Fix: Handle unnamed index/dimension in wave.resource.surface_elevatio… #35
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: Py 3.10, 3.11 | Windows Mac Linux | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| jobs: | |
| set-os: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix_os: ${{ steps.set-matrix.outputs.matrix_os }} | |
| steps: | |
| - id: set-matrix | |
| run: | | |
| if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "develop" ]]; then | |
| echo "matrix_os=[ \"ubuntu-latest\"]" >> $GITHUB_OUTPUT | |
| else | |
| echo "matrix_os=[\"windows-latest\", \"ubuntu-latest\", \"macos-latest\"]" >> $GITHUB_OUTPUT | |
| fi | |
| check-changes: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| wave_io_hindcast_changed: ${{ steps.changes.outputs.wave_io_hindcast }} | |
| should-run-hindcast: ${{ steps.hindcast-logic.outputs.should-run-hindcast }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Check for changes in wave/io/hindcast | |
| id: changes | |
| uses: dorny/paths-filter@v3 | |
| with: | |
| filters: | | |
| wave_io_hindcast: | |
| - 'mhkit/wave/io/hindcast/**' | |
| - 'mhkit/tests/wave/io/hindcast/**' | |
| - id: hindcast-logic | |
| run: | | |
| if [[ "${{ github.event.pull_request.base.ref }}" == "master" || "${{ steps.changes.outputs.wave_io_hindcast }}" == "true" ]]; then | |
| echo "should-run-hindcast=true" >> "$GITHUB_OUTPUT" | |
| else | |
| echo "should-run-hindcast=false" >> "$GITHUB_OUTPUT" | |
| fi | |
| prepare-nonhindcast-cache: | |
| runs-on: ubuntu-latest | |
| env: | |
| PYTHON_VER: 3.11 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| python-version: ${{ env.PYTHON_VER }} | |
| activate-environment: TESTconda | |
| use-only-tar-bz2: true | |
| - name: Setup Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda install numpy cython pip hdf5 libnetcdf cftime netcdf4 --strict-channel-priority | |
| pip install -e . --force-reinstall | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install coverage pytest coveralls . | |
| - name: Prepare non-hindcast API data | |
| shell: bash -l {0} | |
| run: | | |
| pytest mhkit/tests/river/test_io_usgs.py | |
| pytest mhkit/tests/tidal/test_io.py | |
| pytest mhkit/tests/wave/io/test_cdip.py | |
| - name: Upload data as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: data | |
| path: ~/.cache/mhkit | |
| prepare-wave-hindcast-cache: | |
| needs: [check-changes] | |
| runs-on: ubuntu-latest | |
| env: | |
| PYTHON_VER: 3.11 | |
| if: (needs.check-changes.outputs.should-run-hindcast == 'true') | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| activate-environment: TEST | |
| python-version: ${{ env.PYTHON_VER }} | |
| use-only-tar-bz2: true | |
| - name: Setup Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4 coverage --strict-channel-priority | |
| pip install -e . --force-reinstall | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install coverage pytest coveralls . | |
| - name: Prepare Wave Hindcast data | |
| shell: bash -l {0} | |
| run: | | |
| pytest mhkit/tests/wave/io/hindcast/test_hindcast.py | |
| - name: Upload Wave Hindcast data as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wave-hindcast-data | |
| path: ~/.cache/mhkit | |
| prepare-wind-hindcast-cache: | |
| needs: [check-changes, prepare-wave-hindcast-cache] | |
| runs-on: ubuntu-latest | |
| env: | |
| PYTHON_VER: 3.11 | |
| if: (needs.check-changes.outputs.should-run-hindcast == 'true') | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| activate-environment: TEST | |
| python-version: ${{ env.PYTHON_VER }} | |
| use-only-tar-bz2: true | |
| - name: Setup Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4 coverage --strict-channel-priority | |
| pip install -e . --no-deps --force-reinstall | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install coverage pytest coveralls . | |
| - name: Prepare Wind Hindcast data | |
| shell: bash -l {0} | |
| run: | | |
| pytest mhkit/tests/wave/io/hindcast/test_wind_toolkit.py | |
| - name: Upload Wind Hindcast data as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wind-hindcast-data | |
| path: ~/.cache/mhkit | |
| conda-build: | |
| name: conda-${{ matrix.os }}/${{ matrix.python-version }} | |
| needs: [set-os, prepare-nonhindcast-cache] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ${{fromJson(needs.set-os.outputs.matrix_os)}} | |
| python-version: ['3.10', '3.11'] | |
