added container (docker) functionality to the run statement #322
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| name: cgatcore | |
| 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 | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda/environments/cgat-core.yml') }} | |
| - name: Set installer URL | |
| id: set-installer-url | |
| run: | | |
| if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then | |
| echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" >> $GITHUB_ENV | |
| elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then | |
| echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh" >> $GITHUB_ENV | |
| fi | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| installer-url: ${{ env.installer-url }} | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge, bioconda, defaults | |
| channel-priority: true | |
| activate-environment: cgat-core | |
| environment-file: conda/environments/cgat-core.yml | |
| - name: Configure Conda Paths | |
| run: echo "/usr/share/miniconda3/condabin" >> $GITHUB_PATH | |
| - name: Show conda | |
| run: | | |
| conda info | |
| conda list | |
| - name: Debug Python Environment | |
| run: | | |
| python --version | |
| pip list | |
| openssl version | |
| - name: Test | |
| run: | | |
| pip install . | |
| ./all-tests.sh | |
| deploy_docs: | |
| name: Deploy MkDocs Documentation | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install MkDocs and Dependencies | |
| run: | | |
| pip install mkdocs mkdocs-material mkdocstrings[python] | |
| - name: Build and Deploy MkDocs Site | |
| run: mkdocs gh-deploy --force --clean | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} |