ipython notebook test #1019
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| 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: ${{ fromJson(needs.notebook-matrix.outputs.matrix) }} | |
| if: | | |
| always() | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| python-version: '3.11' | |
| activate-environment: TESTconda | |
| use-only-tar-bz2: true | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda install numpy cython pip hdf5 libnetcdf cftime netcdf4 --strict-channel-priority | |
| pip install -e . --force-reinstall | |
| python -m pip install --upgrade pip wheel | |
| pip install nbval jupyter | |
| pip install utm folium | |
| - name: Ensure Conda environment is activated | |
| shell: bash -l {0} | |
| run: | | |
| echo "source ~/miniconda3/etc/profile.d/conda.sh" >> ~/.bashrc | |
| echo "conda activate TESTconda" >> ~/.bashrc | |
| source ~/.bashrc | |
| - name: Run notebook | |
| shell: bash -l {0} | |
| run: | | |
| if [[ "${{ 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 }} |