Test #20
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |