github.com/scientific-python/specs/pull/325
+  # At the time of writing, release critical workflows such as
+  # pypa/gh-action-pypi-publish should use hash-based versioning for security
+  # reasons. This strategy may be generalized to all other github actions
+  # in the future.
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      actions:
+        patterns:
+          - "*"
+    labels:
+      - "Build / CI"
+      - "dependencies"
+    reviewers:
+      - "scikit-learn/core-devs"

.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/assign.yml

@@ -19,8 +19,11 @@ jobs:
        && !github.event.issue.assignee
     steps:
       - run: |
+          # Using REST API directly because assigning through gh has some severe limitations. For more details, see
+          # https://github.com/scikit-learn/scikit-learn/issues/29395#issuecomment-2206776963
           echo "Assigning issue ${{ github.event.issue.number }} to ${{ github.event.comment.user.login }}"
-          gh issue edit $ISSUE --add-assignee ${{ github.event.comment.user.login }}
+          curl -H "Authorization: token $GH_TOKEN" -d '{"assignees": ["${{ github.event.comment.user.login }}"]}' \
+              https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/assignees
           gh issue edit $ISSUE --remove-label "help wanted"
         env:
           GH_TOKEN: ${{ github.token }}

.github/workflows/check-changelog.yml

@@ -16,7 +16,7 @@ jobs:
         run: |
           echo "PR_NUMBER=${{ github.event.pull_request.number }}" >> $GITHUB_ENV
           echo "TAGGED_MILESTONE=${{ github.event.pull_request.milestone.title }}" >> $GITHUB_ENV
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: '0'
       - name: Check the changelog entry

.github/workflows/check-sdist.yml

@@ -11,7 +11,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: '3.9'

.github/workflows/cuda-ci.yml

@@ -0,0 +1,45 @@
+name: CUDA GPU
+
+# Only run this workflow when a Pull Request is labeled with the
+# 'CUDA CI' label.
+on:
+  pull_request:
+    types:
+      - labeled
+
+jobs:
+  tests:
+    if: contains(github.event.pull_request.labels.*.name, 'CUDA CI')
+    runs-on:
+      group: cuda-gpu-runner-group
+    # Set this high enough so that the tests can comforatble run. We set a
+    # timeout to make abusing this workflow less attractive.
+    timeout-minutes: 20
+    name: Run Array API unit tests
+    steps:
+      - uses: actions/setup-python@v5
+        with:
+          # 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
+      - name: Cache conda environment
+        id: cache-conda
+        uses: actions/cache@v4
+        with:
+          path: ~/conda
+          key: ${{ runner.os }}-build-${{ hashFiles('build_tools/github/create_gpu_environment.sh') }}-${{ hashFiles('build_tools/github/pylatest_conda_forge_cuda_array-api_linux-64_conda.lock') }}
+      - name: Install miniforge
+        if: ${{ steps.cache-conda.outputs.cache-hit != 'true' }}
+        run: bash build_tools/github/create_gpu_environment.sh
+      - name: Install scikit-learn
+        run: |
+          source "${HOME}/conda/etc/profile.d/conda.sh"
+          conda activate sklearn
+          pip install --verbose --no-build-isolation --config-settings editable-verbose=true --editable .
+      - name: Run array API tests
+        run: |
+          source "${HOME}/conda/etc/profile.d/conda.sh"
+          conda activate sklearn
+          pytest -k 'array_api'

.github/workflows/cuda-label-remover.yml

@@ -0,0 +1,23 @@
+name: Remove "CUDA CI" Label
+
+# This workflow removes the "CUDA CI" label that triggers the actual
+# CUDA CI. It is separate so that we can use the `pull_request_target`
+# trigger which has a API token with write access.
+on:
+  pull_request_target:
+    types:
+      - labeled
+
+# In order to remove the "CUDA CI" label we need to have write permissions for PRs
+permissions:
+  pull-requests: write
+
+jobs:
+  label-remover:
+    if: contains(github.event.pull_request.labels.*.name, 'CUDA CI')
+    name: Remove "CUDA CI" Label
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions-ecosystem/action-remove-labels@v1
+        with:
+          labels: CUDA CI

.github/workflows/labeler-title-regex.yml

@@ -15,7 +15,7 @@ jobs:
   labeler:
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
         python-version: '3.9'

.github/workflows/lint.yml

@@ -20,7 +20,7 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
@@ -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
@@ -52,7 +52,7 @@ jobs:
 
       - name: Upload Artifact
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: lint-log
           path: |
@@ -72,7 +72,7 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -84,7 +84,7 @@ jobs:
 
       - name: Download artifact
         id: download-artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: lint-log
 

.github/workflows/publish_pypi.yml

@@ -18,7 +18,7 @@ jobs:
       # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
         python-version: '3.8'
@@ -39,10 +39,13 @@ jobs:
       run: |
         python build_tools/github/check_wheels.py
     - name: Publish package to TestPyPI
-      uses: pypa/gh-action-pypi-publish@v1.8.5
+      uses: pypa/gh-action-pypi-publish@ec4db0b4ddc65acdf4bff5fa45ac92d78b56bdf0 # v1.9.0
       with:
-        repository_url: https://test.pypi.org/legacy/
+        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@v1.8.5
+      uses: pypa/gh-action-pypi-publish@ec4db0b4ddc65acdf4bff5fa45ac92d78b56bdf0 # v1.9.0
       if: ${{ github.event.inputs.pypi_repo == 'pypi' }}
+      with:
+        print-hash: true

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

@@ -6,6 +6,10 @@ 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'
@@ -25,9 +29,8 @@ jobs:
           - name: cirrus-arm
             update_script_args: "--select-tag arm"
             additional_commit_message: "[cirrus arm]"
-          - name: pypy
-            update_script_args: "--select-tag pypy"
-            additional_commit_message: "[pypy]"
+          - name: array-api
+            update_script_args: "--select-tag cuda"
 
     steps:
       - uses: actions/checkout@v4
@@ -43,7 +46,7 @@ jobs:
 
       - name: Create Pull Request
         id: cpr
-        uses: peter-evans/create-pull-request@v5
+        uses: peter-evans/create-pull-request@v6
         with:
           token: ${{ secrets.BOT_GITHUB_TOKEN }}
           push-to-fork: scikit-learn-bot/scikit-learn
@@ -59,6 +62,14 @@ jobs:
             ### Note
             If the CI tasks fail, create a new branch based on this PR and add the required fixes to that branch.
 
+      # The CUDA workflow needs to be triggered explicitly as it uses an expensive runner
+      - name: Trigger additional tests
+        if: steps.cpr.outputs.pull-request-number != '' && matrix.name == 'array-api'
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          gh pr edit ${{steps.cpr.outputs.pull-request-number}} --add-label "CUDA CI"
+
       - name: Check Pull Request
         if: steps.cpr.outputs.pull-request-number != ''
         run: |

.github/workflows/update_tracking_issue.yml

@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository == 'scikit-learn/scikit-learn' && github.event_name == 'schedule'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: '3.9'