anndata/.github/workflows/test-cpu.yml at 8ac298708802c6231a398db8c2a07edd4ed37322 · scverse/anndata · GitHub

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name: CI

on:
  push:
    branches:
      - main
      - "[0-9]+.[0-9]+.x"
  pull_request:

env:
  PYTEST_ADDOPTS: "-v --color=yes -n auto --instafail"
  FORCE_COLOR: "1"

defaults:
  run:
    shell: bash -el {0}

# Cancel the job if new commits are pushed
# https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: false  # TODO: set to `true` again

jobs:
  pytest:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        include:
          - python-version: '3.13'
            test-type: coverage
          - python-version: '3.11'
            test-type: standard
          - python-version: '3.13'
            dependencies-version: pre-release
            test-type: strict-warning
          #- python-version: '3.11'
          #  dependencies-version: minimum
          #  test-type: coverage
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
          filter: blob:none

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install UV
        uses: astral-sh/setup-uv@v5
        with:
          enable-cache: true
          cache-dependency-glob: pyproject.toml

      - name: Install dependencies
        if: matrix.dependencies-version == null
        run: uv pip install --system --compile "anndata[dev,test-full] @ ." -c ci/constraints.txt

      - name: Install minimum dependencies
        if: matrix.dependencies-version == 'minimum'
        run: |
          uv pip install --system --compile tomli packaging
          deps=$(python3 ci/scripts/min-deps.py pyproject.toml --extra dev test)
          uv pip install --system --compile $deps "anndata @ ."

      - name: Install dependencies release candidates
        if: matrix.dependencies-version == 'pre-release'
        run: uv pip install -v --system --compile --pre "anndata[dev,test-full] @ ." -c ci/constraints.txt

      - name: Display installed versions
        run: uv pip list

      - name: Run Pytest
        if: matrix.test-type == 'standard'
        run: pytest

      - name: Run Pytest (coverage)
        if: matrix.test-type == 'coverage'
        run: coverage run -m pytest --cov --cov-report=xml

      - name: Run Pytest (treat warnings as errors)
        if: matrix.test-type == 'strict-warning'
        run: pytest --strict-warnings

      - uses: codecov/codecov-action@v4
        if: matrix.test-type == 'coverage'
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          fail_ci_if_error: true
          files: test-data/coverage.xml

  check-build:
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
          filter: blob:none

      - name: Set up Python 3.13
        uses: actions/setup-python@v5
        with:
          python-version: '3.13'

      - name: Install build tools and requirements
        run: |
          python -m pip install --upgrade pip
          pip install build twine

      - name: Display installed versions
        run: pip list

      - name: Build & Twine check
        run: |
          python -m build --sdist --wheel .
          twine check dist/*

      - name: Check runtime version
        run: |
          pip install dist/*.whl
          python -c 'import anndata; print(anndata.__version__)'