Fix CI environment and version related issues #919
Workflow file for this run
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| name: tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - '**.py' | |
| - '.github/workflows/tests.yml' | |
| - 'pyproject.toml' | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| lint: | |
| name: lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: clone repository | |
| uses: actions/checkout@v4 | |
| - name: install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: load cached Python installation | |
| id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: lint-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} | |
| - name: install linters | |
| run: pip install flake8 oitnb | |
| - name: lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: lint with oitnb | |
| run: oitnb . --check | |
| test: | |
| needs: lint | |
| name: test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ ubuntu-latest, macos-latest ] | |
| python-version: [ '3.9', '3.10', '3.11' ] | |
| steps: | |
| - name: clone repository | |
| uses: actions/checkout@v4 | |
| - name: conda virtual environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| init-shell: bash | |
| environment-name: ci-env | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| libnetcdf | |
| hdf5 | |
| udunits2 | |
| - name: install dependencies | |
| run: pip install ".[testing]" | |
| shell: micromamba-shell {0} | |
| - name: run tests | |
| run: pytest --numprocesses auto | |
| shell: micromamba-shell {0} | |
| test_with_coverage: | |
| needs: [ lint, test ] | |
| name: test with coverage | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: clone repository | |
| uses: actions/checkout@v4 | |
| - name: install Python | |
| uses: actions/setup-python@v5 | |
| # due to coupledmodeldriver dependency python 3.10 cannot be supported | |
| with: | |
| python-version: 3.9 | |
| - name: install linux dependencies | |
| run: | | |
| sudo apt update | |
| sudo apt install libhdf5-dev | |
| sudo apt install libnetcdf-dev | |
| if: runner.os == 'Linux' | |
| - name: install macos dependencies | |
| run: | | |
| brew install hdf5 | |
| brew install netcdf | |
| if: runner.os == 'macOS' | |
| - name: load cached Python installation | |
| id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} | |
| - name: install dependencies | |
| run: pip install ".[testing]" | |
| - name: rebuild netcdf from source | |
| run: python -m pip install --upgrade --force-reinstall --no-deps --no-cache-dir netcdf4 --no-binary netcdf4 | |
| if: runner.os == 'Linux' | |
| - name: run tests with coverage | |
| run: pytest --numprocesses auto --cov . --cov-report xml:coverage.xml | |
| - name: show coverage report | |
| run: coverage report | |
| - name: upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: coverage.xml | |
| fail_ci_if_error: true |