[bugfix] more CI/CD fixes #134
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| name: Tests | |
| on: | |
| push: | |
| #pull_request: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/main' }} | |
| jobs: | |
| static_tests: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: false | |
| - name: Install conda environment dependencies | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| miniforge-variant: Miniforge3 | |
| # python-version: "*" | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: lint | |
| auto-update-conda: false | |
| environment-file: tests/conda_lint_env.yaml | |
| - name: README formatting for PyPI | |
| run: rst-lint README.rst | |
| runtime_tests: | |
| strategy: | |
| max-parallel: 5 | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] #, macos-latest] | |
| python-version: ["3.12"] #, "3.11"] | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| # NOTE login shell: to force loading conda profile | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: false | |
| # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS | |
| - name: Fetch test-data | |
| # NOTE to save on bandwidth costs, pull data from BSSE's GitLab LFS instead | |
| run: | | |
| git config --file .lfsconfig lfs.url "https://git.bsse.ethz.ch/cbg/viruses/smallgenomeutilities.git/info/lfs" | |
| git lfs install | |
| git lfs pull | |
| git lfs checkout | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| # miniforge-variant: Miniforge3 | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: testsmgu | |
| auto-update-conda: false | |
| environment-file: tests/conda_testsgmu_env.yaml | |
| - name: Build package | |
| run: | | |
| pip install --no-deps . | |
| - name: dummy run | |
| run: | | |
| frameshift_deletions_checks --version | |
| - name: Test package | |
| run: | | |
| pytest -v |