Container workflow overhaul #732
Workflow file for this run
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| name: Test SPRAS | |
| on: [push, pull_request] | |
| jobs: | |
| # Installs the conda environment but does not run tests because the tests require Linux Docker images | |
| conda-only: | |
| name: Test conda environment | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [macos-latest, windows-latest] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Install conda environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: spras | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| miniconda-version: 'latest' | |
| # Log conda environment contents | |
| - name: Log conda environment | |
| shell: bash --login {0} | |
| run: conda list | |
| # Runs the test code and Snakemake workflow in the conda environment | |
| test: | |
| name: Run test cases and workflow | |
| # The Docker images will be pulled in both the docker job and this test job | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Install conda environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: spras | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| miniconda-version: 'latest' | |
| # Log conda environment contents | |
| - name: Log conda environment | |
| shell: bash --login {0} | |
| run: conda list | |
| # Formerly used Singularity instead of Apptainer (see https://github.com/eWaterCycle/setup-singularity/issues/6) | |
| - name: Install Apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| # Choose version from https://github.com/apptainer/apptainer/releases | |
| apptainer-version: 1.2.2 | |
| - name: Run tests | |
| shell: bash --login {0} | |
| # Verbose output and disable stdout and stderr capturing | |
| run: pytest -vs | |
| - name: Run Snakemake workflow | |
| shell: bash --login {0} | |
| run: snakemake --cores 2 --configfile config/config.yaml --show-failed-logs | |
| # Run pre-commit checks on source files | |
| pre-commit: | |
| name: Run pre-commit checks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' # Match this to the version specified in environment.yml | |
| - name: Run pre-commit checks | |
| uses: pre-commit/[email protected] |