Merge pull request #10 from sequana/copilot/fix-apptainer-workflow-fa… #37
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| workflow_dispatch: | |
| pull_request: | |
| branches-ignore: [] | |
| schedule: | |
| - cron: '0 0 30 * *' | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| python: ['3.11','3.12'] | |
| fail-fast: false | |
| steps: | |
| - name: install graphviz | |
| run: | | |
| sudo apt-get update -qq | |
| sudo apt-get install -y graphviz | |
| - name: checkout git repo | |
| uses: actions/checkout@v4 | |
| - name: conda/mamba | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: environment.yml | |
| create-args: >- | |
| python=${{ matrix.python }} | |
| cache-environment: true | |
| cache-downloads: true | |
| generate-run-shell: true | |
| - name: install package itself | |
| shell: micromamba-shell {0} | |
| run: | | |
| pip install . | |
| - name: Install dependencies | |
| shell: micromamba-shell {0} | |
| run: | | |
| pip install coveralls pytest-cov pytest pytest-xdist | |
| - name: testing | |
| shell: micromamba-shell {0} | |
| run: | | |
| pytest -v --cov-report term-missing --cov=sequana_pipelines.quality_control | |
| - name: coveralls | |
| continue-on-error: true | |
| shell: micromamba-shell {0} | |
| run: | | |
| echo $COVERALLS_REPO_TOKEN | |
| coveralls --service=github | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} |