diff --git a/.binder/postBuild b/.binder/postBuild old mode 100644 new mode 100755 index c33605a68456c..00e8d39b93549 --- a/.binder/postBuild +++ b/.binder/postBuild @@ -6,9 +6,9 @@ set -e # inside a git checkout of the scikit-learn/scikit-learn repo. This script is # generating notebooks from the scikit-learn python examples. -if [[ ! -f /.dockerenv ]]; then - echo "This script was written for repo2docker and is supposed to run inside a docker container." - echo "Exiting because this script can delete data if run outside of a docker container." +if [[ -z "${REPO_DIR}" ]]; then + echo "This script was written for repo2docker and the REPO_DIR environment variable is supposed to be set." + echo "Exiting because this script can delete data if run outside of a repo2docker context." exit 1 fi @@ -23,7 +23,7 @@ find . -delete GENERATED_NOTEBOOKS_DIR=.generated-notebooks cp -r $TMP_CONTENT_DIR/examples $GENERATED_NOTEBOOKS_DIR -find $GENERATED_NOTEBOOKS_DIR -name '*.py' -exec sphx_glr_python_to_jupyter.py '{}' + +find $GENERATED_NOTEBOOKS_DIR -name '*.py' -exec sphinx_gallery_py2jupyter '{}' + NON_NOTEBOOKS=$(find $GENERATED_NOTEBOOKS_DIR -type f | grep -v '\.ipynb') rm -f $NON_NOTEBOOKS diff --git a/.circleci/config.yml b/.circleci/config.yml index 1f9a1a02e0f62..bd4914056fe10 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -3,7 +3,7 @@ version: 2.1 jobs: lint: docker: - - image: cimg/python:3.9.18 + - image: cimg/python:3.10.16 steps: - checkout - run: @@ -11,14 +11,14 @@ 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) $(get_dep mypy min) cython-lint - run: name: linting command: ./build_tools/linting.sh doc-min-dependencies: docker: - - image: cimg/python:3.9.18 + - image: cimg/base:current-22.04 environment: - MKL_NUM_THREADS: 2 - OPENBLAS_NUM_THREADS: 2 @@ -56,7 +56,7 @@ jobs: doc: docker: - - image: cimg/python:3.9.18 + - image: cimg/base:current-22.04 environment: - MKL_NUM_THREADS: 2 - OPENBLAS_NUM_THREADS: 2 @@ -98,7 +98,7 @@ jobs: deploy: docker: - - image: cimg/python:3.9.18 + - image: cimg/base:current-22.04 steps: - checkout - run: ./build_tools/circle/checkout_merge_commit.sh @@ -107,7 +107,7 @@ jobs: - attach_workspace: at: doc/_build/html - run: ls -ltrh doc/_build/html/stable - - deploy: + - run: command: | if [[ "${CIRCLE_BRANCH}" =~ ^main$|^[0-9]+\.[0-9]+\.X$ ]]; then bash build_tools/circle/push_doc.sh doc/_build/html/stable diff --git a/.cirrus.star b/.cirrus.star deleted file mode 100644 index f0b458d74289a..0000000000000 --- a/.cirrus.star +++ /dev/null @@ -1,37 +0,0 @@ -# This script uses starlark for configuring when a cirrus CI job runs: -# https://cirrus-ci.org/guide/programming-tasks/ - -load("cirrus", "env", "fs", "http") - -def main(ctx): - # Only run for scikit-learn/scikit-learn. For debugging on a fork, you can - # comment out the following condition. - if env.get("CIRRUS_REPO_FULL_NAME") != "scikit-learn/scikit-learn": - return [] - - arm_wheel_yaml = "build_tools/cirrus/arm_wheel.yml" - arm_tests_yaml = "build_tools/cirrus/arm_tests.yml" - - # Nightly jobs always run - if env.get("CIRRUS_CRON", "") == "nightly": - return fs.read(arm_wheel_yaml) + fs.read(arm_tests_yaml) - - # Get commit message for event. We can not use `git` here because there is - # no command line access in starlark. Thus we need to query the GitHub API - # for the commit message. Note that `CIRRUS_CHANGE_MESSAGE` can not be used - # because it is set to the PR's title and not the latest commit message. - SHA = env.get("CIRRUS_CHANGE_IN_REPO") - REPO = env.get("CIRRUS_REPO_FULL_NAME") - url = "https://api.github.com/repos/" + REPO + "/git/commits/" + SHA - response = http.get(url).json() - commit_msg = response["message"] - - jobs_to_run = "" - - if "[cd build]" in commit_msg or "[cd build cirrus]" in commit_msg: - jobs_to_run += fs.read(arm_wheel_yaml) - - if "[cirrus arm]" in commit_msg: - jobs_to_run += fs.read(arm_tests_yaml) - - return jobs_to_run diff --git a/.codecov.yml b/.codecov.yml index 54ce77b9c1b0e..f4ecd6e7d8fee 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -30,5 +30,4 @@ ignore: - "sklearn/_build_utils" - "sklearn/__check_build" - "sklearn/_min_dependencies.py" -- "**/setup.py" - "**/conftest.py" diff --git a/.coveragerc b/.coveragerc index a8601458a0b07..0d5f02b3edafc 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,9 +1,11 @@ [run] -branch = True +# Use statement coverage rather than branch coverage because +# COVERAGE_CORE=sysmon can make branch coverage slower rather than faster. See +# https://github.com/nedbat/coveragepy/issues/1812 for more details. +branch = False source = sklearn parallel = True omit = */sklearn/externals/* */sklearn/_build_utils/* */benchmarks/* - **/setup.py diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index b261320543fa7..77fb878ee8fe7 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -32,5 +32,17 @@ d4aad64b1eb2e42e76f49db2ccfbe4b4660d092b # PR 26649: Add isort and ruff rules 42173fdb34b5aded79664e045cada719dfbe39dc -# PR #28802: Update black to 24.3.0 +# PR 28802: Update black to 24.3.0 c4c546355667b070edd5c892b206aa4a97af9a0b + +# PR 30694: Enforce ruff rules (RUF) +fe7c4176828af5231f526e76683fb9bdb9ea0367 + +# PR 30695: Apply ruff/flake8-implicit-str-concat rules (ISC) +5cdbbf15e3fade7cc2462ef66dc4ea0f37f390e3 + +# PR 31015: black -> ruff format +ff78e258ccf11068e2b3a433c51517ae56234f88 + +# PR 31226: Enforce ruff/pygrep-hooks rules +b98dc797c480b1b9495f918e201d45ee07f29feb diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 8d9c592ccdc13..0ebed8c85161b 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,4 +1,4 @@ -blank_issues_enabled: true +blank_issues_enabled: false contact_links: - name: Discussions url: https://github.com/scikit-learn/scikit-learn/discussions/new @@ -13,5 +13,5 @@ contact_links: url: https://discord.gg/h9qyrK8Jc8 about: Developers and users can be found on the Discord server - name: Blank issue - url: https://github.com/scikit-learn/scikit-learn/issues/new + url: https://github.com/scikit-learn/scikit-learn/issues/new?template=BLANK_ISSUE about: Please note that GitHub Discussions should be used in most cases instead diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000000000..7ac17eb0442ad --- /dev/null +++ b/.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" diff --git a/.github/workflows/arm-unit-tests.yml b/.github/workflows/arm-unit-tests.yml new file mode 100644 index 0000000000000..e7636d55d7945 --- /dev/null +++ b/.github/workflows/arm-unit-tests.yml @@ -0,0 +1,54 @@ +name: Unit test for ARM +permissions: + contents: read + +on: + push: + pull_request: + +concurrency: + group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} + cancel-in-progress: true + +jobs: + lint: + name: Lint + runs-on: ubuntu-latest + if: github.repository == 'scikit-learn/scikit-learn' + + steps: + - name: Checkout + uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: '3.12' + 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 + - name: Run linters + run: ./build_tools/linting.sh + - name: Run Meson OpenMP checks + run: | + pip install ninja meson scipy + python build_tools/check-meson-openmp-dependencies.py + + run-unit-tests: + name: Run unit tests + runs-on: ubuntu-24.04-arm + if: github.repository == 'scikit-learn/scikit-learn' + needs: [lint] + steps: + - name: Checkout + uses: actions/checkout@v4 + - uses: mamba-org/setup-micromamba@v2 + with: + environment-file: build_tools/github/pymin_conda_forge_arm_linux-aarch64_conda.lock + environment-name: ci + cache-environment: true + + - name: Build and run tests + shell: bash -el {0} + run: bash build_tools/github/build_test_arm.sh diff --git a/.github/workflows/artifact-redirector.yml b/.github/workflows/artifact-redirector.yml index 3fdbc06fac386..690cacefda935 100644 --- a/.github/workflows/artifact-redirector.yml +++ b/.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 }} diff --git a/.github/workflows/assign.yml b/.github/workflows/assign.yml index fa3b6f95a5e95..a69b60ee0f0a0 100644 --- a/.github/workflows/assign.yml +++ b/.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 }} diff --git a/.github/workflows/check-changelog.yml b/.github/workflows/check-changelog.yml index d5bfc8ef0f430..00e6a81f8cd0b 100644 --- a/.github/workflows/check-changelog.yml +++ b/.github/workflows/check-changelog.yml @@ -1,68 +1,36 @@ name: Check Changelog +permissions: + contents: read + # This check makes sure that the changelog is properly updated # when a PR introduces a change in a test file. # To bypass this check, label the PR with "No Changelog Needed". on: pull_request: - types: [opened, edited, labeled, unlabeled, synchronize] + types: [opened, synchronize, labeled, unlabeled] jobs: check: name: A reviewer will let you know if it is required or can be bypassed runs-on: ubuntu-latest - if: ${{ contains(github.event.pull_request.labels.*.name, 'No Changelog Needed') == 0 }} steps: - - name: Get PR number and milestone - run: | - echo "PR_NUMBER=${{ github.event.pull_request.number }}" >> $GITHUB_ENV - echo "TAGGED_MILESTONE=${{ github.event.pull_request.milestone.title }}" >> $GITHUB_ENV - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: '0' - - name: Check the changelog entry + - name: Check if tests have changed + id: tests_changed run: | set -xe changed_files=$(git diff --name-only origin/main) # Changelog should be updated only if tests have been modified - if [[ ! "$changed_files" =~ tests ]] + if [[ "$changed_files" =~ tests ]] then - exit 0 - fi - all_changelogs=$(cat ./doc/whats_new/v*.rst) - if [[ "$all_changelogs" =~ :pr:\`$PR_NUMBER\` ]] - then - echo "Changelog has been updated." - # If the pull request is milestoned check the correspondent changelog - if exist -f ./doc/whats_new/v${TAGGED_MILESTONE:0:4}.rst - then - expected_changelog=$(cat ./doc/whats_new/v${TAGGED_MILESTONE:0:4}.rst) - if [[ "$expected_changelog" =~ :pr:\`$PR_NUMBER\` ]] - then - echo "Changelog and milestone correspond." - else - echo "Changelog and milestone do not correspond." - echo "If you see this error make sure that the tagged milestone for the PR" - echo "and the edited changelog filename properly match." - exit 1 - fi - fi - else - echo "A Changelog entry is missing." - echo "" - echo "Please add an entry to the changelog at 'doc/whats_new/v*.rst'" - echo "to document your change assuming that the PR will be merged" - echo "in time for the next release of scikit-learn." - echo "" - echo "Look at other entries in that file for inspiration and please" - echo "reference this pull request using the ':pr:' directive and" - echo "credit yourself (and other contributors if applicable) with" - echo "the ':user:' directive." - echo "" - echo "If you see this error and there is already a changelog entry," - echo "check that the PR number is correct." - echo "" - echo "If you believe that this PR does not warrant a changelog" - echo "entry, say so in a comment so that a maintainer will label" - echo "the PR with 'No Changelog Needed' to bypass this check." - exit 1 + echo "check_changelog=true" >> $GITHUB_OUTPUT fi + + - name: Check changelog entry + if: steps.tests_changed.outputs.check_changelog == 'true' + uses: scientific-python/action-towncrier-changelog@v1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + BOT_USERNAME: changelog-bot diff --git a/.github/workflows/check-sdist.yml b/.github/workflows/check-sdist.yml index c02af711bdb6c..d97236dae1e40 100644 --- a/.github/workflows/check-sdist.yml +++ b/.github/workflows/check-sdist.yml @@ -1,4 +1,6 @@ name: "Check sdist" +permissions: + contents: read on: schedule: @@ -11,10 +13,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: - python-version: '3.9' + python-version: '3.10' - name: Install dependencies # scipy and cython are required to build sdist run: | diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 4d38b22d71ab8..58b8fbf5c4ce7 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -29,7 +29,7 @@ jobs: strategy: fail-fast: false matrix: - language: [ 'javascript-typescript', 'python' ] + language: [ 'javascript-typescript', 'python', 'actions' ] # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ] # Use only 'java-kotlin' to analyze code written in Java, Kotlin or both # Use only 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both diff --git a/.github/workflows/cuda-ci.yml b/.github/workflows/cuda-ci.yml new file mode 100644 index 0000000000000..028ff06903e8a --- /dev/null +++ b/.github/workflows/cuda-ci.yml @@ -0,0 +1,78 @@ +name: CUDA GPU +permissions: + contents: read + +# Only run this workflow when a Pull Request is labeled with the +# 'CUDA CI' label. +on: + pull_request: + types: + - labeled + +jobs: + build_wheel: + if: contains(github.event.pull_request.labels.*.name, 'CUDA CI') + runs-on: "ubuntu-latest" + name: Build wheel for Pull Request + steps: + - uses: actions/checkout@v4 + + - name: Build wheels + uses: pypa/cibuildwheel@faf86a6ed7efa889faf6996aa23820831055001a + env: + CIBW_BUILD: cp313-manylinux_x86_64 + CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014 + CIBW_BUILD_VERBOSITY: 1 + CIBW_ARCHS: x86_64 + + - uses: actions/upload-artifact@v4 + with: + name: cibw-wheels + path: ./wheelhouse/*.whl + + tests: + if: contains(github.event.pull_request.labels.*.name, 'CUDA CI') + needs: [build_wheel] + 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/download-artifact@v4 + with: + pattern: cibw-wheels + path: ~/dist + + - 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 ~/dist/cibw-wheels/$(ls ~/dist/cibw-wheels) + + - name: Run array API tests + run: | + source "${HOME}/conda/etc/profile.d/conda.sh" + conda activate sklearn + python -c "import sklearn; sklearn.show_versions()" + + SCIPY_ARRAY_API=1 pytest --pyargs sklearn -k 'array_api' -v + # Run in /home/runner to not load sklearn from the checkout repo + working-directory: /home/runner diff --git a/.github/workflows/cuda-label-remover.yml b/.github/workflows/cuda-label-remover.yml new file mode 100644 index 0000000000000..bb87f5419b662 --- /dev/null +++ b/.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-24.04 + steps: + - uses: actions-ecosystem/action-remove-labels@v1 + with: + labels: CUDA CI diff --git a/.github/workflows/emscripten.yml b/.github/workflows/emscripten.yml new file mode 100644 index 0000000000000..47e54f6125638 --- /dev/null +++ b/.github/workflows/emscripten.yml @@ -0,0 +1,106 @@ +name: Test Emscripten/Pyodide build + +on: + schedule: + # Nightly build at 3:42 A.M. + - cron: "42 3 */1 * *" + push: + branches: + - main + # Release branches + - "[0-9]+.[0-9]+.X" + pull_request: + branches: + - main + - "[0-9]+.[0-9]+.X" + # Manual run + workflow_dispatch: + +env: + FORCE_COLOR: 3 + +concurrency: + group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} + cancel-in-progress: true + +permissions: + contents: read + +jobs: + check_build_trigger: + name: Check build trigger + runs-on: ubuntu-latest + if: github.repository == 'scikit-learn/scikit-learn' + outputs: + build: ${{ steps.check_build_trigger.outputs.build }} + steps: + - name: Checkout scikit-learn + uses: actions/checkout@v4 + with: + ref: ${{ github.event.pull_request.head.sha }} + persist-credentials: false + + - id: check_build_trigger + name: Check build trigger + shell: bash + run: | + set -e + set -x + + COMMIT_MSG=$(git log --no-merges -1 --oneline) + + # The commit marker "[pyodide]" will trigger the build when required + if [[ "$GITHUB_EVENT_NAME" == schedule || + "$GITHUB_EVENT_NAME" == workflow_dispatch || + "$COMMIT_MSG" =~ \[pyodide\] ]]; then + echo "build=true" >> $GITHUB_OUTPUT + fi + + build_wasm_wheel: + name: Build WASM wheel + runs-on: ubuntu-latest + needs: check_build_trigger + if: needs.check_build_trigger.outputs.build + steps: + - name: Checkout scikit-learn + uses: actions/checkout@v4 + with: + persist-credentials: false + + - uses: pypa/cibuildwheel@faf86a6ed7efa889faf6996aa23820831055001a + env: + CIBW_PLATFORM: pyodide + SKLEARN_SKIP_OPENMP_TEST: "true" + SKLEARN_SKIP_NETWORK_TESTS: 1 + CIBW_TEST_REQUIRES: "pytest pandas" + # -s pytest argument is needed to avoid an issue in pytest output capturing with Pyodide + CIBW_TEST_COMMAND: "python -m pytest -svra --pyargs sklearn --durations 20 --showlocals" + + - name: Upload wheel artifact + uses: actions/upload-artifact@v4 + with: + name: pyodide_wheel + path: ./wheelhouse/*.whl + if-no-files-found: error + + # Push to https://anaconda.org/scientific-python-nightly-wheels/scikit-learn + # WARNING: this job will overwrite any existing WASM wheels. + upload-wheels: + name: Upload scikit-learn WASM wheels to Anaconda.org + runs-on: ubuntu-latest + permissions: {} + environment: upload_anaconda + needs: [build_wasm_wheel] + if: github.repository == 'scikit-learn/scikit-learn' && github.event_name != 'pull_request' + steps: + - name: Download wheel artifact + uses: actions/download-artifact@v4 + with: + path: wheelhouse/ + merge-multiple: true + + - name: Push to Anaconda PyPI index + uses: scientific-python/upload-nightly-action@b36e8c0c10dbcfd2e05bf95f17ef8c14fd708dbf # 0.6.2 + with: + artifacts_path: wheelhouse/ + anaconda_nightly_upload_token: ${{ secrets.SCIKIT_LEARN_NIGHTLY_UPLOAD_TOKEN }} diff --git a/.github/workflows/label-blank-issue.yml b/.github/workflows/label-blank-issue.yml index fce4fe6f9c74e..7c00984d1169f 100644 --- a/.github/workflows/label-blank-issue.yml +++ b/.github/workflows/label-blank-issue.yml @@ -1,4 +1,6 @@ name: Labels Blank issues +permissions: + issues: write on: issues: diff --git a/.github/workflows/labeler-title-regex.yml b/.github/workflows/labeler-title-regex.yml index 10195eca13a73..8b127925cbdae 100644 --- a/.github/workflows/labeler-title-regex.yml +++ b/.github/workflows/labeler-title-regex.yml @@ -13,9 +13,9 @@ permissions: jobs: labeler: - runs-on: ubuntu-20.04 + runs-on: ubuntu-24.04 steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: python-version: '3.9' diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index fdc993c1b3fdd..f8075e779c56b 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -20,7 +20,7 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: ref: ${{ github.event.pull_request.head.sha }} @@ -31,13 +31,13 @@ jobs: - name: Install dependencies run: | + curl https://raw.githubusercontent.com/${{ github.repository }}/main/build_tools/shared.sh --retry 5 -o ./build_tools/shared.sh 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) 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 - python -c "from importlib.metadata import version; print(f\"black={version('black')}\")" >> /tmp/versions.txt python -c "from importlib.metadata import version; print(f\"cython-lint={version('cython-lint')}\")" >> /tmp/versions.txt - name: Run linting @@ -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 diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml index b8940ae133ad9..ad24ea805eb8a 100644 --- a/.github/workflows/publish_pypi.yml +++ b/.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@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4 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@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4 if: ${{ github.event.inputs.pypi_repo == 'pypi' }} + with: + print-hash: true diff --git a/.github/workflows/update-lock-files.yml b/.github/workflows/update-lock-files.yml index 8301b45fa37fa..3d67bd9f70701 100644 --- a/.github/workflows/update-lock-files.yml +++ b/.github/workflows/update-lock-files.yml @@ -1,5 +1,7 @@ # Workflow to update lock files name: Update lock files +permissions: + contents: read on: workflow_dispatch: @@ -22,9 +24,11 @@ jobs: - name: scipy-dev update_script_args: "--select-tag scipy-dev" additional_commit_message: "[scipy-dev]" - - name: cirrus-arm - update_script_args: "--select-tag arm" - additional_commit_message: "[cirrus arm]" + - name: free-threaded + update_script_args: "--select-tag free-threaded" + additional_commit_message: "[free-threaded]" + - name: array-api + update_script_args: "--select-tag cuda" steps: - uses: actions/checkout@v4 @@ -32,6 +36,7 @@ jobs: run: | source build_tools/shared.sh source $CONDA/bin/activate + conda update -n base --all conda install -n base conda conda-libmamba-solver -y conda config --set solver libmamba conda install -c conda-forge "$(get_dep conda-lock min)" -y @@ -40,7 +45,7 @@ jobs: - name: Create Pull Request id: cpr - uses: peter-evans/create-pull-request@v5 + uses: peter-evans/create-pull-request@v7 with: token: ${{ secrets.BOT_GITHUB_TOKEN }} push-to-fork: scikit-learn-bot/scikit-learn @@ -56,6 +61,21 @@ 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: ${{ secrets.BOT_GITHUB_TOKEN }} + PR_NUMBER: ${{steps.cpr.outputs.pull-request-number}} + run: | + curl -L \ + -X POST \ + -H "Accept: application/vnd.github+json" \ + -H "Authorization: Bearer $GH_TOKEN" \ + -H "X-GitHub-Api-Version: 2022-11-28" \ + https://api.github.com/repos/scikit-learn/scikit-learn/issues/$PR_NUMBER/labels \ + -d '{"labels":["CUDA CI"]}' + - name: Check Pull Request if: steps.cpr.outputs.pull-request-number != '' run: | diff --git a/.github/workflows/update_tracking_issue.yml b/.github/workflows/update_tracking_issue.yml index d4538fe6848d8..54db3f50bc43b 100644 --- a/.github/workflows/update_tracking_issue.yml +++ b/.github/workflows/update_tracking_issue.yml @@ -11,6 +11,9 @@ # Where JOB_NAME is contains the status of the job you are interested in name: "Update tracking issue" +permissions: + contents: read + on: workflow_call: inputs: @@ -26,7 +29,7 @@ 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' diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml index 8bd7ffc17beca..33e8897c147f7 100644 --- a/.github/workflows/wheels.yml +++ b/.github/workflows/wheels.yml @@ -1,5 +1,7 @@ # Workflow to build and test wheels name: Wheel builder +permissions: + contents: read on: schedule: @@ -32,7 +34,7 @@ jobs: steps: - name: Checkout scikit-learn - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: ref: ${{ github.event.pull_request.head.sha }} @@ -44,6 +46,11 @@ jobs: build_wheels: name: Build wheel for cp${{ matrix.python }}-${{ matrix.platform_id }}-${{ matrix.manylinux_image }} runs-on: ${{ matrix.os }} + + # For conda-incubator/setup-miniconda to work + defaults: + run: + shell: bash -el {0} needs: check_build_trigger if: needs.check_build_trigger.outputs.build @@ -53,9 +60,6 @@ jobs: matrix: include: # Window 64 bit - - os: windows-latest - python: 39 - platform_id: win_amd64 - os: windows-latest python: 310 platform_id: win_amd64 @@ -65,19 +69,19 @@ jobs: - os: windows-latest python: 312 platform_id: win_amd64 + - os: windows-latest + python: 313 + platform_id: win_amd64 + - os: windows-latest + python: 313t + platform_id: win_amd64 + free_threaded_support: True # Linux 64 bit manylinux2014 - - os: ubuntu-latest - python: 39 - platform_id: manylinux_x86_64 - manylinux_image: manylinux2014 - - # NumPy on Python 3.10 only supports 64bit and is only available with manylinux2014 - os: ubuntu-latest python: 310 platform_id: manylinux_x86_64 manylinux_image: manylinux2014 - - os: ubuntu-latest python: 311 platform_id: manylinux_x86_64 @@ -86,25 +90,53 @@ 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 + free_threaded_support: True + + # # Linux 64 bit manylinux2014 + - os: ubuntu-24.04-arm + python: 310 + platform_id: manylinux_aarch64 + manylinux_image: manylinux2014 + - os: ubuntu-24.04-arm + python: 311 + platform_id: manylinux_aarch64 + manylinux_image: manylinux2014 + - os: ubuntu-24.04-arm + python: 312 + platform_id: manylinux_aarch64 + manylinux_image: manylinux2014 + - os: ubuntu-24.04-arm + python: 313 + platform_id: manylinux_aarch64 + manylinux_image: manylinux2014 # MacOS x86_64 - - os: macos-12 - python: 39 - platform_id: macosx_x86_64 - - os: macos-12 + - os: macos-13 python: 310 platform_id: macosx_x86_64 - - os: macos-12 + - os: macos-13 python: 311 platform_id: macosx_x86_64 - - os: macos-12 + - os: macos-13 python: 312 platform_id: macosx_x86_64 + - os: macos-13 + python: 313 + platform_id: macosx_x86_64 + - os: macos-13 + python: 313t + platform_id: macosx_x86_64 + free_threaded_support: True # MacOS arm64 - - os: macos-14 - python: 39 - platform_id: macosx_arm64 - os: macos-14 python: 310 platform_id: macosx_arm64 @@ -114,49 +146,31 @@ 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 - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Setup Python uses: actions/setup-python@v5 with: python-version: "3.11" # update once build dependencies are available - - name: Install conda for macos arm64 - if: ${{ matrix.platform_id == 'macosx_arm64' }} - run: | - set -ex - # macos arm64 runners do not have conda installed. Thus we much install conda manually - EXPECTED_SHA="dd832d8a65a861b5592b2cf1d55f26031f7c1491b30321754443931e7b1e6832" - MINIFORGE_URL="https://github.com/conda-forge/miniforge/releases/download/23.11.0-0/Mambaforge-23.11.0-0-MacOSX-arm64.sh" - curl -L --retry 10 $MINIFORGE_URL -o miniforge.sh - - # Check SHA - file_sha=$(shasum -a 256 miniforge.sh | awk '{print $1}') - if [ "$EXPECTED_SHA" != "$file_sha" ]; then - echo "SHA values did not match!" - exit 1 - fi - - # Install miniforge - MINIFORGE_PATH=$HOME/miniforge - bash ./miniforge.sh -b -p $MINIFORGE_PATH - echo "$MINIFORGE_PATH/bin" >> $GITHUB_PATH - echo "CONDA_HOME=$MINIFORGE_PATH" >> $GITHUB_ENV - - - name: Set conda environment for non-macos arm64 environments - if: ${{ matrix.platform_id != 'macosx_arm64' }} - run: | - # Non-macos arm64 envrionments already have conda installed - echo "CONDA_HOME=/usr/local/miniconda" >> $GITHUB_ENV + - uses: conda-incubator/setup-miniconda@v3 + if: ${{ startsWith(matrix.platform_id, 'macosx') }} - 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 }} CIBW_ARCHS: all CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.manylinux_image }} @@ -166,17 +180,24 @@ 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_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 ${{ matrix.python }} {project} CIBW_BUILD_VERBOSITY: 1 run: bash build_tools/wheels/build_wheels.sh - name: Store artifacts - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: + name: cibw-wheels-cp${{ matrix.python }}-${{ matrix.platform_id }} path: wheelhouse/*.whl update-tracker: @@ -197,17 +218,15 @@ jobs: steps: - name: Checkout scikit-learn - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Setup Python uses: actions/setup-python@v5 with: - python-version: "3.9" # update once build dependencies are available + python-version: "3.12" - name: Build source distribution run: bash build_tools/github/build_source.sh - env: - SKLEARN_BUILD_PARALLEL: 3 - name: Test source distribution run: bash build_tools/github/test_source.sh @@ -215,8 +234,9 @@ jobs: SKLEARN_SKIP_NETWORK_TESTS: 1 - name: Store artifacts - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: + name: cibw-sdist path: dist/*.tar.gz # Upload the wheels and the source distribution @@ -230,12 +250,14 @@ jobs: steps: - name: Checkout scikit-learn - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Download artifacts - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: + pattern: cibw-* path: dist + merge-multiple: true - name: Setup Python uses: actions/setup-python@v5 @@ -245,6 +267,6 @@ 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 diff --git a/.gitignore b/.gitignore index 61c89bcb96491..7e00b8802bd01 100644 --- a/.gitignore +++ b/.gitignore @@ -21,9 +21,13 @@ doc/css/* !doc/css/.gitkeep doc/modules/generated/ doc/datasets/generated/ +doc/developers/maintainer.rst doc/index.rst doc/min_dependency_table.rst doc/min_dependency_substitutions.rst +# release notes generated by towncrier +doc/whats_new/notes-towncrier.rst + *.pdf pip-log.txt scikit_learn.egg-info/ @@ -87,31 +91,8 @@ _configtest.o.d # virtualenv from advanced installation guide sklearn-env/ -# files generated from a template -sklearn/_loss/_loss.pyx -sklearn/utils/_seq_dataset.pyx -sklearn/utils/_seq_dataset.pxd -sklearn/utils/_weight_vector.pyx -sklearn/utils/_weight_vector.pxd -sklearn/linear_model/_sag_fast.pyx -sklearn/linear_model/_sgd_fast.pyx -sklearn/metrics/_dist_metrics.pyx -sklearn/metrics/_dist_metrics.pxd -sklearn/metrics/_pairwise_distances_reduction/_argkmin.pxd -sklearn/metrics/_pairwise_distances_reduction/_argkmin.pyx -sklearn/metrics/_pairwise_distances_reduction/_argkmin_classmode.pyx -sklearn/metrics/_pairwise_distances_reduction/_base.pxd -sklearn/metrics/_pairwise_distances_reduction/_base.pyx -sklearn/metrics/_pairwise_distances_reduction/_datasets_pair.pxd -sklearn/metrics/_pairwise_distances_reduction/_datasets_pair.pyx -sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.pxd -sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.pyx -sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.pxd -sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.pyx -sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_classmode.pyx -sklearn/neighbors/_ball_tree.pyx -sklearn/neighbors/_binary_tree.pxi -sklearn/neighbors/_kd_tree.pyx - # Default JupyterLite content jupyterlite_contents + +# file recognised by vscode IDEs containing env variables +.env diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index abe14acc7778c..48871d2a4abed 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,28 +1,25 @@ +exclude: '^(.git/|sklearn/externals/|asv_benchmarks/env/)' repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.3.0 + rev: v5.0.0 hooks: - id: check-yaml - id: end-of-file-fixer - id: trailing-whitespace - repo: https://github.com/astral-sh/ruff-pre-commit - # Ruff version. - rev: v0.2.1 + rev: v0.11.7 hooks: - id: ruff args: ["--fix", "--output-format=full"] -- repo: https://github.com/psf/black - rev: 24.3.0 - hooks: - - id: black + - id: ruff-format - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.9.0 + rev: v1.15.0 hooks: - id: mypy files: sklearn/ additional_dependencies: [pytest==6.2.4] - repo: https://github.com/MarcoGorelli/cython-lint - rev: v0.15.0 + rev: v0.16.6 hooks: # TODO: add the double-quote-cython-strings hook when it's usability has improved: # possibility to pass a directory and use it as a check instead of auto-formatter. diff --git a/.spin/cmds.py b/.spin/cmds.py new file mode 100644 index 0000000000000..954749b8005c2 --- /dev/null +++ b/.spin/cmds.py @@ -0,0 +1,29 @@ +import shutil +import sys + +import click +from spin.cmds import util + + +@click.command() +def clean(): + """🪥 Clean build folder. + + Very rarely needed since meson-python recompiles as needed when sklearn is + imported. + + One known use case where "spin clean" is useful: avoid compilation errors + when switching from numpy<2 to numpy>=2 in the same conda environment or + virtualenv. + """ + util.run([sys.executable, "-m", "pip", "uninstall", "scikit-learn", "-y"]) + default_meson_build_dir = ( + f"build/cp{sys.version_info.major}{sys.version_info.minor}" + ) + click.secho( + f"removing default Meson build dir: {default_meson_build_dir}", + bold=True, + fg="bright_blue", + ) + + shutil.rmtree(default_meson_build_dir, ignore_errors=True) diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000000000..c3e367c124f81 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,48 @@ +cff-version: 1.2.0 +title: scikit-learn +type: software +authors: + - name: "The scikit-learn developers" +message: "If you use scikit-learn in a scientific publication, we would appreciate citations to the following paper:" +preferred-citation: + type: article + title: "Scikit-learn: Machine Learning in Python" + authors: + - family-names: "Pedregosa" + given-names: "Fabian" + - family-names: "Varoquaux" + given-names: "Gaël" + - family-names: "Gramfort" + given-names: "Alexandre" + - family-names: "Michel" + given-names: "Vincent" + - family-names: "Thirion" + given-names: "Bertrand" + - family-names: "Grisel" + given-names: "Olivier" + - family-names: "Blondel" + given-names: "Mathieu" + - family-names: "Prettenhofer" + given-names: "Peter" + - family-names: "Weiss" + given-names: "Ron" + - family-names: "Dubourg" + given-names: "Vincent" + - family-names: "Vanderplas" + given-names: "Jake" + - family-names: "Passos" + given-names: "Alexandre" + - family-names: "Cournapeau" + given-names: "David" + - family-names: "Brucher" + given-names: "Matthieu" + - family-names: "Perrot" + given-names: "Matthieu" + - family-names: "Duchesnay" + given-names: "Édouard" + journal: "Journal of Machine Learning Research" + volume: 12 + start: 2825 + end: 2830 + year: 2011 + url: "https://jmlr.csail.mit.edu/papers/v12/pedregosa11a.html" diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 23016563a5f6e..b4e1709e67c3f 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -13,4 +13,3 @@ all priceless contributions. We abide by the principles of openness, respect, and consideration of others of the Python Software Foundation: https://www.python.org/psf/codeofconduct/ - diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 1596d4cd011df..0000000000000 --- a/MANIFEST.in +++ /dev/null @@ -1,36 +0,0 @@ -include *.rst -include *.build -recursive-include sklearn *.build -recursive-include doc * -recursive-include examples * -recursive-include sklearn *.c *.cpp *.h *.pyx *.pxd *.pxi *.tp -recursive-include sklearn/datasets *.csv *.csv.gz *.rst *.jpg *.txt *.arff.gz *.json.gz -include COPYING -include README.rst -include pyproject.toml -include sklearn/externals/README -include sklearn/svm/src/liblinear/COPYRIGHT -include sklearn/svm/src/libsvm/LIBSVM_CHANGES -include conftest.py -include Makefile -include MANIFEST.in -include .coveragerc - -# exclude from sdist -recursive-exclude asv_benchmarks * -recursive-exclude benchmarks * -recursive-exclude build_tools * -recursive-exclude maint_tools * -recursive-exclude benchmarks * -recursive-exclude .binder * -recursive-exclude .circleci * -exclude .cirrus.star -exclude .codecov.yml -exclude .git-blame-ignore-revs -exclude .mailmap -exclude .pre-commit-config.yaml -exclude azure-pipelines.yml -exclude CODE_OF_CONDUCT.md -exclude CONTRIBUTING.md -exclude SECURITY.md -exclude PULL_REQUEST_TEMPLATE.md diff --git a/Makefile b/Makefile index 52374ba44ff79..eb6ec39edcbdc 100644 --- a/Makefile +++ b/Makefile @@ -1,70 +1,27 @@ # 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 -CTAGS ?