[pre-commit.ci] pre-commit autoupdate #250
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| name: tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| concurrency: | |
| group: test-${{ github.head_ref }} | |
| cancel-in-progress: true | |
| env: | |
| PYTHONUNBUFFERED: "1" | |
| FORCE_COLOR: "1" | |
| # Needed for mamba to work | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python: ["3.7", "3.8", "3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up JDK 8 # to match beast2 conda recipe | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: 8 | |
| - name: Setup Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install mambaforge | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| channel-priority: strict # Snakemake errors otherwise | |
| - name: Install Poetry and nox | |
| run: | | |
| curl -sSL https://install.python-poetry.org | python3 - | |
| pip install nox nox-poetry | |
| - name: Set up cache for nox | |
| uses: actions/cache@v2 | |
| id: cached-nox-datadir | |
| with: | |
| path: .nox | |
| key: nox-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/pyproject.toml') }}-${{ env.CACHE_NUMBER }} | |
| env: | |
| # Increase this value to reset cache if pyproject.toml has not changed | |
| CACHE_NUMBER: 0 | |
| - name: Get Date | |
| id: get-date | |
| run: echo "::set-output name=today::$(/bin/date -u '+%Y%m%d')" | |
| shell: bash | |
| - name: Set up cache for conda | |
| uses: actions/cache@v2 | |
| id: cached-conda-envsdir | |
| with: | |
| path: tests/.conda | |
| key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('mccoy/workflow/envs/*') }}-${{ env.CACHE_NUMBER }} | |
| env: | |
| # Increase this value to reset cache if the env files have not changed | |
| CACHE_NUMBER: 2 | |
| - name: Set up cache for beast extensions | |
| uses: actions/cache@v2 | |
| id: cached-beast-extensions | |
| with: | |
| path: ~/.beast | |
| key: beast_exts-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('mccoy/workflow/envs/beast*') }}-${{ env.CACHE_NUMBER }} | |
| env: | |
| # Increase this value to reset cache if the env files have not changed | |
| CACHE_NUMBER: 1 | |
| - name: Run nox | |
| # Run nox using the version of Python in `PATH` | |
| run: nox --force-python python |