update sagehen graph postprocessing #1104
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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]+*" | |
| workflow_dispatch: | |
| inputs: | |
| debug_enabled: | |
| type: boolean | |
| description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' | |
| required: false | |
| default: false | |
| 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@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Upgrade pip and install build and twine | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install wheel build 'twine<5.0.0' 'importlib_metadata<=7.0.1' 'setuptools<=72.2.0' 'numpy<2.0' | |
| - 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@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| pip install wheel | |
| pip install . | |
| pip install ".[lint]" | |
| - name: Version info | |
| run: | | |
| pip -V | |
| pip list | |
| - name: Lint | |
| run: ruff check . | |
| - name: Format | |
| run: ruff format --check . | |
| 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: ["3.10", "3.11"] | |
| steps: | |
| - name: Free Disk Space (Ubuntu) | |
| if: runner.os == 'Linux' | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| tool-cache: false | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: true | |
| swap-storage: true | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Setup tmate session | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }} | |
| - name: Set environment variables | |
| run: | | |
| echo "PYTHON_VERSION=${{ 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=develop # if not develop, submit an issue | |
| echo $MF6_REF | |
| if [[ "$MF6_REF" != "$req_ref" ]]; then exit 1; fi | |
| req_remote=MODFLOW-USGS/modflow6 | |
| echo $MF6_REMOTE | |
| if [[ "$MF6_REMOTE" != "$req_remote" ]]; then echo "bad mf6 remote in .mf6_ci_ref_remote"; exit 1; fi | |
| - name: Setup gfortran | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: 11 | |
| - name: Link gfortran dylibs on Mac | |
| if: runner.os == 'macOS' | |
| run: .github/scripts/symlink_gfortran_mac.sh | |
| - name: Install Dependencies via Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| log-level: debug | |
| environment-file: environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| create-args: >- | |
| python=${{matrix.python-version}} | |
| - name: Checkout MODFLOW 6 | |
| uses: actions/checkout@v4 | |
| 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 mf6 nightly build binaries | |
| uses: modflowpy/install-modflow-action@v1 | |
| with: | |
| repo: modflow6-nightly-build | |
| - name: Install pywatershed | |
| run: | | |
| pip install . | |
| - name: Version info | |
| run: | | |
| pip -V | |
| pip list | |
| - name: Get GIS files for tests | |
| run: | | |
| python pywatershed/utils/gis_files.py | |
| - name: domainless - run tests not requiring domain data | |
| working-directory: autotest | |
| run: pytest -m domainless -n=auto -vv | |
| - name: sagehen_5yr_no_cascades - generate and manage test data domain, run PRMS and convert csv output to NetCDF | |
| working-directory: autotest | |
| run: | | |
| python generate_test_data.py \ | |
| -n=auto --domain=sagehen_5yr --control_pattern=sagehen_no_cascades.control \ | |
| --remove_prms_csvs --remove_prms_output_dirs | |
| - name: sagehen_5yr_no_cascades - list netcdf input files | |
| working-directory: test_data | |
| run: | | |
| find sagehen_5yr/output_no_cascades -name '*.nc' | |
| - name: sagehen_5yr_no_cascades - pywatershed tests | |
| working-directory: autotest | |
| run: pytest | |
| -vv | |
| -rs | |
| -n=auto | |
| -m "not domainless" | |
| --domain=sagehen_5yr | |
| --control_pattern=sagehen_no_cascades.control | |
| --durations=0 | |
| --cov=pywatershed | |
| --cov-report=xml | |
| --junitxml=pytest_sagehen_5yr_no_cascades.xml | |
| - name: hru_1_nhm - generate and manage test data domain, run PRMS and convert csv output to NetCDF | |
| working-directory: autotest | |
| run: | | |
| python generate_test_data.py \ | |
| -n=auto --domain=hru_1 --control_pattern=nhm.control \ | |
| --remove_prms_csvs --remove_prms_output_dirs | |
| - name: hru_1_nhm - list netcdf input files | |
| working-directory: test_data | |
| run: | | |
| find hru_1/output -name '*.nc' | |
| - name: hru_1_nhm - pywatershed tests | |
| working-directory: autotest | |
| run: pytest | |
| -vv | |
| -rs | |
| -n=auto | |
| -m "not domainless" | |
| --domain=hru_1 | |
| --control_pattern=nhm.control | |
| --durations=0 | |
| --cov=pywatershed | |
| --cov-report=xml | |
| --junitxml=pytest_hru_1_nhm.xml | |
| - name: drb_2yr with and without dprst and obsin - generate and manage test data | |
| working-directory: autotest | |
| run: | | |
| python generate_test_data.py \ | |
| -n=auto --domain=drb_2yr \ | |
| --remove_prms_csvs --remove_prms_output_dirs | |
| - name: drb_2yr_nhm - list netcdf input files | |
| working-directory: test_data | |
| run: | | |
| find drb_2yr/output -name '*.nc' | |
| - name: drb_2yr_no_dprst - list netcdf input files | |
| working-directory: test_data | |
| run: | | |
| find drb_2yr/output_no_dprst -name '*.nc' | |
| - name: drb_2yr_nhm - pywatershed tests | |
| working-directory: autotest | |
| run: pytest | |
| -vv | |
| -rs | |
| -n=auto | |
| -m "not domainless" | |
| --domain=drb_2yr | |
| --control_pattern=nhm.control | |
| --durations=0 | |
| --cov=pywatershed | |
| --cov-report=xml | |
| --junitxml=pytest_drb_2yr_nhm.xml | |
| # Specific tests not redundant with dprst | |
| - name: drb_2yr_no_dprst - pywatershed tests | |
| working-directory: autotest | |
| run: pytest | |
| test_prms_runoff.py | |
| test_prms_soilzone.py | |
| test_prms_groundwater.py | |
| test_prms_above_snow.py | |
| test_prms_below_snow.py | |
| -vv | |
| -rs | |
| -n=auto | |
| -m "not domainless" | |
| --domain=drb_2yr | |
| --control_pattern=no_dprst | |
| --durations=0 | |
| --cov=pywatershed | |
| --cov-report=xml | |
| --junitxml=pytest_drb_2yr_no_dprst.xml | |
| # Specific tests not redundant with dprst | |
| - name: drb_2yr_obsin - pywatershed tests | |
| working-directory: autotest | |
| run: pytest | |
| test_obsin_flow_node.py | |
| -vv | |
| -n=0 | |
| -m "not domainless" | |
| --domain=drb_2yr | |
| --control_pattern=nhm_obsin.control | |
| --durations=0 | |
| --cov=pywatershed | |
| --cov-report=xml | |
| --junitxml=pytest_drb_2yr_no_dprst.xml | |
| - name: ucb_2yr_nhm - generate and manage test data | |
| working-directory: autotest | |
| run: | | |
| python generate_test_data.py \ | |
| -n=auto --domain=ucb_2yr --control_pattern=nhm.control \ | |
| --remove_prms_csvs --remove_prms_output_dirs | |
| - name: ucb_2yr_nhm - list netcdf input files | |
| working-directory: test_data | |
| run: | | |
| find ucb_2yr/output -name '*.nc' | |
| - name: ucb_2yr_nhm - pywatershed tests | |
| working-directory: autotest | |
| run: pytest | |
| -vv | |
| -n=auto | |
| -m "not domainless" | |
| --domain=ucb_2yr | |
| --control_pattern=nhm.control | |
| --durations=0 | |
| --cov=pywatershed | |
| --cov-report=xml | |
| --junitxml=pytest_ucb_2yr_nhm.xml | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Test results for ${{ runner.os }}-${{ matrix.python-version }} | |
| path: | | |
| ./autotest/pytest_hru_1_nhm.xml | |
| ./autotest/pytest_drb_2yr_nhm.xml | |
| ./autotest/pytest_drb_2yr_no_dprst.xml | |
| ./autotest/pytest_ucb_2yr_nhm.xml | |
| - name: Upload code coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: ./autotest/coverage.xml # should be just the ucb result | |
| # flags: unittests | |
| env_vars: RUNNER_OS,PYTHON_VERSION | |
| # name: codecov-umbrella | |
| fail_ci_if_error: false | |
| version: "v0.1.15" |