Merge branch '4.x' #3
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| name: Test | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| schedule: | |
| - cron: "0 5 1,15 * *" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} # -e to fail on error | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-13] | |
| python: ["3.7", "3.8", "3.9", "3.10", "3.11"] | |
| name: ${{ matrix.name }} Python ${{ matrix.python }} | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # - name: Set up Python ${{ matrix.python }} | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: ${{ matrix.python }} | |
| # cache: "pip" | |
| # cache-dependency-path: "**/pyproject.toml" | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| mamba-version: "*" | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| python-version: ${{ matrix.python }} | |
| channels: conda-forge, bioconda, defaults | |
| activate-environment: test_dbcan | |
| environment-file: envs/test.yml | |
| - name: export test_dbcan environment | |
| run: mamba env export | |
| # - name: Install test dependencies | |
| # run: | | |
| # python -m pip install --upgrade pip wheel | |
| # - name: create run_dbcan environment | |
| # run: conda create -n run_dbcan python=${{ matrix.python }} | |
| # - name: activate run_dbcan environment | |
| # run: conda activate run_dbcan | |
| - name: Install dependencies | |
| run: | | |
| pip install ${{ matrix.pip-flags }} ".[dev,test]" | |
| # - name: Add conda to PATH | |
| # run: | | |
| # echo ::add-path::$CONDA/bin | |
| - name: Build dbCAN Database | |
| run: | | |
| dbcan_build --cpus 1 --db-dir db --clean | |
| # conda install -y -c bioconda -c conda-forge hmmer diamond blast prodigal | |
| - name: Test | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| run: | | |
| coverage run -m pytest -v --color=yes |