| env: | |
| PYTHON_VER: ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| environment-file: environment.yml | |
| activate-environment: TEST | |
| python-version: ${{ matrix.python-version }} | |
| use-only-tar-bz2: false | |
| - name: Create and setup Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c conda-forge pytest coverage=7.5.0 coveralls --strict-channel-priority | |
| pip install -e . --force-reinstall | |
| - name: Download data from artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: data | |
| path: ~/.cache/mhkit | |
| - name: Run pytest & generate coverage report | |
| shell: bash -l {0} | |
| run: | | |
| coverage run --rcfile=.github/workflows/.coveragerc --source=./mhkit/ -m pytest -c .github/workflows/pytest.ini | |
| coverage lcov | |
| - name: Upload coverage data to coveralls.io | |
| uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| flag-name: conda-${{ runner.os }}-py${{ matrix.python-version }} | |
| parallel: true | |
| path-to-lcov: ./coverage.lcov | |
| pip-build: | |
| name: pip-${{ matrix.os }}/${{ matrix.python-version }} | |
| needs: [set-os, prepare-nonhindcast-cache] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ${{fromJson(needs.set-os.outputs.matrix_os)}} | |
| python-version: ['3.10', '3.11'] | |
| steps: | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Set up Git repository | |
| uses: actions/checkout@v4 | |
| - name: Download data from artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: data | |
| path: ~/.cache/mhkit | |
| - name: Update and install packages | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install coverage pytest coveralls . | |
| - name: Run pytest & generate coverage report | |
| shell: bash -l {0} | |
| run: | | |
| coverage run --rcfile=.github/workflows/.coveragerc --source=./mhkit/ -m pytest -c .github/workflows/pytest.ini | |
| coverage lcov | |
| - name: Upload coverage data to coveralls.io | |
| uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| flag-name: pip-${{ runner.os }}-py${{ matrix.python-version }} | |
| parallel: true | |
| path-to-lcov: ./coverage.lcov | |
| hindcast-calls: | |
| name: hindcast-${{ matrix.os }}/${{ matrix.python-version }} | |
| needs: | |
| [ | |
| check-changes, | |
| prepare-wave-hindcast-cache, | |
| prepare-wind-hindcast-cache, | |
| set-os, | |
| ] | |
| if: (needs.check-changes.outputs.should-run-hindcast == 'true') | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 1 | |
| fail-fast: false | |
| matrix: | |
| os: ${{fromJson(needs.set-os.outputs.matrix_os)}} | |
| python-version: ['3.10', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| environment-file: environment.yml | |
| activate-environment: TEST | |
| python-version: ${{ matrix.python-version }} | |
| use-only-tar-bz2: false | |
| - name: Setup Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c conda-forge pytest coverage=7.5.0 coveralls --strict-channel-priority | |
| pip install -e . --force-reinstall | |
| - name: Download Wave Hindcast data from artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: wave-hindcast-data | |
| path: ~/.cache/mhkit/wave-hindcast | |
| - name: Download Wind Hindcast data from artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: wind-hindcast-data | |
| path: ~/.cache/mhkit/wind-hindcast | |
| - name: Consolidate hindcast data | |
| run: | | |
| mkdir -p ~/.cache/mhkit/hindcast | |
| mv ~/.cache/mhkit/wave-hindcast/hindcast/* ~/.cache/mhkit/hindcast/ | |
| mv ~/.cache/mhkit/wind-hindcast/hindcast/* ~/.cache/mhkit/hindcast/ | |
| shell: bash | |
| - name: Install MHKiT and run pytest | |
| shell: bash -l {0} | |
| run: | | |
| coverage run --rcfile=.github/workflows/.coveragehindcastrc -m pytest -c .github/workflows/pytest-hindcast.ini | |
| coverage lcov | |
| - name: Upload coverage data to coveralls.io | |
| uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| flag-name: hindcast-${{ runner.os }}-py${{ matrix.python-version }} | |
| parallel: true | |
| path-to-lcov: ./coverage.lcov | |
| notebook-matrix: | |
| runs-on: ubuntu-latest | |
| needs: | |
| [ | |
| check-changes, | |
| prepare-nonhindcast-cache, | |
| prepare-wave-hindcast-cache, | |
| prepare-wind-hindcast-cache, | |
| ] | |
| if: | | |
| always() && | |
| ( | |
| ( | |
| needs.prepare-nonhindcast-cache.result == 'success' && | |
| needs.prepare-wave-hindcast-cache.result == 'skipped' && | |