= ctags - -# skip doctests on 32bit python -BITS := $(shell python -c 'import struct; print(8 * struct.calcsize("P"))') +DEFAULT_MESON_BUILD_DIR = build/cp$(shell python -c 'import sys; print(f"{sys.version_info.major}{sys.version_info.minor}")' ) -all: clean inplace test +all: + @echo "Please use 'make ' where is one of" + @echo " dev build scikit-learn with Meson" + @echo " clean clean scikit-learn Meson build. Very rarely needed," + @echo " since meson-python recompiles on import." -clean-ctags: - rm -f tags +.PHONY: all -clean: clean-ctags - $(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 . --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 - -trailing-spaces: - find sklearn -name "*.py" -exec perl -pi -e 's/[ \t]*$$//' {} \; - -cython: - python setup.py build_src - -ctags: - # make tags for symbol based navigation in emacs and vim - # Install with: sudo apt-get install exuberant-ctags - $(CTAGS) --python-kinds=-i -R sklearn - -doc: inplace - $(MAKE) -C doc html - -doc-noplot: inplace - $(MAKE) -C doc html-noplot - -code-analysis: - build_tools/linting.sh + # It seems in some cases removing the folder avoids weird compilation + # errors (e.g. when switching from numpy>=2 to numpy<2). For some + # reason ninja clean -C $(DEFAULT_MESON_BUILD_DIR) is not + # enough. + rm -rf $(DEFAULT_MESON_BUILD_DIR) diff --git a/README.rst b/README.rst index 4ac297063c26e..4f4741a090dee 100644 --- a/README.rst +++ b/README.rst @@ -1,6 +1,6 @@ .. -*- mode: rst -*- -|Azure| |CirrusCI| |Codecov| |CircleCI| |Nightly wheels| |Black| |PythonVersion| |PyPi| |DOI| |Benchmark| +|Azure| |Codecov| |CircleCI| |Nightly wheels| |Ruff| |PythonVersion| |PyPi| |DOI| |Benchmark| .. |Azure| image:: https://dev.azure.com/scikit-learn/scikit-learn/_apis/build/status/scikit-learn.scikit-learn?branchName=main :target: https://dev.azure.com/scikit-learn/scikit-learn/_build/latest?definitionId=1&branchName=main @@ -8,38 +8,35 @@ .. |CircleCI| image:: https://circleci.com/gh/scikit-learn/scikit-learn/tree/main.svg?style=shield :target: https://circleci.com/gh/scikit-learn/scikit-learn -.. |CirrusCI| image:: https://img.shields.io/cirrus/github/scikit-learn/scikit-learn/main?label=Cirrus%20CI - :target: https://cirrus-ci.com/github/scikit-learn/scikit-learn/main - .. |Codecov| image:: https://codecov.io/gh/scikit-learn/scikit-learn/branch/main/graph/badge.svg?token=Pk8G9gg3y9 :target: https://codecov.io/gh/scikit-learn/scikit-learn .. |Nightly wheels| image:: https://github.com/scikit-learn/scikit-learn/workflows/Wheel%20builder/badge.svg?event=schedule :target: https://github.com/scikit-learn/scikit-learn/actions?query=workflow%3A%22Wheel+builder%22+event%3Aschedule +.. |Ruff| image:: https://img.shields.io/badge/code%20style-ruff-000000.svg + :target: https://github.com/astral-sh/ruff + .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/scikit-learn.svg :target: https://pypi.org/project/scikit-learn/ .. |PyPi| image:: https://img.shields.io/pypi/v/scikit-learn :target: https://pypi.org/project/scikit-learn -.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg - :target: https://github.com/psf/black - .. |DOI| image:: https://zenodo.org/badge/21369/scikit-learn/scikit-learn.svg :target: https://zenodo.org/badge/latestdoi/21369/scikit-learn/scikit-learn .. |Benchmark| image:: https://img.shields.io/badge/Benchmarked%20by-asv-blue :target: https://scikit-learn.org/scikit-learn-benchmarks -.. |PythonMinVersion| replace:: 3.9 -.. |NumPyMinVersion| replace:: 1.19.5 -.. |SciPyMinVersion| replace:: 1.6.0 +.. |PythonMinVersion| replace:: 3.10 +.. |NumPyMinVersion| replace:: 1.22.0 +.. |SciPyMinVersion| replace:: 1.8.0 .. |JoblibMinVersion| replace:: 1.2.0 .. |ThreadpoolctlMinVersion| replace:: 3.1.0 -.. |MatplotlibMinVersion| replace:: 3.3.4 -.. |Scikit-ImageMinVersion| replace:: 0.17.2 -.. |PandasMinVersion| replace:: 1.1.5 +.. |MatplotlibMinVersion| replace:: 3.5.0 +.. |Scikit-ImageMinVersion| replace:: 0.19.0 +.. |PandasMinVersion| replace:: 1.4.0 .. |SeabornMinVersion| replace:: 0.9.0 .. |PytestMinVersion| replace:: 7.1.2 .. |PlotlyMinVersion| replace:: 5.14.0 @@ -75,10 +72,6 @@ scikit-learn requires: ======= -**Scikit-learn 0.20 was the last version to support Python 2.7 and Python 3.4.** -scikit-learn 1.0 and later require Python 3.7 or newer. -scikit-learn 1.1 and later require Python 3.8 or newer. - Scikit-learn plotting capabilities (i.e., functions start with ``plot_`` and classes end with ``Display``) require Matplotlib (>= |MatplotlibMinVersion|). For running the examples Matplotlib >= |MatplotlibMinVersion| is required. @@ -187,16 +180,16 @@ Communication - Logos & Branding: https://github.com/scikit-learn/scikit-learn/tree/main/doc/logos - Blog: https://blog.scikit-learn.org - Calendar: https://blog.scikit-learn.org/calendar/ -- Twitter: https://twitter.com/scikit_learn - Stack Overflow: https://stackoverflow.com/questions/tagged/scikit-learn - GitHub Discussions: https://github.com/scikit-learn/scikit-learn/discussions - Website: https://scikit-learn.org - LinkedIn: https://www.linkedin.com/company/scikit-learn +- Bluesky: https://bsky.app/profile/scikit-learn.org +- Mastodon: https://mastodon.social/@sklearn@fosstodon.org - YouTube: https://www.youtube.com/channel/UCJosFjYm0ZYVUARxuOZqnnw/playlists - Facebook: https://www.facebook.com/scikitlearnofficial/ - Instagram: https://www.instagram.com/scikitlearnofficial/ - TikTok: https://www.tiktok.com/@scikit.learn -- Mastodon: https://mastodon.social/@sklearn@fosstodon.org - Discord: https://discord.gg/h9qyrK8Jc8 diff --git a/SECURITY.md b/SECURITY.md index c961966d3ea5e..cfc0bc34c738d 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -4,17 +4,20 @@ | Version | Supported | | ------------- | ------------------ | -| 1.5.0 | :white_check_mark: | -| < 1.5.0 | :x: | +| 1.6.1 | :white_check_mark: | +| < 1.6.1 | :x: | ## Reporting a Vulnerability -Please report security vulnerabilities by email to `security@scikit-learn.org`. -This email is an alias to a subset of the scikit-learn maintainers' team. +Please report security vulnerabilities by opening a new [GitHub security +advisory](https://github.com/scikit-learn/scikit-learn/security/advisories/new). + +You can also send an email to `security@scikit-learn.org`, which is an alias to +a subset of the scikit-learn maintainers' team. If the security vulnerability is accepted, a patch will be crafted privately in order to prepare a dedicated bugfix release as timely as possible (depending on the complexity of the fix). -In addition to sending the report by email, you can also report security -vulnerabilities to [tidelift](https://tidelift.com/security). +In addition to the options above, you can also report security vulnerabilities +to [tidelift](https://tidelift.com/security). diff --git a/asv_benchmarks/asv.conf.json b/asv_benchmarks/asv.conf.json index 3392925d7a488..3b16389139c0c 100644 --- a/asv_benchmarks/asv.conf.json +++ b/asv_benchmarks/asv.conf.json @@ -7,31 +7,21 @@ "project": "scikit-learn", // The project's homepage - "project_url": "scikit-learn.org/", + "project_url": "https://scikit-learn.org/", // The URL or local path of the source code repository for the // project being benchmarked "repo": "..", - // The Python project's subdirectory in your repo. If missing or - // the empty string, the project is assumed to be located at the root - // of the repository. - // "repo_subdir": "", - // Customizable commands for building, installing, and // uninstalling the project. See asv.conf.json documentation. - // - // "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}" - // ], + "install_command": ["python -mpip install {wheel_file}"], + "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"], + "build_command": ["python -m build --wheel -o {build_cache_dir} {build_dir}"], - // List of branches to benchmark. If not provided, defaults to "master + // List of branches to benchmark. If not provided, defaults to "main" // (for git) or "default" (for mercurial). "branches": ["main"], - // "branches": ["default"], // for mercurial // The DVCS being used. If not set, it will be automatically // determined from "repo" by looking at the protocol in the URL @@ -50,19 +40,19 @@ // defaults to 10 min //"install_timeout": 600, + // timeout in seconds all benchmarks, can be overridden per benchmark + // defaults to 1 min + //"default_benchmark_timeout": 60, + // the base URL to show a commit for the project. "show_commit_url": "https://github.com/scikit-learn/scikit-learn/commit/", - // The Pythons you'd like to test against. If not provided, defaults + // The Pythons you'd like to test against. If not provided, defaults // to the current version of Python used to run `asv`. - // "pythons": ["3.6"], + // "pythons": ["3.12"], - // The list of conda channel names to be searched for benchmark - // dependency packages in the specified order - // "conda_channels": ["conda-forge", "defaults"] - - // The matrix of dependencies to test. Each key is the name of a - // package (in PyPI) and the values are version numbers. An empty + // The matrix of dependencies to test. Each key is the name of a + // package (in PyPI) and the values are version numbers. An empty // list or empty string indicates to just test against the default // (latest) version. null indicates that the package is to not be // installed. If the package to be tested is only available from @@ -76,12 +66,12 @@ // those due to dependency changes. // "matrix": { - "numpy": ["1.25.2"], - "scipy": ["1.11.2"], + "numpy": ["2.0.0"], + "scipy": ["1.14.0"], "cython": ["3.0.10"], "joblib": ["1.3.2"], "threadpoolctl": ["3.2.0"], - "pandas": ["2.1.0"] + "pandas": ["2.2.2"] }, // Combinations of libraries/python versions can be excluded/included @@ -111,10 +101,10 @@ // ], // // "include": [ - // // additional env for python2.7 - // {"python": "2.7", "numpy": "1.8"}, + // // additional env for python3.12 + // {"python": "3.12", "numpy": "1.26"}, // // additional env if run on windows+conda - // {"platform": "win32", "environment_type": "conda", "python": "2.7", "libpython": ""}, + // {"sys_platform": "win32", "environment_type": "conda", "python": "3.12", "libpython": ""}, // ], // The directory (relative to the current directory) that benchmarks are @@ -136,10 +126,10 @@ // The number of characters to retain in the commit hashes. // "hash_length": 8, - // `asv` will cache results of the recent builds in each + // `asv` will cache wheels of the recent builds in each // environment, making them faster to install next time. This is - // the number of builds to keep, per environment. - // "build_cache_size": 2, + // number of builds to keep, per environment. + // "build_cache_size": 0 // The commits after which the regression search in `asv publish` // should start looking for regressions. Dictionary whose keys are @@ -152,16 +142,5 @@ // "regressions_first_commits": { // "some_benchmark": "352cdf", // Consider regressions only after this commit // "another_benchmark": null, // Skip regression detection altogether - // }, - - // The thresholds for relative change in results, after which `asv - // publish` starts reporting regressions. Dictionary of the same - // form as in ``regressions_first_commits``, with values - // indicating the thresholds. If multiple entries match, the - // maximum is taken. If no entry matches, the default is 5%. - // - // "regressions_thresholds": { - // "some_benchmark": 0.01, // Threshold of 1% - // "another_benchmark": 0.5, // Threshold of 50% - // }, + // } } diff --git a/asv_benchmarks/benchmarks/config.json b/asv_benchmarks/benchmarks/config.json index f50827cdbd7b7..b5a10b930e60b 100644 --- a/asv_benchmarks/benchmarks/config.json +++ b/asv_benchmarks/benchmarks/config.json @@ -9,7 +9,7 @@ // Can be overridden by environment variable SKLBENCH_PROFILE. "profile": "regular", - // List of values of n_jobs to use for estimators which accept this + // List of values of n_jobs to use for estimators which accept this // parameter (-1 means all cores). An empty list means all values from 1 to // the maximum number of available cores. // Can be overridden by environment variable SKLBENCH_NJOBS. diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 1ce5244124d4d..804214f97808a 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -11,7 +11,7 @@ jobs: - job: git_commit displayName: Get Git Commit pool: - vmImage: ubuntu-20.04 + vmImage: ubuntu-24.04 steps: - bash: python build_tools/azure/get_commit_message.py name: commit @@ -27,24 +27,29 @@ jobs: ) displayName: Linting pool: - vmImage: ubuntu-20.04 + vmImage: ubuntu-24.04 steps: - task: UsePythonVersion@0 inputs: - versionSpec: '3.9' + versionSpec: '3.12' - 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) cython-lint displayName: Install linters - bash: | ./build_tools/linting.sh displayName: Run linters + - bash: | + pip install ninja meson scipy + python build_tools/check-meson-openmp-dependencies.py + displayName: Run Meson OpenMP checks + - template: build_tools/azure/posix.yml parameters: name: Linux_Nightly - vmImage: ubuntu-20.04 + vmImage: ubuntu-22.04 dependsOn: [git_commit, linting] condition: | and( @@ -62,80 +67,34 @@ jobs: SKLEARN_WARNINGS_AS_ERRORS: '1' CHECK_PYTEST_SOFT_DEPENDENCY: 'true' -- template: build_tools/azure/posix-docker.yml - # Experimental CPython branch without the Global Interpreter Lock: - # https://github.com/colesbury/nogil/ - # - # The nogil build relies on a dedicated PyPI-style index to install patched - # versions of NumPy, SciPy and Cython maintained by @colesbury and that - # include specific fixes to make them run correctly without relying on the GIL. - # - # The goal of this CI entry is to make sure that we do not introduce any - # dependency on the GIL in scikit-learn itself. An auxiliary goal is to early - # detect any regression in the patched build dependencies to report them - # upstream. The long-term goal is to be able to stop having to maintain - # multiprocessing based workaround / hacks in joblib / loky to make multi-CPU - # computing in scikit-learn efficient by default using regular threads. - # - # If this experimental entry becomes too unstable, feel free to disable it. +- template: build_tools/azure/posix.yml + # CPython 3.13 free-threaded build parameters: - name: Linux_nogil - vmImage: ubuntu-20.04 + name: Linux_free_threaded + vmImage: ubuntu-22.04 dependsOn: [git_commit, linting] condition: | and( succeeded(), not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')), or(eq(variables['Build.Reason'], 'Schedule'), - contains(dependencies['git_commit']['outputs']['commit.message'], '[nogil]' + contains(dependencies['git_commit']['outputs']['commit.message'], '[free-threaded]' ) ) ) matrix: - pylatest_pip_nogil: - DOCKER_CONTAINER: 'nogil/python' - DISTRIB: 'pip-nogil' - LOCK_FILE: './build_tools/azure/python_nogil_lock.txt' + pylatest_free_threaded: + PYTHON_GIL: '0' + DISTRIB: 'conda-free-threaded' + LOCK_FILE: './build_tools/azure/pylatest_free_threaded_linux-64_conda.lock' COVERAGE: 'false' - -- job: Linux_Nightly_Pyodide - pool: - vmImage: ubuntu-22.04 - variables: - # Need to match Python version and Emscripten version for the correct - # Pyodide version. For example, for Pyodide version 0.25.1, see - # https://github.com/pyodide/pyodide/blob/0.25.1/Makefile.envs - PYODIDE_VERSION: '0.25.1' - EMSCRIPTEN_VERSION: '3.1.46' - PYTHON_VERSION: '3.11.3' - - dependsOn: [git_commit, linting] - condition: | - and( - succeeded(), - not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')), - or(eq(variables['Build.Reason'], 'Schedule'), - contains(dependencies['git_commit']['outputs']['commit.message'], '[pyodide]' - ) - ) - ) - steps: - - task: UsePythonVersion@0 - inputs: - versionSpec: $(PYTHON_VERSION) - addToPath: true - - - bash: bash build_tools/azure/install_pyodide.sh - displayName: Build Pyodide wheel - - - bash: bash build_tools/azure/test_script_pyodide.sh - displayName: Test Pyodide wheel + SKLEARN_FAULTHANDLER_TIMEOUT: '1800' # 30 * 60 seconds # Will run all the time regardless of linting outcome. - template: build_tools/azure/posix.yml parameters: name: Linux_Runs - vmImage: ubuntu-20.04 + vmImage: ubuntu-22.04 dependsOn: [git_commit] condition: | and( @@ -152,6 +111,7 @@ jobs: # Here we make sure, that they are still run on a regular basis. ${{ if eq(variables['Build.Reason'], 'Schedule') }}: SKLEARN_SKIP_NETWORK_TESTS: '0' + SCIPY_ARRAY_API: '1' # Check compilation with Ubuntu 22.04 LTS (Jammy Jellyfish) and scipy from conda-forge # By default the CI is sequential, where `Ubuntu_Jammy_Jellyfish` runs first and @@ -181,7 +141,7 @@ jobs: - template: build_tools/azure/posix.yml parameters: name: Ubuntu_Atlas - vmImage: ubuntu-22.04 + vmImage: ubuntu-24.04 dependsOn: [linting, git_commit, Ubuntu_Jammy_Jellyfish] # Runs when dependencies succeeded or skipped condition: | @@ -191,8 +151,8 @@ jobs: ) matrix: # Linux environment to test that scikit-learn can be built against - # versions of numpy, scipy with ATLAS that comes with Ubuntu Jammy Jellyfish 22.04 - # i.e. numpy 1.21.5 and scipy 1.8.0 + # versions of numpy, scipy with ATLAS that comes with Ubuntu 24.04 Noble Numbat + # i.e. numpy 1.26.4 and scipy 1.11.4 ubuntu_atlas: DISTRIB: 'ubuntu' LOCK_FILE: './build_tools/azure/ubuntu_atlas_lock.txt' @@ -202,7 +162,7 @@ jobs: - template: build_tools/azure/posix.yml parameters: name: Linux - vmImage: ubuntu-20.04 + vmImage: ubuntu-22.04 dependsOn: [linting, git_commit, Ubuntu_Jammy_Jellyfish] # Runs when dependencies succeeded or skipped condition: | @@ -211,10 +171,10 @@ jobs: not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')) ) matrix: - # Linux + Python 3.9 build with OpenBLAS and without pandas - pymin_conda_defaults_openblas: + # Linux build with minimum supported version of dependencies + pymin_conda_forge_openblas_min_dependencies: DISTRIB: 'conda' - LOCK_FILE: './build_tools/azure/pymin_conda_defaults_openblas_linux-64_conda.lock' + LOCK_FILE: './build_tools/azure/pymin_conda_forge_openblas_min_dependencies_linux-64_conda.lock' # Enable debug Cython directives to capture IndexError exceptions in # combination with the -Werror::pytest.PytestUnraisableExceptionWarning # flag for pytest. @@ -222,7 +182,6 @@ jobs: SKLEARN_ENABLE_DEBUG_CYTHON_DIRECTIVES: '1' SKLEARN_RUN_FLOAT32_TESTS: '1' SKLEARN_TESTS_GLOBAL_RANDOM_SEED: '2' # non-default seed - BUILD_WITH_SETUPTOOLS: 'true' # Linux environment to test the latest available dependencies. # It runs tests requiring lightgbm, pandas and PyAMG. pylatest_pip_openblas_pandas: @@ -236,11 +195,12 @@ jobs: # makes sure that they are single threaded in each xdist subprocess. PYTEST_XDIST_VERSION: 'none' PIP_BUILD_ISOLATION: 'true' + SCIPY_ARRAY_API: '1' - template: build_tools/azure/posix-docker.yml parameters: name: Linux_Docker - vmImage: ubuntu-20.04 + vmImage: ubuntu-24.04 dependsOn: [linting, git_commit, Ubuntu_Jammy_Jellyfish] # Runs when dependencies succeeded or skipped condition: | @@ -249,11 +209,11 @@ jobs: not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')) ) matrix: - debian_atlas_32bit: - DOCKER_CONTAINER: 'i386/debian:11.2' + debian_32bit: + DOCKER_CONTAINER: 'i386/debian:trixie' DISTRIB: 'debian-32' COVERAGE: "true" - LOCK_FILE: './build_tools/azure/debian_atlas_32bit_lock.txt' + LOCK_FILE: './build_tools/azure/debian_32bit_lock.txt' # disable pytest xdist due to unknown bug with 32-bit container PYTEST_XDIST_VERSION: 'none' SKLEARN_TESTS_GLOBAL_RANDOM_SEED: '4' # non-default seed @@ -261,7 +221,7 @@ jobs: - template: build_tools/azure/posix.yml parameters: name: macOS - vmImage: macOS-11 + vmImage: macOS-13 dependsOn: [linting, git_commit, Ubuntu_Jammy_Jellyfish] # Runs when dependencies succeeded or skipped condition: | @@ -274,6 +234,7 @@ jobs: DISTRIB: 'conda' LOCK_FILE: './build_tools/azure/pylatest_conda_forge_mkl_osx-64_conda.lock' SKLEARN_TESTS_GLOBAL_RANDOM_SEED: '5' # non-default seed + SCIPY_ARRAY_API: '1' pylatest_conda_mkl_no_openmp: DISTRIB: 'conda' LOCK_FILE: './build_tools/azure/pylatest_conda_mkl_no_openmp_osx-64_conda.lock' diff --git a/benchmarks/bench_20newsgroups.py b/benchmarks/bench_20newsgroups.py index 44a117f1ad42d..a559bc59b5f8a 100644 --- a/benchmarks/bench_20newsgroups.py +++ b/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), } diff --git a/benchmarks/bench_covertype.py b/benchmarks/bench_covertype.py index 5b8cdd588c8ee..243cce03a632f 100644 --- a/benchmarks/bench_covertype.py +++ b/benchmarks/bench_covertype.py @@ -41,9 +41,8 @@ """ -# Author: Peter Prettenhofer -# Arnaud Joly -# License: BSD 3 clause +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause import argparse import os diff --git a/benchmarks/bench_hist_gradient_boosting_adult.py b/benchmarks/bench_hist_gradient_boosting_adult.py index 97c762e8e9230..4d5ce48cded81 100644 --- a/benchmarks/bench_hist_gradient_boosting_adult.py +++ b/benchmarks/bench_hist_gradient_boosting_adult.py @@ -46,7 +46,7 @@ def predict(est, data_test, target_test): toc = time() roc_auc = roc_auc_score(target_test, predicted_proba_test[:, 1]) acc = accuracy_score(target_test, predicted_test) - print(f"predicted in {toc - tic:.3f}s, ROC AUC: {roc_auc:.4f}, ACC: {acc :.4f}") + print(f"predicted in {toc - tic:.3f}s, ROC AUC: {roc_auc:.4f}, ACC: {acc:.4f}") data = fetch_openml(data_id=179, as_frame=True) # adult dataset diff --git a/benchmarks/bench_hist_gradient_boosting_higgsboson.py b/benchmarks/bench_hist_gradient_boosting_higgsboson.py index 20057c50dc810..ceab576bc0a52 100644 --- a/benchmarks/bench_hist_gradient_boosting_higgsboson.py +++ b/benchmarks/bench_hist_gradient_boosting_higgsboson.py @@ -74,7 +74,7 @@ def predict(est, data_test, target_test): toc = time() roc_auc = roc_auc_score(target_test, predicted_proba_test[:, 1]) acc = accuracy_score(target_test, predicted_test) - print(f"predicted in {toc - tic:.3f}s, ROC AUC: {roc_auc:.4f}, ACC: {acc :.4f}") + print(f"predicted in {toc - tic:.3f}s, ROC AUC: {roc_auc:.4f}, ACC: {acc:.4f}") df = load_data() diff --git a/benchmarks/bench_isolation_forest_predict.py b/benchmarks/bench_isolation_forest_predict.py new file mode 100644 index 0000000000000..f16e65cf19511 --- /dev/null +++ b/benchmarks/bench_isolation_forest_predict.py @@ -0,0 +1,213 @@ +""" +========================================== +IsolationForest prediction benchmark +========================================== +A test of IsolationForest on classical anomaly detection datasets. + +The benchmark is run as follows: +1. The dataset is randomly split into a training set and a test set, both +assumed to contain outliers. +2. Isolation Forest is trained on the training set fixed at 1000 samples. +3. The test samples are scored using the trained model at: + - 1000, 10000, 50000 samples + - 10, 100, 1000 features + - 0.01, 0.1, 0.5 contamination + - 1, 2, 3, 4 n_jobs + +We compare the prediction time at the very end. + +Here are instructions for running this benchmark to compare runtime against main branch: + +1. Build and run on a branch or main, e.g. for a branch named `pr`: + +```bash +python bench_isolation_forest_predict.py bench ~/bench_results pr +``` + +2. Plotting to compare two branches `pr` and `main`: + +```bash +python bench_isolation_forest_predict.py plot ~/bench_results pr main results_image.png +``` +""" + +import argparse +from collections import defaultdict +from pathlib import Path +from time import time + +import numpy as np +import pandas as pd +from joblib import parallel_config + +from sklearn.ensemble import IsolationForest + +print(__doc__) + + +def get_data( + n_samples_train, n_samples_test, n_features, contamination=0.1, random_state=0 +): + """Function based on code from: https://scikit-learn.org/stable/ + auto_examples/ensemble/plot_isolation_forest.html#sphx-glr-auto- + examples-ensemble-plot-isolation-forest-py + """ + rng = np.random.RandomState(random_state) + + X = 0.3 * rng.randn(n_samples_train, n_features) + X_train = np.r_[X + 2, X - 2] + + X = 0.3 * rng.randn(n_samples_test, n_features) + X_test = np.r_[X + 2, X - 2] + + n_outliers = int(np.floor(contamination * n_samples_test)) + X_outliers = rng.uniform(low=-4, high=4, size=(n_outliers, n_features)) + + outlier_idx = rng.choice(np.arange(0, n_samples_test), n_outliers, replace=False) + X_test[outlier_idx, :] = X_outliers + + return X_train, X_test + + +def plot(args): + import matplotlib.pyplot as plt + import seaborn as sns + + bench_results = Path(args.bench_results) + pr_name = args.pr_name + main_name = args.main_name + image_path = args.image_path + + results_path = Path(bench_results) + pr_path = results_path / f"{pr_name}.csv" + main_path = results_path / f"{main_name}.csv" + image_path = results_path / image_path + + df_pr = pd.read_csv(pr_path).assign(branch=pr_name) + df_main = pd.read_csv(main_path).assign(branch=main_name) + + # Merge the two datasets on the common columns + merged_data = pd.merge( + df_pr, + df_main, + on=["n_samples_test", "n_jobs"], + suffixes=("_pr", "_main"), + ) + + # Set up the plotting grid + sns.set(style="whitegrid", context="notebook", font_scale=1.5) + + # Create a figure with subplots + fig, axes = plt.subplots(1, 2, figsize=(18, 6), sharex=True, sharey=True) + + # Plot predict time as a function of n_samples_test with different n_jobs + print(merged_data["n_jobs"].unique()) + ax = axes[0] + sns.lineplot( + data=merged_data, + x="n_samples_test", + y="predict_time_pr", + hue="n_jobs", + style="n_jobs", + markers="o", + ax=ax, + legend="full", + ) + ax.set_title(f"Predict Time vs. n_samples_test - {pr_name} branch") + ax.set_ylabel("Predict Time (Seconds)") + ax.set_xlabel("n_samples_test") + + ax = axes[1] + sns.lineplot( + data=merged_data, + x="n_samples_test", + y="predict_time_main", + hue="n_jobs", + style="n_jobs", + markers="X", + dashes=True, + ax=ax, + legend=None, + ) + ax.set_title(f"Predict Time vs. n_samples_test - {main_name} branch") + ax.set_ylabel("Predict Time") + ax.set_xlabel("n_samples_test") + + # Adjust layout and display the plots + plt.tight_layout() + fig.savefig(image_path, bbox_inches="tight") + print(f"Saved image to {image_path}") + + +def bench(args): + results_dir = Path(args.bench_results) + branch = args.branch + random_state = 1 + + results = defaultdict(list) + + # Loop over all datasets for fitting and scoring the estimator: + n_samples_train = 1000 + for n_samples_test in [ + 1000, + 10000, + 50000, + ]: + for n_features in [10, 100, 1000]: + for contamination in [0.01, 0.1, 0.5]: + for n_jobs in [1, 2, 3, 4]: + X_train, X_test = get_data( + n_samples_train, + n_samples_test, + n_features, + contamination, + random_state, + ) + + print("--- Fitting the IsolationForest estimator...") + model = IsolationForest(n_jobs=-1, random_state=random_state) + tstart = time() + model.fit(X_train) + fit_time = time() - tstart + + # clearcache + for _ in range(1000): + 1 + 1 + with parallel_config("threading", n_jobs=n_jobs): + tstart = time() + model.decision_function(X_test) # the lower, the more abnormal + predict_time = time() - tstart + + results["predict_time"].append(predict_time) + results["fit_time"].append(fit_time) + results["n_samples_train"].append(n_samples_train) + results["n_samples_test"].append(n_samples_test) + results["n_features"].append(n_features) + results["contamination"].append(contamination) + results["n_jobs"].append(n_jobs) + + df = pd.DataFrame(results) + df.to_csv(results_dir / f"{branch}.csv", index=False) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + + # parse arguments for benchmarking + subparsers = parser.add_subparsers() + bench_parser = subparsers.add_parser("bench") + bench_parser.add_argument("bench_results") + bench_parser.add_argument("branch") + bench_parser.set_defaults(func=bench) + + # parse arguments for plotting + plot_parser = subparsers.add_parser("plot") + plot_parser.add_argument("bench_results") + plot_parser.add_argument("pr_name") + plot_parser.add_argument("main_name") + plot_parser.add_argument("image_path") + plot_parser.set_defaults(func=plot) + + # enable the parser and run the relevant function + args = parser.parse_args() + args.func(args) diff --git a/benchmarks/bench_kernel_pca_solvers_time_vs_n_components.py b/benchmarks/bench_kernel_pca_solvers_time_vs_n_components.py index 26789c173688f..a468f7b3e1abf 100644 --- a/benchmarks/bench_kernel_pca_solvers_time_vs_n_components.py +++ b/benchmarks/bench_kernel_pca_solvers_time_vs_n_components.py @@ -36,8 +36,6 @@ of components (this takes more time). """ -# Authors: Sylvain MARIE, Schneider Electric - import time import matplotlib.pyplot as plt diff --git a/benchmarks/bench_mnist.py b/benchmarks/bench_mnist.py index 334e69ed5a30a..5745a6d1e3882 100644 --- a/benchmarks/bench_mnist.py +++ b/benchmarks/bench_mnist.py @@ -26,9 +26,8 @@ dummy 0.00s 0.01s 0.8973 """ -# Author: Issam H. Laradji -# Arnaud Joly -# License: BSD 3 clause +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause import argparse import os diff --git a/benchmarks/bench_plot_fastkmeans.py b/benchmarks/bench_plot_fastkmeans.py index 1d420d1dabe5d..d5a2d10fbf22d 100644 --- a/benchmarks/bench_plot_fastkmeans.py +++ b/benchmarks/bench_plot_fastkmeans.py @@ -97,8 +97,8 @@ def compute_bench_2(chunks): if __name__ == "__main__": - from mpl_toolkits.mplot3d import axes3d # noqa register the 3d projection import matplotlib.pyplot as plt + from mpl_toolkits.mplot3d import axes3d # register the 3d projection # noqa: F401 samples_range = np.linspace(50, 150, 5).astype(int) features_range = np.linspace(150, 50000, 5).astype(int) diff --git a/benchmarks/bench_plot_lasso_path.py b/benchmarks/bench_plot_lasso_path.py index 3b46e447401cb..9acc1b4b35952 100644 --- a/benchmarks/bench_plot_lasso_path.py +++ b/benchmarks/bench_plot_lasso_path.py @@ -80,8 +80,8 @@ def compute_bench(samples_range, features_range): if __name__ == "__main__": - from mpl_toolkits.mplot3d import axes3d # noqa register the 3d projection import matplotlib.pyplot as plt + from mpl_toolkits.mplot3d import axes3d # register the 3d projection # noqa: F401 samples_range = np.linspace(10, 2000, 5).astype(int) features_range = np.linspace(10, 2000, 5).astype(int) diff --git a/benchmarks/bench_plot_nmf.py b/benchmarks/bench_plot_nmf.py index f05ede117191b..76d1a6de8286c 100644 --- a/benchmarks/bench_plot_nmf.py +++ b/benchmarks/bench_plot_nmf.py @@ -2,10 +2,8 @@ Benchmarks of Non-Negative Matrix Factorization """ -# Authors: Tom Dupre la Tour (benchmark) -# Chih-Jen Linn (original projected gradient NMF implementation) -# Anthony Di Franco (projected gradient, Python and NumPy port) -# License: BSD 3 clause +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause import numbers import sys diff --git a/benchmarks/bench_plot_parallel_pairwise.py b/benchmarks/bench_plot_parallel_pairwise.py index ca12972f9be6c..5b7cf81f8fce4 100644 --- a/benchmarks/bench_plot_parallel_pairwise.py +++ b/benchmarks/bench_plot_parallel_pairwise.py @@ -1,5 +1,6 @@ -# Author: Mathieu Blondel -# License: BSD 3 clause +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + import time import matplotlib.pyplot as plt diff --git a/benchmarks/bench_plot_polynomial_kernel_approximation.py b/benchmarks/bench_plot_polynomial_kernel_approximation.py index a80455e21c255..1e23e0a3c79ad 100644 --- a/benchmarks/bench_plot_polynomial_kernel_approximation.py +++ b/benchmarks/bench_plot_polynomial_kernel_approximation.py @@ -39,8 +39,8 @@ """ -# Author: Daniel Lopez-Sanchez -# License: BSD 3 clause +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause # Load data manipulation functions # Will use this for timing results diff --git a/benchmarks/bench_plot_randomized_svd.py b/benchmarks/bench_plot_randomized_svd.py index 6bb5618b3633f..e955be64cdee3 100644 --- a/benchmarks/bench_plot_randomized_svd.py +++ b/benchmarks/bench_plot_randomized_svd.py @@ -63,7 +63,8 @@ A. Szlam et al. 2014 """ -# Author: Giorgio Patrini +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause import gc import os.path diff --git a/benchmarks/bench_plot_svd.py b/benchmarks/bench_plot_svd.py index ed99d1c44e2fd..f93920cae5305 100644 --- a/benchmarks/bench_plot_svd.py +++ b/benchmarks/bench_plot_svd.py @@ -54,8 +54,8 @@ def compute_bench(samples_range, features_range, n_iter=3, rank=50): if __name__ == "__main__": - from mpl_toolkits.mplot3d import axes3d # noqa register the 3d projection import matplotlib.pyplot as plt + from mpl_toolkits.mplot3d import axes3d # register the 3d projection # noqa: F401 samples_range = np.linspace(2, 1000, 4).astype(int) features_range = np.linspace(2, 1000, 4).astype(int) diff --git a/benchmarks/bench_rcv1_logreg_convergence.py b/benchmarks/bench_rcv1_logreg_convergence.py index 166c6c2f5f9d1..27e730736a3de 100644 --- a/benchmarks/bench_rcv1_logreg_convergence.py +++ b/benchmarks/bench_rcv1_logreg_convergence.py @@ -1,7 +1,5 @@ -# Authors: Tom Dupre la Tour -# Olivier Grisel -# -# License: BSD 3 clause +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause import gc import time diff --git a/benchmarks/bench_sgd_regression.py b/benchmarks/bench_sgd_regression.py index 4b1b902795feb..bd00615e3d5f9 100644 --- a/benchmarks/bench_sgd_regression.py +++ b/benchmarks/bench_sgd_regression.py @@ -1,5 +1,5 @@ -# Author: Peter Prettenhofer -# License: BSD 3 clause +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause import gc from time import time diff --git a/benchmarks/bench_tsne_mnist.py b/benchmarks/bench_tsne_mnist.py index 813fffcf29141..8649c7a46b629 100644 --- a/benchmarks/bench_tsne_mnist.py +++ b/benchmarks/bench_tsne_mnist.py @@ -5,7 +5,7 @@ """ -# License: BSD 3 clause +# SPDX-License-Identifier: BSD-3-Clause import argparse import json diff --git a/build_tools/azure/debian_32bit_lock.txt b/build_tools/azure/debian_32bit_lock.txt new file mode 100644 index 0000000000000..051a8b8ef7e48 --- /dev/null +++ b/build_tools/azure/debian_32bit_lock.txt @@ -0,0 +1,37 @@ +# +# This file is autogenerated by pip-compile with Python 3.12 +# by the following command: +# +# pip-compile --output-file=build_tools/azure/debian_32bit_lock.txt build_tools/azure/debian_32bit_requirements.txt +# +coverage[toml]==7.8.0 + # via pytest-cov +cython==3.0.12 + # via -r build_tools/azure/debian_32bit_requirements.txt +iniconfig==2.1.0 + # via pytest +joblib==1.5.0 + # via -r build_tools/azure/debian_32bit_requirements.txt +meson==1.8.0 + # via meson-python +meson-python==0.17.1 + # via -r build_tools/azure/debian_32bit_requirements.txt +ninja==1.11.1.4 + # via -r build_tools/azure/debian_32bit_requirements.txt +packaging==25.0 + # via + # meson-python + # pyproject-metadata + # pytest +pluggy==1.5.0 + # via pytest +pyproject-metadata==0.9.1 + # via meson-python +pytest==8.3.5 + # via + # -r build_tools/azure/debian_32bit_requirements.txt + # pytest-cov +pytest-cov==6.1.1 + # via -r build_tools/azure/debian_32bit_requirements.txt +threadpoolctl==3.6.0 + # via -r build_tools/azure/debian_32bit_requirements.txt diff --git a/build_tools/azure/debian_atlas_32bit_requirements.txt b/build_tools/azure/debian_32bit_requirements.txt similarity index 65% rename from build_tools/azure/debian_atlas_32bit_requirements.txt rename to build_tools/azure/debian_32bit_requirements.txt index 615193a71fc6b..6dcf67d11c58d 100644 --- a/build_tools/azure/debian_atlas_32bit_requirements.txt +++ b/build_tools/azure/debian_32bit_requirements.txt @@ -1,10 +1,10 @@ # 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 -cython==3.0.10 # min -joblib==1.2.0 # min -threadpoolctl==3.1.0 -pytest==7.1.2 # min -pytest-cov==2.9.0 # min +cython +joblib +threadpoolctl +pytest +pytest-cov ninja meson-python diff --git a/build_tools/azure/debian_atlas_32bit_lock.txt b/build_tools/azure/debian_atlas_32bit_lock.txt deleted file mode 100644 index 92b4b864fb9f5..0000000000000 --- a/build_tools/azure/debian_atlas_32bit_lock.txt +++ /dev/null @@ -1,45 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.9 -# by the following command: -# -# pip-compile --output-file=build_tools/azure/debian_atlas_32bit_lock.txt build_tools/azure/debian_atlas_32bit_requirements.txt -# -attrs==23.2.0 - # via pytest -coverage==7.5.2 - # via pytest-cov -cython==3.0.10 - # via -r build_tools/azure/debian_atlas_32bit_requirements.txt -iniconfig==2.0.0 - # via pytest -joblib==1.2.0 - # via -r build_tools/azure/debian_atlas_32bit_requirements.txt -meson==1.4.0 - # via meson-python -meson-python==0.16.0 - # via -r build_tools/azure/debian_atlas_32bit_requirements.txt -ninja==1.11.1.1 - # via -r build_tools/azure/debian_atlas_32bit_requirements.txt -packaging==24.0 - # via - # meson-python - # pyproject-metadata - # pytest -pluggy==1.5.0 - # via pytest -py==1.11.0 - # via pytest -pyproject-metadata==0.8.0 - # via meson-python -pytest==7.1.2 - # via - # -r build_tools/azure/debian_atlas_32bit_requirements.txt - # pytest-cov -pytest-cov==2.9.0 - # via -r build_tools/azure/debian_atlas_32bit_requirements.txt -threadpoolctl==3.1.0 - # via -r build_tools/azure/debian_atlas_32bit_requirements.txt -tomli==2.0.1 - # via - # meson-python - # pytest diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh index 35f8f768eeced..c009e2972036e 100755 --- a/build_tools/azure/install.sh +++ b/build_tools/azure/install.sh @@ -24,6 +24,9 @@ setup_ccache() { done export PATH="${CCACHE_LINKS_DIR}:${PATH}" ccache -M 256M + + # Zeroing statistics so that ccache statistics are shown only for this build + ccache -z fi } @@ -36,7 +39,7 @@ pre_python_environment_install() { elif [[ "$DISTRIB" == "debian-32" ]]; then apt-get update apt-get install -y python3-dev python3-numpy python3-scipy \ - python3-matplotlib libatlas3-base libatlas-base-dev \ + python3-matplotlib libopenblas-dev \ python3-virtualenv python3-pandas ccache git fi } @@ -44,7 +47,7 @@ pre_python_environment_install() { check_packages_dev_version() { for package in $@; do package_version=$(python -c "import $package; print($package.__version__)") - if ! [[ $package_version =~ "dev" ]]; then + if [[ $package_version =~ "^[.0-9]+$" ]]; then echo "$package is not a development version: $package_version" exit 1 fi @@ -53,44 +56,39 @@ check_packages_dev_version() { python_environment_install_and_activate() { if [[ "$DISTRIB" == "conda"* ]]; then - # Install/update conda with the libmamba solver because the legacy - # solver can be slow at installing a specific version of conda-lock. - conda install -n base conda conda-libmamba-solver -y - conda config --set solver libmamba - conda install -c conda-forge "$(get_dep conda-lock min)" -y - conda-lock install --name $VIRTUALENV $LOCK_FILE - source activate $VIRTUALENV + create_conda_environment_from_lock_file $VIRTUALENV $LOCK_FILE + activate_environment elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" ]]; then python3 -m virtualenv --system-site-packages --python=python3 $VIRTUALENV - source $VIRTUALENV/bin/activate + activate_environment pip install -r "${LOCK_FILE}" - elif [[ "$DISTRIB" == "pip-nogil" ]]; then - python -m venv $VIRTUALENV - source $VIRTUALENV/bin/activate - pip install -r "${LOCK_FILE}" fi - if [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then + # Install additional packages on top of the lock-file in specific cases + if [[ "$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 echo "Installing development dependency wheels" dev_anaconda_url=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple - dev_packages="numpy scipy pandas" - pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url $dev_packages + dev_packages="numpy scipy pandas Cython" + pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url $dev_packages --only-binary :all: check_packages_dev_version $dev_packages - echo "Installing Cython from latest sources" - pip install https://github.com/cython/cython/archive/master.zip echo "Installing joblib from latest sources" pip install https://github.com/joblib/joblib/archive/master.zip echo "Installing pillow from latest sources" pip install https://github.com/python-pillow/Pillow/archive/main.zip - - elif [[ "$DISTRIB" == "pip-nogil" ]]; then - apt-get -yq update - apt-get install -yq ccache - fi } @@ -98,10 +96,6 @@ scikit_learn_install() { setup_ccache show_installed_libraries - # Set parallelism to 3 to overlap IO bound tasks with CPU bound tasks on CI - # workers with 2 cores when building the compiled extensions of scikit-learn. - export SKLEARN_BUILD_PARALLEL=3 - if [[ "$UNAMESTR" == "Darwin" && "$SKLEARN_TEST_NO_OPENMP" == "true" ]]; then # Without openmp, we use the system clang. Here we use /usr/bin/ar # instead because llvm-ar errors @@ -112,6 +106,11 @@ scikit_learn_install() { # brings in openmp so that you end up having the omp.h include inside # the conda environment. find $CONDA_PREFIX -name omp.h -delete -print + # meson >= 1.5 detects OpenMP installed with brew and OpenMP may be installed + # with brew in CI runner. OpenMP was installed with brew in macOS-12 CI + # runners which doesn't seem to be the case in macOS-13 runners anymore, + # but we keep the next line just to be safe ... + brew uninstall --ignore-dependencies --force libomp fi if [[ "$UNAMESTR" == "Linux" ]]; then @@ -120,9 +119,7 @@ scikit_learn_install() { export LDFLAGS="$LDFLAGS -Wl,--sysroot=/" fi - if [[ "$BUILD_WITH_SETUPTOOLS" == "true" ]]; then - python setup.py develop - elif [[ "$PIP_BUILD_ISOLATION" == "true" ]]; then + if [[ "$PIP_BUILD_ISOLATION" == "true" ]]; then # Check that pip can automatically build scikit-learn with the build # dependencies specified in pyproject.toml using an isolated build # environment: diff --git a/build_tools/azure/install_pyodide.sh b/build_tools/azure/install_pyodide.sh deleted file mode 100644 index 58d0348a53202..0000000000000 --- a/build_tools/azure/install_pyodide.sh +++ /dev/null @@ -1,20 +0,0 @@ -#!/bin/bash - -set -e - -git clone https://github.com/emscripten-core/emsdk.git -cd emsdk -./emsdk install $EMSCRIPTEN_VERSION -./emsdk activate $EMSCRIPTEN_VERSION -source emsdk_env.sh -cd - - -pip install pyodide-build==$PYODIDE_VERSION pyodide-cli - -pyodide build - -ls -ltrh dist - -# The Pyodide js library is needed by build_tools/azure/test_script_pyodide.sh -# to run tests inside Pyodide -npm install pyodide@$PYODIDE_VERSION diff --git a/build_tools/azure/install_setup_conda.sh b/build_tools/azure/install_setup_conda.sh new file mode 100755 index 0000000000000..d09a02cda5a9f --- /dev/null +++ b/build_tools/azure/install_setup_conda.sh @@ -0,0 +1,24 @@ +#!/bin/bash + +set -e +set -x + +if [[ -z "${CONDA}" ]]; then + # In some runners (macOS-13 and macOS-14 in October 2024) conda is not + # installed so we install it ourselves + MINIFORGE_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" + wget ${MINIFORGE_URL} -O miniforge.sh + bash miniforge.sh -b -u -p $HOME/miniforge3 + CONDA="$HOME/miniforge3" +else + # In most runners (in October 2024) conda is installed, + # but in a system folder and we want it user writable + sudo chown -R $USER $CONDA +fi + +# Add conda to the PATH so that it can be used in further Azure CI steps. +# Need set +x for ##vso Azure magic otherwise it may add a quote in the PATH. +# For more details, see https://github.com/microsoft/azure-pipelines-tasks/issues/10331 +set +x +echo "##vso[task.prependpath]$CONDA/bin" +set -x diff --git a/build_tools/azure/posix-docker.yml b/build_tools/azure/posix-docker.yml index b00ca66c378ca..49b0eb5f0f356 100644 --- a/build_tools/azure/posix-docker.yml +++ b/build_tools/azure/posix-docker.yml @@ -131,3 +131,4 @@ jobs: retryCountOnTaskFailure: 5 env: CODECOV_TOKEN: $(CODECOV_TOKEN) + JUNIT_FILE: $(TEST_DIR)/$(JUNITXML) diff --git a/build_tools/azure/posix.yml b/build_tools/azure/posix.yml index 35e5165d22c83..e0f504ba540db 100644 --- a/build_tools/azure/posix.yml +++ b/build_tools/azure/posix.yml @@ -36,11 +36,8 @@ jobs: - bash: $(pyTools.pythonLocation)/bin/python build_tools/azure/get_selected_tests.py displayName: Check selected tests for all random seeds condition: eq(variables['Build.Reason'], 'PullRequest') - - bash: echo "##vso[task.prependpath]$CONDA/bin" - displayName: Add conda to PATH - condition: startsWith(variables['DISTRIB'], 'conda') - - bash: sudo chown -R $USER $CONDA - displayName: Take ownership of conda installation + - bash: build_tools/azure/install_setup_conda.sh + displayName: Install conda if necessary and set it up condition: startsWith(variables['DISTRIB'], 'conda') - task: Cache@2 inputs: @@ -109,3 +106,4 @@ jobs: retryCountOnTaskFailure: 5 env: CODECOV_TOKEN: $(CODECOV_TOKEN) + JUNIT_FILE: $(TEST_DIR)/$(JUNITXML) diff --git a/build_tools/azure/pylatest_conda_forge_mkl_linux-64_conda.lock b/build_tools/azure/pylatest_conda_forge_mkl_linux-64_conda.lock index bf4b0087c662b..9b452e7ecba3d 100644 --- a/build_tools/azure/pylatest_conda_forge_mkl_linux-64_conda.lock +++ b/build_tools/azure/pylatest_conda_forge_mkl_linux-64_conda.lock @@ -1,221 +1,248 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 50fed47bc507d9ee3dbf5ff7a2247cb88944928bd5797e534ebdf8ece2d858ec +# input_hash: 15de7a0d1a0d046ada825ffa5ad3547c790bf903bd5d9b03e7c0e9a6a62c680d @EXPLICIT -https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb -https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_1.conda#33b7851c39c25da14f6a233a8ccbeeca -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406 -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-4_cp311.conda#d786502c97404c94d7d58d258a445a65 -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 +https://conda.anaconda.org/conda-forge/linux-64/libopentelemetry-cpp-headers-1.20.0-ha770c72_0.conda#96806e6c31dc89253daff2134aeb58f3 +https://conda.anaconda.org/conda-forge/linux-64/mkl-include-2024.2.2-ha957f24_16.conda#42b0d14354b5910a9f41e29289914f6b 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coverage - ccache - - pytorch=1.13 + - pytorch - pytorch-cpu - polars - pyarrow - - array-api-compat - array-api-strict + - scipy-doctest diff --git a/build_tools/azure/pylatest_conda_forge_mkl_osx-64_conda.lock b/build_tools/azure/pylatest_conda_forge_mkl_osx-64_conda.lock index 833ce559e02b9..4def307b28f84 100644 --- a/build_tools/azure/pylatest_conda_forge_mkl_osx-64_conda.lock +++ b/build_tools/azure/pylatest_conda_forge_mkl_osx-64_conda.lock @@ -1,129 +1,132 @@ # Generated by conda-lock. # platform: osx-64 -# input_hash: e7c2bc2b07721ef735f30d3b1cf0b2a780b5bf5c138d9d18ad174611bfbd32bf +# input_hash: b4e9eb0fbe1a7a6d067e4f4b43ca9e632309794c2a76d5c254ce023cb2fa2d99 @EXPLICIT -https://conda.anaconda.org/conda-forge/osx-64/bzip2-1.0.8-h10d778d_5.conda#6097a6ca9ada32699b5fc4312dd6ef18 -https://conda.anaconda.org/conda-forge/osx-64/ca-certificates-2024.2.2-h8857fd0_0.conda#f2eacee8c33c43692f1ccfd33d0f50b1 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a/build_tools/azure/pylatest_conda_mkl_no_openmp_environment.yml b/build_tools/azure/pylatest_conda_mkl_no_openmp_environment.yml index 7e85b28b3f6c4..0c2eec344c26b 100644 --- a/build_tools/azure/pylatest_conda_mkl_no_openmp_environment.yml +++ b/build_tools/azure/pylatest_conda_mkl_no_openmp_environment.yml @@ -25,3 +25,4 @@ dependencies: - cython - threadpoolctl - meson-python + - meson diff --git a/build_tools/azure/pylatest_conda_mkl_no_openmp_osx-64_conda.lock b/build_tools/azure/pylatest_conda_mkl_no_openmp_osx-64_conda.lock index 956622fe0008e..ed4af051f10c6 100644 --- a/build_tools/azure/pylatest_conda_mkl_no_openmp_osx-64_conda.lock +++ b/build_tools/azure/pylatest_conda_mkl_no_openmp_osx-64_conda.lock @@ -1,86 +1,82 @@ # Generated by conda-lock. # platform: osx-64 -# input_hash: 33a102d2ccde4e14e315a98b50340349af349f802403dd49589375b2b889f2d3 +# input_hash: 037fecf9454db91c21c8a57ee632e7221447f0bcfd9a5850dfcd6d727a30b086 @EXPLICIT 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-https://repo.anaconda.com/pkgs/main/osx-64/contourpy-1.2.0-py312ha357a0b_0.conda#57d384ad07152375b40a6293f79e3f0c -https://repo.anaconda.com/pkgs/main/osx-64/matplotlib-3.8.4-py312hecd8cb5_0.conda#6886c230c2ec2f47621b5cca4c7d493a -https://repo.anaconda.com/pkgs/main/osx-64/matplotlib-base-3.8.4-py312h7f12edd_0.conda#a4eee14a4dcaa89b306ca33d2d479fa4 +https://repo.anaconda.com/pkgs/main/osx-64/pytest-cov-6.0.0-py312hecd8cb5_0.conda#db697e319a4d1145363246a51eef0352 +https://repo.anaconda.com/pkgs/main/osx-64/pytest-xdist-3.6.1-py312hecd8cb5_0.conda#38df9520774ee82bf143218f1271f936 +https://repo.anaconda.com/pkgs/main/osx-64/bottleneck-1.4.2-py312ha2b695f_0.conda#7efb63b6a5b33829a3b2c7a3efcf53ce +https://repo.anaconda.com/pkgs/main/osx-64/contourpy-1.3.1-py312h1962661_0.conda#41499d3a415721b0514f0cccb8288cb1 +https://repo.anaconda.com/pkgs/main/osx-64/matplotlib-3.10.0-py312hecd8cb5_0.conda#2977e81a7775be7963daf49df981b6e0 +https://repo.anaconda.com/pkgs/main/osx-64/matplotlib-base-3.10.0-py312h919b35b_0.conda#afc11bf311f5921ca4674ebac9592cf8 https://repo.anaconda.com/pkgs/main/osx-64/mkl_fft-1.3.8-py312h6c40b1e_0.conda#d59d01b940493f2b6a84aac922fd0c76 https://repo.anaconda.com/pkgs/main/osx-64/mkl_random-1.2.4-py312ha357a0b_0.conda#c1ea9c8eee79a5af3399f3c31be0e9c6 https://repo.anaconda.com/pkgs/main/osx-64/numpy-1.26.4-py312hac873b0_0.conda#3150bac1e382156f82a153229e1ebd06 https://repo.anaconda.com/pkgs/main/osx-64/numexpr-2.8.7-py312hac873b0_0.conda#6303ba071636ef57fddf69eb6f440ec1 https://repo.anaconda.com/pkgs/main/osx-64/scipy-1.11.4-py312h81688c2_0.conda#7d57b4c21a9261f97fa511e0940c5d93 -https://repo.anaconda.com/pkgs/main/osx-64/pandas-2.2.1-py312he282a81_0.conda#021b70a1e40efb75b89eb8ebdb347132 -https://repo.anaconda.com/pkgs/main/osx-64/pyamg-4.2.3-py312h44cbcf4_0.conda#3bdc7be74087b3a5a83c520a74e1e8eb -# pip cython @ https://files.pythonhosted.org/packages/d5/6d/06c08d75adb98cdf72af18801e193d22580cc86ca553610f430f18ea26b3/Cython-3.0.10-cp312-cp312-macosx_10_9_x86_64.whl#sha256=8f2864ab5fcd27a346f0b50f901ebeb8f60b25a60a575ccfd982e7f3e9674914 -# pip meson @ https://files.pythonhosted.org/packages/33/75/b1a37fa7b2dbca8c0dbb04d5cdd7e2720c8ef6febe41b4a74866350e041c/meson-1.4.0-py3-none-any.whl#sha256=476a458d51fcfa322a6bdc64da5138997c542d08e6b2e49b9fa68c46fd7c4475 -# pip threadpoolctl @ https://files.pythonhosted.org/packages/4b/2c/ffbf7a134b9ab11a67b0cf0726453cedd9c5043a4fe7a35d1cefa9a1bcfb/threadpoolctl-3.5.0-py3-none-any.whl#sha256=56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467 -# pip pyproject-metadata @ https://files.pythonhosted.org/packages/aa/5f/bb5970d3d04173b46c9037109f7f05fc8904ff5be073ee49bb6ff00301bc/pyproject_metadata-0.8.0-py3-none-any.whl#sha256=ad858d448e1d3a1fb408ac5bac9ea7743e7a8bbb472f2693aaa334d2db42f526 -# pip meson-python @ https://files.pythonhosted.org/packages/91/c0/104cb6244c83fe6bc3886f144cc433db0c0c78efac5dc00e409a5a08c87d/meson_python-0.16.0-py3-none-any.whl#sha256=842dc9f5dc29e55fc769ff1b6fe328412fe6c870220fc321060a1d2d395e69e8 +https://repo.anaconda.com/pkgs/main/osx-64/pandas-2.2.3-py312h6d0c2b6_0.conda#84ce5b8ec4a986d13a5df17811f556a2 +https://repo.anaconda.com/pkgs/main/osx-64/pyamg-5.2.1-py312h1962661_0.conda#58881950d4ce74c9302b56961f97a43c +# pip cython @ https://files.pythonhosted.org/packages/e6/6c/3be501a6520a93449b1e7e6f63e598ec56f3b5d1bc7ad14167c72a22ddf7/Cython-3.0.12-cp312-cp312-macosx_10_9_x86_64.whl#sha256=fe030d4a00afb2844f5f70896b7f2a1a0d7da09bf3aa3d884cbe5f73fff5d310 +# pip meson @ https://files.pythonhosted.org/packages/df/d7/f1c8acf0e597d4d07532f519780ee6e11ba285a9b092f18706b4c9118331/meson-1.8.0-py3-none-any.whl#sha256=472b7b25da286447333d32872b82d1c6f1a34024fb8ee017d7308056c25fec1f +# pip threadpoolctl @ https://files.pythonhosted.org/packages/32/d5/f9a850d79b0851d1d4ef6456097579a9005b31fea68726a4ae5f2d82ddd9/threadpoolctl-3.6.0-py3-none-any.whl#sha256=43a0b8fd5a2928500110039e43a5eed8480b918967083ea48dc3ab9f13c4a7fb +# pip pyproject-metadata @ https://files.pythonhosted.org/packages/7e/b1/8e63033b259e0a4e40dd1ec4a9fee17718016845048b43a36ec67d62e6fe/pyproject_metadata-0.9.1-py3-none-any.whl#sha256=ee5efde548c3ed9b75a354fc319d5afd25e9585fa918a34f62f904cc731973ad +# pip meson-python @ https://files.pythonhosted.org/packages/7d/ec/40c0ddd29ef4daa6689a2b9c5ced47d5b58fa54ae149b19e9a97f4979c8c/meson_python-0.17.1-py3-none-any.whl#sha256=30a75c52578ef14aff8392677b09c39346e0a24d2b2c6204b8ed30583c11269c diff --git a/build_tools/azure/pylatest_free_threaded_environment.yml b/build_tools/azure/pylatest_free_threaded_environment.yml new file mode 100644 index 0000000000000..b947f31beb14a --- /dev/null +++ b/build_tools/azure/pylatest_free_threaded_environment.yml @@ -0,0 +1,16 @@ +# 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 +channels: + - conda-forge +dependencies: + - python-freethreading + - numpy + - joblib + - threadpoolctl + - pytest + - pytest-xdist + - ninja + - meson-python + - ccache + - pip diff --git a/build_tools/azure/pylatest_free_threaded_linux-64_conda.lock b/build_tools/azure/pylatest_free_threaded_linux-64_conda.lock new file mode 100644 index 0000000000000..39b5e6021d170 --- /dev/null +++ b/build_tools/azure/pylatest_free_threaded_linux-64_conda.lock @@ -0,0 +1,58 @@ +# Generated by conda-lock. +# platform: linux-64 +# input_hash: a4b2a317ef7733b7244b987f8b6b61126b9e647153cd112ba9565ae8eb5558e8 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.13-5_cp313t.conda#ea4c21b96e8280414d9e243da0ec3201 +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/_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/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/liblzma-5.8.1-hb9d3cd8_0.conda#0e87378639676987af32fee53ba32258 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-h8f9b012_2.conda#a78c856b6dc6bf4ea8daeb9beaaa3fb0 +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/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/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/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/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 +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-31_h59b9bed_openblas.conda#728dbebd0f7a20337218beacffd37916 +https://conda.anaconda.org/conda-forge/linux-64/libhiredis-1.0.2-h2cc385e_0.tar.bz2#b34907d3a81a3cd8095ee83d174c074a +https://conda.anaconda.org/conda-forge/noarch/meson-1.8.0-pyh29332c3_0.conda#8e25221b702272394b86b0f4d7217f77 +https://conda.anaconda.org/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda#58335b26c38bf4a20f399384c33cbcf9 +https://conda.anaconda.org/conda-forge/noarch/pip-25.1.1-pyh145f28c_0.conda#01384ff1639c6330a0924791413b8714 +https://conda.anaconda.org/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_1.conda#e9dcbce5f45f9ee500e728ae58b605b6 +https://conda.anaconda.org/conda-forge/noarch/setuptools-80.1.0-pyhff2d567_0.conda#f6f72d0837c79eaec77661be43e8a691 +https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.6.0-pyhecae5ae_0.conda#9d64911b31d57ca443e9f1e36b04385f +https://conda.anaconda.org/conda-forge/noarch/tomli-2.2.1-pyhd8ed1ab_1.conda#ac944244f1fed2eb49bae07193ae8215 +https://conda.anaconda.org/conda-forge/linux-64/ccache-4.11.3-h80c52d3_0.conda#eb517c6a2b960c3ccb6f1db1005f063a +https://conda.anaconda.org/conda-forge/noarch/joblib-1.5.0-pyhd8ed1ab_0.conda#3d7257f0a61c9aa4ffa3e324a887416b +https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-31_he106b2a_openblas.conda#abb32c727da370c481a1c206f5159ce9 +https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-31_h7ac8fdf_openblas.conda#452b98eafe050ecff932f0ec832dd03f +https://conda.anaconda.org/conda-forge/noarch/pyproject-metadata-0.9.1-pyhd8ed1ab_0.conda#22ae7c6ea81e0c8661ef32168dda929b +https://conda.anaconda.org/conda-forge/noarch/pytest-8.3.5-pyhd8ed1ab_0.conda#c3c9316209dec74a705a36797970c6be +https://conda.anaconda.org/conda-forge/noarch/python-freethreading-3.13.3-h92d6c8b_1.conda#4fa25290aec662a01642ba4b3c0ff5c1 +https://conda.anaconda.org/conda-forge/noarch/meson-python-0.17.1-pyh70fd9c4_1.conda#7a02679229c6c2092571b4c025055440 +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 diff --git a/build_tools/azure/pylatest_pip_openblas_pandas_environment.yml b/build_tools/azure/pylatest_pip_openblas_pandas_environment.yml index adb7add7622e1..6c3da4bb863b4 100644 --- a/build_tools/azure/pylatest_pip_openblas_pandas_environment.yml +++ b/build_tools/azure/pylatest_pip_openblas_pandas_environment.yml @@ -4,7 +4,7 @@ channels: - defaults dependencies: - - python=3.9 + - python - ccache - pip - pip: @@ -27,3 +27,5 @@ dependencies: - numpydoc - lightgbm - scikit-image + - array-api-strict + - scipy-doctest diff --git a/build_tools/azure/pylatest_pip_openblas_pandas_linux-64_conda.lock b/build_tools/azure/pylatest_pip_openblas_pandas_linux-64_conda.lock index fb409d975c5a4..edffbc7d70f46 100644 --- a/build_tools/azure/pylatest_pip_openblas_pandas_linux-64_conda.lock +++ b/build_tools/azure/pylatest_pip_openblas_pandas_linux-64_conda.lock @@ -1,88 +1,91 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 37f8029b6bb116e0d5856093424791a8c1ddc3f493e20fcb5d02cd32d516523d +# input_hash: 830b1d953ebfc9e46b73f639e733ee09b5171952cf987981d569b1d5abd16292 @EXPLICIT https://repo.anaconda.com/pkgs/main/linux-64/_libgcc_mutex-0.1-main.conda#c3473ff8bdb3d124ed5ff11ec380d6f9 -https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2024.3.11-h06a4308_0.conda#08529eb3504712baabcbda266a19feb7 -https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.38-h1181459_1.conda#68eedfd9c06f2b0e6888d8db345b7f5b -https://repo.anaconda.com/pkgs/main/noarch/tzdata-2024a-h04d1e81_0.conda#452af53adae0a5b06eb5d05c707b2f25 +https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2025.2.25-h06a4308_0.conda#495015d24da8ad929e3ae2d18571016d +https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.40-h12ee557_0.conda#ee672b5f635340734f58d618b7bca024 +https://repo.anaconda.com/pkgs/main/linux-64/python_abi-3.13-0_cp313.conda#d4009c49dd2b54ffded7f1365b5f6505 +https://repo.anaconda.com/pkgs/main/noarch/tzdata-2025b-h04d1e81_0.conda#1d027393db3427ab22a02aa44a56f143 https://repo.anaconda.com/pkgs/main/linux-64/libgomp-11.2.0-h1234567_1.conda#b372c0eea9b60732fdae4b817a63c8cd https://repo.anaconda.com/pkgs/main/linux-64/libstdcxx-ng-11.2.0-h1234567_1.conda#57623d10a70e09e1d048c2b2b6f4e2dd https://repo.anaconda.com/pkgs/main/linux-64/_openmp_mutex-5.1-1_gnu.conda#71d281e9c2192cb3fa425655a8defb85 https://repo.anaconda.com/pkgs/main/linux-64/libgcc-ng-11.2.0-h1234567_1.conda#a87728dabf3151fb9cfa990bd2eb0464 +https://repo.anaconda.com/pkgs/main/linux-64/bzip2-1.0.8-h5eee18b_6.conda#f21a3ff51c1b271977f53ce956a69297 +https://repo.anaconda.com/pkgs/main/linux-64/expat-2.7.1-h6a678d5_0.conda#269942a9f3f943e2e5d8a2516a861f7c https://repo.anaconda.com/pkgs/main/linux-64/libffi-3.4.4-h6a678d5_1.conda#70646cc713f0c43926cfdcfe9b695fe0 +https://repo.anaconda.com/pkgs/main/linux-64/libmpdec-4.0.0-h5eee18b_0.conda#feb10f42b1a7b523acbf85461be41a3e +https://repo.anaconda.com/pkgs/main/linux-64/libuuid-1.41.5-h5eee18b_0.conda#4a6a2354414c9080327274aa514e5299 https://repo.anaconda.com/pkgs/main/linux-64/ncurses-6.4-h6a678d5_0.conda#5558eec6e2191741a92f832ea826251c -https://repo.anaconda.com/pkgs/main/linux-64/openssl-3.0.13-h7f8727e_2.conda#0019453c25f5e72129f99236e60febaa -https://repo.anaconda.com/pkgs/main/linux-64/xz-5.4.6-h5eee18b_1.conda#1562802f843297ee776a50b9329597ed +https://repo.anaconda.com/pkgs/main/linux-64/openssl-3.0.16-h5eee18b_0.conda#5875526739afa058cfa84da1fa7a2ef4 +https://repo.anaconda.com/pkgs/main/linux-64/xz-5.6.4-h5eee18b_1.conda#3581505fa450962d631bd82b8616350e https://repo.anaconda.com/pkgs/main/linux-64/zlib-1.2.13-h5eee18b_1.conda#92e42d8310108b0a440fb2e60b2b2a25 https://repo.anaconda.com/pkgs/main/linux-64/ccache-3.7.9-hfe4627d_0.conda#bef6fc681c273bb7bd0c67d1a591365e https://repo.anaconda.com/pkgs/main/linux-64/readline-8.2-h5eee18b_0.conda#be42180685cce6e6b0329201d9f48efb https://repo.anaconda.com/pkgs/main/linux-64/tk-8.6.14-h39e8969_0.conda#78dbc5e3c69143ebc037fc5d5b22e597 https://repo.anaconda.com/pkgs/main/linux-64/sqlite-3.45.3-h5eee18b_0.conda#acf93d6aceb74d6110e20b44cc45939e -https://repo.anaconda.com/pkgs/main/linux-64/python-3.9.19-h955ad1f_1.conda#4b453281859c293c9d577271f3b18a0d -https://repo.anaconda.com/pkgs/main/linux-64/setuptools-69.5.1-py39h06a4308_0.conda#3eb144d481b39c0fbbced789dd9b76b3 -https://repo.anaconda.com/pkgs/main/linux-64/wheel-0.43.0-py39h06a4308_0.conda#40bb60408c7433d767fd8c65b35bc4a0 -https://repo.anaconda.com/pkgs/main/linux-64/pip-24.0-py39h06a4308_0.conda#7f8ce3af15cfecd12e4dda8c5cef5fb7 -# pip alabaster @ https://files.pythonhosted.org/packages/32/34/d4e1c02d3bee589efb5dfa17f88ea08bdb3e3eac12bc475462aec52ed223/alabaster-0.7.16-py3-none-any.whl#sha256=b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92 -# pip babel @ https://files.pythonhosted.org/packages/27/45/377f7e32a5c93d94cd56542349b34efab5ca3f9e2fd5a68c5e93169aa32d/Babel-2.15.0-py3-none-any.whl#sha256=08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb -# pip certifi @ https://files.pythonhosted.org/packages/ba/06/a07f096c664aeb9f01624f858c3add0a4e913d6c96257acb4fce61e7de14/certifi-2024.2.2-py3-none-any.whl#sha256=dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1 -# pip charset-normalizer @ https://files.pythonhosted.org/packages/98/69/5d8751b4b670d623aa7a47bef061d69c279e9f922f6705147983aa76c3ce/charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=b261ccdec7821281dade748d088bb6e9b69e6d15b30652b74cbbac25e280b796 +https://repo.anaconda.com/pkgs/main/linux-64/python-3.13.2-hf623796_100_cp313.conda#bf836f30ac4c16fd3d71c1aaa25da08c +https://repo.anaconda.com/pkgs/main/linux-64/setuptools-78.1.1-py313h06a4308_0.conda#8f8e1c1e3af9d2d371aaa0ee8316ae7c +https://repo.anaconda.com/pkgs/main/linux-64/wheel-0.45.1-py313h06a4308_0.conda#29057e876eedce0e37c2388c138a19f9 +https://repo.anaconda.com/pkgs/main/noarch/pip-25.1-pyhc872135_2.conda#2778327d2a700153fefe0e69438b18e1 +# pip alabaster @ https://files.pythonhosted.org/packages/7e/b3/6b4067be973ae96ba0d615946e314c5ae35f9f993eca561b356540bb0c2b/alabaster-1.0.0-py3-none-any.whl#sha256=fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b +# pip babel @ https://files.pythonhosted.org/packages/b7/b8/3fe70c75fe32afc4bb507f75563d39bc5642255d1d94f1f23604725780bf/babel-2.17.0-py3-none-any.whl#sha256=4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2 +# pip certifi @ https://files.pythonhosted.org/packages/4a/7e/3db2bd1b1f9e95f7cddca6d6e75e2f2bd9f51b1246e546d88addca0106bd/certifi-2025.4.26-py3-none-any.whl#sha256=30350364dfe371162649852c63336a15c70c6510c2ad5015b21c2345311805f3 +# pip charset-normalizer @ https://files.pythonhosted.org/packages/e2/28/ffc026b26f441fc67bd21ab7f03b313ab3fe46714a14b516f931abe1a2d8/charset_normalizer-3.4.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=6c9379d65defcab82d07b2a9dfbfc2e95bc8fe0ebb1b176a3190230a3ef0e07c +# pip coverage @ https://files.pythonhosted.org/packages/cb/74/2f8cc196643b15bc096d60e073691dadb3dca48418f08bc78dd6e899383e/coverage-7.8.0-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=5aaeb00761f985007b38cf463b1d160a14a22c34eb3f6a39d9ad6fc27cb73008 # pip cycler @ https://files.pythonhosted.org/packages/e7/05/c19819d5e3d95294a6f5947fb9b9629efb316b96de511b418c53d245aae6/cycler-0.12.1-py3-none-any.whl#sha256=85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30 -# pip cython @ https://files.pythonhosted.org/packages/a7/f5/3dde4d96076888ceaa981827b098274c2b45ddd4b20d75a8cfaa92b91eec/Cython-3.0.10-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=651a15a8534ebfb9b58cb0b87c269c70984b6f9c88bfe65e4f635f0e3f07dfcd +# pip cython @ https://files.pythonhosted.org/packages/a8/30/7f48207ea13dab46604db0dd388e807d53513ba6ad1c34462892072f8f8c/Cython-3.0.12-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=879ae9023958d63c0675015369384642d0afb9c9d1f3473df9186c42f7a9d265 # pip docutils @ https://files.pythonhosted.org/packages/8f/d7/9322c609343d929e75e7e5e6255e614fcc67572cfd083959cdef3b7aad79/docutils-0.21.2-py3-none-any.whl#sha256=dafca5b9e384f0e419294eb4d2ff9fa826435bf15f15b7bd45723e8ad76811b2 -# pip exceptiongroup @ https://files.pythonhosted.org/packages/01/90/79fe92dd413a9cab314ef5c591b5aa9b9ba787ae4cadab75055b0ae00b33/exceptiongroup-1.2.1-py3-none-any.whl#sha256=5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad # pip execnet @ https://files.pythonhosted.org/packages/43/09/2aea36ff60d16dd8879bdb2f5b3ee0ba8d08cbbdcdfe870e695ce3784385/execnet-2.1.1-py3-none-any.whl#sha256=26dee51f1b80cebd6d0ca8e74dd8745419761d3bef34163928cbebbdc4749fdc -# pip fonttools @ https://files.pythonhosted.org/packages/22/56/8b2ffe792b0a11d481ed797e0c246ee914b86370e317476c84d4fc537d95/fonttools-4.52.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=ee2a8c1101d06cc8fca7851dceb67afd53dd6fc0288bacaa632e647bc5afff58 -# pip idna @ https://files.pythonhosted.org/packages/e5/3e/741d8c82801c347547f8a2a06aa57dbb1992be9e948df2ea0eda2c8b79e8/idna-3.7-py3-none-any.whl#sha256=82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0 +# pip fonttools @ https://files.pythonhosted.org/packages/f8/ad/c25116352f456c0d1287545a7aa24e98987b6d99c5b0456c4bd14321f20f/fonttools-4.57.0-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=4dea5893b58d4637ffa925536462ba626f8a1b9ffbe2f5c272cdf2c6ebadb817 +# pip idna @ https://files.pythonhosted.org/packages/76/c6/c88e154df9c4e1a2a66ccf0005a88dfb2650c1dffb6f5ce603dfbd452ce3/idna-3.10-py3-none-any.whl#sha256=946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3 # pip imagesize @ https://files.pythonhosted.org/packages/ff/62/85c4c919272577931d407be5ba5d71c20f0b616d31a0befe0ae45bb79abd/imagesize-1.4.1-py2.py3-none-any.whl#sha256=0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b -# pip iniconfig @ https://files.pythonhosted.org/packages/ef/a6/62565a6e1cf69e10f5727360368e451d4b7f58beeac6173dc9db836a5b46/iniconfig-2.0.0-py3-none-any.whl#sha256=b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374 -# pip joblib @ https://files.pythonhosted.org/packages/91/29/df4b9b42f2be0b623cbd5e2140cafcaa2bef0759a00b7b70104dcfe2fb51/joblib-1.4.2-py3-none-any.whl#sha256=06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6 -# pip kiwisolver @ https://files.pythonhosted.org/packages/c0/a8/841594f11d0b88d8aeb26991bc4dac38baa909dc58d0c4262a4f7893bcbf/kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=6c3bd3cde54cafb87d74d8db50b909705c62b17c2099b8f2e25b461882e544ff -# pip markupsafe @ https://files.pythonhosted.org/packages/5f/5a/360da85076688755ea0cceb92472923086993e86b5613bbae9fbc14136b0/MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=17b950fccb810b3293638215058e432159d2b71005c74371d784862b7e4683f3 -# pip meson @ https://files.pythonhosted.org/packages/33/75/b1a37fa7b2dbca8c0dbb04d5cdd7e2720c8ef6febe41b4a74866350e041c/meson-1.4.0-py3-none-any.whl#sha256=476a458d51fcfa322a6bdc64da5138997c542d08e6b2e49b9fa68c46fd7c4475 -# pip networkx @ https://files.pythonhosted.org/packages/d5/f0/8fbc882ca80cf077f1b246c0e3c3465f7f415439bdea6b899f6b19f61f70/networkx-3.2.1-py3-none-any.whl#sha256=f18c69adc97877c42332c170849c96cefa91881c99a7cb3e95b7c659ebdc1ec2 -# pip ninja @ https://files.pythonhosted.org/packages/6d/92/8d7aebd4430ab5ff65df2bfee6d5745f95c004284db2d8ca76dcbfd9de47/ninja-1.11.1.1-py2.py3-none-manylinux1_x86_64.manylinux_2_5_x86_64.whl#sha256=84502ec98f02a037a169c4b0d5d86075eaf6afc55e1879003d6cab51ced2ea4b -# pip numpy @ https://files.pythonhosted.org/packages/54/30/c2a907b9443cf42b90c17ad10c1e8fa801975f01cb9764f3f8eb8aea638b/numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=f870204a840a60da0b12273ef34f7051e98c3b5961b61b0c2c1be6dfd64fbcd3 -# pip packaging @ https://files.pythonhosted.org/packages/49/df/1fceb2f8900f8639e278b056416d49134fb8d84c5942ffaa01ad34782422/packaging-24.0-py3-none-any.whl#sha256=2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5 -# pip pillow @ https://files.pythonhosted.org/packages/f5/6d/52e82352670e850f468de9e6bccced4202a09f58e7ea5ecdbf08283d85cb/pillow-10.3.0-cp39-cp39-manylinux_2_28_x86_64.whl#sha256=1dfc94946bc60ea375cc39cff0b8da6c7e5f8fcdc1d946beb8da5c216156ddd8 +# pip 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https://files.pythonhosted.org/packages/d3/6d/45837c5b3d0005a5a9b04729b218a16bf3aa195701c6b33b2cc39ae943b6/matplotlib-3.9.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=81c40af649d19c85f8073e25e5806926986806fa6d54be506fbf02aef47d5a89 -# pip meson-python @ https://files.pythonhosted.org/packages/91/c0/104cb6244c83fe6bc3886f144cc433db0c0c78efac5dc00e409a5a08c87d/meson_python-0.16.0-py3-none-any.whl#sha256=842dc9f5dc29e55fc769ff1b6fe328412fe6c870220fc321060a1d2d395e69e8 -# pip pandas @ https://files.pythonhosted.org/packages/bb/30/f6f1f1ac36250f50c421b1b6af08c35e5a8b5a84385ef928625336b93e6f/pandas-2.2.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=66b479b0bd07204e37583c191535505410daa8df638fd8e75ae1b383851fe921 -# pip pyamg @ https://files.pythonhosted.org/packages/68/a9/aed9f557e7eb779d2cb4fa090663f8540979e0c04dadd16e9a0bdc9632c5/pyamg-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=5817d4567fb240dab4779bb1630bbb3035b3827731fcdaeb9ecc9c8814319995 -# pip pytest-cov @ https://files.pythonhosted.org/packages/78/3a/af5b4fa5961d9a1e6237b530eb87dd04aea6eb83da09d2a4073d81b54ccf/pytest_cov-5.0.0-py3-none-any.whl#sha256=4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652 +# pip requests @ https://files.pythonhosted.org/packages/f9/9b/335f9764261e915ed497fcdeb11df5dfd6f7bf257d4a6a2a686d80da4d54/requests-2.32.3-py3-none-any.whl#sha256=70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6 +# pip scipy @ https://files.pythonhosted.org/packages/03/5a/fc34bf1aa14dc7c0e701691fa8685f3faec80e57d816615e3625f28feb43/scipy-1.15.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=fb530e4794fc8ea76a4a21ccb67dea33e5e0e60f07fc38a49e821e1eae3b71a0 +# pip tifffile @ https://files.pythonhosted.org/packages/6e/be/10d23cfd4078fbec6aba768a357eff9e70c0b6d2a07398425985c524ad2a/tifffile-2025.3.30-py3-none-any.whl#sha256=0ed6eee7b66771db2d1bfc42262a51b01887505d35539daef118f4ff8c0f629c +# pip lightgbm @ https://files.pythonhosted.org/packages/42/86/dabda8fbcb1b00bcfb0003c3776e8ade1aa7b413dff0a2c08f457dace22f/lightgbm-4.6.0-py3-none-manylinux_2_28_x86_64.whl#sha256=cb19b5afea55b5b61cbb2131095f50538bd608a00655f23ad5d25ae3e3bf1c8d +# pip matplotlib @ https://files.pythonhosted.org/packages/51/d0/2bc4368abf766203e548dc7ab57cf7e9c621f1a3c72b516cc7715347b179/matplotlib-3.10.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=7e496c01441be4c7d5f96d4e40f7fca06e20dcb40e44c8daa2e740e1757ad9e6 +# pip meson-python @ https://files.pythonhosted.org/packages/7d/ec/40c0ddd29ef4daa6689a2b9c5ced47d5b58fa54ae149b19e9a97f4979c8c/meson_python-0.17.1-py3-none-any.whl#sha256=30a75c52578ef14aff8392677b09c39346e0a24d2b2c6204b8ed30583c11269c +# pip pandas @ https://files.pythonhosted.org/packages/e8/31/aa8da88ca0eadbabd0a639788a6da13bb2ff6edbbb9f29aa786450a30a91/pandas-2.2.3-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=f3a255b2c19987fbbe62a9dfd6cff7ff2aa9ccab3fc75218fd4b7530f01efa24 +# pip pyamg @ https://files.pythonhosted.org/packages/cd/a7/0df731cbfb09e73979a1a032fc7bc5be0eba617d798b998a0f887afe8ade/pyamg-5.2.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=6999b351ab969c79faacb81faa74c0fa9682feeff3954979212872a3ee40c298 +# pip pytest-cov @ https://files.pythonhosted.org/packages/28/d0/def53b4a790cfb21483016430ed828f64830dd981ebe1089971cd10cab25/pytest_cov-6.1.1-py3-none-any.whl#sha256=bddf29ed2d0ab6f4df17b4c55b0a657287db8684af9c42ea546b21b1041b3dde # pip pytest-xdist @ https://files.pythonhosted.org/packages/6d/82/1d96bf03ee4c0fdc3c0cbe61470070e659ca78dc0086fb88b66c185e2449/pytest_xdist-3.6.1-py3-none-any.whl#sha256=9ed4adfb68a016610848639bb7e02c9352d5d9f03d04809919e2dafc3be4cca7 -# pip scikit-image @ https://files.pythonhosted.org/packages/a3/7e/4cd853a855ac34b4ef3ef6a5c3d1c2e96eaca1154fc6be75db55ffa87393/scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=3b7a6c89e8d6252332121b58f50e1625c35f7d6a85489c0b6b7ee4f5155d547a -# pip sphinx @ https://files.pythonhosted.org/packages/b4/fa/130c32ed94cf270e3d0b9ded16fb7b2c8fea86fa7263c29a696a30c1dde7/sphinx-7.3.7-py3-none-any.whl#sha256=413f75440be4cacf328f580b4274ada4565fb2187d696a84970c23f77b64d8c3 -# pip numpydoc @ https://files.pythonhosted.org/packages/f0/fa/dcfe0f65660661db757ee9ebd84e170ff98edd5d80235f62457d9088f85f/numpydoc-1.7.0-py3-none-any.whl#sha256=5a56419d931310d79a06cfc2a126d1558700feeb9b4f3d8dcae1a8134be829c9 +# pip scikit-image @ https://files.pythonhosted.org/packages/cd/9b/c3da56a145f52cd61a68b8465d6a29d9503bc45bc993bb45e84371c97d94/scikit_image-0.25.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=b8abd3c805ce6944b941cfed0406d88faeb19bab3ed3d4b50187af55cf24d147 +# pip scipy-doctest @ https://files.pythonhosted.org/packages/76/eb/668949f884d5fe8a0d231dcba42c02e7b84626b35ca9072d6283c3aae773/scipy_doctest-1.7.1-py3-none-any.whl#sha256=dece106ec5ac8c595cc6372480d724e68c684450124dd0ddeb6be487ad62b365 +# pip sphinx @ https://files.pythonhosted.org/packages/2f/72/9a437a9dc5393c0eabba447bdb6233a7b02bb23e84975f17ad9a9ca86677/sphinx-8.3.0-py3-none-any.whl#sha256=bd8fcf35ab2c4240b01c74a411c948350a3aebd6aa175579363754ed380d350a +# pip numpydoc @ https://files.pythonhosted.org/packages/6c/45/56d99ba9366476cd8548527667f01869279cedb9e66b28eb4dfb27701679/numpydoc-1.8.0-py3-none-any.whl#sha256=72024c7fd5e17375dec3608a27c03303e8ad00c81292667955c6fea7a3ccf541 diff --git a/build_tools/azure/pylatest_pip_scipy_dev_linux-64_conda.lock b/build_tools/azure/pylatest_pip_scipy_dev_linux-64_conda.lock index c7212167a0b5e..068aee47c99a3 100644 --- a/build_tools/azure/pylatest_pip_scipy_dev_linux-64_conda.lock +++ b/build_tools/azure/pylatest_pip_scipy_dev_linux-64_conda.lock @@ -1,67 +1,70 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 8a4a203136d97ff3b2c8657fce2dd2228215bfbf9c1cfbe271e401f934bdf1a7 +# input_hash: 45bccf0e77c6967a2f49b8c304ef02337f7bd84c59e63221f8c0cb0e75dfe269 @EXPLICIT https://repo.anaconda.com/pkgs/main/linux-64/_libgcc_mutex-0.1-main.conda#c3473ff8bdb3d124ed5ff11ec380d6f9 -https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2024.3.11-h06a4308_0.conda#08529eb3504712baabcbda266a19feb7 -https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.38-h1181459_1.conda#68eedfd9c06f2b0e6888d8db345b7f5b -https://repo.anaconda.com/pkgs/main/noarch/tzdata-2024a-h04d1e81_0.conda#452af53adae0a5b06eb5d05c707b2f25 +https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2025.2.25-h06a4308_0.conda#495015d24da8ad929e3ae2d18571016d +https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.40-h12ee557_0.conda#ee672b5f635340734f58d618b7bca024 +https://repo.anaconda.com/pkgs/main/linux-64/python_abi-3.13-0_cp313.conda#d4009c49dd2b54ffded7f1365b5f6505 +https://repo.anaconda.com/pkgs/main/noarch/tzdata-2025b-h04d1e81_0.conda#1d027393db3427ab22a02aa44a56f143 https://repo.anaconda.com/pkgs/main/linux-64/libgomp-11.2.0-h1234567_1.conda#b372c0eea9b60732fdae4b817a63c8cd https://repo.anaconda.com/pkgs/main/linux-64/libstdcxx-ng-11.2.0-h1234567_1.conda#57623d10a70e09e1d048c2b2b6f4e2dd https://repo.anaconda.com/pkgs/main/linux-64/_openmp_mutex-5.1-1_gnu.conda#71d281e9c2192cb3fa425655a8defb85 https://repo.anaconda.com/pkgs/main/linux-64/libgcc-ng-11.2.0-h1234567_1.conda#a87728dabf3151fb9cfa990bd2eb0464 https://repo.anaconda.com/pkgs/main/linux-64/bzip2-1.0.8-h5eee18b_6.conda#f21a3ff51c1b271977f53ce956a69297 -https://repo.anaconda.com/pkgs/main/linux-64/expat-2.6.2-h6a678d5_0.conda#55049db2772dae035f6b8a95f72b5970 +https://repo.anaconda.com/pkgs/main/linux-64/expat-2.7.1-h6a678d5_0.conda#269942a9f3f943e2e5d8a2516a861f7c https://repo.anaconda.com/pkgs/main/linux-64/libffi-3.4.4-h6a678d5_1.conda#70646cc713f0c43926cfdcfe9b695fe0 +https://repo.anaconda.com/pkgs/main/linux-64/libmpdec-4.0.0-h5eee18b_0.conda#feb10f42b1a7b523acbf85461be41a3e https://repo.anaconda.com/pkgs/main/linux-64/libuuid-1.41.5-h5eee18b_0.conda#4a6a2354414c9080327274aa514e5299 https://repo.anaconda.com/pkgs/main/linux-64/ncurses-6.4-h6a678d5_0.conda#5558eec6e2191741a92f832ea826251c -https://repo.anaconda.com/pkgs/main/linux-64/openssl-3.0.13-h7f8727e_2.conda#0019453c25f5e72129f99236e60febaa -https://repo.anaconda.com/pkgs/main/linux-64/xz-5.4.6-h5eee18b_1.conda#1562802f843297ee776a50b9329597ed +https://repo.anaconda.com/pkgs/main/linux-64/openssl-3.0.16-h5eee18b_0.conda#5875526739afa058cfa84da1fa7a2ef4 +https://repo.anaconda.com/pkgs/main/linux-64/xz-5.6.4-h5eee18b_1.conda#3581505fa450962d631bd82b8616350e https://repo.anaconda.com/pkgs/main/linux-64/zlib-1.2.13-h5eee18b_1.conda#92e42d8310108b0a440fb2e60b2b2a25 https://repo.anaconda.com/pkgs/main/linux-64/ccache-3.7.9-hfe4627d_0.conda#bef6fc681c273bb7bd0c67d1a591365e https://repo.anaconda.com/pkgs/main/linux-64/readline-8.2-h5eee18b_0.conda#be42180685cce6e6b0329201d9f48efb https://repo.anaconda.com/pkgs/main/linux-64/tk-8.6.14-h39e8969_0.conda#78dbc5e3c69143ebc037fc5d5b22e597 https://repo.anaconda.com/pkgs/main/linux-64/sqlite-3.45.3-h5eee18b_0.conda#acf93d6aceb74d6110e20b44cc45939e -https://repo.anaconda.com/pkgs/main/linux-64/python-3.12.3-h996f2a0_1.conda#0e22ed7e6df024e4f7467e75c8575301 -https://repo.anaconda.com/pkgs/main/linux-64/setuptools-69.5.1-py312h06a4308_0.conda#ce85d9a864a73e0b12d31a97733c9fca -https://repo.anaconda.com/pkgs/main/linux-64/wheel-0.43.0-py312h06a4308_0.conda#18d5f3b68a175c72576876db4afc9e9e -https://repo.anaconda.com/pkgs/main/linux-64/pip-24.0-py312h06a4308_0.conda#6d9697bb8b9f3212be10b3b8e01a12b9 -# pip alabaster @ https://files.pythonhosted.org/packages/32/34/d4e1c02d3bee589efb5dfa17f88ea08bdb3e3eac12bc475462aec52ed223/alabaster-0.7.16-py3-none-any.whl#sha256=b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92 -# pip babel @ https://files.pythonhosted.org/packages/27/45/377f7e32a5c93d94cd56542349b34efab5ca3f9e2fd5a68c5e93169aa32d/Babel-2.15.0-py3-none-any.whl#sha256=08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb -# pip certifi @ https://files.pythonhosted.org/packages/5b/11/1e78951465b4a225519b8c3ad29769c49e0d8d157a070f681d5b6d64737f/certifi-2024.6.2-py3-none-any.whl#sha256=ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56 -# pip charset-normalizer @ https://files.pythonhosted.org/packages/ee/fb/14d30eb4956408ee3ae09ad34299131fb383c47df355ddb428a7331cfa1e/charset_normalizer-3.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=90d558489962fd4918143277a773316e56c72da56ec7aa3dc3dbbe20fdfed15b -# pip coverage @ https://files.pythonhosted.org/packages/0e/39/c44111cfc5e40fc1681a41b96911fba6560b51172b59c204b08b75d58495/coverage-7.5.3-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=b1196e13c45e327d6cd0b6e471530a1882f1017eb83c6229fc613cd1a11b53cd +https://repo.anaconda.com/pkgs/main/linux-64/python-3.13.2-hf623796_100_cp313.conda#bf836f30ac4c16fd3d71c1aaa25da08c +https://repo.anaconda.com/pkgs/main/linux-64/setuptools-78.1.1-py313h06a4308_0.conda#8f8e1c1e3af9d2d371aaa0ee8316ae7c +https://repo.anaconda.com/pkgs/main/linux-64/wheel-0.45.1-py313h06a4308_0.conda#29057e876eedce0e37c2388c138a19f9 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https://files.pythonhosted.org/packages/f0/fa/dcfe0f65660661db757ee9ebd84e170ff98edd5d80235f62457d9088f85f/numpydoc-1.7.0-py3-none-any.whl#sha256=5a56419d931310d79a06cfc2a126d1558700feeb9b4f3d8dcae1a8134be829c9 +# pip sphinx @ https://files.pythonhosted.org/packages/2f/72/9a437a9dc5393c0eabba447bdb6233a7b02bb23e84975f17ad9a9ca86677/sphinx-8.3.0-py3-none-any.whl#sha256=bd8fcf35ab2c4240b01c74a411c948350a3aebd6aa175579363754ed380d350a +# pip numpydoc @ https://files.pythonhosted.org/packages/6c/45/56d99ba9366476cd8548527667f01869279cedb9e66b28eb4dfb27701679/numpydoc-1.8.0-py3-none-any.whl#sha256=72024c7fd5e17375dec3608a27c03303e8ad00c81292667955c6fea7a3ccf541 diff --git a/build_tools/azure/pymin_conda_defaults_openblas_linux-64_conda.lock b/build_tools/azure/pymin_conda_defaults_openblas_linux-64_conda.lock deleted file mode 100644 index deb9f11010bd9..0000000000000 --- a/build_tools/azure/pymin_conda_defaults_openblas_linux-64_conda.lock +++ /dev/null @@ -1,99 +0,0 @@ -# Generated by 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-https://repo.anaconda.com/pkgs/main/linux-64/libgomp-11.2.0-h1234567_1.conda#b372c0eea9b60732fdae4b817a63c8cd -https://repo.anaconda.com/pkgs/main/linux-64/libstdcxx-ng-11.2.0-h1234567_1.conda#57623d10a70e09e1d048c2b2b6f4e2dd -https://repo.anaconda.com/pkgs/main/linux-64/_openmp_mutex-5.1-1_gnu.conda#71d281e9c2192cb3fa425655a8defb85 -https://repo.anaconda.com/pkgs/main/linux-64/libgcc-ng-11.2.0-h1234567_1.conda#a87728dabf3151fb9cfa990bd2eb0464 -https://repo.anaconda.com/pkgs/main/linux-64/bzip2-1.0.8-h5eee18b_6.conda#f21a3ff51c1b271977f53ce956a69297 -https://repo.anaconda.com/pkgs/main/linux-64/expat-2.6.2-h6a678d5_0.conda#55049db2772dae035f6b8a95f72b5970 -https://repo.anaconda.com/pkgs/main/linux-64/fftw-3.3.9-h5eee18b_2.conda#db1df41113accc18ec59a99f1631bfcd -https://repo.anaconda.com/pkgs/main/linux-64/icu-73.1-h6a678d5_0.conda#6d09df641fc23f7d277a04dc7ea32dd4 -https://repo.anaconda.com/pkgs/main/linux-64/jpeg-9e-h5eee18b_1.conda#ac373800fda872108412d1ccfe3fa572 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-https://repo.anaconda.com/pkgs/main/linux-64/ncurses-6.4-h6a678d5_0.conda#5558eec6e2191741a92f832ea826251c -https://repo.anaconda.com/pkgs/main/linux-64/openssl-3.0.13-h7f8727e_2.conda#0019453c25f5e72129f99236e60febaa -https://repo.anaconda.com/pkgs/main/linux-64/xz-5.4.6-h5eee18b_1.conda#1562802f843297ee776a50b9329597ed -https://repo.anaconda.com/pkgs/main/linux-64/zlib-1.2.13-h5eee18b_1.conda#92e42d8310108b0a440fb2e60b2b2a25 -https://repo.anaconda.com/pkgs/main/linux-64/ccache-3.7.9-hfe4627d_0.conda#bef6fc681c273bb7bd0c67d1a591365e -https://repo.anaconda.com/pkgs/main/linux-64/libcups-2.4.2-h2d74bed_1.conda#3f265c2172a9e8c90a74037b6fa13685 -https://repo.anaconda.com/pkgs/main/linux-64/libedit-3.1.20230828-h5eee18b_0.conda#850eb5a9d2d7d3c66cce12e84406ca08 -https://repo.anaconda.com/pkgs/main/linux-64/libllvm14-14.0.6-hdb19cb5_3.conda#aefea2b45cf32f12b4f1ffaa70aa3201 -https://repo.anaconda.com/pkgs/main/linux-64/libpng-1.6.39-h5eee18b_0.conda#f6aee38184512eb05b06c2e94d39ab22 -https://repo.anaconda.com/pkgs/main/linux-64/libxml2-2.10.4-hfdd30dd_2.conda#ff7a0e3b92afb3c99b82c9f0ba8b5670 -https://repo.anaconda.com/pkgs/main/linux-64/pcre2-10.42-hebb0a14_1.conda#727e15c3cfa02b032da4eb0c1123e977 -https://repo.anaconda.com/pkgs/main/linux-64/readline-8.2-h5eee18b_0.conda#be42180685cce6e6b0329201d9f48efb -https://repo.anaconda.com/pkgs/main/linux-64/tk-8.6.14-h39e8969_0.conda#78dbc5e3c69143ebc037fc5d5b22e597 -https://repo.anaconda.com/pkgs/main/linux-64/zstd-1.5.5-hc292b87_2.conda#3b7fe809e5b429b4f90fe064842a2370 -https://repo.anaconda.com/pkgs/main/linux-64/freetype-2.12.1-h4a9f257_0.conda#bdc7b5952e9c5dca01bc2f4ccef2f974 -https://repo.anaconda.com/pkgs/main/linux-64/krb5-1.20.1-h143b758_1.conda#cf1accc86321fa25d6b978cc748039ae -https://repo.anaconda.com/pkgs/main/linux-64/libclang13-14.0.6-default_he11475f_1.conda#44890feda1cf51639d9c94afbacce011 -https://repo.anaconda.com/pkgs/main/linux-64/libglib-2.78.4-hdc74915_0.conda#2f6d27741e931d5b6ba56e1a1312aaf0 -https://repo.anaconda.com/pkgs/main/linux-64/libtiff-4.5.1-h6a678d5_0.conda#235a671f74f0c4ecad9f9b3b107e3566 -https://repo.anaconda.com/pkgs/main/linux-64/libxkbcommon-1.0.1-h5eee18b_1.conda#888b2e8f1bbf21017c503826e2d24b50 -https://repo.anaconda.com/pkgs/main/linux-64/sqlite-3.45.3-h5eee18b_0.conda#acf93d6aceb74d6110e20b44cc45939e -https://repo.anaconda.com/pkgs/main/linux-64/cyrus-sasl-2.1.28-h52b45da_1.conda#d634af1577e4008f9228ae96ce671c44 -https://repo.anaconda.com/pkgs/main/linux-64/fontconfig-2.14.1-h4c34cd2_2.conda#f0b472f5b544f8d57beb09ed4a2932e1 -https://repo.anaconda.com/pkgs/main/linux-64/glib-tools-2.78.4-h6a678d5_0.conda#3dbe6227cd59818dca9afb75ccb70708 -https://repo.anaconda.com/pkgs/main/linux-64/lcms2-2.12-h3be6417_0.conda#719db47afba9f6586eecb5eacac70bff -https://repo.anaconda.com/pkgs/main/linux-64/libclang-14.0.6-default_hc6dbbc7_1.conda#8f12583c4027b2861cff470f6b8837c4 -https://repo.anaconda.com/pkgs/main/linux-64/libpq-12.17-hdbd6064_0.conda#6bed363e25859faff66bf546a11c10e8 -https://repo.anaconda.com/pkgs/main/linux-64/openjpeg-2.4.0-h3ad879b_0.conda#86baecb47ecaa7f7ff2657a1f03b90c9 -https://repo.anaconda.com/pkgs/main/linux-64/python-3.9.19-h955ad1f_1.conda#4b453281859c293c9d577271f3b18a0d -https://repo.anaconda.com/pkgs/main/linux-64/certifi-2024.2.2-py39h06a4308_0.conda#2bc1db9166ecbb968f61252e6f08c2ce -https://repo.anaconda.com/pkgs/main/noarch/cycler-0.11.0-pyhd3eb1b0_0.conda#f5e365d2cdb66d547eb8c3ab93843aab -https://repo.anaconda.com/pkgs/main/linux-64/cython-3.0.10-py39h5eee18b_0.conda#1419a658ed2b4d5c3ac1964f33143b64 -https://repo.anaconda.com/pkgs/main/linux-64/exceptiongroup-1.2.0-py39h06a4308_0.conda#960e2cb83ac5134df8e593a130aa11af -https://repo.anaconda.com/pkgs/main/noarch/execnet-1.9.0-pyhd3eb1b0_0.conda#f895937671af67cebb8af617494b3513 -https://repo.anaconda.com/pkgs/main/linux-64/glib-2.78.4-h6a678d5_0.conda#045ff487547f7b2b7ff01648681b8ebe -https://repo.anaconda.com/pkgs/main/noarch/iniconfig-1.1.1-pyhd3eb1b0_0.tar.bz2#e40edff2c5708f342cef43c7f280c507 -https://repo.anaconda.com/pkgs/main/linux-64/joblib-1.2.0-py39h06a4308_0.conda#ac1f5687d70aa1128cbecb26bc9e559d -https://repo.anaconda.com/pkgs/main/linux-64/kiwisolver-1.4.4-py39h6a678d5_0.conda#3d57aedbfbd054ce57fb3c1e4448828c -https://repo.anaconda.com/pkgs/main/linux-64/mysql-5.7.24-h721c034_2.conda#dfc19ca2466d275c4c1f73b62c57f37b -https://repo.anaconda.com/pkgs/main/linux-64/numpy-base-1.21.6-py39h375b286_1.conda#0061d9193658774ab79fc85d143a94fc -https://repo.anaconda.com/pkgs/main/linux-64/packaging-23.2-py39h06a4308_0.conda#b3f88f45f31bde016e49be3e941e5272 -https://repo.anaconda.com/pkgs/main/linux-64/pillow-10.3.0-py39h5eee18b_0.conda#b346d6c71267c1553b6c18d3db5fdf6d -https://repo.anaconda.com/pkgs/main/linux-64/pluggy-1.0.0-py39h06a4308_1.conda#fb4fed11ed43cf727dbd51883cc1d9fa -https://repo.anaconda.com/pkgs/main/linux-64/ply-3.11-py39h06a4308_0.conda#6c89bf6d2fdf6d24126e34cb83fd10f1 -https://repo.anaconda.com/pkgs/main/linux-64/pyparsing-3.0.9-py39h06a4308_0.conda#3a0537468e59760404f63b4f04369828 -https://repo.anaconda.com/pkgs/main/linux-64/pyqt5-sip-12.13.0-py39h5eee18b_0.conda#256840c3841b52346ea5743be8490ede -https://repo.anaconda.com/pkgs/main/linux-64/setuptools-69.5.1-py39h06a4308_0.conda#3eb144d481b39c0fbbced789dd9b76b3 -https://repo.anaconda.com/pkgs/main/noarch/six-1.16.0-pyhd3eb1b0_1.conda#34586824d411d36af2fa40e799c172d0 -https://repo.anaconda.com/pkgs/main/noarch/toml-0.10.2-pyhd3eb1b0_0.conda#cda05f5f6d8509529d1a2743288d197a -https://repo.anaconda.com/pkgs/main/linux-64/tomli-2.0.1-py39h06a4308_0.conda#b06dffe7ddca2645ed72f5116f0a087d -https://repo.anaconda.com/pkgs/main/linux-64/tornado-6.3.3-py39h5eee18b_0.conda#9c4bd985bb8adcd12f47e790e95a9333 -https://repo.anaconda.com/pkgs/main/linux-64/wheel-0.43.0-py39h06a4308_0.conda#40bb60408c7433d767fd8c65b35bc4a0 -https://repo.anaconda.com/pkgs/main/linux-64/coverage-7.2.2-py39h5eee18b_0.conda#e9da151b7e1f56be2cb569c65949a1d2 -https://repo.anaconda.com/pkgs/main/linux-64/dbus-1.13.18-hb2f20db_0.conda#6a6a6f1391f807847404344489ef6cf4 -https://repo.anaconda.com/pkgs/main/linux-64/gstreamer-1.14.1-h5eee18b_1.conda#f2f26e6f869b5d87f41bd059fae47c3e -https://repo.anaconda.com/pkgs/main/linux-64/numpy-1.21.6-py39hac523dd_1.conda#f379f92039f666828a193fadd18c9819 -https://repo.anaconda.com/pkgs/main/linux-64/pip-24.0-py39h06a4308_0.conda#7f8ce3af15cfecd12e4dda8c5cef5fb7 -https://repo.anaconda.com/pkgs/main/linux-64/pytest-7.4.0-py39h06a4308_0.conda#99d92a7a39f7e615de84f8cc5606c49a -https://repo.anaconda.com/pkgs/main/linux-64/python-dateutil-2.9.0post0-py39h06a4308_2.conda#d6566c6d6a0140e45f22787ae58ed6e8 -https://repo.anaconda.com/pkgs/main/linux-64/sip-6.7.12-py39h6a678d5_0.conda#6988a3e12fcacfedcac523c1e4c3167c -https://repo.anaconda.com/pkgs/main/linux-64/gst-plugins-base-1.14.1-h6a678d5_1.conda#afd9cbe949d670d24cc0a007aaec1fe1 -https://repo.anaconda.com/pkgs/main/linux-64/matplotlib-base-3.3.4-py39h62a2d02_0.conda#dbab28222c740af8e21a3e5e2882c178 -https://repo.anaconda.com/pkgs/main/linux-64/pytest-cov-4.1.0-py39h06a4308_1.conda#8f41fce21670b120bf7fa8a7883380d9 -https://repo.anaconda.com/pkgs/main/linux-64/pytest-xdist-3.5.0-py39h06a4308_0.conda#e1d7ffcb1ee2ed9a84800f5c4bbbd7ae -https://repo.anaconda.com/pkgs/main/linux-64/scipy-1.7.3-py39hf838250_2.conda#0667ea5ac14d35e26da19a0f068739da -https://repo.anaconda.com/pkgs/main/linux-64/pyamg-4.2.3-py39h79cecc1_0.conda#afc634da8b81dc504179d53d334e6e55 -https://repo.anaconda.com/pkgs/main/linux-64/qt-main-5.15.2-h53bd1ea_10.conda#bd0c79e82df6323f638bdcb871891b61 -https://repo.anaconda.com/pkgs/main/linux-64/pyqt-5.15.10-py39h6a678d5_0.conda#52da5ff9b1144b078d2f41bab0b213f2 -https://repo.anaconda.com/pkgs/main/linux-64/matplotlib-3.3.4-py39h06a4308_0.conda#384fc5e01ebfcf30e7161119d3029b5a -# pip threadpoolctl @ https://files.pythonhosted.org/packages/61/cf/6e354304bcb9c6413c4e02a747b600061c21d38ba51e7e544ac7bc66aecc/threadpoolctl-3.1.0-py3-none-any.whl#sha256=8b99adda265feb6773280df41eece7b2e6561b772d21ffd52e372f999024907b diff --git a/build_tools/azure/pymin_conda_forge_mkl_environment.yml b/build_tools/azure/pymin_conda_forge_mkl_environment.yml index a219e4b3daa8f..fe6ce91950e4a 100644 --- a/build_tools/azure/pymin_conda_forge_mkl_environment.yml +++ b/build_tools/azure/pymin_conda_forge_mkl_environment.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - - python=3.9 + - python=3.10 - numpy - blas[build=mkl] - scipy diff --git a/build_tools/azure/pymin_conda_forge_mkl_win-64_conda.lock b/build_tools/azure/pymin_conda_forge_mkl_win-64_conda.lock index f4c2f51b1ea88..051a5041f1138 100644 --- a/build_tools/azure/pymin_conda_forge_mkl_win-64_conda.lock +++ b/build_tools/azure/pymin_conda_forge_mkl_win-64_conda.lock @@ -1,118 +1,117 @@ # Generated by conda-lock. # platform: win-64 -# input_hash: ea607aaeb7b1d1f8a1f821a9f505b3601083a218ec4763e2d72d3d3d800e718c +# input_hash: b3869076628274fd49d96cadc2692c963f26cbed79ec7498ecbfd50011a55e67 @EXPLICIT -https://conda.anaconda.org/conda-forge/win-64/ca-certificates-2024.2.2-h56e8100_0.conda#63da060240ab8087b60d1357051ea7d6 -https://conda.anaconda.org/conda-forge/win-64/intel-openmp-2024.1.0-h57928b3_966.conda#35d7ea07ad6c878bd7240d2d6c1b8657 -https://conda.anaconda.org/conda-forge/win-64/mkl-include-2024.1.0-h66d3029_692.conda#60233966dc7c0261c9a443120b43c477 -https://conda.anaconda.org/conda-forge/win-64/msys2-conda-epoch-20160418-1.tar.bz2#b0309b72560df66f71a9d5e34a5efdfa -https://conda.anaconda.org/conda-forge/win-64/python_abi-3.9-4_cp39.conda#948b0d93d4ab1372d8fd45e1560afd47 -https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/win-64/ucrt-10.0.22621.0-h57928b3_0.tar.bz2#72608f6cd3e5898229c3ea16deb1ac43 -https://conda.anaconda.org/conda-forge/win-64/m2w64-gmp-6.1.0-2.tar.bz2#53a1c73e1e3d185516d7e3af177596d9 -https://conda.anaconda.org/conda-forge/win-64/m2w64-libwinpthread-git-5.0.0.4634.697f757-2.tar.bz2#774130a326dee16f1ceb05cc687ee4f0 -https://conda.anaconda.org/conda-forge/win-64/vc14_runtime-14.38.33135-h835141b_20.conda#e971b35a5765862fabc4ba6e5ddf9470 -https://conda.anaconda.org/conda-forge/win-64/m2w64-gcc-libs-core-5.3.0-7.tar.bz2#4289d80fb4d272f1f3b56cfe87ac90bd -https://conda.anaconda.org/conda-forge/win-64/vc-14.3-ha32ba9b_20.conda#2abfb5cb1b9d41a50f765d60f0be563d -https://conda.anaconda.org/conda-forge/win-64/vs2015_runtime-14.38.33135-h22015db_20.conda#bb4f5ab332e46e1b022d8842e72905b1 -https://conda.anaconda.org/conda-forge/win-64/bzip2-1.0.8-hcfcfb64_5.conda#26eb8ca6ea332b675e11704cce84a3be -https://conda.anaconda.org/conda-forge/win-64/icu-73.2-h63175ca_0.conda#0f47d9e3192d9e09ae300da0d28e0f56 -https://conda.anaconda.org/conda-forge/win-64/lerc-4.0.0-h63175ca_0.tar.bz2#1900cb3cab5055833cfddb0ba233b074 -https://conda.anaconda.org/conda-forge/win-64/libbrotlicommon-1.1.0-hcfcfb64_1.conda#f77f319fb82980166569e1280d5b2864 -https://conda.anaconda.org/conda-forge/win-64/libdeflate-1.20-hcfcfb64_0.conda#b12b5bde5eb201a1df75e49320cc938a -https://conda.anaconda.org/conda-forge/win-64/libffi-3.4.2-h8ffe710_5.tar.bz2#2c96d1b6915b408893f9472569dee135 -https://conda.anaconda.org/conda-forge/win-64/libiconv-1.17-hcfcfb64_2.conda#e1eb10b1cca179f2baa3601e4efc8712 -https://conda.anaconda.org/conda-forge/win-64/libjpeg-turbo-3.0.0-hcfcfb64_1.conda#3f1b948619c45b1ca714d60c7389092c -https://conda.anaconda.org/conda-forge/win-64/libogg-1.3.4-h8ffe710_1.tar.bz2#04286d905a0dcb7f7d4a12bdfe02516d -https://conda.anaconda.org/conda-forge/win-64/libsqlite-3.45.3-hcfcfb64_0.conda#73f5dc8e2d55d9a1e14b11f49c3b4a28 -https://conda.anaconda.org/conda-forge/win-64/libwebp-base-1.4.0-hcfcfb64_0.conda#abd61d0ab127ec5cd68f62c2969e6f34 -https://conda.anaconda.org/conda-forge/win-64/libzlib-1.2.13-hcfcfb64_5.conda#5fdb9c6a113b6b6cb5e517fd972d5f41 -https://conda.anaconda.org/conda-forge/win-64/m2w64-gcc-libgfortran-5.3.0-6.tar.bz2#066552ac6b907ec6d72c0ddab29050dc -https://conda.anaconda.org/conda-forge/win-64/ninja-1.12.1-hc790b64_0.conda#a557dde55343e03c68cd7e29e7f87279 -https://conda.anaconda.org/conda-forge/win-64/openssl-3.3.0-h2466b09_3.conda#d7fec5d3bb8fc0c8e266bf1ad350cec5 -https://conda.anaconda.org/conda-forge/win-64/pthreads-win32-2.9.1-hfa6e2cd_3.tar.bz2#e2da8758d7d51ff6aa78a14dfb9dbed4 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 +https://conda.anaconda.org/conda-forge/win-64/intel-openmp-2024.2.1-h57928b3_1083.conda#2d89243bfb53652c182a7c73182cce4f +https://conda.anaconda.org/conda-forge/win-64/mkl-include-2024.2.2-h66d3029_15.conda#e2f516189b44b6e042199d13e7015361 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a/build_tools/azure/pymin_conda_defaults_openblas_environment.yml +++ b/build_tools/azure/pymin_conda_forge_openblas_min_dependencies_environment.yml @@ -2,22 +2,25 @@ # following script to centralize the configuration for CI builds: # build_tools/update_environments_and_lock_files.py channels: - - defaults + - conda-forge dependencies: - - python=3.9 - - numpy=1.21 + - python=3.10 + - numpy=1.22.0 # min - blas[build=openblas] - - scipy=1.7 + - scipy=1.8.0 # min - cython=3.0.10 # min - joblib=1.2.0 # min - - matplotlib=3.3.4 # min - - pyamg + - threadpoolctl=3.1.0 # min + - matplotlib=3.5.0 # min + - pandas=1.4.0 # min + - pyamg=4.2.1 # min - pytest - pytest-xdist - pillow + - pip + - ninja + - meson-python=0.16.0 # min - pytest-cov - coverage - ccache - - pip - - pip: - - threadpoolctl==3.1.0 # min + - polars=0.20.30 # min diff --git a/build_tools/azure/pymin_conda_forge_openblas_min_dependencies_linux-64_conda.lock b/build_tools/azure/pymin_conda_forge_openblas_min_dependencies_linux-64_conda.lock new file mode 100644 index 0000000000000..5d0b23f9e2f41 --- /dev/null +++ b/build_tools/azure/pymin_conda_forge_openblas_min_dependencies_linux-64_conda.lock @@ -0,0 +1,190 @@ +# Generated by conda-lock. +# platform: linux-64 +# input_hash: fbba4fe2a9e1ebfa6e5d79269f12618306ade6ba86f95bb43c9719cd8dbe0e38 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 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b/build_tools/azure/pymin_conda_forge_openblas_ubuntu_2204_environment.yml @@ -4,14 +4,13 @@ channels: - conda-forge dependencies: - - python=3.9 + - python=3.10 - numpy - blas[build=openblas] - scipy - cython - joblib - threadpoolctl - - matplotlib - pandas - pyamg - pytest diff --git a/build_tools/azure/pymin_conda_forge_openblas_ubuntu_2204_linux-64_conda.lock b/build_tools/azure/pymin_conda_forge_openblas_ubuntu_2204_linux-64_conda.lock index 66cd5eced566b..009d15a7d3713 100644 --- a/build_tools/azure/pymin_conda_forge_openblas_ubuntu_2204_linux-64_conda.lock +++ b/build_tools/azure/pymin_conda_forge_openblas_ubuntu_2204_linux-64_conda.lock @@ -1,205 +1,116 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 3974f9847d888a2fd37ba5fcfb76cb09bba4c9b84b6200932500fc94e3b0c4ae +# input_hash: ec41f4a9538671e542d266b999ea055a685df8323c3c879f7d01fb2c259197cb @EXPLICIT 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+https://conda.anaconda.org/conda-forge/noarch/sphinx-8.1.3-pyhd8ed1ab_1.conda#1a3281a0dc355c02b5506d87db2d78ac +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_1.conda#3bc61f7161d28137797e038263c04c54 diff --git a/build_tools/azure/pytest-pyodide.js b/build_tools/azure/pytest-pyodide.js deleted file mode 100644 index c195940ce3b5b..0000000000000 --- a/build_tools/azure/pytest-pyodide.js +++ /dev/null @@ -1,53 +0,0 @@ -const { opendir } = require('node:fs/promises'); -const { loadPyodide } = require("pyodide"); - -async function main() { - let exit_code = 0; - try { - global.pyodide = await loadPyodide(); - let pyodide = global.pyodide; - const FS = pyodide.FS; - const NODEFS = FS.filesystems.NODEFS; - - let mountDir = "/mnt"; - pyodide.FS.mkdir(mountDir); - pyodide.FS.mount(pyodide.FS.filesystems.NODEFS, { root: "." }, mountDir); - - await pyodide.loadPackage(["micropip"]); - await pyodide.runPythonAsync(` - import glob - import micropip - - wheels = glob.glob('/mnt/dist/*.whl') - wheels = [f'emfs://{wheel}' for wheel in wheels] - print(f'installing wheels: {wheels}') - await micropip.install(wheels); - - pkg_list = micropip.list() - print(pkg_list) - `); - - // Pyodide is built without OpenMP, need to set environment variable to - // skip related test - await pyodide.runPythonAsync(` - import os - os.environ['SKLEARN_SKIP_OPENMP_TEST'] = 'true' - `); - - await pyodide.runPythonAsync("import micropip; micropip.install('pytest')"); - let pytest = pyodide.pyimport("pytest"); - let args = process.argv.slice(2); - console.log('pytest args:', args); - exit_code = pytest.main(pyodide.toPy(args)); - } catch (e) { - console.error(e); - // Arbitrary exit code here. I have seen this code reached instead of a - // Pyodide fatal error sometimes - exit_code = 66; - - } finally { - process.exit(exit_code); - } -} - -main(); diff --git a/build_tools/azure/python_nogil_lock.txt b/build_tools/azure/python_nogil_lock.txt deleted file mode 100644 index 7f67a48842dea..0000000000000 --- a/build_tools/azure/python_nogil_lock.txt +++ /dev/null @@ -1,73 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.9 -# by the following command: -# -# pip-compile --output-file=/scikit-learn/build_tools/azure/python_nogil_lock.txt /scikit-learn/build_tools/azure/python_nogil_requirements.txt -# ---index-url https://d1yxz45j0ypngg.cloudfront.net/ ---extra-index-url https://pypi.org/simple - -contourpy==1.1.1 - # via matplotlib -cycler==0.12.1 - # via matplotlib -cython==3.0.10 - # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt -exceptiongroup==1.2.1 - # via pytest -execnet==2.1.1 - # via pytest-xdist -fonttools==4.51.0 - # via matplotlib -iniconfig==2.0.0 - # via pytest -joblib==1.4.2 - # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt -kiwisolver==1.4.4 - # via matplotlib -matplotlib==3.6.2 - # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt -meson==1.4.0 - # via meson-python -meson-python==0.16.0 - # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt -ninja==1.11.1.1 - # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt -numpy==1.24.0 - # via - # -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt - # contourpy - # matplotlib - # scipy -packaging==24.0 - # via - # matplotlib - # meson-python - # pyproject-metadata - # pytest -pillow==9.5.0 - # via matplotlib -pluggy==1.5.0 - # via pytest -pyparsing==3.1.2 - # via matplotlib -pyproject-metadata==0.8.0 - # via meson-python -pytest==7.4.4 - # via - # -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt - # pytest-xdist -pytest-xdist==3.6.1 - # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt -python-dateutil==2.9.0.post0 - # via matplotlib -scipy==1.9.3 - # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt -six==1.16.0 - # via python-dateutil -threadpoolctl==3.5.0 - # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt -tomli==2.0.1 - # via - # meson-python - # pytest diff --git a/build_tools/azure/python_nogil_requirements.txt b/build_tools/azure/python_nogil_requirements.txt deleted file mode 100644 index 2cebad9a03b25..0000000000000 --- a/build_tools/azure/python_nogil_requirements.txt +++ /dev/null @@ -1,20 +0,0 @@ -# To generate python_nogil_lock.txt, use the following command: -# docker run -v $PWD:/scikit-learn -it nogil/python bash -c 'pip install pip-tools; pip-compile --upgrade /scikit-learn/build_tools/azure/python_nogil_requirements.txt -o /scikit-learn/build_tools/azure/python_nogil_lock.txt' -# -# The reason behind it is that you need python-nogil to generate the pip lock -# file. Using pip-compile --index and --extra-index will not work, for example -# the latest cython will be picked up from PyPI, rather than the one from the -# python-nogil index -matplotlib -numpy -scipy -cython -joblib -threadpoolctl -# TODO: somehow pytest 8 does not seem to work with meson editable -# install. Exit code is 5, i.e. no test collected -# This would be fixed by https://github.com/mesonbuild/meson-python/pull/569 -pytest<8 -pytest-xdist -meson-python -ninja diff --git a/build_tools/azure/test_docs.sh b/build_tools/azure/test_docs.sh index 61e855425786b..f3f824d5806b0 100755 --- a/build_tools/azure/test_docs.sh +++ b/build_tools/azure/test_docs.sh @@ -1,11 +1,21 @@ #!/bin/bash -set -e +set -ex -if [[ "$DISTRIB" =~ ^conda.* ]]; then - source activate $VIRTUALENV -elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "pip-nogil" ]]; then - source $VIRTUALENV/bin/activate -fi +source build_tools/shared.sh +activate_environment -make test-doc +scipy_doctest_installed=$(python -c 'import scipy_doctest' && echo "True" || echo "False") +if [[ "$scipy_doctest_installed" == "True" ]]; then + doc_rst_files=$(find $PWD/doc -name '*.rst' | sort) + # Changing dir, as we do in build_tools/azure/test_script.sh, avoids an + # error when importing sklearn. Not sure why this happens ... I am going to + # wild guess that it has something to do with the bespoke way we set up + # conda with putting conda in the PATH and source activate, rather than + # source /etc/profile.d/conda.sh + conda activate. + cd $TEST_DIR + # with scipy-doctest, --doctest-modules only runs doctests (in contrary to + # vanilla pytest where it runs doctests on top of normal tests) + python -m pytest --doctest-modules --pyargs sklearn + python -m pytest --doctest-modules $doc_rst_files +fi diff --git a/build_tools/azure/test_script.sh b/build_tools/azure/test_script.sh index f3f0cd0663bfc..d8152bd7c3ae2 100755 --- a/build_tools/azure/test_script.sh +++ b/build_tools/azure/test_script.sh @@ -11,7 +11,10 @@ if [[ "$BUILD_REASON" == "Schedule" ]]; then # Enable global random seed randomization to discover seed-sensitive tests # only on nightly builds. # https://scikit-learn.org/stable/computing/parallelism.html#environment-variables - export SKLEARN_TESTS_GLOBAL_RANDOM_SEED="any" + export SKLEARN_TESTS_GLOBAL_RANDOM_SEED=$(($RANDOM % 100)) + echo "To reproduce this test run, set the following environment variable:" + echo " SKLEARN_TESTS_GLOBAL_RANDOM_SEED=$SKLEARN_TESTS_GLOBAL_RANDOM_SEED", + echo "See: https://scikit-learn.org/dev/computing/parallelism.html#sklearn-tests-global-random-seed" # Enable global dtype fixture for all nightly builds to discover # numerical-sensitive tests. @@ -27,7 +30,7 @@ if [[ "$COMMIT_MESSAGE" =~ \[float32\] ]]; then fi mkdir -p $TEST_DIR -cp setup.cfg $TEST_DIR +cp pyproject.toml $TEST_DIR cd $TEST_DIR python -c "import joblib; print(f'Number of cores (physical): \ @@ -36,7 +39,7 @@ python -c "import sklearn; sklearn.show_versions()" show_installed_libraries -TEST_CMD="python -m pytest --showlocals --durations=20 --junitxml=$JUNITXML" +TEST_CMD="python -m pytest --showlocals --durations=20 --junitxml=$JUNITXML -o junit_family=legacy" if [[ "$COVERAGE" == "true" ]]; then # Note: --cov-report= is used to disable to long text output report in the @@ -45,6 +48,12 @@ if [[ "$COVERAGE" == "true" ]]; then # report that otherwise hides the test failures and forces long scrolls in # the CI logs. export COVERAGE_PROCESS_START="$BUILD_SOURCESDIRECTORY/.coveragerc" + + # Use sys.monitoring to make coverage faster for Python >= 3.12 + HAS_SYSMON=$(python -c 'import sys; print(sys.version_info >= (3, 12))') + if [[ "$HAS_SYSMON" == "True" ]]; then + export COVERAGE_CORE=sysmon + fi TEST_CMD="$TEST_CMD --cov-config='$COVERAGE_PROCESS_START' --cov sklearn --cov-report=" fi @@ -60,6 +69,12 @@ if [[ -n "$SELECTED_TESTS" ]]; then export SKLEARN_TESTS_GLOBAL_RANDOM_SEED="all" fi +if which lscpu ; then + lscpu +else + echo "Could not inspect CPU architecture." +fi + TEST_CMD="$TEST_CMD --pyargs sklearn" set -x diff --git a/build_tools/azure/test_script_pyodide.sh b/build_tools/azure/test_script_pyodide.sh deleted file mode 100644 index d1aa207f864a2..0000000000000 --- a/build_tools/azure/test_script_pyodide.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -set -e - -# We are using a pytest js wrapper script to run tests inside Pyodide. Maybe -# one day we can use a Pyodide venv instead but at the time of writing -# (2023-09-27) there is an issue with scipy.linalg in a Pyodide venv, see -# https://github.com/pyodide/pyodide/issues/3865 for more details. -node build_tools/azure/pytest-pyodide.js --pyargs sklearn --durations 20 --showlocals diff --git a/build_tools/azure/ubuntu_atlas_lock.txt b/build_tools/azure/ubuntu_atlas_lock.txt index e66f5ca8943fd..ea978eeabcb51 100644 --- a/build_tools/azure/ubuntu_atlas_lock.txt +++ b/build_tools/azure/ubuntu_atlas_lock.txt @@ -6,30 +6,30 @@ # cython==3.0.10 # via -r build_tools/azure/ubuntu_atlas_requirements.txt -exceptiongroup==1.2.1 +exceptiongroup==1.2.2 # via pytest execnet==2.1.1 # via pytest-xdist -iniconfig==2.0.0 +iniconfig==2.1.0 # via pytest joblib==1.2.0 # via -r build_tools/azure/ubuntu_atlas_requirements.txt -meson==1.4.0 +meson==1.8.0 # via meson-python -meson-python==0.16.0 +meson-python==0.17.1 # via -r build_tools/azure/ubuntu_atlas_requirements.txt -ninja==1.11.1.1 +ninja==1.11.1.4 # via -r build_tools/azure/ubuntu_atlas_requirements.txt -packaging==24.0 +packaging==25.0 # via # meson-python # pyproject-metadata # pytest pluggy==1.5.0 # via pytest -pyproject-metadata==0.8.0 +pyproject-metadata==0.9.1 # via meson-python -pytest==8.2.1 +pytest==8.3.5 # via # -r build_tools/azure/ubuntu_atlas_requirements.txt # pytest-xdist @@ -37,7 +37,7 @@ pytest-xdist==3.6.1 # via -r build_tools/azure/ubuntu_atlas_requirements.txt threadpoolctl==3.1.0 # via -r build_tools/azure/ubuntu_atlas_requirements.txt -tomli==2.0.1 +tomli==2.2.1 # via # meson-python # pytest diff --git a/build_tools/azure/upload_codecov.sh b/build_tools/azure/upload_codecov.sh index 0e87b2dafc8b4..4c3db8fe8bbd6 100755 --- a/build_tools/azure/upload_codecov.sh +++ b/build_tools/azure/upload_codecov.sh @@ -9,8 +9,8 @@ fi # When we update the codecov uploader version, we need to update the checksums. # The checksum for each codecov binary is available at -# https://uploader.codecov.io e.g. for linux -# https://uploader.codecov.io/v0.7.1/linux/codecov.SHA256SUM. +# https://cli.codecov.io e.g. for linux +# https://cli.codecov.io/v10.2.1/linux/codecov.SHA256SUM. # Instead of hardcoding a specific version and signature in this script, it # would be possible to use the "latest" symlink URL but then we need to @@ -20,9 +20,8 @@ fi # However this approach would yield a larger number of downloads from # codecov.io and keybase.io, therefore increasing the risk of running into # network failures. -CODECOV_UPLOADER_VERSION=0.7.1 -CODECOV_BASE_URL="https://uploader.codecov.io/v$CODECOV_UPLOADER_VERSION" - +CODECOV_CLI_VERSION=10.2.1 +CODECOV_BASE_URL="https://cli.codecov.io/v$CODECOV_CLI_VERSION" # Check that the git repo is located at the expected location: if [[ ! -d "$BUILD_REPOSITORY_LOCALPATH/.git" ]]; then @@ -39,19 +38,22 @@ fi if [[ $OSTYPE == *"linux"* ]]; then curl -Os "$CODECOV_BASE_URL/linux/codecov" - SHA256SUM="b9282b8b43eef83f722646d8992c4dd36563046afe0806722184e7e9923a6d7b codecov" + SHA256SUM="39dd112393680356daf701c07f375303aef5de62f06fc80b466b5c3571336014 codecov" echo "$SHA256SUM" | shasum -a256 -c chmod +x codecov - ./codecov -t ${CODECOV_TOKEN} -R $BUILD_REPOSITORY_LOCALPATH -f coverage.xml -Z --verbose + ./codecov upload-coverage -t ${CODECOV_TOKEN} -f coverage.xml -Z + ./codecov do-upload --disable-search --report-type test_results --file $JUNIT_FILE elif [[ $OSTYPE == *"darwin"* ]]; then curl -Os "$CODECOV_BASE_URL/macos/codecov" - SHA256SUM="e4ce34c144d3195eccb7f8b9ca8de092d2a4be114d927ca942500f3a6326225c codecov" + SHA256SUM="01183f6367c7baff4947cce389eaa511b7a6d938e37ae579b08a86b51f769fd9 codecov" echo "$SHA256SUM" | shasum -a256 -c chmod +x codecov - ./codecov -t ${CODECOV_TOKEN} -R $BUILD_REPOSITORY_LOCALPATH -f coverage.xml -Z --verbose + ./codecov upload-coverage -t ${CODECOV_TOKEN} -f coverage.xml -Z + ./codecov do-upload --disable-search --report-type test_results --file $JUNIT_FILE else curl -Os "$CODECOV_BASE_URL/windows/codecov.exe" - SHA256SUM="f5de88026f061ff08b88a5895f9c11855523924ceb8174e027403dd20fa5e4d6 codecov.exe" + SHA256SUM="e54e9520428701a510ef451001db56b56fb17f9b0484a266f184b73dd27b77e7 codecov.exe" echo "$SHA256SUM" | sha256sum -c - ./codecov.exe -t ${CODECOV_TOKEN} -R $BUILD_REPOSITORY_LOCALPATH -f coverage.xml -Z --verbose + ./codecov.exe upload-coverage -t ${CODECOV_TOKEN} -f coverage.xml -Z + ./codecov.exe do-upload --disable-search --report-type test_results --file $JUNIT_FILE fi diff --git a/build_tools/azure/windows.yml b/build_tools/azure/windows.yml index 1727da4138f07..b3fcf130f9350 100644 --- a/build_tools/azure/windows.yml +++ b/build_tools/azure/windows.yml @@ -83,3 +83,4 @@ jobs: retryCountOnTaskFailure: 5 env: CODECOV_TOKEN: $(CODECOV_TOKEN) + JUNIT_FILE: $(TEST_DIR)/$(JUNITXML) diff --git a/build_tools/check-meson-openmp-dependencies.py b/build_tools/check-meson-openmp-dependencies.py new file mode 100644 index 0000000000000..43a7426494160 --- /dev/null +++ b/build_tools/check-meson-openmp-dependencies.py @@ -0,0 +1,172 @@ +""" +Check that OpenMP dependencies are correctly defined in meson.build files. + +This is based on trying to make sure the the following two things match: +- the Cython files using OpenMP (based on a git grep regex) +- the Cython extension modules that are built with OpenMP compiler flags (based + on meson introspect json output) +""" + +import json +import re +import subprocess +from pathlib import Path + + +def has_source_openmp_flags(target_source): + return any("openmp" in arg for arg in target_source["parameters"]) + + +def has_openmp_flags(target): + """Return whether target sources use OpenMP flags. + + Make sure that both compiler and linker source use OpenMP. + Look at `get_meson_info` docstring to see what `target` looks like. + """ + target_sources = target["target_sources"] + + target_use_openmp_flags = any( + has_source_openmp_flags(target_source) for target_source in target_sources + ) + + if not target_use_openmp_flags: + return False + + # When the target use OpenMP we expect a compiler + linker source and we + # want to make sure that both the compiler and the linker use OpenMP + assert len(target_sources) == 2 + compiler_source, linker_source = target_sources + assert "compiler" in compiler_source + assert "linker" in linker_source + + compiler_use_openmp_flags = any( + "openmp" in arg for arg in compiler_source["parameters"] + ) + linker_use_openmp_flags = any( + "openmp" in arg for arg in linker_source["parameters"] + ) + + assert compiler_use_openmp_flags == linker_use_openmp_flags + return compiler_use_openmp_flags + + +def get_canonical_name_meson(target, build_path): + """Return a name based on generated shared library. + + The goal is to return a name that can be easily matched with the output + from `git_grep_info`. + + Look at `get_meson_info` docstring to see what `target` looks like. + """ + # Expect a list with one element with the name of the shared library + assert len(target["filename"]) == 1 + shared_library_path = Path(target["filename"][0]) + shared_library_relative_path = shared_library_path.relative_to( + build_path.absolute() + ) + # Needed on Windows to match git grep output + rel_path = shared_library_relative_path.as_posix() + # OS-specific naming of the shared library .cpython- on POSIX and + # something like .cp312- on Windows + pattern = r"\.(cpython|cp\d+)-.+" + return re.sub(pattern, "", str(rel_path)) + + +def get_canonical_name_git_grep(filename): + """Return name based on filename. + + The goal is to return a name that can easily be matched with the output + from `get_meson_info`. + """ + return re.sub(r"\.pyx(\.tp)?", "", filename) + + +def get_meson_info(): + """Return names of extension that use OpenMP based on meson introspect output. + + The meson introspect json info is a list of targets where a target is a dict + that looks like this (parts not used in this script are not shown for simplicity): + { + 'name': '_k_means_elkan.cpython-312-x86_64-linux-gnu', + 'filename': [ + '/sklearn/cluster/_k_means_elkan.cpython-312-x86_64-linux-gnu.so' + ], + 'target_sources': [ + { + 'compiler': ['ccache', 'cc'], + 'parameters': [ + '-Wall', + '-std=c11', + '-fopenmp', + ... + ], + ... + }, + { + 'linker': ['cc'], + 'parameters': [ + '-shared', + '-fPIC', + '-fopenmp', + ... + ] + } + ] + } + """ + build_path = Path("build/introspect") + subprocess.check_call(["meson", "setup", build_path, "--reconfigure"]) + + json_out = subprocess.check_output( + ["meson", "introspect", build_path, "--targets"], text=True + ) + target_list = json.loads(json_out) + meson_targets = [target for target in target_list if has_openmp_flags(target)] + + return [get_canonical_name_meson(each, build_path) for each in meson_targets] + + +def get_git_grep_info(): + """Return names of extensions that use OpenMP based on git grep regex.""" + git_grep_filenames = subprocess.check_output( + ["git", "grep", "-lP", "cython.*parallel|_openmp_helpers"], text=True + ).splitlines() + git_grep_filenames = [f for f in git_grep_filenames if ".pyx" in f] + + return [get_canonical_name_git_grep(each) for each in git_grep_filenames] + + +def main(): + from_meson = set(get_meson_info()) + from_git_grep = set(get_git_grep_info()) + + only_in_git_grep = from_git_grep - from_meson + only_in_meson = from_meson - from_git_grep + + msg = "" + if only_in_git_grep: + only_in_git_grep_msg = "\n".join( + [f" {each}" for each in sorted(only_in_git_grep)] + ) + msg += ( + "Some Cython files use OpenMP," + " but their meson.build is missing the openmp_dep dependency:\n" + f"{only_in_git_grep_msg}\n\n" + ) + + if only_in_meson: + only_in_meson_msg = "\n".join([f" {each}" for each in sorted(only_in_meson)]) + msg += ( + "Some Cython files do not use OpenMP," + " you should remove openmp_dep from their meson.build:\n" + f"{only_in_meson_msg}\n\n" + ) + + if from_meson != from_git_grep: + raise ValueError( + f"Some issues have been found in Meson OpenMP dependencies:\n\n{msg}" + ) + + +if __name__ == "__main__": + main() diff --git a/build_tools/circle/build_doc.sh b/build_tools/circle/build_doc.sh index c569f4913d4d8..e85f3ab15e617 100755 --- a/build_tools/circle/build_doc.sh +++ b/build_tools/circle/build_doc.sh @@ -1,5 +1,6 @@ #!