resolve issues with different ways of specifiying netcdf output optio… #729
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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/[email protected] | |
| 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" |