ci: smoke test with/out optional dependencies, mark more tests #1045
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| name: FloPy continuous integration | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| - ci-diagnose* | |
| - notebooks | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| jobs: | |
| build: | |
| name: Build | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| timeout-minutes: 10 | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| cache: 'pip' | |
| cache-dependency-path: pyproject.toml | |
| - name: Install Python dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install build twine | |
| pip install . | |
| python -c "import flopy; print(f'{flopy.__version__}')" | |
| - name: Build package | |
| run: | | |
| python -m build | |
| - name: Check package | |
| run: | | |
| twine check --strict dist/* | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| timeout-minutes: 10 | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| cache: 'pip' | |
| cache-dependency-path: pyproject.toml | |
| - name: Install Python dependencies | |
| run: | | |
| pip install . | |
| pip install ".[lint]" | |
| - name: Run isort | |
| run: | | |
| echo "if isort check fails update isort using" | |
| echo " pip install isort --upgrade" | |
| echo "and run" | |
| echo " isort ./flopy" | |
| echo "and then commit the changes." | |
| isort --check --diff ./flopy | |
| - name: Run black | |
| run: | | |
| echo "if black check fails update black using" | |
| echo " pip install black --upgrade" | |
| echo "and run" | |
| echo " black ./flopy" | |
| echo "and then commit the changes." | |
| black --check --diff ./flopy | |
| - name: Run flake8 | |
| run: | | |
| flake8 --count --show-source --exit-zero ./flopy | |
| - name: Run pylint | |
| run: | | |
| pylint --jobs=2 --errors-only --exit-zero ./flopy | |
| - name: Check CITATION.cff | |
| run: | | |
| cffconvert --validate | |
| cffconvert -f apalike | |
| cffconvert -f bibtex | |
| smoke: | |
| name: Smoke test | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| timeout-minutes: 10 | |
| env: | |
| PYTHON_VERSION: 3.8 | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| optdeps: | |
| - "all optional dependencies" | |
| - "no optional dependencies" | |
| - "some optional dependencies" | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: 'pip' | |
| cache-dependency-path: pyproject.toml | |
| - name: Install Python dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install . | |
| pip install ".[test]" | |
| if [[ ! "${{ matrix.optdeps }}" == *"no"* ]]; then | |
| pip install ".[optional]" | |
| fi | |
| if [[ "${{ matrix.optdeps }}" == *"some"* ]]; then | |
| deps=$(sed '/optional =/,/]/!d' pyproject.toml | sed -e '1d;$d' -e 's/\"//g' -e 's/,//g' | tr -d ' ' | cut -f 1 -d ';') | |
| rmvd=$(echo $deps | tr ' ' '\n' | shuf --random-source <(yes date +%d.%m.%y) | head -n 3) | |
| echo "Removing optional dependencies: $rmvd" >> removed_dependencies.txt | |
| cat removed_dependencies.txt | |
| pip uninstall --yes $rmvd | |
| fi | |
| - name: Upload removed dependencies log | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: smoke-test-removed-dependencies | |
| path: ./removed_dependencies.txt | |
| - name: Install Modflow executables | |
| uses: modflowpy/install-modflow-action@v1 | |
| - name: Smoke test (${{ matrix.optdeps }}) | |
| working-directory: autotest | |
| run: pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Upload failed test outputs | |
| uses: actions/upload-artifact@v3 | |
| if: failure() | |
| with: | |
| name: failed-smoke-${{ runner.os }}-${{ env.PYTHON_VERSION }} | |
| path: ./autotest/.failed/** | |
| - name: Upload coverage | |
| if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request') | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| files: ./autotest/coverage.xml | |
| test: | |
| name: Test | |
| needs: smoke | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest, macos-latest, windows-latest ] | |
| python-version: [ 3.8, 3.9, "3.10", "3.11" ] | |
| exclude: | |
| # avoid shutil.copytree infinite recursion bug | |
| # https://github.com/python/cpython/pull/17098 | |
| - python-version: '3.8.0' | |
| defaults: | |
| run: | |
| shell: bash | |
| timeout-minutes: 45 | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| if: runner.os != 'Windows' | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| cache-dependency-path: pyproject.toml | |
| - name: Install Python dependencies | |
| if: runner.os != 'Windows' | |
| run: | | |
| pip install --upgrade pip | |
| pip install . | |
| pip install ".[test, optional]" | |
| - name: Setup Micromamba | |
| if: runner.os == 'Windows' | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: etc/environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| init-shell: >- | |
| bash | |
| powershell | |
| - name: Install Python dependencies | |
| shell: bash -l {0} | |
| if: runner.os == 'Windows' | |
| run: | | |
| pip install xmipy | |
| pip install . | |
| - name: Install Modflow-related executables | |
| uses: modflowpy/install-modflow-action@v1 | |
| - name: Install Modflow dev build executables | |
| uses: modflowpy/install-modflow-action@v1 | |
| with: | |
| repo: modflow6-nightly-build | |
| - name: Update FloPy packages | |
| if: runner.os != 'Windows' | |
| run: python -c 'import flopy; flopy.mf6.utils.generate_classes(ref="develop", backup=False)' | |
| - name: Update FloPy packages | |
| if: runner.os == 'Windows' | |
| shell: bash -l {0} | |
| run: python -c 'import flopy; flopy.mf6.utils.generate_classes(ref="develop", backup=False)' | |
| - name: Run tests | |
| if: runner.os != 'Windows' | |
| working-directory: ./autotest | |
| run: | | |
| pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile | |
| coverage report | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Run tests | |
| if: runner.os == 'Windows' | |
| shell: bash -l {0} | |
| working-directory: ./autotest | |
| run: | | |
| pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile | |
| coverage report | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Upload failed test outputs | |
| uses: actions/upload-artifact@v3 | |
| if: failure() | |
| with: | |
| name: failed-${{ matrix.os }}-${{ matrix.python-version }} | |
| path: | | |
| ./autotest/.failed/** | |
| - name: Upload coverage | |
| if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request') | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| files: ./autotest/coverage.xml |