/usr/bin/env bash set -e +set -x # Decide what kind of documentation build to run, and run it. # @@ -30,11 +31,18 @@ then then CIRCLE_BRANCH=$GITHUB_HEAD_REF CI_PULL_REQUEST=true + CI_TARGET_BRANCH=$GITHUB_BASE_REF else CIRCLE_BRANCH=$GITHUB_REF_NAME fi fi +if [[ -n "$CI_PULL_REQUEST" && -z "$CI_TARGET_BRANCH" ]] +then + # Get the target branch name when using CircleCI + CI_TARGET_BRANCH=$(curl -s "https://api.github.com/repos/scikit-learn/scikit-learn/pulls/$CIRCLE_PR_NUMBER" | jq -r .base.ref) +fi + get_build_type() { if [ -z "$CIRCLE_SHA1" ] then @@ -159,34 +167,46 @@ if [[ `type -t deactivate` ]]; then deactivate fi -MAMBAFORGE_PATH=$HOME/mambaforge -# Install dependencies with mamba -wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \ - -O mambaforge.sh -chmod +x mambaforge.sh && ./mambaforge.sh -b -p $MAMBAFORGE_PATH -export PATH="/usr/lib/ccache:$MAMBAFORGE_PATH/bin:$PATH" +# Install Miniforge +MINIFORGE_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" +curl -L --retry 10 $MINIFORGE_URL -o miniconda.sh +MINIFORGE_PATH=$HOME/miniforge3 +bash ./miniconda.sh -b -p $MINIFORGE_PATH +source $MINIFORGE_PATH/etc/profile.d/conda.sh +conda activate -ccache -M 512M -export CCACHE_COMPRESS=1 -# pin conda-lock to latest released version (needs manual update from time to time) -mamba install "$(get_dep conda-lock min)" -y +create_conda_environment_from_lock_file $CONDA_ENV_NAME $LOCK_FILE +conda activate $CONDA_ENV_NAME -conda-lock install --log-level DEBUG --name $CONDA_ENV_NAME $LOCK_FILE -source activate $CONDA_ENV_NAME +# Sets up ccache when using system compiler +export PATH="/usr/lib/ccache:$PATH" +# Sets up ccache when using conda-forge compilers (needs to be after conda +# activate which sets CC and CXX) +export CC="ccache $CC" +export CXX="ccache $CXX" +ccache -M 512M +export CCACHE_COMPRESS=1 +# Zeroing statistics so that ccache statistics are shown only for this build +ccache -z show_installed_libraries -# Set parallelism to 3 to overlap IO bound tasks with CPU bound tasks on CI -# workers with 2 cores when building the compiled extensions of scikit-learn. -export SKLEARN_BUILD_PARALLEL=3 -pip install -e . --no-build-isolation +# Specify explicitly ninja -j argument because ninja does not handle cgroups v2 and +# use the same default rule as ninja (-j3 since we have 2 cores on CircleCI), see +# https://github.com/scikit-learn/scikit-learn/pull/30333 +pip install -e . --no-build-isolation --config-settings=compile-args="-j 3" echo "ccache build summary:" ccache -s export OMP_NUM_THREADS=1 +if [[ "$CIRCLE_BRANCH" == "main" || "$CI_TARGET_BRANCH" == "main" ]] +then + towncrier build --yes +fi + if [[ "$CIRCLE_BRANCH" =~ ^main$ && -z "$CI_PULL_REQUEST" ]] then # List available documentation versions if on main @@ -201,8 +221,16 @@ cd - set +o pipefail affected_doc_paths() { + scikit_learn_version=$(python -c 'import re; import sklearn; print(re.sub(r"(\d+\.\d+).+", r"\1", sklearn.__version__))') files=$(git diff --name-only origin/main...$CIRCLE_SHA1) - echo "$files" | grep ^doc/.*\.rst | sed 's/^doc\/\(.*\)\.rst$/\1.html/' + # use sed to replace files ending by .rst or .rst.template by .html + echo "$files" | grep -vP 'upcoming_changes/.*/\d+.*\.rst' | grep ^doc/.*\.rst | \ + sed 's/^doc\/\(.*\)\.rst$/\1.html/; s/^doc\/\(.*\)\.rst\.template$/\1.html/' + # replace towncrier fragment files by link to changelog. uniq is used + # because in some edge cases multiple fragments can be added and we want a + # single link to the changelog. + echo "$files" | grep -P 'upcoming_changes/.*/\d+.*\.rst' | sed "s@.*@whats_new/v${scikit_learn_version}.html@" | uniq + echo "$files" | grep ^examples/.*.py | sed 's/^\(.*\)\.py$/auto_\1.html/' sklearn_files=$(echo "$files" | grep '^sklearn/') if [ -n "$sklearn_files" ] diff --git a/build_tools/circle/doc_environment.yml b/build_tools/circle/doc_environment.yml index ea930fadcb528..bc36e178de058 100644 --- a/build_tools/circle/doc_environment.yml +++ b/build_tools/circle/doc_environment.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - - python=3.9 + - python=3.10 - numpy - blas - scipy @@ -36,6 +36,7 @@ dependencies: - sphinx-remove-toctrees - sphinx-design - pydata-sphinx-theme + - towncrier - pip - pip: - jupyterlite-sphinx diff --git a/build_tools/circle/doc_linux-64_conda.lock b/build_tools/circle/doc_linux-64_conda.lock index 0d925375b643b..c489e4f01a9f7 100644 --- a/build_tools/circle/doc_linux-64_conda.lock +++ b/build_tools/circle/doc_linux-64_conda.lock @@ -1,328 +1,332 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+https://conda.anaconda.org/conda-forge/noarch/sphinx-remove-toctrees-1.0.0.post1-pyhd8ed1ab_1.conda#b275c865b753413caaa8548b9d44c024 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-2.0.0-pyhd8ed1ab_1.conda#16e3f039c0aa6446513e94ab18a8784b +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-2.0.0-pyhd8ed1ab_1.conda#910f28a05c178feba832f842155cbfff +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.1.0-pyhd8ed1ab_1.conda#e9fb3fe8a5b758b4aff187d434f94f03 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-2.0.0-pyhd8ed1ab_1.conda#00534ebcc0375929b45c3039b5ba7636 https://conda.anaconda.org/conda-forge/noarch/sphinx-7.3.7-pyhd8ed1ab_0.conda#7b1465205e28d75d2c0e1a868ee00a67 -https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda#e507335cb4ca9cff4c3d0fa9cdab255e +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_1.conda#3bc61f7161d28137797e038263c04c54 # pip libsass @ https://files.pythonhosted.org/packages/fd/5a/eb5b62641df0459a3291fc206cf5bd669c0feed7814dded8edef4ade8512/libsass-0.23.0-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=4a218406d605f325d234e4678bd57126a66a88841cb95bee2caeafdc6f138306 # pip sphinxcontrib-sass @ https://files.pythonhosted.org/packages/2e/87/7c2eb08e3ca1d6baae32c0a5e005330fe1cec93a36aa085e714c3b3a3c7d/sphinxcontrib_sass-0.3.4-py2.py3-none-any.whl#sha256=a0c79a44ae8b8935c02dc340ebe40c9e002c839331201c899dc93708970c355a # pip sphinxext-opengraph @ https://files.pythonhosted.org/packages/92/0a/970b80b4fa1feeb6deb6f2e22d4cb14e388b27b315a1afdb9db930ff91a4/sphinxext_opengraph-0.9.1-py3-none-any.whl#sha256=b3b230cc6a5b5189139df937f0d9c7b23c7c204493b22646273687969dcb760e diff --git a/build_tools/circle/list_versions.py b/build_tools/circle/list_versions.py index e1f8d54b84ec5..00526f062f200 100755 --- a/build_tools/circle/list_versions.py +++ b/build_tools/circle/list_versions.py @@ -71,10 +71,8 @@ def get_file_size(version): "Web-based documentation is available for versions listed below:\n", ] -ROOT_URL = ( - "https://api.github.com/repos/scikit-learn/scikit-learn.github.io/contents/" # noqa -) -RAW_FMT = "https://raw.githubusercontent.com/scikit-learn/scikit-learn.github.io/master/%s/index.html" # noqa +ROOT_URL = "https://api.github.com/repos/scikit-learn/scikit-learn.github.io/contents/" +RAW_FMT = "https://raw.githubusercontent.com/scikit-learn/scikit-learn.github.io/master/%s/index.html" VERSION_RE = re.compile(r"scikit-learn ([\w\.\-]+) documentation") NAMED_DIRS = ["dev", "stable"] diff --git a/build_tools/cirrus/arm_tests.yml b/build_tools/cirrus/arm_tests.yml deleted file mode 100644 index 09874e081b460..0000000000000 --- a/build_tools/cirrus/arm_tests.yml +++ /dev/null @@ -1,34 +0,0 @@ -linux_aarch64_test_task: - compute_engine_instance: - image_project: cirrus-images - image: family/docker-builder-arm64 - architecture: arm64 - platform: linux - cpu: 4 - memory: 6G - env: - CONDA_ENV_NAME: testenv - LOCK_FILE: build_tools/cirrus/pymin_conda_forge_linux-aarch64_conda.lock - CONDA_PKGS_DIRS: /root/.conda/pkgs - HOME: / # $HOME is not defined in image and is required to install mambaforge - # Upload tokens have been encrypted via the CirrusCI interface: - # https://cirrus-ci.org/guide/writing-tasks/#encrypted-variables - # See `maint_tools/update_tracking_issue.py` for details on the permissions the token requires. - BOT_GITHUB_TOKEN: ENCRYPTED[9b50205e2693f9e4ce9a3f0fcb897a259289062fda2f5a3b8aaa6c56d839e0854a15872f894a70fca337dd4787274e0f] - ccache_cache: - folder: /root/.cache/ccache - conda_cache: - folder: /root/.conda/pkgs - fingerprint_script: cat build_tools/cirrus/pymin_conda_forge_linux-aarch64_conda.lock - - install_python_script: | - # Install python so that update_tracking_issue has access to a Python - apt install -y python3 python-is-python3 - - test_script: | - bash build_tools/cirrus/build_test_arm.sh - # On success, this script is run updating the issue. - bash build_tools/cirrus/update_tracking_issue.sh true - - on_failure: - update_tracker_script: bash build_tools/cirrus/update_tracking_issue.sh false diff --git a/build_tools/cirrus/arm_wheel.yml b/build_tools/cirrus/arm_wheel.yml deleted file mode 100644 index c3dfcfbc53ad9..0000000000000 --- a/build_tools/cirrus/arm_wheel.yml +++ /dev/null @@ -1,76 +0,0 @@ -linux_arm64_wheel_task: - compute_engine_instance: - image_project: cirrus-images - image: family/docker-builder-arm64 - architecture: arm64 - platform: linux - cpu: 4 - memory: 4G - env: - CIBW_ENVIRONMENT: SKLEARN_SKIP_NETWORK_TESTS=1 - SKLEARN_BUILD_PARALLEL=5 - CIBW_TEST_COMMAND: bash {project}/build_tools/wheels/test_wheels.sh - CIBW_TEST_REQUIRES: pytest pandas threadpoolctl pytest-xdist - CIBW_BUILD_VERBOSITY: 1 - # Upload tokens have been encrypted via the CirrusCI interface: - # https://cirrus-ci.org/guide/writing-tasks/#encrypted-variables - # See `maint_tools/update_tracking_issue.py` for details on the permissions the token requires. - BOT_GITHUB_TOKEN: ENCRYPTED[9b50205e2693f9e4ce9a3f0fcb897a259289062fda2f5a3b8aaa6c56d839e0854a15872f894a70fca337dd4787274e0f] - matrix: - # Only the latest Python version is tested - - env: - CIBW_BUILD: cp39-manylinux_aarch64 - CIBW_TEST_SKIP: "*_aarch64" - - env: - CIBW_BUILD: cp310-manylinux_aarch64 - CIBW_TEST_SKIP: "*_aarch64" - - env: - CIBW_BUILD: cp311-manylinux_aarch64 - CIBW_TEST_SKIP: "*_aarch64" - - env: - CIBW_BUILD: cp312-manylinux_aarch64 - - cibuildwheel_script: - - apt install -y python3 python-is-python3 - - bash build_tools/wheels/build_wheels.sh - - on_failure: - update_tracker_script: - - bash build_tools/cirrus/update_tracking_issue.sh false - - wheels_artifacts: - path: "wheelhouse/*" - -# Update tracker when all jobs are successful -update_tracker_success: - depends_on: - - linux_arm64_wheel - container: - image: python:3.11 - # Only update tracker for nightly builds - only_if: $CIRRUS_CRON == "nightly" - update_script: - - bash build_tools/cirrus/update_tracking_issue.sh true - -wheels_upload_task: - depends_on: - - linux_arm64_wheel - container: - image: continuumio/miniconda3:22.11.1 - # Artifacts are not uploaded on PRs - only_if: $CIRRUS_PR == "" - env: - # Upload tokens have been encrypted via the CirrusCI interface: - # https://cirrus-ci.org/guide/writing-tasks/#encrypted-variables - SCIKIT_LEARN_NIGHTLY_UPLOAD_TOKEN: ENCRYPTED[9cf0529227577d503f2e19ef31cb690a2272cb243a217fb9a1ceda5cc608e8ccc292050fde9dca94cab766e1dd418519] - SCIKIT_LEARN_STAGING_UPLOAD_TOKEN: ENCRYPTED[8fade46af37fa645e57bd1ee21683337aa369ba56f6307ce13889f1e74df94e5bdd21d323baac21e332fd87b8949659a] - ARTIFACTS_PATH: wheelhouse - upload_script: | - conda install curl unzip -y - - # Download and show wheels - curl https://api.cirrus-ci.com/v1/artifact/build/$CIRRUS_BUILD_ID/wheels.zip --output wheels.zip - unzip wheels.zip - ls wheelhouse - - bash build_tools/github/upload_anaconda.sh diff --git a/build_tools/cirrus/pymin_conda_forge_linux-aarch64_conda.lock b/build_tools/cirrus/pymin_conda_forge_linux-aarch64_conda.lock deleted file mode 100644 index 7c36386889867..0000000000000 --- a/build_tools/cirrus/pymin_conda_forge_linux-aarch64_conda.lock +++ /dev/null @@ -1,94 +0,0 @@ -# Generated by conda-lock. -# platform: linux-aarch64 -# input_hash: 2d8c526ab7c0c2f0ca509bfec3f035e5bd33b8096f194f0747f167c8aff66383 -@EXPLICIT -https://conda.anaconda.org/conda-forge/linux-aarch64/ca-certificates-2024.6.2-hcefe29a_0.conda#3ef6b1a30375f8a973a593698e317191 -https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.40-h9fc2d93_1.conda#8a90b17a5d12ba55b7d90534f38579d0 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-https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-10.3.0-py39h71661b1_0.conda#dae548b7b537d7ef796d1d4c38a55319 -https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 -https://conda.anaconda.org/conda-forge/noarch/pyproject-metadata-0.8.0-pyhd8ed1ab_0.conda#573fe09d7bd0cd4bcc210d8369b5ca47 -https://conda.anaconda.org/conda-forge/noarch/pytest-8.2.1-pyhd8ed1ab_0.conda#e4418e8bdbaa8eea28e047531e6763c8 -https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda#2cf4264fffb9e6eff6031c5b6884d61c -https://conda.anaconda.org/conda-forge/noarch/importlib-resources-6.4.0-pyhd8ed1ab_0.conda#dcbadab7a68738a028e195ab68ab2d2e -https://conda.anaconda.org/conda-forge/linux-aarch64/liblapacke-3.9.0-22_linuxaarch64_openblas.conda#5acf669e0be669f30f4b813d2ecda7b8 -https://conda.anaconda.org/conda-forge/noarch/meson-python-0.16.0-pyh0c530f3_0.conda#e16f0dbf502da873be9f9adb0dc52547 -https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-1.26.4-py39h91c28bb_0.conda#d88e195f11a9f27e649aea408b54cb48 -https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-3.5.0-pyhd8ed1ab_0.conda#d5f595da2daead898ca958ac62f0307b -https://conda.anaconda.org/conda-forge/linux-aarch64/blas-devel-3.9.0-22_linuxaarch64_openblas.conda#a5b77b6c6807661afd716f33e85814b3 -https://conda.anaconda.org/conda-forge/linux-aarch64/contourpy-1.2.1-py39hd16970a_0.conda#66b9718539ecdd38876b0176c315bcad -https://conda.anaconda.org/conda-forge/linux-aarch64/scipy-1.13.1-py39hb921187_0.conda#1aac9080de661e03d286f18fb71e5240 -https://conda.anaconda.org/conda-forge/linux-aarch64/blas-2.122-openblas.conda#65bc48b3bc85f8eeeab54311443a83aa -https://conda.anaconda.org/conda-forge/linux-aarch64/matplotlib-base-3.8.4-py39hf44f4b6_2.conda#fadf734d38ed608c9f0b5c91fe79cfb4 -https://conda.anaconda.org/conda-forge/linux-aarch64/matplotlib-3.8.4-py39ha65689a_2.conda#c0472e3c4b3f007de6d643317c30963b diff --git a/build_tools/cirrus/update_tracking_issue.sh b/build_tools/cirrus/update_tracking_issue.sh deleted file mode 100644 index 9166210ac0007..0000000000000 --- a/build_tools/cirrus/update_tracking_issue.sh +++ /dev/null @@ -1,22 +0,0 @@ -# Update tracking issue if Cirrus fails nightly job - -if [[ "$CIRRUS_CRON" != "nightly" ]]; then - exit 0 -fi - -# TEST_PASSED is either "true" or "false" -TEST_PASSED="$1" - -python -m venv .venv -source .venv/bin/activate -python -m pip install defusedxml PyGithub - -LINK_TO_RUN="https://cirrus-ci.com/build/$CIRRUS_BUILD_ID" - -python maint_tools/update_tracking_issue.py \ - $BOT_GITHUB_TOKEN \ - $CIRRUS_TASK_NAME \ - $CIRRUS_REPO_FULL_NAME \ - $LINK_TO_RUN \ - --tests-passed $TEST_PASSED \ - --auto-close false diff --git a/build_tools/codespell_ignore_words.txt b/build_tools/codespell_ignore_words.txt index fbe501d04f29f..6b942a2eabe6d 100644 --- a/build_tools/codespell_ignore_words.txt +++ b/build_tools/codespell_ignore_words.txt @@ -1,13 +1,17 @@ +achin aggresive aline ba basf boun bre +bu cach +chanel complies coo copys +datas deine didi feld @@ -17,20 +21,25 @@ fro fwe gool hart +heping hist ines inout ist jaques +lamas linke lod mape +mis mor nd nmae ocur pullrequest +repid ro +ser soler suh suprised @@ -40,6 +49,8 @@ teh thi usal vie +vor wan +whis winn yau diff --git a/build_tools/generate_authors_table.py b/build_tools/generate_authors_table.py index 483dc3739506e..6dcddda40af4d 100644 --- a/build_tools/generate_authors_table.py +++ b/build_tools/generate_authors_table.py @@ -15,9 +15,9 @@ import requests -print("user:", file=sys.stderr) +print("Input user:", file=sys.stderr) user = input() -token = getpass.getpass("access token:\n") +token = getpass.getpass("Input access token:\n") auth = (user, token) LOGO_URL = "https://avatars2.githubusercontent.com/u/365630?v=4" @@ -63,11 +63,13 @@ def get_contributors(): ), (core_devs, contributor_experience_team, comm_team, documentation_team), ): + print(f"Retrieving {team_slug}\n") for page in [1, 2]: # 30 per page reply = get(f"{entry_point}teams/{team_slug}/members?page={page}") lst.extend(reply.json()) # get members of scikit-learn on GitHub + print("Retrieving members\n") members = [] for page in [1, 2, 3]: # 30 per page reply = get(f"{entry_point}members?page={page}") @@ -214,6 +216,7 @@ def generate_list(contributors): documentation_team, ) = get_contributors() + print("Generating rst files") with open( REPO_FOLDER / "doc" / "maintainers.rst", "w+", encoding="utf-8" ) as rst_file: diff --git a/build_tools/get_comment.py b/build_tools/get_comment.py index b357c68f23e3e..48ff14a058c9a 100644 --- a/build_tools/get_comment.py +++ b/build_tools/get_comment.py @@ -55,10 +55,7 @@ def get_step_message(log, start, end, title, message, details): if end not in log: return "" res = ( - "-----------------------------------------------\n" - + f"### {title}\n\n" - + message - + "\n\n" + f"-----------------------------------------------\n### {title}\n\n{message}\n\n" ) if details: res += ( @@ -93,33 +90,31 @@ def get_message(log_file, repo, pr_number, sha, run_id, details, versions): message = "" - # black + # ruff check message += get_step_message( log, - start="### Running black ###", - end="Problems detected by black", - title="`black`", + start="### Running the ruff linter ###", + end="Problems detected by ruff check", + title="`ruff check`", message=( - "`black` detected issues. Please run `black .` locally and push " - "the changes. Here you can see the detected issues. Note that " - "running black might also fix some of the issues which might be " - "detected by `ruff`. Note that the installed `black` version is " - f"`black={versions['black']}`." + "`ruff` detected issues. Please run " + "`ruff check --fix --output-format=full` locally, fix the remaining " + "issues, and push the changes. Here you can see the detected issues. Note " + f"that the installed `ruff` version is `ruff={versions['ruff']}`." ), details=details, ) - # ruff + # ruff format message += get_step_message( log, - start="### Running ruff ###", - end="Problems detected by ruff", - title="`ruff`", + start="### Running the ruff formatter ###", + end="Problems detected by ruff format", + title="`ruff format`", message=( - "`ruff` detected issues. Please run " - "`ruff check --fix --output-format=full .` locally, fix the remaining " - "issues, and push the changes. Here you can see the detected issues. Note " - f"that the installed `ruff` version is `ruff={versions['ruff']}`." + "`ruff` detected issues. Please run `ruff format` locally and push " + "the changes. Here you can see the detected issues. Note that the " + f"installed `ruff` version is `ruff={versions['ruff']}`." ), details=details, ) @@ -240,7 +235,7 @@ def get_headers(token): def find_lint_bot_comments(repo, token, pr_number): """Get the comment from the linting bot.""" # repo is in the form of "org/repo" - # API doc: https://docs.github.com/en/rest/issues/comments?apiVersion=2022-11-28#list-issue-comments # noqa + # API doc: https://docs.github.com/en/rest/issues/comments?apiVersion=2022-11-28#list-issue-comments response = requests.get( f"https://api.github.com/repos/{repo}/issues/{pr_number}/comments", headers=get_headers(token), @@ -275,7 +270,7 @@ def create_or_update_comment(comment, message, repo, pr_number, token): # repo is in the form of "org/repo" if comment is not None: print("updating existing comment") - # API doc: https://docs.github.com/en/rest/issues/comments?apiVersion=2022-11-28#update-an-issue-comment # noqa + # API doc: https://docs.github.com/en/rest/issues/comments?apiVersion=2022-11-28#update-an-issue-comment response = requests.patch( f"https://api.github.com/repos/{repo}/issues/comments/{comment['id']}", headers=get_headers(token), @@ -283,7 +278,7 @@ def create_or_update_comment(comment, message, repo, pr_number, token): ) else: print("creating new comment") - # API doc: https://docs.github.com/en/rest/issues/comments?apiVersion=2022-11-28#create-an-issue-comment # noqa + # API doc: https://docs.github.com/en/rest/issues/comments?apiVersion=2022-11-28#create-an-issue-comment response = requests.post( f"https://api.github.com/repos/{repo}/issues/{pr_number}/comments", headers=get_headers(token), diff --git a/build_tools/github/Windows b/build_tools/github/Windows deleted file mode 100644 index a9971aa525581..0000000000000 --- a/build_tools/github/Windows +++ /dev/null @@ -1,13 +0,0 @@ -# Get the Python version of the base image from a build argument -ARG PYTHON_VERSION -FROM winamd64/python:$PYTHON_VERSION-windowsservercore - -ARG WHEEL_NAME -ARG CIBW_TEST_REQUIRES - -# Copy and install the Windows wheel -COPY $WHEEL_NAME $WHEEL_NAME -RUN pip install $env:WHEEL_NAME - -# Install the testing dependencies -RUN pip install $env:CIBW_TEST_REQUIRES.split(" ") diff --git a/build_tools/github/build_minimal_windows_image.sh b/build_tools/github/build_minimal_windows_image.sh index 2995b6906c535..8cc9af937dfd9 100755 --- a/build_tools/github/build_minimal_windows_image.sh +++ b/build_tools/github/build_minimal_windows_image.sh @@ -5,21 +5,47 @@ set -x PYTHON_VERSION=$1 -TEMP_FOLDER="$HOME/AppData/Local/Temp" -WHEEL_PATH=$(ls -d $TEMP_FOLDER/**/*/repaired_wheel/*) -WHEEL_NAME=$(basename $WHEEL_PATH) +FREE_THREADED_BUILD="$(python -c"import sysconfig; print(bool(sysconfig.get_config_var('Py_GIL_DISABLED')))")" -cp $WHEEL_PATH $WHEEL_NAME +if [[ $FREE_THREADED_BUILD == "False" ]]; then + # Prepare a minimal Windows environment without any developer runtime libraries + # installed to check that the scikit-learn wheel does not implicitly rely on + # external DLLs when running the tests. + TEMP_FOLDER="$HOME/AppData/Local/Temp" + WHEEL_PATH=$(ls -d $TEMP_FOLDER/**/*/repaired_wheel/*) + WHEEL_NAME=$(basename $WHEEL_PATH) -# Dot the Python version for identyfing the base Docker image -PYTHON_VERSION=$(echo ${PYTHON_VERSION:0:1}.${PYTHON_VERSION:1:2}) + cp $WHEEL_PATH $WHEEL_NAME -if [[ "$CIBW_PRERELEASE_PYTHONS" == "True" ]]; then - PYTHON_VERSION="$PYTHON_VERSION-rc" + # Dot the Python version for identifying the base Docker image + PYTHON_DOCKER_IMAGE_PART=$(echo ${PYTHON_VERSION:0:1}.${PYTHON_VERSION:1:2}) + + if [[ "$CIBW_PRERELEASE_PYTHONS" =~ [tT]rue ]]; then + PYTHON_DOCKER_IMAGE_PART="${PYTHON_DOCKER_IMAGE_PART}-rc" + fi + + # We could have all of the following logic in a Dockerfile but it's a lot + # easier to do it in bash rather than figure out how to do it in Powershell + # inside the Dockerfile ... + DOCKER_IMAGE="winamd64/python:${PYTHON_DOCKER_IMAGE_PART}-windowsservercore" + MNT_FOLDER="C:/mnt" + CONTAINER_ID=$(docker run -it -v "$(cygpath -w $PWD):$MNT_FOLDER" -d $DOCKER_IMAGE) + + function exec_inside_container() { + docker exec $CONTAINER_ID powershell -Command $1 + } + + exec_inside_container "python -m pip install $MNT_FOLDER/$WHEEL_NAME" + exec_inside_container "python -m pip install $CIBW_TEST_REQUIRES" + + # Save container state to scikit-learn/minimal-windows image. On Windows the + # container needs to be stopped first. + docker stop $CONTAINER_ID + docker commit $CONTAINER_ID scikit-learn/minimal-windows +else + # This is too cumbersome to use a Docker image in the free-threaded case + # TODO When pandas has a release with a Windows free-threaded wheel we can + # replace the next line with + # python -m pip install CIBW_TEST_REQUIRES + python -m pip install pytest fi -# Build a minimal Windows Docker image for testing the wheels -docker build --build-arg PYTHON_VERSION=$PYTHON_VERSION \ - --build-arg WHEEL_NAME=$WHEEL_NAME \ - --build-arg CIBW_TEST_REQUIRES="$CIBW_TEST_REQUIRES" \ - -f build_tools/github/Windows \ - -t scikit-learn/minimal-windows . diff --git a/build_tools/cirrus/build_test_arm.sh b/build_tools/github/build_test_arm.sh similarity index 57% rename from build_tools/cirrus/build_test_arm.sh rename to build_tools/github/build_test_arm.sh index 551dc3689e010..db11fdc0e82f0 100755 --- a/build_tools/cirrus/build_test_arm.sh +++ b/build_tools/github/build_test_arm.sh @@ -22,28 +22,10 @@ setup_ccache() { ccache -M 0 } -MAMBAFORGE_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh" - -# Install Mambaforge -curl -L --retry 10 $MAMBAFORGE_URL -o mambaforge.sh -MAMBAFORGE_PATH=$HOME/mambaforge -bash ./mambaforge.sh -b -p $MAMBAFORGE_PATH -export PATH=$MAMBAFORGE_PATH/bin:$PATH -mamba init --all --verbose -mamba update --yes mamba -mamba update --yes conda -mamba install "$(get_dep conda-lock min)" -y -conda-lock install --name $CONDA_ENV_NAME $LOCK_FILE -source activate $CONDA_ENV_NAME - setup_ccache python --version -# Set parallelism to $N_CORES + 1 to overlap IO bound tasks with CPU bound tasks on CI -# workers with $N_CORES cores when building the compiled extensions of scikit-learn. -export SKLEARN_BUILD_PARALLEL=$(($N_CORES + 1)) - # Disable the build isolation and build in the tree so that the same folder can be # cached between CI runs. pip install --verbose --no-build-isolation . @@ -51,7 +33,7 @@ pip install --verbose --no-build-isolation . # Report cache usage ccache -s --verbose -mamba list +micromamba list # Changing directory not to have module resolution use scikit-learn source # directory but to the installed package. diff --git a/build_tools/github/check_build_trigger.sh b/build_tools/github/check_build_trigger.sh index 3a38924aa23a7..e6bc77b00e71f 100755 --- a/build_tools/github/check_build_trigger.sh +++ b/build_tools/github/check_build_trigger.sh @@ -5,9 +5,9 @@ set -x COMMIT_MSG=$(git log --no-merges -1 --oneline) -# The commit marker "[cd build]" or "[cd build gh]" will trigger the build when required +# The commit marker "[cd build]" will trigger the build when required if [[ "$GITHUB_EVENT_NAME" == schedule || - "$COMMIT_MSG" =~ \[cd\ build\] || - "$COMMIT_MSG" =~ \[cd\ build\ gh\] ]]; then + "$GITHUB_EVENT_NAME" == workflow_dispatch || + "$COMMIT_MSG" =~ \[cd\ build\] ]]; then echo "build=true" >> $GITHUB_OUTPUT fi diff --git a/build_tools/github/check_wheels.py b/build_tools/github/check_wheels.py index 5579d86c5ce3e..21c9a529b265b 100644 --- a/build_tools/github/check_wheels.py +++ b/build_tools/github/check_wheels.py @@ -16,13 +16,6 @@ # plus one more for the sdist n_wheels += 1 -# arm64 builds from cirrus -cirrus_path = Path.cwd() / "build_tools" / "cirrus" / "arm_wheel.yml" -with cirrus_path.open("r") as f: - cirrus_config = yaml.safe_load(f) - -n_wheels += len(cirrus_config["linux_arm64_wheel_task"]["matrix"]) - dist_files = list(Path("dist").glob("**/*")) n_dist_files = len(dist_files) diff --git a/build_tools/github/create_gpu_environment.sh b/build_tools/github/create_gpu_environment.sh new file mode 100755 index 0000000000000..96a62d7678566 --- /dev/null +++ b/build_tools/github/create_gpu_environment.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +set -e +set -x + +curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" +bash Miniforge3-$(uname)-$(uname -m).sh -b -p "${HOME}/conda" +source "${HOME}/conda/etc/profile.d/conda.sh" + + +# defines the get_dep and show_installed_libraries functions +source build_tools/shared.sh +conda activate base + +CONDA_ENV_NAME=sklearn +LOCK_FILE=build_tools/github/pylatest_conda_forge_cuda_array-api_linux-64_conda.lock +create_conda_environment_from_lock_file $CONDA_ENV_NAME $LOCK_FILE + +conda activate $CONDA_ENV_NAME +conda list diff --git a/build_tools/github/pylatest_conda_forge_cuda_array-api_linux-64_conda.lock b/build_tools/github/pylatest_conda_forge_cuda_array-api_linux-64_conda.lock new file mode 100644 index 0000000000000..8a707637fbc9b --- /dev/null +++ b/build_tools/github/pylatest_conda_forge_cuda_array-api_linux-64_conda.lock @@ -0,0 +1,254 @@ +# Generated by conda-lock. +# platform: linux-64 +# input_hash: e141e0789f4a2b4be527fb91bb83f873bd14718407fa58b8790d2198f61bc6f5 +@EXPLICIT 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- blas + - scipy + - cython + - joblib + - threadpoolctl + - matplotlib + - pandas + - pyamg + - pytest + - pytest-xdist + - pillow + - pip + - ninja + - meson-python + - pytest-cov + - coverage + - ccache + - pytorch-gpu + - polars + - pyarrow + - cupy + - array-api-strict diff --git a/build_tools/cirrus/pymin_conda_forge_environment.yml b/build_tools/github/pymin_conda_forge_arm_environment.yml similarity index 96% rename from build_tools/cirrus/pymin_conda_forge_environment.yml rename to build_tools/github/pymin_conda_forge_arm_environment.yml index e41cc7f610ac0..c65ab4aaecf14 100644 --- a/build_tools/cirrus/pymin_conda_forge_environment.yml +++ b/build_tools/github/pymin_conda_forge_arm_environment.