| needs.prepare-wind-hindcast-cache.result == 'skipped' && | |
| needs.check-changes.outputs.should-run-hindcast == 'false' | |
| ) || | |
| ( | |
| needs.prepare-nonhindcast-cache.result == 'success' && | |
| needs.prepare-wave-hindcast-cache.result == 'success' && | |
| needs.prepare-wind-hindcast-cache.result == 'success' && | |
| needs.check-changes.outputs.should-run-hindcast == 'true' | |
| ) | |
| ) | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.11' | |
| - name: Generate matrix | |
| id: set-matrix | |
| run: | | |
| matrix_json=$(python .github/workflows/generate_notebook_matrix.py) | |
| echo "$matrix_json" >> $GITHUB_OUTPUT | |
| test-notebooks: | |
| needs: | |
| [ | |
| notebook-matrix, | |
| check-changes, | |
| prepare-nonhindcast-cache, | |
| prepare-wave-hindcast-cache, | |
| prepare-wind-hindcast-cache, | |
| ] | |
| strategy: | |
| matrix: ${{ fromJson(needs.notebook-matrix.outputs.matrix) }} | |
| if: | | |
| always() | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| python-version: '3.11' | |
| activate-environment: TESTconda | |
| use-only-tar-bz2: true | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda install numpy cython pip hdf5 libnetcdf cftime netcdf4 --strict-channel-priority | |
| pip install -e . --force-reinstall | |
| python -m pip install --upgrade pip wheel | |
| pip install nbval jupyter | |
| pip install utm folium | |
| - name: Ensure Conda environment is activated | |
| shell: bash -l {0} | |
| run: | | |
| echo "source ~/miniconda3/etc/profile.d/conda.sh" >> ~/.bashrc | |
| echo "conda activate TESTconda" >> ~/.bashrc | |
| source ~/.bashrc | |
| - name: Download non-hindcast data | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: data | |
| path: ~/.cache/mhkit | |
| - name: Download Wave Hindcast data (if available) | |
| if: (needs.check-changes.outputs.should-run-hindcast == 'true') | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: wave-hindcast-data | |
| path: ~/.cache/mhkit/wave-hindcast | |
| - name: Download Wind Hindcast data (if available) | |
| if: (needs.check-changes.outputs.should-run-hindcast == 'true') | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: wind-hindcast-data | |
| path: ~/.cache/mhkit/wind-hindcast | |
| - name: Consolidate hindcast data | |
| if: (needs.check-changes.outputs.should-run-hindcast == 'true') | |
| run: | | |
| mkdir -p ~/.cache/mhkit/hindcast | |
| mv ~/.cache/mhkit/wave-hindcast/hindcast/* ~/.cache/mhkit/hindcast/ | |
| mv ~/.cache/mhkit/wind-hindcast/hindcast/* ~/.cache/mhkit/hindcast/ | |
| shell: bash | |
| - name: Copy .hscfg file to examples directory | |
| shell: bash -l {0} | |
| run: | | |
| cp .hscfg examples/ | |
| - name: Run notebook | |
| shell: bash -l {0} | |
| run: | | |
| if [[ "${{ matrix.notebook }}" == "examples/metocean_example.ipynb" || "${{ matrix.notebook }}" == "examples/WPTO_hindcast_example.ipynb" ]]; then | |
| if [[ "${{ needs.check-changes.outputs.should-run-hindcast }}" == 'true' ]]; then | |
| jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=${{ matrix.timeout }} "${{ matrix.notebook }}" | |
| else | |
| echo "Skipping ${{ matrix.notebook }}" | |
| fi | |
| else | |
| jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=${{ matrix.timeout }} "${{ matrix.notebook }}" | |
| fi | |
| coveralls: | |
| name: Indicate completion to coveralls.io | |
| needs: | |
| [ | |
| prepare-wave-hindcast-cache, | |
| prepare-wind-hindcast-cache, | |
| conda-build, | |
| pip-build, | |
| hindcast-calls, | |
| ] | |
| if: | | |
| always() && | |
| ( | |
| ( | |
| needs.conda-build.result == 'success' && | |
| needs.pip-build.result == 'success' && | |
| needs.prepare-wave-hindcast-cache.result == 'skipped' && | |
| needs.prepare-wind-hindcast-cache.result == 'skipped' && | |
| needs.hindcast-calls.result == 'skipped' | |
| ) || | |
| ( | |
| needs.conda-build.result == 'success' && | |
| needs.pip-build.result == 'success' && | |
| needs.prepare-wave-hindcast-cache.result == 'success' && | |
| needs.prepare-wind-hindcast-cache.result == 'success' && | |
| needs.hindcast-calls.result == 'success' | |
| ) | |
| ) | |
| runs-on: ubuntu-latest | |
| container: python:3-slim | |
| steps: | |
| - name: Coveralls Finished | |
| uses: coverallsapp/github-action@master | |
| with: | |
| parallel-finished: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |