added container (docker) functionality to the run statement #345
Workflow file for this run
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: 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 }} |