Ac setup #448
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| name: cgat-apps | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest"] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Cache conda | |
| uses: actions/cache@v3 # Updated to the latest cache action version | |
| env: | |
| # Increase this value to reset cache if conda/environments/cgat-core.yml has not changed | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda/environments/cgat-apps.yml') }} | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" # Optional: if you prefer using mamba | |
| python-version: ${{ matrix.python-version }} | |
| miniforge-version: "latest" # Added to ensure Miniforge is installed | |
| channels: conda-forge, bioconda, defaults | |
| channel-priority: true | |
| activate-environment: cgat-a | |
| environment-file: conda/environments/cgat-apps.yml | |
| - name: Show conda | |
| run: | | |
| conda info | |
| conda list | |
| - name: Test | |
| run: | | |
| pip install . | |
| pip install pytest | |
| pytest -v tests/test_style.py | |
| pytest -v tests/test_scripts.py | |
| pytest -v tests/test_import.py |