bioconda-utils/.github/workflows/GithubActionTests.yml at c473ae5184f0ae28754dfa520e7cfced75da8aee · bioconda/bioconda-utils · GitHub

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name: PR Tests
on: [pull_request]
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  qc:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6
      - uses: astral-sh/ruff-action@v4.0.0
        name: ruff check
      - uses: astral-sh/ruff-action@v4.0.0
        name: ruff format
        with:
          args: "format --check --diff"
      - uses: prefix-dev/setup-pixi@v0
        with:
          pixi-version: latest
          environments: dev
          activate-environment: true
      - name: Check generated requirements
        run: pixi run python scripts/generate-requirements-txt.py --check
      - name: ty check
        run: ty check .
      - name: shellcheck
        run: pixi run just shellcheck
  test-linux:
    name: Linux tests
    runs-on: ubuntu-latest
    strategy:
      matrix:
        py_test_marker:
          - not long_running_1 and not long_running_2
          - long_running_1
          - long_running_2

    steps:
      - uses: actions/checkout@v6
        with:
          fetch-depth: 0

      - uses: prefix-dev/setup-pixi@v0
        with:
          pixi-version: latest
          environments: default
          activate-environment: true

      - name: Install bioconda-utils
        run: pixi run python -m pip install --no-deps --no-build-isolation .

      - name: List installed packages
        run: pixi list

      - name: Build docker container
        run: |
          docker build -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest ./
          docker history quay.io/bioconda/bioconda-utils-build-env-cos7:latest
          docker run --rm -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest sh -lec 'type -t conda && conda info --verbose && conda list'
          docker build -t quay.io/bioconda/bioconda-utils-test-env-cos7:latest -f ./Dockerfile.test ./

      - name: Run tests '${{ matrix.py_test_marker }}'
        run: |
          if git diff --name-only origin/master...HEAD | grep -vE ^docs; then
              py.test --durations=0 test/ -v --log-level=DEBUG --tb=native -m '${{ matrix.py_test_marker }}'
          else
              echo "Skipping pytest - only docs modified"
          fi
  test-macosx:
    name: OSX ARM tests
    runs-on: macos-26
    steps:
      - uses: actions/checkout@v6
        with:
          fetch-depth: 0

      - uses: prefix-dev/setup-pixi@v0
        with:
          pixi-version: latest
          environments: default
          activate-environment: true

      - name: Install bioconda-utils
        run: pixi run python -m pip install --no-deps --no-build-isolation .

      - name: List installed packages
        run: pixi list

      - name: Run tests
        run: |
          if git diff --name-only origin/master...HEAD | grep -vE ^docs; then
              py.test --durations=0 test/ -v --log-level=DEBUG -k "not docker" --tb=native
          else
              echo "Skipping pytest - only docs modified"
          fi

  autobump-test:
    name: autobump test
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6

      - uses: prefix-dev/setup-pixi@v0
        with:
          pixi-version: latest
          environments: default
          activate-environment: true

      - name: Install bioconda-utils
        run: pixi run python -m pip install --no-deps --no-build-isolation .

      - name: List installed packages
        run: pixi list

      - name: Test autobump
        run: |
          git clone --depth 1 https://github.com/bioconda/bioconda-recipes.git
          cd bioconda-recipes
          git config user.name Autobump
          git config user.email bioconda@users.noreply.github.com
          mkdir /tmp/artifacts
          bioconda-utils autobump \
            --packages "a*" \
            --unparsed-urls /tmp/artifacts/unparsed_urls.txt \
            --failed-urls /tmp/artifacts/failed_urls.txt \
            --recipe-status /tmp/artifacts/status.txt \
            --create-pr \
            --no-check-pinnings \
            --no-check-pending-deps \
            --no-follow-graph \
            --exclude bioconductor-* \
            --commit-as BiocondaBot 47040946+BiocondaBot@users.noreply.github.com \
            --max-updates 5 \
            --dry-run