Update CI with micromamba #41
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| name: morphMan CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| schedule: | |
| - cron: '0 8 * * *' | |
| env: | |
| CACHE_NUMBER: 2 # Increase to reset cache | |
| jobs: | |
| check-code: | |
| name: Check code | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies and project | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| python -m pip install '.[test]' | |
| - name: Run linting and checks | |
| run: | | |
| bash linting.sh | |
| test-code: | |
| needs: check-code | |
| strategy: | |
| matrix: | |
| include: | |
| - os: ubuntu-latest | |
| label: linux-64 | |
| prefix: /usr/share/miniconda3/envs/morphman-env | |
| # Workaround for arm64: https://github.com/vmtk/vmtk/issues/452#issuecomment-1489829429 | |
| - os: macos-13 | |
| label: osx-64 # No support for arm64 | |
| prefix: /Users/runner/miniconda3/envs/morphman-env | |
| - os: windows-latest | |
| label: win-64 | |
| prefix: C:/Miniconda3/envs/morphman-env | |
| name: Test morphMan on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| init-shell: bash | |
| cache-environment: true | |
| # | |
| # - uses: conda-incubator/setup-miniconda@v3 | |
| # with: | |
| # mamba-version: '*' | |
| # channels: conda-forge,vmtk | |
| # channel-priority: flexible | |
| # activate-environment: morphman-env | |
| # environment-file: environment.yml | |
| # python-version: '3.10' | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ${{ matrix.prefix }} | |
| key: ${{ matrix.label }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} | |
| restore-keys: ${{ matrix.label }}-${{ env.CACHE_NUMBER }}- | |
| - name: Install morphMan | |
| run: | | |
| python -m pip install '.[test]' | |
| - name: Run tests | |
| run: | | |
| python -m pytest tests | |
| - name: Upload coverage report to Codecov | |
| if: matrix.os == 'ubuntu-latest' | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage.xml | |
| fail_ci_if_error: false | |
| verbose: true |