Update deps with confpass deps #108
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: Continuous Integration / Deployment | |
| on: [pull_request, push] | |
| jobs: | |
| Format: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Apply formatting | |
| uses: github/super-linter@v4 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| VALIDATE_PYTHON_PYLINT: true | |
| VALIDATE_PYTHON_FLAKE8: true | |
| VALIDATE_PYTHON_ISORT: true | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| IGNORE_GITIGNORED_FILES: true | |
| Test_Linux: | |
| needs: | |
| - Format | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: 4.9.2-4 | |
| use-mamba: true | |
| environment-file: envs/linux.yml | |
| use-only-tar-bz2: true | |
| auto-activate-base: false | |
| activate-environment: isicle | |
| - name: Install ISiCLE | |
| run: pip install --no-deps . | |
| # - name: Test environment | |
| # run: | | |
| # pytest | |
| Test_Mac: | |
| needs: | |
| - Format | |
| runs-on: macos-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: 4.9.2-4 | |
| use-mamba: true | |
| environment-file: envs/osx.yml | |
| use-only-tar-bz2: true | |
| auto-activate-base: false | |
| activate-environment: isicle | |
| - name: Install ISiCLE | |
| run: pip install --no-deps . | |
| # - name: Test environment | |
| # run: | | |
| # pytest | |
| Deploy: | |
| needs: | |
| - Test_Linux | |
| - Test_Mac | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: 4.9.2-4 | |
| use-mamba: true | |
| python-version: 3.9 | |
| channels: conda-forge,bioconda | |
| use-only-tar-bz2: true | |
| auto-activate-base: true | |
| - name: Install dependencies | |
| run: | | |
| mamba install boa anaconda-client conda-verify | |
| - name: Build conda package | |
| run: | | |
| mkdir build/ | |
| conda mambabuild conda-recipe/ --output-folder build/ | |
| conda index build/ | |
| - name: Convert to osx-64 | |
| run: conda convert -p osx-64 build/linux-64/*.tar.bz2 -o build/ | |
| - name: Upload packages | |
| env: | |
| ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| run: | | |
| anaconda upload build/linux-64/*.tar.bz2 | |
| anaconda upload build/osx-64/*.tar.bz2 |