sprocket/.github/workflows/python-ci.yml at 228aeae8d75954c3eb4c097d2133c037e93a0f3d · stjude-rust-labs/sprocket · GitHub

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name: Python CI

permissions:
  contents: read

on:
  push:
    branches:
      - main
  pull_request:
  workflow_dispatch:

env:
  RUST_BACKTRACE: full
  CARGO_TERM_COLOR: always
  FORCE_COLOR: 1
  IN_CI: 1
  # Only include the debug info necessary for backtraces (file names and line numbers). Any extra
  # debug info provided by `debuginfo=1` or `debuginfo=2` require an interactive debugger like
  # `lldb` or `gdb`.
  RUSTFLAGS: -C debuginfo=line-tables-only

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [windows-latest, macos-latest, ubuntu-latest]
    steps:
      - name: Checkout repository
        uses: actions/checkout@v6

      - name: Update Rust
        run: rustup update stable && rustup default stable && rustup component add llvm-tools

      - name: Setup Python
        uses: actions/setup-python@v6
        with:
          python-version-file: .python-version

      - name: Install cargo-llvm-cov
        uses: taiki-e/install-action@v2
        with:
          tool: cargo-llvm-cov@0.8

      - name: Create virtual environment
        run: python -m venv --upgrade-deps .venv

      - name: Activate virtual environment and code coverage (Windows)
        if: ${{ matrix.os == 'windows-latest' }}
        run: |
          # Activate virtual environment.
          Add-Content -Value "VIRTUAL_ENV=$PWD\.venv" -Path $Env:GITHUB_ENV
          Add-Content -Value "$PWD\.venv\Scripts" -Path $Env:GITHUB_PATH

          # Activate code coverage.
          cargo llvm-cov show-env >> $Env:GITHUB_ENV

      - name: Activate virtual environment and code coverage (non-Windows)
        if: ${{ matrix.os != 'windows-latest' }}
        run: |
          # Activate virtual environment.
          echo "VIRTUAL_ENV=$(pwd)/.venv" >> "${GITHUB_ENV}"
          echo "$(pwd)/.venv/bin" >> "${GITHUB_PATH}"

          # Activate code coverage. We remove single quotes from `llvm-cov`'s output, as Github
          # Actions does not understand them.
          cargo llvm-cov show-env | tr -d "'" >> "${GITHUB_ENV}"

      - name: Build package
        uses: PyO3/maturin-action@v1
        with:
          command: develop
          args: --group=cov --locked

      - name: Run tests
        run: pytest --cov=python/sprocket_bio --cov-report=json:codecov-py.json

      - name: Generate llvm-cov report
        run: cargo llvm-cov report -p sprocket-py -p wdl-diagnostics -p wdl-grammar -p wdl-ast --codecov --output-path=codecov-rust.json

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v6
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: codecov-py.json,codecov-rust.json
          fail_ci_if_error: true

  type-check:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v6

      - name: Update Rust
        run: rustup update stable && rustup default stable

      - name: Setup Python
        uses: actions/setup-python@v6
        with:
          python-version-file: .python-version

      - name: Create virtual environment
        run: python -m venv --upgrade-deps .venv

      - name: Activate virtual environment
        run: |
          echo "VIRTUAL_ENV=$(pwd)/.venv" >> "${GITHUB_ENV}"
          echo "$(pwd)/.venv/bin" >> "${GITHUB_PATH}"

      - name: Build package
        uses: PyO3/maturin-action@v1
        with:
          command: develop
          args: --locked

      - name: Check types
        run: mypy python

      - name: Check stubs
        run: python -m mypy.stubtest sprocket_bio

  format:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v6

      - name: Check formatting
        uses: psf/black@stable
        with:
          use_pyproject: true

  sort-imports:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v6

      - name: Setup Python
        uses: actions/setup-python@v6
        with:
          python-version-file: .python-version

      # `isort` requires third-party dependencies to be installed before running. We skip this
      # because `sprocket_bio` doesn't have any dependencies.
      - name: Check import sorting
        run: |
          python -m pip install "isort~=8.0"
          isort --check-only --diff python/