refactor test data generation #757
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "*" | |
| - "!v[0-9]+.[0-9]+.[0-9]+*" | |
| pull_request: | |
| branches: | |
| - "*" | |
| - "!v[0-9]+.[0-9]+.[0-9]+*" | |
| jobs: | |
| pyws_setup: | |
| name: standard installation | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Upgrade pip and install build and twine | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install wheel build twine | |
| - name: Base installation | |
| run: | | |
| pip --verbose install . | |
| - name: Print pyhmn version | |
| run: | | |
| python -c "import pywatershed; print(pywatershed.__version__)" | |
| - name: Build pywatershed, check dist outputs | |
| run: | | |
| python -m build | |
| twine check --strict dist/* | |
| pyws_lint: | |
| name: linting | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| pip install wheel | |
| pip install . | |
| pip install ".[lint]" | |
| - name: Version info | |
| run: | | |
| pip -V | |
| pip list | |
| - name: Run isort | |
| run: | | |
| echo "if isort check fails update isort using" | |
| echo " pip install isort --upgrade" | |
| echo "and run" | |
| echo " isort ./pywatershed ./autotest" | |
| echo "and then commit the changes." | |
| isort --check --diff ./pywatershed ./autotest | |
| - name: Run black | |
| run: | | |
| echo "if black check fails update black using" | |
| echo " pip install black --upgrade" | |
| echo "and run" | |
| echo " black ./pywatershed ./autotest" | |
| echo "and then commit the changes." | |
| black --check --diff ./pywatershed ./autotest | |
| - name: Run flake8 | |
| run: | | |
| flake8 --count --show-source --exit-zero ./pywatershed ./autotest | |
| - name: Run pylint | |
| run: | | |
| pylint --jobs=2 --errors-only --exit-zero ./pywatershed ./autotest | |
| test: | |
| name: ${{ matrix.os}} py${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ "ubuntu-latest", "macos-latest", "windows-latest" ] | |
| python-version: ["3.9", "3.10"] | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Set environment variables | |
| run: | | |
| echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV | |
| echo "PYWS_FORTRAN=true" >> $GITHUB_ENV | |
| echo 'SETUPTOOLS_ENABLE_FEATURES="legacy-editable"' >> $GITHUB_ENV | |
| cat .mf6_ci_ref_remote >> $GITHUB_ENV | |
| - name: Enforce MF6 ref and remote merge to main | |
| if: github.base_ref == 'main' | |
| run: | | |
| echo Merge commit: GITHUB_BASE_REF = $GITHUB_BASE_REF | |
| req_ref=feat-snf # if not develop, submit an issue | |
| echo $MF6_REF | |
| if [[ "$MF6_REF" != "$req_ref" ]]; then exit 1; fi | |
| req_remote=langevin-usgs/modflow6 # if not MODFLOW-USGS/modflow6, submit an issue | |
| echo $MF6_REMOTE | |
| if [[ "$MF6_REMOTE" != "$req_remote" ]]; then exit 1; fi | |
| - name: Setup gfortran | |
| uses: awvwgk/setup-fortran@main | |
| with: | |
| compiler: gcc | |
| version: 11 | |
| - name: Link gfortran dylibs on Mac | |
| if: runner.os == 'macOS' | |
| run: .github/scripts/symlink_gfortran_mac.sh | |
| - name: Install Dependencies via Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| create-args: >- | |
| python=${{matrix.python-version}} | |
| conda | |
| - name: Checkout MODFLOW 6 | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{ env.MF6_REMOTE }} | |
| ref: ${{ env.MF6_REF }} | |
| path: modflow6 | |
| - name: Update flopy MODFLOW 6 classes | |
| working-directory: modflow6/autotest | |
| run: | | |
| python update_flopy.py | |
| - name: Install pywatershed | |
| run: | | |
| pip install . | |
| - name: Version info | |
| run: | | |
| pip -V | |
| pip list | |
| - name: Run available domains with PRMS and convert csv output to NetCDF | |
| working-directory: test_data/scripts | |
| run: | | |
| pytest -v -n=auto --durations=0 test_run_domains.py | |
| pytest -v -n=auto --durations=0 test_nc_domains.py | |
| - name: List all NetCDF files in test_data directory | |
| working-directory: test_data | |
| run: | | |
| find . -name "*.nc" | |
| - name: Run tests | |
| working-directory: autotest | |
| run: pytest | |
| -v | |
| -n=auto | |
| --durations=0 | |
| --all_domains | |
| --cov=pywatershed | |
| --cov-report=xml | |
| --junitxml=pytest.xml | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: Test results for ${{ runner.os }}-${{ matrix.python-version }} | |
| path: ./autotest/pytest.xml | |
| - name: Upload code coverage to Codecov | |
| uses: codecov/codecov-action@v2.1.0 | |
| with: | |
| file: ./autotest/coverage.xml | |
| # flags: unittests | |
| env_vars: RUNNER_OS,PYTHON_VERSION | |
| # name: codecov-umbrella | |
| fail_ci_if_error: false | |
| version: "v0.1.15" |