Continuous Integration #119
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| name: Continuous Integration | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: '0 4 * * 1' | |
| defaults: | |
| run: | |
| # This is needed for miniconda, see: | |
| # https://github.com/marketplace/actions/setup-miniconda#important. | |
| shell: bash -l {0} | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| test: | |
| - sanity | |
| - dry-run | |
| - integration | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: snakemake-project | |
| use-mamba: true | |
| # This is used to invalidate the conda environment every week | |
| - name: Get week number | |
| id: get-date | |
| run: echo "week=$(/bin/date -u '+%Y-w%V')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Cache conda environment | |
| id: conda-cache | |
| uses: actions/cache@v4 | |
| env: | |
| # Increase this value to manually invalidate the cache | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-v${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}-${{ steps.get-date.outputs.week }} | |
| - name: Update conda environment | |
| run: mamba env update -f environment.yml | |
| if: steps.conda-cache.outputs.cache-hit != 'true' | |
| - name: Install singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: Cache singularity images | |
| uses: actions/cache@v4 | |
| env: | |
| # Increase this value to manually invalidate the cache | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: | |
| ~/.singularity/cache/snakemake | |
| key: singularity-v${{ env.CACHE_NUMBER }}-${{ hashFiles('common.smk') }} | |
| - name: Run test in conda evironment | |
| run: >- | |
| pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }} | |
| - name: Check job stderr messages in case of failure | |
| if: ${{ failure() }} | |
| run: >- | |
| bash -c ' | |
| for file in $(find /tmp/pytest_workflow_* -name log.err); do | |
| echo $file; cat $file | |
| done | |
| ' | |
| - name: Check job stdout messages in case of failure | |
| if: ${{ failure() }} | |
| run: >- | |
| bash -c ' | |
| for file in $(find /tmp/pytest_workflow_* -name log.out); do | |
| echo $file; cat $file | |
| done | |
| ' |