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - - python=3.9 + - python=3.10 - numpy - blas - scipy diff --git a/build_tools/github/pymin_conda_forge_arm_linux-aarch64_conda.lock b/build_tools/github/pymin_conda_forge_arm_linux-aarch64_conda.lock new file mode 100644 index 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+https://conda.anaconda.org/conda-forge/linux-aarch64/blas-devel-3.9.0-31_h9678261_openblas.conda#a2cc143d7e25e52a915cb320e5b0d592 +https://conda.anaconda.org/conda-forge/linux-aarch64/cairo-1.18.4-h83712da_0.conda#cd55953a67ec727db5dc32b167201aa6 +https://conda.anaconda.org/conda-forge/linux-aarch64/contourpy-1.3.2-py310hf54e67a_0.conda#779694434d1f0a67c5260db76b7b7907 +https://conda.anaconda.org/conda-forge/linux-aarch64/scipy-1.15.2-py310hf37559f_0.conda#5c9b72f10d2118d943a5eaaf2f396891 +https://conda.anaconda.org/conda-forge/linux-aarch64/blas-2.131-openblas.conda#51c5f346e1ebee750f76066490059df9 +https://conda.anaconda.org/conda-forge/linux-aarch64/harfbuzz-11.1.0-h405b6a2_0.conda#6fd48c127b76a95ed3858c47fa9db7b0 +https://conda.anaconda.org/conda-forge/linux-aarch64/matplotlib-base-3.10.1-py310h2cc5e2d_0.conda#5652e355346f4823f6b4bfdd4860359d +https://conda.anaconda.org/conda-forge/linux-aarch64/qt6-main-6.9.0-ha483c8b_1.conda#fb32973c68de1f23a7e4de3651442b15 +https://conda.anaconda.org/conda-forge/linux-aarch64/pyside6-6.9.0-py310hee8ad4f_0.conda#68f556281ac23f1780381f00de99d66d +https://conda.anaconda.org/conda-forge/linux-aarch64/matplotlib-3.10.1-py310hbbe02a8_0.conda#c6aa0ea00ec104d0ad260c2ed2bb5582 diff --git a/build_tools/github/test_windows_wheels.sh b/build_tools/github/test_windows_wheels.sh index 07954a7a91970..c96ec4ad89d3e 100755 --- a/build_tools/github/test_windows_wheels.sh +++ b/build_tools/github/test_windows_wheels.sh @@ -4,12 +4,27 @@ set -e set -x PYTHON_VERSION=$1 +PROJECT_DIR=$2 -docker container run \ - --rm scikit-learn/minimal-windows \ - powershell -Command "python -c 'import sklearn; sklearn.show_versions()'" +python $PROJECT_DIR/build_tools/wheels/check_license.py -docker container run \ - -e SKLEARN_SKIP_NETWORK_TESTS=1 \ - --rm scikit-learn/minimal-windows \ - powershell -Command "pytest --pyargs sklearn" +FREE_THREADED_BUILD="$(python -c"import sysconfig; print(bool(sysconfig.get_config_var('Py_GIL_DISABLED')))")" + +if [[ $FREE_THREADED_BUILD == "False" ]]; then + # Run the tests for the scikit-learn wheel in a minimal Windows environment + # without any developer runtime libraries installed to ensure that it does not + # implicitly rely on the presence of the DLLs of such runtime libraries. + docker container run \ + --rm scikit-learn/minimal-windows \ + powershell -Command "python -c 'import sklearn; sklearn.show_versions()'" + + docker container run \ + -e SKLEARN_SKIP_NETWORK_TESTS=1 \ + --rm scikit-learn/minimal-windows \ + powershell -Command "pytest --pyargs sklearn" +else + # This is too cumbersome to use a Docker image in the free-threaded case + export PYTHON_GIL=0 + python -c "import sklearn; sklearn.show_versions()" + pytest --pyargs sklearn +fi diff --git a/build_tools/github/upload_anaconda.sh b/build_tools/github/upload_anaconda.sh index 5054b32a53c61..b53f27b75e72b 100755 --- a/build_tools/github/upload_anaconda.sh +++ b/build_tools/github/upload_anaconda.sh @@ -3,8 +3,8 @@ set -e set -x -# Note: build_wheels.sh has the same branch (only for NumPy 2.0 transition) -if [[ "$GITHUB_EVENT_NAME" == "schedule" || "$CIRRUS_CRON" == "nightly" ]]; then +if [[ "$GITHUB_EVENT_NAME" == "schedule" \ + || "$GITHUB_EVENT_NAME" == "workflow_dispatch" ]]; then ANACONDA_ORG="scientific-python-nightly-wheels" ANACONDA_TOKEN="$SCIKIT_LEARN_NIGHTLY_UPLOAD_TOKEN" else @@ -12,11 +12,9 @@ else ANACONDA_TOKEN="$SCIKIT_LEARN_STAGING_UPLOAD_TOKEN" fi -# Install Python 3.8 because of a bug with Python 3.9 export PATH=$CONDA/bin:$PATH -conda create -n upload -y python=3.8 +conda create -n upload -y anaconda-client source activate upload -conda install -y anaconda-client # Force a replacement if the remote file already exists anaconda -t $ANACONDA_TOKEN upload --force -u $ANACONDA_ORG $ARTIFACTS_PATH/* diff --git a/build_tools/linting.sh b/build_tools/linting.sh index aefabfae7b3f5..34b37530e10ff 100755 --- a/build_tools/linting.sh +++ b/build_tools/linting.sh @@ -10,26 +10,25 @@ set -o pipefail global_status=0 -echo -e "### Running black ###\n" -black --check --diff . +echo -e "### Running the ruff linter ###\n" +ruff check --output-format=full status=$? - if [[ $status -eq 0 ]] then - echo -e "No problem detected by black\n" + echo -e "No problem detected by the ruff linter\n" else - echo -e "Problems detected by black, please run black and commit the result\n" + echo -e "Problems detected by ruff check, please fix them\n" global_status=1 fi -echo -e "### Running ruff ###\n" -ruff check --output-format=full . +echo -e "### Running the ruff formatter ###\n" +ruff format --diff status=$? if [[ $status -eq 0 ]] then - echo -e "No problem detected by ruff\n" + echo -e "No problem detected by the ruff formatter\n" else - echo -e "Problems detected by ruff, please fix them\n" + echo -e "Problems detected by ruff format, please run ruff format and commit the result\n" global_status=1 fi @@ -89,16 +88,15 @@ else fi # Check for joblib.delayed and joblib.Parallel imports -# TODO(1.7): remove ":!sklearn/utils/_joblib.py" echo -e "### Checking for joblib imports ###\n" joblib_status=0 -joblib_delayed_import="$(git grep -l -A 10 -E "joblib import.+delayed" -- "*.py" ":!sklearn/utils/_joblib.py" ":!sklearn/utils/parallel.py")" +joblib_delayed_import="$(git grep -l -A 10 -E "joblib import.+delayed" -- "*.py" ":!sklearn/utils/parallel.py")" if [ ! -z "$joblib_delayed_import" ]; then echo "Use from sklearn.utils.parallel import delayed instead of joblib delayed. The following files contains imports to joblib.delayed:" echo "$joblib_delayed_import" joblib_status=1 fi -joblib_Parallel_import="$(git grep -l -A 10 -E "joblib import.+Parallel" -- "*.py" ":!sklearn/utils/_joblib.py" ":!sklearn/utils/parallel.py")" +joblib_Parallel_import="$(git grep -l -A 10 -E "joblib import.+Parallel" -- "*.py" ":!sklearn/utils/parallel.py")" if [ ! -z "$joblib_Parallel_import" ]; then echo "Use from sklearn.utils.parallel import Parallel instead of joblib Parallel. The following files contains imports to joblib.Parallel:" echo "$joblib_Parallel_import" diff --git a/build_tools/shared.sh b/build_tools/shared.sh index 4866c149d506f..3c6f238385506 100644 --- a/build_tools/shared.sh +++ b/build_tools/shared.sh @@ -29,7 +29,23 @@ show_installed_libraries(){ activate_environment() { if [[ "$DISTRIB" =~ ^conda.* ]]; then source activate $VIRTUALENV - elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" || "$DISTRIB" == "pip-nogil" ]]; then + elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" ]]; then source $VIRTUALENV/bin/activate fi } + +create_conda_environment_from_lock_file() { + ENV_NAME=$1 + LOCK_FILE=$2 + # Because we are using lock-files with the "explicit" format, conda can + # install them directly, provided the lock-file does not contain pip solved + # packages. For more details, see + # https://conda.github.io/conda-lock/output/#explicit-lockfile + lock_file_has_pip_packages=$(grep -q files.pythonhosted.org $LOCK_FILE && echo "true" || echo "false") + if [[ "$lock_file_has_pip_packages" == "false" ]]; then + conda create --name $ENV_NAME --file $LOCK_FILE + else + python -m pip install "$(get_dep conda-lock min)" + conda-lock install --name $ENV_NAME $LOCK_FILE + fi +} diff --git a/build_tools/update_environments_and_lock_files.py b/build_tools/update_environments_and_lock_files.py index 92d97709386d1..0edf62b5a0d7b 100644 --- a/build_tools/update_environments_and_lock_files.py +++ b/build_tools/update_environments_and_lock_files.py @@ -7,7 +7,7 @@ - make sure that the latest versions of all the dependencies are used in the CI. There is a scheduled workflow that does this, see .github/workflows/update-lock-files.yml. This is still useful to run this - script when when the automated PR fails and for example some packages need to + script when the automated PR fails and for example some packages need to be pinned. You can add the pins to this script, run it, and open a PR with the changes. - bump minimum dependencies in sklearn/_min_dependencies.py. Running this @@ -26,6 +26,7 @@ with pip. To run this script you need: +- conda - conda-lock. The version should match the one used in the CI in sklearn/_min_dependencies.py - pip-tools @@ -90,13 +91,30 @@ def remove_from(alist, to_remove): build_metadata_list = [ + { + "name": "pylatest_conda_forge_cuda_array-api_linux-64", + "type": "conda", + "tag": "cuda", + "folder": "build_tools/github", + "platform": "linux-64", + "channels": ["conda-forge", "pytorch", "nvidia"], + "conda_dependencies": common_dependencies + + [ + "ccache", + "pytorch-gpu", + "polars", + "pyarrow", + "cupy", + "array-api-strict", + ], + }, { "name": "pylatest_conda_forge_mkl_linux-64", "type": "conda", "tag": "main-ci", "folder": "build_tools/azure", "platform": "linux-64", - "channel": "conda-forge", + "channels": ["conda-forge"], "conda_dependencies": common_dependencies + [ "ccache", @@ -104,12 +122,11 @@ def remove_from(alist, to_remove): "pytorch-cpu", "polars", "pyarrow", - "array-api-compat", "array-api-strict", + "scipy-doctest", ], "package_constraints": { "blas": "[build=mkl]", - "pytorch": "1.13", }, }, { @@ -118,7 +135,7 @@ def remove_from(alist, to_remove): "tag": "main-ci", "folder": "build_tools/azure", "platform": "osx-64", - "channel": "conda-forge", + "channels": ["conda-forge"], "conda_dependencies": common_dependencies + [ "ccache", @@ -135,7 +152,7 @@ def remove_from(alist, to_remove): "tag": "main-ci", "folder": "build_tools/azure", "platform": "osx-64", - "channel": "defaults", + "channels": ["defaults"], "conda_dependencies": remove_from( common_dependencies, ["cython", "threadpoolctl", "meson-python"] ) @@ -149,33 +166,30 @@ def remove_from(alist, to_remove): }, # TODO: put cython, threadpoolctl and meson-python back to conda # dependencies when required version is available on the main channel - "pip_dependencies": ["cython", "threadpoolctl", "meson-python"], + "pip_dependencies": ["cython", "threadpoolctl", "meson-python", "meson"], }, { - "name": "pymin_conda_defaults_openblas", + "name": "pymin_conda_forge_openblas_min_dependencies", "type": "conda", "tag": "main-ci", "folder": "build_tools/azure", "platform": "linux-64", - "channel": "defaults", - "conda_dependencies": remove_from( - common_dependencies, - ["pandas", "threadpoolctl", "pip", "ninja", "meson-python"], - ) - + ["ccache"], + "channels": ["conda-forge"], + "conda_dependencies": common_dependencies + ["ccache", "polars"], "package_constraints": { - "python": "3.9", + "python": "3.10", "blas": "[build=openblas]", - "numpy": "1.21", # the min version is not available on the defaults channel - "scipy": "1.7", # the min version has some low level crashes + "numpy": "min", + "scipy": "min", "matplotlib": "min", "cython": "min", "joblib": "min", "threadpoolctl": "min", + "meson-python": "min", + "pandas": "min", + "polars": "min", + "pyamg": "min", }, - # TODO: put pip dependencies back to conda dependencies when required - # version is available on the defaults channel. - "pip_dependencies": ["threadpoolctl"], }, { "name": "pymin_conda_forge_openblas_ubuntu_2204", @@ -183,14 +197,14 @@ def remove_from(alist, to_remove): "tag": "main-ci", "folder": "build_tools/azure", "platform": "linux-64", - "channel": "conda-forge", + "channels": ["conda-forge"], "conda_dependencies": ( - common_dependencies_without_coverage + remove_from(common_dependencies_without_coverage, ["matplotlib"]) + docstring_test_dependencies + ["ccache"] ), "package_constraints": { - "python": "3.9", + "python": "3.10", "blas": "[build=openblas]", }, }, @@ -200,16 +214,18 @@ def remove_from(alist, to_remove): "tag": "main-ci", "folder": "build_tools/azure", "platform": "linux-64", - "channel": "defaults", + "channels": ["defaults"], "conda_dependencies": ["python", "ccache"], "pip_dependencies": ( remove_from(common_dependencies, ["python", "blas", "pip"]) + docstring_test_dependencies + # Test with some optional dependencies + ["lightgbm", "scikit-image"] + # Test array API on CPU without PyTorch + + ["array-api-strict"] + # doctests dependencies + + ["scipy-doctest"] ), - "package_constraints": { - "python": "3.9", - }, }, { "name": "pylatest_pip_scipy_dev", @@ -217,7 +233,7 @@ def remove_from(alist, to_remove): "tag": "scipy-dev", "folder": "build_tools/azure", "platform": "linux-64", - "channel": "defaults", + "channels": ["defaults"], "conda_dependencies": ["python", "ccache"], "pip_dependencies": ( remove_from( @@ -245,20 +261,45 @@ def remove_from(alist, to_remove): + ["python-dateutil"] ), }, + { + "name": "pylatest_free_threaded", + "type": "conda", + "tag": "free-threaded", + "folder": "build_tools/azure", + "platform": "linux-64", + "channels": ["conda-forge"], + "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. + "joblib", + "threadpoolctl", + "pytest", + "pytest-xdist", + "ninja", + "meson-python", + "ccache", + "pip", + ], + }, { "name": "pymin_conda_forge_mkl", "type": "conda", "tag": "main-ci", "folder": "build_tools/azure", "platform": "win-64", - "channel": "conda-forge", + "channels": ["conda-forge"], "conda_dependencies": remove_from(common_dependencies, ["pandas", "pyamg"]) + [ "wheel", "pip", ], "package_constraints": { - "python": "3.9", + "python": "3.10", "blas": "[build=mkl]", }, }, @@ -268,7 +309,7 @@ def remove_from(alist, to_remove): "tag": "main-ci", "folder": "build_tools/circle", "platform": "linux-64", - "channel": "conda-forge", + "channels": ["conda-forge"], "conda_dependencies": common_dependencies_without_coverage + [ "scikit-image", @@ -286,13 +327,14 @@ def remove_from(alist, to_remove): "sphinx-remove-toctrees", "sphinx-design", "pydata-sphinx-theme", + "towncrier", ], "pip_dependencies": [ "sphinxext-opengraph", "sphinxcontrib-sass", ], "package_constraints": { - "python": "3.9", + "python": "3.10", "numpy": "min", "scipy": "min", "matplotlib": "min", @@ -308,10 +350,12 @@ def remove_from(alist, to_remove): "plotly": "min", "polars": "min", "pooch": "min", + "pyamg": "min", "sphinx-design": "min", "sphinxcontrib-sass": "min", "sphinx-remove-toctrees": "min", "pydata-sphinx-theme": "min", + "towncrier": "min", }, }, { @@ -320,7 +364,7 @@ def remove_from(alist, to_remove): "tag": "main-ci", "folder": "build_tools/circle", "platform": "linux-64", - "channel": "conda-forge", + "channels": ["conda-forge"], "conda_dependencies": common_dependencies_without_coverage + [ "scikit-image", @@ -339,6 +383,7 @@ def remove_from(alist, to_remove): "sphinx-remove-toctrees", "sphinx-design", "pydata-sphinx-theme", + "towncrier", ], "pip_dependencies": [ "jupyterlite-sphinx", @@ -346,26 +391,26 @@ def remove_from(alist, to_remove): "sphinxcontrib-sass", ], "package_constraints": { - "python": "3.9", + "python": "3.10", }, }, { - "name": "pymin_conda_forge", + "name": "pymin_conda_forge_arm", "type": "conda", - "tag": "arm", - "folder": "build_tools/cirrus", + "tag": "main-ci", + "folder": "build_tools/github", "platform": "linux-aarch64", - "channel": "conda-forge", + "channels": ["conda-forge"], "conda_dependencies": remove_from( common_dependencies_without_coverage, ["pandas", "pyamg"] ) + ["pip", "ccache"], "package_constraints": { - "python": "3.9", + "python": "3.10", }, }, { - "name": "debian_atlas_32bit", + "name": "debian_32bit", "type": "pip", "tag": "main-ci", "folder": "build_tools/azure", @@ -378,16 +423,9 @@ def remove_from(alist, to_remove): "ninja", "meson-python", ], - "package_constraints": { - "joblib": "min", - "threadpoolctl": "3.1.0", - "pytest": "min", - "pytest-cov": "min", - # no pytest-xdist because it causes issue on 32bit - "cython": "min", - }, - # same Python version as in debian-32 build - "python_version": "3.9.2", + # Python version from the python3 APT package in the debian-32 docker + # image. + "python_version": "3.12.5", }, { "name": "ubuntu_atlas", @@ -472,7 +510,9 @@ def get_conda_environment_content(build_metadata): # following script to centralize the configuration for CI builds: # build_tools/update_environments_and_lock_files.py channels: - - {{ build_metadata['channel'] }} + {% for channel in build_metadata['channels'] %} + - {{ channel }} + {% endfor %} dependencies: {% for conda_dep in build_metadata['conda_dependencies'] %} - {{ conda_dep | get_package_with_constraint(build_metadata) }} @@ -603,9 +643,9 @@ def write_pip_lock_file(build_metadata): json_output = execute_command(["conda", "info", "--json"]) conda_info = json.loads(json_output) - environment_folder = [ + environment_folder = next( each for each in conda_info["envs"] if each.endswith(environment_name) - ][0] + ) environment_path = Path(environment_folder) pip_compile_path = environment_path / "bin" / "pip-compile" @@ -720,6 +760,7 @@ def main(select_build, skip_build, select_tag, verbose, very_verbose): filtered_conda_build_metadata_list = [ each for each in filtered_build_metadata_list if each["type"] == "conda" ] + if filtered_conda_build_metadata_list: logger.info("# Writing conda environments") write_all_conda_environments(filtered_conda_build_metadata_list) diff --git a/build_tools/wheels/LICENSE_linux.txt b/build_tools/wheels/LICENSE_linux.txt new file mode 100644 index 0000000000000..057656fcc789d --- /dev/null +++ b/build_tools/wheels/LICENSE_linux.txt @@ -0,0 +1,80 @@ +This binary distribution of scikit-learn also bundles the following software: + +---- + +Name: GCC runtime library +Files: scikit_learn.libs/libgomp*.so* +Availability: https://gcc.gnu.org/git/?p=gcc.git;a=tree;f=libgomp + +GCC RUNTIME LIBRARY EXCEPTION + +Version 3.1, 31 March 2009 + +Copyright (C) 2009 Free Software Foundation, Inc. + +Everyone is permitted to copy and distribute verbatim copies of this +license document, but changing it is not allowed. + +This GCC Runtime Library Exception ("Exception") is an additional +permission under section 7 of the GNU General Public License, version +3 ("GPLv3"). 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All such code will be identified clearly using at least one of two +mechanisms: +1) It will be in a separate directory tree with its own `LICENSE.txt` or + `LICENSE` file at the top containing the specific license and restrictions + which apply to that software, or +2) It will contain specific license and restriction terms at the top of every + file. + +============================================================================== +Legacy LLVM License (https://llvm.org/docs/DeveloperPolicy.html#legacy): +============================================================================== +University of Illinois/NCSA +Open Source License + +Copyright (c) 2003-2019 University of Illinois at Urbana-Champaign. +All rights reserved. + +Developed by: + + LLVM Team + + University of Illinois at Urbana-Champaign + + http://llvm.org + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal with +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is furnished to do +so, subject to the following conditions: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimers. + + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimers in the + documentation and/or other materials provided with the distribution. + + * Neither the names of the LLVM Team, University of Illinois at + Urbana-Champaign, nor the names of its contributors may be used to + endorse or promote products derived from this Software without specific + prior written permission. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS +FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE +SOFTWARE. diff --git a/build_tools/wheels/LICENSE_windows.txt b/build_tools/wheels/LICENSE_windows.txt new file mode 100644 index 0000000000000..9e98ad8defac2 --- /dev/null +++ b/build_tools/wheels/LICENSE_windows.txt @@ -0,0 +1,25 @@ +This binary distribution of scikit-learn also bundles the following software: + +---- + +Name: Microsoft Visual C++ Runtime Files +Files: sklearn\.libs\*.dll +Availability: https://learn.microsoft.com/en-us/visualstudio/releases/2015/2015-redistribution-vs + +Subject to the License Terms for the software, you may copy and distribute with your +program any of the files within the followng folder and its subfolders except as noted +below. You may not modify these files. + +C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\redist + +You may not distribute the contents of the following folders: + +C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\redist\debug_nonredist +C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\redist\onecore\debug_nonredist + +Subject to the License Terms for the software, you may copy and distribute the following +files with your program in your program’s application local folder or by deploying them +into the Global Assembly Cache (GAC): + +VC\atlmfc\lib\mfcmifc80.dll +VC\atlmfc\lib\amd64\mfcmifc80.dll diff --git a/build_tools/wheels/build_wheels.sh b/build_tools/wheels/build_wheels.sh index d2df4e3936829..02b05bc8a2795 100755 --- a/build_tools/wheels/build_wheels.sh +++ b/build_tools/wheels/build_wheels.sh @@ -38,8 +38,8 @@ if [[ $(uname) == "Darwin" ]]; then OPENMP_URL="https://anaconda.org/conda-forge/llvm-openmp/11.1.0/download/osx-64/llvm-openmp-11.1.0-hda6cdc1_1.tar.bz2" fi - sudo conda create -n build $OPENMP_URL - PREFIX="$CONDA_HOME/envs/build" + conda create -n build $OPENMP_URL + PREFIX="$HOME/miniconda3/envs/build" export CC=/usr/bin/clang export CXX=/usr/bin/clang++ @@ -49,14 +49,11 @@ if [[ $(uname) == "Darwin" ]]; then export LDFLAGS="$LDFLAGS -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lomp" fi - -if [[ "$GITHUB_EVENT_NAME" == "schedule" || "$CIRRUS_CRON" == "nightly" ]]; then - # Nightly build: See also `../github/upload_anaconda.sh` (same branching). - # To help with NumPy 2.0 transition, ensure that we use the NumPy 2.0 - # nightlies. This lives on the edge and opts-in to all pre-releases. - # That could be an issue, in which case no-build-isolation and a targeted - # NumPy install may be necessary, instead. - export CIBW_BUILD_FRONTEND='pip; args: --pre --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"' +if [[ "$CIBW_FREE_THREADED_SUPPORT" =~ [tT]rue ]]; then + # Numpy, scipy, Cython only have free-threaded wheels on scientific-python-nightly-wheels + # TODO: remove this after CPython 3.13 is released (scheduled October 2024) + # and our dependencies have free-threaded wheels on PyPI + export CIBW_BUILD_FRONTEND='pip; args: --pre --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" --only-binary :all:' fi # The version of the built dependencies are specified diff --git a/build_tools/wheels/check_license.py b/build_tools/wheels/check_license.py new file mode 100644 index 0000000000000..00fe4169be65d --- /dev/null +++ b/build_tools/wheels/check_license.py @@ -0,0 +1,30 @@ +"""Checks the bundled license is installed with the wheel.""" + +import platform +import site +from itertools import chain +from pathlib import Path + +site_packages = site.getsitepackages() + +site_packages_path = (Path(p) for p in site_packages) + +try: + distinfo_path = next( + chain( + s + for site_package in site_packages_path + for s in site_package.glob("scikit_learn-*.dist-info") + ) + ) +except StopIteration as e: + raise RuntimeError("Unable to find scikit-learn's dist-info") from e + +license_text = (distinfo_path / "COPYING").read_text() + +assert "Copyright (c)" in license_text + +assert ( + "This binary distribution of scikit-learn also bundles the following software" + in license_text +), f"Unable to find bundled license for {platform.system()}" diff --git a/build_tools/wheels/cibw_before_build.sh b/build_tools/wheels/cibw_before_build.sh new file mode 100755 index 0000000000000..4e4558db5a5bc --- /dev/null +++ b/build_tools/wheels/cibw_before_build.sh @@ -0,0 +1,18 @@ +#!/bin/bash + +set -euxo pipefail + +PROJECT_DIR="$1" +LICENSE_FILE="$PROJECT_DIR/COPYING" + +echo "" >>"$LICENSE_FILE" +echo "----" >>"$LICENSE_FILE" +echo "" >>"$LICENSE_FILE" + +if [[ $RUNNER_OS == "Linux" ]]; then + cat $PROJECT_DIR/build_tools/wheels/LICENSE_linux.txt >>"$LICENSE_FILE" +elif [[ $RUNNER_OS == "macOS" ]]; then + cat $PROJECT_DIR/build_tools/wheels/LICENSE_macos.txt >>"$LICENSE_FILE" +elif [[ $RUNNER_OS == "Windows" ]]; then + cat $PROJECT_DIR/build_tools/wheels/LICENSE_windows.txt >>"$LICENSE_FILE" +fi diff --git a/build_tools/wheels/test_wheels.sh b/build_tools/wheels/test_wheels.sh index e8cdf4b3ea8a2..1d6ee19bda8a8 100755 --- a/build_tools/wheels/test_wheels.sh +++ b/build_tools/wheels/test_wheels.sh @@ -3,9 +3,21 @@ set -e set -x +PROJECT_DIR="$1" + +python $PROJECT_DIR/build_tools/wheels/check_license.py + python -c "import joblib; print(f'Number of cores (physical): \ {joblib.cpu_count()} ({joblib.cpu_count(only_physical_cores=True)})')" +FREE_THREADED_BUILD="$(python -c"import sysconfig; print(bool(sysconfig.get_config_var('Py_GIL_DISABLED')))")" +if [[ $FREE_THREADED_BUILD == "True" ]]; then + # TODO: delete when importing numpy no longer enables the GIL + # setting to zero ensures the GIL is disabled while running the + # tests under free-threaded python + export PYTHON_GIL=0 +fi + # Test that there are no links to system libraries in the # threadpoolctl output section of the show_versions output: python -c "import sklearn; sklearn.show_versions()" diff --git a/doc/Makefile b/doc/Makefile index f84d3c78b8051..1419bac49316d 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -2,7 +2,7 @@ # # You can set these variables from the command line. -SPHINXOPTS = -T +SPHINXOPTS ?= -T SPHINXBUILD ?= sphinx-build PAPER = BUILDDIR = _build @@ -66,6 +66,7 @@ clean: # https://github.com/scikit-learn/scikit-learn/pull/25809 html: SPHINX_NUMJOBS ?= 1 html: + @echo $(ALLSPHINXOPTS) # These two lines make the build a bit more lengthy, and the # the embedding of images more robust rm -rf $(BUILDDIR)/html/_images diff --git a/doc/about.rst b/doc/about.rst index 47d57e4737318..4db39f9709e73 100644 --- a/doc/about.rst +++ b/doc/about.rst @@ -1,26 +1,28 @@ .. _about: +======== About us ======== History -------- +======= This project was started in 2007 as a Google Summer of Code project by -David Cournapeau. Later that year, Matthieu Brucher started work on -this project as part of his thesis. +David Cournapeau. Later that year, Matthieu Brucher started working on this project +as part of his thesis. In 2010 Fabian Pedregosa, Gael Varoquaux, Alexandre Gramfort and Vincent Michel of INRIA took leadership of the project and made the first public release, February the 1st 2010. Since then, several releases have appeared following an approximately 3-month cycle, and a thriving international -community has been leading the development. +community has been leading the development. As a result, INRIA holds the +copyright over the work done by people who were employed by INRIA at the +time of the contribution. Governance ----------- +========== -The decision making process and governance structure of scikit-learn is laid -out in the :ref:`governance document `. +The decision making process and governance structure of scikit-learn, like roles and responsibilities, is laid out in the :ref:`governance document `. .. The "author" anchors below is there to ensure that old html links (in the form of "about.html#author" still work) @@ -28,14 +30,17 @@ out in the :ref:`governance document `. .. _authors: The people behind scikit-learn ------------------------------- +============================== Scikit-learn is a community project, developed by a large group of -people, all across the world. A few teams, listed below, have central -roles, however a more complete list of contributors can be found `on +people, all across the world. A few core contributor teams, listed below, have +central roles, however a more complete list of contributors can be found `on github `__. +Active Core Contributors +------------------------ + Maintainers Team ................ @@ -79,8 +84,11 @@ The following people help with :ref:`communication around scikit-learn .. include:: communication_team.rst -Emeritus Core Developers -........................ +Emeritus Core Contributors +-------------------------- + +Emeritus Maintainers Team +......................... The following people have been active contributors in the past, but are no longer active in the project: @@ -106,7 +114,7 @@ past: .. _citing-scikit-learn: Citing scikit-learn -------------------- +=================== If you use scikit-learn in a scientific publication, we would appreciate citations to the following paper: @@ -151,7 +159,7 @@ Bibtex entry:: } Artwork -------- +======= High quality PNG and SVG logos are available in the `doc/logos/ `_ @@ -161,7 +169,7 @@ source directory. :align: center Funding -------- +======= Scikit-learn is a community driven project, however institutional and private grants help to assure its sustainability. @@ -174,8 +182,9 @@ The project would like to thank the following funders. .. div:: text-box - `:probabl. `_ funds Adrin Jalali, Arturo Amor, François Goupil, - Guillaume Lemaitre, Jérémie du Boisberranger, Olivier Grisel, and Stefanie Senger. + `:probabl. `_ employs Adrin Jalali, Arturo Amor, + François Goupil, Guillaume Lemaitre, Jérémie du Boisberranger, Loïc Estève, + Olivier Grisel, and Stefanie Senger. .. div:: image-box @@ -196,9 +205,6 @@ The project would like to thank the following funders. .. |dataiku| image:: images/dataiku.png :target: https://www.dataiku.com/ -.. |hf| image:: images/huggingface_logo-noborder.png - :target: https://huggingface.co - .. |nvidia| image:: images/nvidia.png :target: https://www.nvidia.com @@ -243,7 +249,7 @@ The project would like to thank the following funders. +----------+-----------+ | |axa| | |bnp| | +----------+-----------+ - | |nvidia| | |hf| | + | |nvidia| | +----------+-----------+ | |dataiku| | +----------+-----------+ @@ -292,6 +298,35 @@ The project would like to thank the following funders. ........... +.. |czi| image:: images/czi.png + :target: https://chanzuckerberg.com + +.. |wellcome| image:: images/wellcome-trust.png + :target: https://wellcome.org/ + +.. div:: sk-text-image-grid-small + + .. div:: text-box + + `The Chan-Zuckerberg Initiative `_ and + `Wellcome Trust `_ fund scikit-learn through the + `Essential Open Source Software for Science (EOSS) `_ + cycle 6. + + It supports Lucy Liu and diversity & inclusion initiatives that will + be announced in the future. + + .. div:: image-box + + .. table:: + :class: image-subtable + + +----------+----------------+ + | |czi| | |wellcome| | + +----------+----------------+ + +........... + .. div:: sk-text-image-grid-small .. div:: text-box @@ -308,7 +343,7 @@ The project would like to thank the following funders. Past Sponsors -............. +------------- .. div:: sk-text-image-grid-small @@ -455,7 +490,7 @@ Past Sponsors .. div:: image-box - .. image:: images/czi_logo.svg + .. image:: images/czi.png :target: https://chanzuckerberg.com ...................... @@ -499,6 +534,9 @@ the past: .. |aphp| image:: images/logo_APHP_text.png :target: https://aphp.fr/ +.. |hf| image:: images/huggingface_logo-noborder.png + :target: https://huggingface.co + .. raw:: html

