CI Add lock files for linting (scikit-learn#34303)

Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>

Author: AnneBeyer

.circleci/config.yml

@@ -9,9 +9,7 @@ jobs:
       - run:
           name: dependencies
           command: |
-            source build_tools/shared.sh
-            # Include pytest compatibility with mypy
-            pip install pytest $(get_dep ruff min) $(get_dep mypy min) cython-lint
+            pip install -r build_tools/github/lint_lock.txt
       - run:
           name: linting
           command: ./build_tools/linting.sh

.github/workflows/lint.yml

@@ -32,10 +32,9 @@ jobs:
 
       - name: Install dependencies
         run: |
-          source build_tools/shared.sh
-          # Include pytest compatibility with mypy
-          pip install pytest $(get_dep ruff min) $(get_dep mypy min) cython-lint
+          pip install -r build_tools/github/lint_lock.txt
           # we save the versions of the linters to be used in the error message later.
+          python -c "from importlib.metadata import version; print(f\"pytest={version('pytest')}\")" >> /tmp/versions.txt
           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
           python -c "from importlib.metadata import version; print(f\"cython-lint={version('cython-lint')}\")" >> /tmp/versions.txt

.github/workflows/unit-tests.yml

@@ -37,9 +37,7 @@ jobs:
           cache: 'pip'
       - name: Install linters
         run: |
-          source build_tools/shared.sh
-          # Include pytest compatibility with mypy
-          pip install pytest $(get_dep ruff min) $(get_dep mypy min) cython-lint
+          pip install -r build_tools/github/lint_lock.txt
       - name: Run linters
         run: ./build_tools/linting.sh
       - name: Run Meson OpenMP checks

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

@@ -29,6 +29,8 @@ jobs:
             additional_commit_message: "[free-threaded]"
           - name: array-api
             update_script_args: "--select-tag cuda"
+          - name: lint
+            update_script_args: "--select-tag lint"
 
     steps:
       - uses: actions/checkout@v7

.pre-commit-config.yaml

@@ -15,12 +15,19 @@ repos:
         args: ["--fix", "--output-format=full"]
     -   id: ruff-format
 -   repo: https://github.com/pre-commit/mirrors-mypy
+    # NOTE if you update the mypy version here, remember to update
+    # sklearn/_min_dependencies.py as well
     rev: v1.15.0
     hooks:
      -  id: mypy
         files: sklearn/
-        additional_dependencies: [pytest==6.2.4]
+        # We set `pytest` to an arbitrary recent version to keep it consistent with the
+        # linting settings in `build_tools/update_environments_and_lock_files.py`. They
+        # should be updated from time to time in both places.
+        additional_dependencies: [pytest==9.1.0]
 -   repo: https://github.com/MarcoGorelli/cython-lint
+    # NOTE if you update the cython-lint version here, remember to update
+    # sklearn/_min_dependencies.py as well
     rev: v0.21.0
     hooks:
     # TODO: add the double-quote-cython-strings hook when it's usability has improved:

build_tools/github/lint_lock.txt

@@ -0,0 +1,32 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --output-file=build_tools/github/lint_lock.txt build_tools/github/lint_requirements.txt
+#
+cython==3.2.5
+    # via cython-lint
+cython-lint==0.20.0
+    # via -r build_tools/github/lint_requirements.txt
+iniconfig==2.3.0
+    # via pytest
+mypy==1.15.0
+    # via -r build_tools/github/lint_requirements.txt
+mypy-extensions==1.1.0
+    # via mypy
+packaging==26.2
+    # via pytest
+pluggy==1.6.0
+    # via pytest
+pycodestyle==2.14.0
+    # via cython-lint
+pygments==2.20.0
+    # via pytest
+pytest==9.1.0
+    # via -r build_tools/github/lint_requirements.txt
+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
+    # via mypy

build_tools/github/lint_requirements.txt

@@ -0,0 +1,7 @@
+# DO NOT EDIT: this file is generated from the specification found in the
+# following script to centralize the configuration for CI builds:
+# build_tools/update_environments_and_lock_files.py
+pytest
+ruff==0.12.2  # min
+mypy==1.15  # min
+cython-lint==0.20  # min

build_tools/update_environments_and_lock_files.py

@@ -482,6 +482,28 @@ def remove_from(alist, to_remove):
         },
         "python_version": "3.12.3",
     },
+    {
+        "name": "lint",
+        "type": "pip",
+        "tag": "lint",
+        "folder": "build_tools/github",
+        "pip_dependencies": ["pytest", "ruff", "mypy", "cython-lint"],
+        "package_constraints": {
+            # We set `pytest` to an arbitrary recent version to keep it consistent with
+            # the settings in `.pre-commit-config.yml`. They should be updated from
+            # time to time in both places.
+            "pytest": "9.1.0",
+            # We fix the version of the linters to some arbitrary version to
+            # avoid changing linting conventions too often.
+            # The meaning of the "min" values is set in `_min_dependencies.py`
+            # and should be updated from time to time when we feel the need
+            # for it.
+            "ruff": "min",
+            "mypy": "min",
+            "cython-lint": "min",
+        },
+        "python_version": "3.11",
+    },
 ]
 
 

pyproject.toml

@@ -87,6 +87,7 @@ tests = [
     "pytest-cov>=2.9.0",
     "ruff>=0.12.2",
     "mypy>=1.15",
+    "cython-lint>=0.21",
     "pyamg>=5.0.0",
     "polars>=0.20.30",
     "pyarrow>=13.0.0",

sklearn/_min_dependencies.py

@@ -35,8 +35,11 @@
     "memory_profiler": ("0.57.0", "benchmark, docs"),
     "pytest": (PYTEST_MIN_VERSION, "tests"),
     "pytest-cov": ("2.9.0", "tests"),
+    # NOTE if you update ruff, mypy or cython-lint here, remember to update
+    # .pre-commit-config.yaml as well
     "ruff": ("0.12.2", "tests"),
     "mypy": ("1.15", "tests"),
+    "cython-lint": ("0.21", "tests"),
     "pyamg": ("5.0.0", "tests"),
     "polars": ("0.20.30", "docs, tests"),
     "pyarrow": ("13.0.0", "tests"),