Incorporate charge handling #124
Workflow file for this run
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| 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 |