-

Lauren Burke

+

Lauren Burke-McCarthy


diff --git a/doc/computing/computational_performance.rst b/doc/computing/computational_performance.rst index a7b6d3a37001e..4af79206dae1c 100644 --- a/doc/computing/computational_performance.rst +++ b/doc/computing/computational_performance.rst @@ -15,9 +15,9 @@ scikit-learn estimators in different contexts and provide some tips and tricks for overcoming performance bottlenecks. Prediction latency is measured as the elapsed time necessary to make a -prediction (e.g. in micro-seconds). Latency is often viewed as a distribution +prediction (e.g. in microseconds). Latency is often viewed as a distribution and operations engineers often focus on the latency at a given percentile of -this distribution (e.g. the 90 percentile). +this distribution (e.g. the 90th percentile). Prediction throughput is defined as the number of predictions the software can deliver in a given amount of time (e.g. in predictions per second). @@ -30,7 +30,7 @@ to take into account the same exact properties of the data as more complex ones. Prediction Latency ------------------ -One of the most straight-forward concerns one may have when using/choosing a +One of the most straightforward concerns one may have when using/choosing a machine learning toolkit is the latency at which predictions can be made in a production environment. @@ -352,7 +352,7 @@ feature selection components in a pipeline once we know which features to keep from a previous run. Finally, it can help reduce processing time and I/O usage upstream in the data access and feature extraction layers by not collecting and building features that are discarded by the model. For instance -if the raw data come from a database, it can make it possible to write simpler +if the raw data come from a database, it is possible to write simpler and faster queries or reduce I/O usage by making the queries return lighter records. At the moment, reshaping needs to be performed manually in scikit-learn. diff --git a/doc/computing/parallelism.rst b/doc/computing/parallelism.rst index 5c15cd9db440e..d2ff106aec3be 100644 --- a/doc/computing/parallelism.rst +++ b/doc/computing/parallelism.rst @@ -72,7 +72,7 @@ In practice, whether parallelism is helpful at improving runtime depends on many factors. It is usually a good idea to experiment rather than assuming that increasing the number of workers is always a good thing. In some cases it can be highly detrimental to performance to run multiple copies of some -estimators or functions in parallel (see oversubscription below). +estimators or functions in parallel (see :ref:`oversubscription` below). Lower-level parallelism with OpenMP ................................... @@ -103,7 +103,7 @@ such as MKL, OpenBLAS or BLIS. You can control the exact number of threads used by BLAS for each library using environment variables, namely: -- ``MKL_NUM_THREADS`` sets the number of thread MKL uses, +- ``MKL_NUM_THREADS`` sets the number of threads MKL uses, - ``OPENBLAS_NUM_THREADS`` sets the number of threads OpenBLAS uses - ``BLIS_NUM_THREADS`` sets the number of threads BLIS uses @@ -122,11 +122,13 @@ for different values of `OMP_NUM_THREADS`: distributed on pypi.org (i.e. the ones installed via ``pip install``) and on the conda-forge channel (i.e. the ones installed via ``conda install --channel conda-forge``) are linked with OpenBLAS, while - NumPy and SciPy packages packages shipped on the ``defaults`` conda + NumPy and SciPy packages shipped on the ``defaults`` conda channel from Anaconda.org (i.e. the ones installed via ``conda install``) are linked by default with MKL. +.. _oversubscription: + Oversubscription: spawning too many threads ........................................... @@ -227,19 +229,17 @@ state of the aforementioned singletons. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Controls the seeding of the random number generator used in tests that rely on -the `global_random_seed`` fixture. +the `global_random_seed` fixture. All tests that use this fixture accept the contract that they should deterministically pass for any seed value from 0 to 99 included. -If the `SKLEARN_TESTS_GLOBAL_RANDOM_SEED` environment variable is set to -`"any"` (which should be the case on nightly builds on the CI), the fixture -will choose an arbitrary seed in the above range (based on the BUILD_NUMBER or -the current day) and all fixtured tests will run for that specific seed. The -goal is to ensure that, over time, our CI will run all tests with different -seeds while keeping the test duration of a single run of the full test suite -limited. This will check that the assertions of tests written to use this -fixture are not dependent on a specific seed value. +In nightly CI builds, the `SKLEARN_TESTS_GLOBAL_RANDOM_SEED` environment +variable is drawn randomly in the above range and all fixtured tests will run +for that specific seed. The goal is to ensure that, over time, our CI will run +all tests with different seeds while keeping the test duration of a single run +of the full test suite limited. This will check that the assertions of tests +written to use this fixture are not dependent on a specific seed value. The range of admissible seed values is limited to [0, 99] because it is often not possible to write a test that can work for any possible seed and we want to @@ -250,8 +250,6 @@ Valid values for `SKLEARN_TESTS_GLOBAL_RANDOM_SEED`: - `SKLEARN_TESTS_GLOBAL_RANDOM_SEED="42"`: run tests with a fixed seed of 42 - `SKLEARN_TESTS_GLOBAL_RANDOM_SEED="40-42"`: run the tests with all seeds between 40 and 42 included -- `SKLEARN_TESTS_GLOBAL_RANDOM_SEED="any"`: run the tests with an arbitrary - seed selected between 0 and 99 included - `SKLEARN_TESTS_GLOBAL_RANDOM_SEED="all"`: run the tests with all seeds between 0 and 99 included. This can take a long time: only use for individual tests, not the full test suite! @@ -300,7 +298,7 @@ segfaults. When this environment variable is set to a non zero value, the debug symbols will be included in the compiled C extensions. Only debug symbols for POSIX -systems is configured. +systems are configured. `SKLEARN_PAIRWISE_DIST_CHUNK_SIZE` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -329,7 +327,7 @@ you can set `SKLEARN_WARNINGS_AS_ERRORS=1`. By default, warnings are not turned into errors. This is the case if `SKLEARN_WARNINGS_AS_ERRORS` is unset, or `SKLEARN_WARNINGS_AS_ERRORS=0`. -This environment variable use specific warning filters to ignore some warnings, +This environment variable uses specific warning filters to ignore some warnings, since sometimes warnings originate from third-party libraries and there is not much we can do about it. You can see the warning filters in the `_get_warnings_filters_info_list` function in `sklearn/utils/_testing.py`. diff --git a/doc/conf.py b/doc/conf.py index db79bfe3f7865..1113d4b2c100a 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -10,12 +10,14 @@ # All configuration values have a default; values that are commented out # serve to show the default. +import json import os import re import sys import warnings from datetime import datetime from pathlib import Path +from urllib.request import urlopen from sklearn.externals._packaging.version import parse from sklearn.utils._testing import turn_warnings_into_errors @@ -30,9 +32,12 @@ import jinja2 import sphinx_gallery from github_link import make_linkcode_resolve +from sphinx.util.logging import getLogger from sphinx_gallery.notebook import add_code_cell, add_markdown_cell from sphinx_gallery.sorting import ExampleTitleSortKey +logger = getLogger(__name__) + try: # Configure plotly to integrate its output into the HTML pages generated by # sphinx-gallery. @@ -69,7 +74,6 @@ "autoshortsummary", "doi_role", "dropdown_anchors", - "move_gallery_links", "override_pst_pagetoc", "sphinx_issues", ] @@ -175,6 +179,7 @@ "templates", "includes", "**/sg_execution_times.rst", + "whats_new/upcoming_changes", ] # The reST default role (used for this markup: `text`) to use for all @@ -202,6 +207,11 @@ # Sphinx are currently 'default' and 'sphinxdoc'. html_theme = "pydata_sphinx_theme" +# This config option is used to generate the canonical links in the header +# of every page. The canonical link is needed to prevent search engines from +# returning results pointing to old scikit-learn versions. +html_baseurl = "https://scikit-learn.org/stable/" + # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. @@ -276,7 +286,16 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-exclude_patterns # In particular, "**" specifies the default for all pages # Use :html_theme.sidebar_secondary.remove: for file-wide removal - "secondary_sidebar_items": {"**": ["page-toc", "sourcelink"]}, + "secondary_sidebar_items": { + "**": [ + "page-toc", + "sourcelink", + # Sphinx-Gallery-specific sidebar components + # https://sphinx-gallery.github.io/stable/advanced.html#using-sphinx-gallery-sidebar-components + "sg_download_links", + "sg_launcher_links", + ], + }, "show_version_warning_banner": True, "announcement": None, } @@ -332,6 +351,7 @@ html_js_files = [ "scripts/dropdown.js", "scripts/version-switcher.js", + "scripts/sg_plotly_resize.js", ] # Compile scss files into css files using sphinxcontrib-sass @@ -359,13 +379,11 @@ def add_js_css_files(app, pagename, templatename, context, doctree): app.add_css_file( "https://cdn.datatables.net/2.0.0/css/dataTables.dataTables.min.css" ) - # Internal: API search intialization and styling + # Internal: API search initialization and styling app.add_js_file("scripts/api-search.js") app.add_css_file("styles/api-search.css") elif pagename == "index": app.add_css_file("styles/index.css") - elif pagename == "install": - app.add_css_file("styles/install.css") elif pagename.startswith("modules/generated/"): app.add_css_file("styles/api.css") @@ -422,6 +440,7 @@ def add_js_css_files(app, pagename, templatename, context, doctree): "contents": "index", "preface": "index", "modules/classes": "api/index", + "tutorial/machine_learning_map/index": "machine_learning_map", "auto_examples/feature_selection/plot_permutation_test_for_classification": ( "auto_examples/model_selection/plot_permutation_tests_for_classification" ), @@ -429,8 +448,17 @@ def add_js_css_files(app, pagename, templatename, context, doctree): "auto_examples/linear_model/plot_bayesian_ridge": ( "auto_examples/linear_model/plot_ard" ), - "auto_examples/model_selection/grid_search_text_feature_extraction.py": ( - "auto_examples/model_selection/plot_grid_search_text_feature_extraction.py" + "auto_examples/model_selection/grid_search_text_feature_extraction": ( + "auto_examples/model_selection/plot_grid_search_text_feature_extraction" + ), + "auto_examples/model_selection/plot_validation_curve": ( + "auto_examples/model_selection/plot_train_error_vs_test_error" + ), + "auto_examples/datasets/plot_digits_last_image": ( + "auto_examples/exercises/plot_digits_classification_exercises" + ), + "auto_examples/datasets/plot_random_dataset": ( + "auto_examples/classification/plot_classifier_comparison" ), "auto_examples/miscellaneous/plot_changed_only_pprint_parameter": ( "auto_examples/miscellaneous/plot_estimator_representation" @@ -445,8 +473,40 @@ def add_js_css_files(app, pagename, templatename, context, doctree): "auto_examples/decomposition/plot_pca_3d": ( "auto_examples/decomposition/plot_pca_iris" ), - "auto_examples/exercises/plot_cv_digits.py": ( - "auto_examples/model_selection/plot_nested_cross_validation_iris.py" + "auto_examples/exercises/plot_cv_digits": ( + "auto_examples/model_selection/plot_nested_cross_validation_iris" + ), + "auto_examples/linear_model/plot_lasso_lars": ( + "auto_examples/linear_model/plot_lasso_lasso_lars_elasticnet_path" + ), + "auto_examples/linear_model/plot_lasso_coordinate_descent_path": ( + "auto_examples/linear_model/plot_lasso_lasso_lars_elasticnet_path" + ), + "auto_examples/cluster/plot_color_quantization": ( + "auto_examples/cluster/plot_face_compress" + ), + "auto_examples/cluster/plot_cluster_iris": ( + "auto_examples/cluster/plot_kmeans_assumptions" + ), + "auto_examples/ensemble/plot_forest_importances_faces": ( + "auto_examples/ensemble/plot_forest_importances" + ), + "auto_examples/ensemble/plot_voting_probas": ( + "auto_examples/ensemble/plot_voting_decision_regions" + ), + "auto_examples/datasets/plot_iris_dataset": ( + "auto_examples/decomposition/plot_pca_iris" + ), + "auto_examples/linear_model/plot_iris_logistic": ( + "auto_examples/linear_model/plot_logistic_multinomial" + ), + "auto_examples/linear_model/plot_ols_3d": ("auto_examples/linear_model/plot_ols"), + "auto_examples/linear_model/plot_ols": "auto_examples/linear_model/plot_ols_ridge", + "auto_examples/linear_model/plot_ols_ridge_variance": ( + "auto_examples/linear_model/plot_ols_ridge" + ), + "auto_examples/linear_model/plot_sgd_comparison": ( + "auto_examples/linear_model/plot_sgd_loss_functions" ), } html_context["redirects"] = redirects @@ -625,6 +685,23 @@ def notebook_modification_function(notebook_content, notebook_filename): # imports inside functions code_lines.extend(["import matplotlib", "import pandas"]) + # Work around https://github.com/jupyterlite/pyodide-kernel/issues/166 + # and https://github.com/pyodide/micropip/issues/223 by installing the + # dependencies first, and then scikit-learn from Anaconda.org. + if "dev" in release: + dev_docs_specific_code = [ + "import piplite", + "import joblib", + "import threadpoolctl", + "import scipy", + "await piplite.install(\n" + f" 'scikit-learn=={release}',\n" + " index_urls='https://pypi.anaconda.org/scientific-python-nightly-wheels/simple',\n" + ")", + ] + + code_lines.extend(dev_docs_specific_code) + if code_lines: code_lines = ["# JupyterLite-specific code"] + code_lines code = "\n".join(code_lines) @@ -674,19 +751,10 @@ def reset_sklearn_config(gallery_conf, fname): "notebook_modification_function": notebook_modification_function } -# Secondary sidebar configuration for pages generated by sphinx-gallery - # For the index page of the gallery and each nested section, we hide the secondary # sidebar by specifying an empty list (no components), because there is no meaningful # in-page toc for these pages, and they are generated so "sourcelink" is not useful # either. - -# For each example page we keep default ["page-toc", "sourcelink"] specified by the -# "**" key. "page-toc" is wanted for these pages. "sourcelink" is also necessary since -# otherwise the secondary sidebar will degenerate when "page-toc" is empty, and the -# script `sphinxext/move_gallery_links.py` will fail (it assumes the existence of the -# secondary sidebar). The script will remove "sourcelink" in the end. - html_theme_options["secondary_sidebar_items"][f"{sg_gallery_dir}/index"] = [] for sub_sg_dir in (Path(".") / sg_examples_dir).iterdir(): if sub_sg_dir.is_dir(): @@ -704,8 +772,10 @@ def reset_sklearn_config(gallery_conf, fname): # enable experimental module so that experimental estimators can be # discovered properly by sphinx -from sklearn.experimental import enable_iterative_imputer # noqa -from sklearn.experimental import enable_halving_search_cv # noqa +from sklearn.experimental import ( # noqa: F401 + enable_halving_search_cv, + enable_iterative_imputer, +) def make_carousel_thumbs(app, exception): @@ -754,6 +824,15 @@ def disable_plot_gallery_for_linkcheck(app): sphinx_gallery_conf["plot_gallery"] = "False" +def skip_properties(app, what, name, obj, skip, options): + """Skip properties that are fitted attributes""" + if isinstance(obj, property): + if name.endswith("_") and not name.startswith("_"): + return True + + return skip + + def setup(app): # do not run the examples when using linkcheck by using a small priority # (default priority is 500 and sphinx-gallery using builder-inited event too) @@ -766,6 +845,8 @@ def setup(app): app.connect("build-finished", make_carousel_thumbs) app.connect("build-finished", filter_search_index) + app.connect("autodoc-skip-member", skip_properties) + # The following is used by sphinx.ext.linkcode to provide links to github linkcode_resolve = make_linkcode_resolve( @@ -867,10 +948,6 @@ def setup(app): "consistently-create-same-random-numpy-array/5837352#comment6712034_5837352", ] -# Config for sphinx-remove-toctrees - -remove_from_toctrees = ["metadata_routing.rst"] - # Use a browser-like user agent to avoid some "403 Client Error: Forbidden for # url" errors. This is taken from the variable navigator.userAgent inside a # browser console. @@ -890,6 +967,51 @@ def setup(app): } +def infer_next_release_versions(): + """Infer the most likely next release versions to make.""" + all_version_full = {"rc": "0.99.0rc1", "final": "0.99.0", "bf": "0.98.1"} + all_version_short = {"rc": "0.99", "final": "0.99", "bf": "0.98"} + all_previous_tag = {"rc": "unused", "final": "0.98.33", "bf": "0.97.22"} + + try: + # Fetch the version switcher JSON; see `html_theme_options` for more details + versions_json = json.loads( + urlopen(html_theme_options["switcher"]["json_url"], timeout=10).read() + ) + + # See `build_tools/circle/list_versions.py`, stable is always the second entry + stable_version = parse(versions_json[1]["version"]) + last_stable_version = parse(versions_json[2]["version"]) + next_major_minor = f"{stable_version.major}.{stable_version.minor + 1}" + + # RC + all_version_full["rc"] = f"{next_major_minor}.0rc1" + all_version_short["rc"] = next_major_minor + + # Major/Minor final + all_version_full["final"] = f"{next_major_minor}.0" + all_version_short["final"] = next_major_minor + all_previous_tag["final"] = stable_version.base_version + + # Bug-fix + all_version_full["bf"] = ( + f"{stable_version.major}.{stable_version.minor}.{stable_version.micro + 1}" + ) + all_version_short["bf"] = f"{stable_version.major}.{stable_version.minor}" + all_previous_tag["bf"] = last_stable_version.base_version + except Exception as e: + logger.warning( + "Failed to infer all possible next release versions because of " + f"{type(e).__name__}: {e}" + ) + + return { + "version_full": all_version_full, + "version_short": all_version_short, + "previous_tag": all_previous_tag, + } + + # -- Convert .rst.template files to .rst --------------------------------------- from api_reference import API_REFERENCE, DEPRECATED_API_REFERENCE @@ -907,6 +1029,11 @@ def setup(app): # Each entry is in the format (template name, file name, kwargs for rendering) rst_templates = [ ("index", "index", {"development_link": development_link}), + ( + "developers/maintainer", + "developers/maintainer", + {"inferred": infer_next_release_versions()}, + ), ( "min_dependency_table", "min_dependency_table", diff --git a/doc/conftest.py b/doc/conftest.py index 48e820e1199dc..ad8d6eb8cfb62 100644 --- a/doc/conftest.py +++ b/doc/conftest.py @@ -1,5 +1,4 @@ import os -import warnings from os import environ from os.path import exists, join @@ -10,7 +9,7 @@ from sklearn.datasets._base import _pkl_filepath from sklearn.datasets._twenty_newsgroups import CACHE_NAME from sklearn.utils._testing import SkipTest, check_skip_network -from sklearn.utils.fixes import np_base_version, parse_version +from sklearn.utils.fixes import np_base_version, parse_version, sp_version def setup_labeled_faces(): @@ -42,7 +41,7 @@ def setup_working_with_text_data(): def setup_loading_other_datasets(): try: - import pandas # noqa + import pandas # noqa: F401 except ImportError: raise SkipTest("Skipping loading_other_datasets.rst, pandas not installed") @@ -57,49 +56,35 @@ def setup_loading_other_datasets(): def setup_compose(): try: - import pandas # noqa + import pandas # noqa: F401 except ImportError: raise SkipTest("Skipping compose.rst, pandas not installed") def setup_impute(): try: - import pandas # noqa + import pandas # noqa: F401 except ImportError: raise SkipTest("Skipping impute.rst, pandas not installed") def setup_grid_search(): try: - import pandas # noqa + import pandas # noqa: F401 except ImportError: raise SkipTest("Skipping grid_search.rst, pandas not installed") def setup_preprocessing(): try: - import pandas # noqa - - if parse_version(pandas.__version__) < parse_version("1.1.0"): - raise SkipTest("Skipping preprocessing.rst, pandas version < 1.1.0") + import pandas # noqa: F401 except ImportError: raise SkipTest("Skipping preprocessing.rst, pandas not installed") -def setup_unsupervised_learning(): - try: - import skimage # noqa - except ImportError: - raise SkipTest("Skipping unsupervised_learning.rst, scikit-image not installed") - # ignore deprecation warnings from scipy.misc.face - warnings.filterwarnings( - "ignore", "The binary mode of fromstring", DeprecationWarning - ) - - def skip_if_matplotlib_not_installed(fname): try: - import matplotlib # noqa + import matplotlib # noqa: F401 except ImportError: basename = os.path.basename(fname) raise SkipTest(f"Skipping doctests for {basename}, matplotlib not installed") @@ -107,7 +92,7 @@ def skip_if_matplotlib_not_installed(fname): def skip_if_cupy_not_installed(fname): try: - import cupy # noqa + import cupy # noqa: F401 except ImportError: basename = os.path.basename(fname) raise SkipTest(f"Skipping doctests for {basename}, cupy not installed") @@ -126,10 +111,6 @@ def pytest_runtest_setup(item): setup_rcv1() elif fname.endswith("datasets/twenty_newsgroups.rst") or is_index: setup_twenty_newsgroups() - elif ( - fname.endswith("tutorial/text_analytics/working_with_text_data.rst") or is_index - ): - setup_working_with_text_data() elif fname.endswith("modules/compose.rst") or is_index: setup_compose() elif fname.endswith("datasets/loading_other_datasets.rst"): @@ -140,14 +121,10 @@ def pytest_runtest_setup(item): setup_grid_search() elif fname.endswith("modules/preprocessing.rst"): setup_preprocessing() - elif fname.endswith("statistical_inference/unsupervised_learning.rst"): - setup_unsupervised_learning() rst_files_requiring_matplotlib = [ "modules/partial_dependence.rst", "modules/tree.rst", - "tutorial/statistical_inference/settings.rst", - "tutorial/statistical_inference/supervised_learning.rst", ] for each in rst_files_requiring_matplotlib: if fname.endswith(each): @@ -176,13 +153,17 @@ def pytest_collection_modifyitems(config, items): items : list of collected items """ skip_doctests = False - if np_base_version >= parse_version("2"): - # Skip doctests when using numpy 2 for now. See the following discussion - # to decide what to do in the longer term: - # https://github.com/scikit-learn/scikit-learn/issues/27339 + if np_base_version < parse_version("2"): + # TODO: configure numpy to output scalar arrays as regular Python scalars + # once possible to improve readability of the tests docstrings. + # https://numpy.org/neps/nep-0051-scalar-representation.html#implementation reason = "Due to NEP 51 numpy scalar repr has changed in numpy 2" skip_doctests = True + if sp_version < parse_version("1.14"): + reason = "Scipy sparse matrix repr has changed in scipy 1.14" + skip_doctests = True + # Normally doctest has the entire module's scope. Here we set globs to an empty dict # to remove the module's scope: # https://docs.python.org/3/library/doctest.html#what-s-the-execution-context diff --git a/doc/contributor_experience_team.rst b/doc/contributor_experience_team.rst index 7d942a07e6a7d..73ccd668b20cd 100644 --- a/doc/contributor_experience_team.rst +++ b/doc/contributor_experience_team.rst @@ -6,6 +6,10 @@ img.avatar {border-radius: 10px;}
+
+

Virgil Chan

+
+

Juan Carlos Alfaro Jiménez

@@ -30,6 +34,10 @@

Norbert Preining

+
+

Stefanie Senger

+
+

Reshama Shaikh

diff --git a/doc/datasets.rst b/doc/datasets.rst index ee767e5843256..f12e5095cc6a8 100644 --- a/doc/datasets.rst +++ b/doc/datasets.rst @@ -6,12 +6,9 @@ Dataset loading utilities .. currentmodule:: sklearn.datasets -The ``sklearn.datasets`` package embeds some small toy datasets -as introduced in the :ref:`Getting Started ` section. - -This package also features helpers to fetch larger datasets commonly -used by the machine learning community to benchmark algorithms on data -that comes from the 'real world'. +The ``sklearn.datasets`` package embeds some small toy datasets and provides helpers +to fetch larger datasets commonly used by the machine learning community to benchmark +algorithms on data that comes from the 'real world'. To evaluate the impact of the scale of the dataset (``n_samples`` and ``n_features``) while controlling the statistical properties of the data @@ -36,7 +33,7 @@ length ``n_samples``, containing the target values, with key ``target``. The Bunch object is a dictionary that exposes its keys as attributes. For more information about Bunch object, see :class:`~sklearn.utils.Bunch`. -It's also possible for almost all of these function to constrain the output +It's also possible for almost all of these functions to constrain the output to be a tuple containing only the data and the target, by setting the ``return_X_y`` parameter to ``True``. diff --git a/doc/datasets/loading_other_datasets.rst b/doc/datasets/loading_other_datasets.rst index 004aa66c001e5..84d042f64c9d3 100644 --- a/doc/datasets/loading_other_datasets.rst +++ b/doc/datasets/loading_other_datasets.rst @@ -19,24 +19,29 @@ and pipelines on 2D data. load_sample_images load_sample_image -.. image:: ../auto_examples/cluster/images/sphx_glr_plot_color_quantization_001.png - :target: ../auto_examples/cluster/plot_color_quantization.html +.. plot:: + :context: close-figs :scale: 30 :align: right + :include-source: False + import matplotlib.pyplot as plt + from sklearn.datasets import load_sample_image + + china = load_sample_image("china.jpg") + plt.imshow(china) + plt.axis('off') + plt.tight_layout() + plt.show() .. warning:: The default coding of images is based on the ``uint8`` dtype to spare memory. Often machine learning algorithms work best if the input is converted to a floating point representation first. Also, - if you plan to use ``matplotlib.pyplpt.imshow``, don't forget to scale to the range + if you plan to use ``matplotlib.pyplot.imshow``, don't forget to scale to the range 0 - 1 as done in the following example. -.. rubric:: Examples - -* :ref:`sphx_glr_auto_examples_cluster_plot_color_quantization.py` - .. _libsvm_loader: Datasets in svmlight / libsvm format @@ -48,7 +53,7 @@ takes the form ``