Fix failing pip tests (#422) #1434
This file contains hidden or 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, 3.12 | Windows Mac Linux | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| - develop | |
| push: | |
| branches: | |
| - main | |
| - 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 }}" == "main" || "${{ steps.changes.outputs.wave_io_hindcast }}" == "true" ]]; then | |
| echo "should-run-hindcast=true" >> "$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: false | |
| - name: Create MHKiT Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -f environment.yml | |
| conda activate mhkit-env | |
| - name: Install testing dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| conda install -y pytest coverage coveralls | |
| - name: Install mhkit | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| pip install -e ".[all,dev]" --no-deps | |
| - name: Prepare non-hindcast API data | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| 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: false | |
| - name: Create MHKiT Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -f environment.yml | |
| conda activate mhkit-env | |
| - name: Install testing dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| conda install -y pytest coverage coveralls | |
| - name: Install mhkit | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| pip install -e ".[all,dev]" --no-deps | |
| - name: Prepare Wave Hindcast data | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| 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: ${{ env.PYTHON_VER }} | |
| use-only-tar-bz2: false | |
| - name: Create MHKiT Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -f environment.yml | |
| conda activate mhkit-env | |
| - name: Install testing dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| conda install -y pytest coverage coveralls | |
| - name: Install mhkit | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| pip install -e ".[all,dev]" --no-deps | |
| - name: Prepare Wind Hindcast data | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| pytest mhkit/tests/wave/io/hindcast/test_wind_toolkit.py | |
| - name: Upload Wind Hindcast data as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wind-hindcast-data | |
| path: ~/.cache/mhkit | |
| conda-build: | |
| name: conda-${{ 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', '3.12'] | |
| 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 MHKiT Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -f environment.yml | |
| conda activate mhkit-env | |
| - name: Install testing dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| conda install -y pytest coverage coveralls | |
| - name: Install mhkit | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| pip install -e . --no-deps | |
| - name: Run pytest & generate coverage report | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| 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', '3.12'] | |
| 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: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install -y libhdf5-dev libnetcdf-dev | |
| - name: Update and install packages | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install -e ".[all,dev]" | |
| - name: Reinstall h5py and netCDF4 with system libraries | |
| if: runner.os == 'Linux' | |
| run: "pip install --force-reinstall --no-binary=:all: h5py netCDF4" | |
| - name: Install setuptools for Python 3.12 | |
| if: matrix.python-version == '3.12' | |
| run: pip install setuptools | |
| - 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', '3.12'] | |
| 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 MHKiT Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -f environment.yml | |
| conda activate mhkit-env | |
| - name: Install testing dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| conda install -y pytest coverage coveralls | |
| - name: Install mhkit | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| pip install -e ".[all,dev]" --no-deps | |
| - 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: Run hindcast pytest | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| 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 | |
| test-wheel-packaging: | |
| name: Test Built Wheel | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build dependencies | |
| run: python -m pip install build --user | |
| - name: Build wheel | |
| run: python -m build --wheel --outdir dist/ . | |
| - name: Install MHKiT from built wheel | |
| run: | | |
| # Install from build wheel in dist/ directory, not from PyPI | |
| # -f, --find-links <url> If a URL or path to an html file, then parse for links to archives such as sdist (.tar.gz) or wheel (.whl) files. | |
| # If a local path or file:// URL that's a directory, then look for archives in the directory listing. | |
| pip install 'mhkit[all]' --find-links dist/ | |
| - name: Test mhkit submodule imports | |
| run: | | |
| python -c " | |
| import mhkit | |
| print(f'Version: {mhkit.__version__}') | |
| # Test all submodules can be imported | |
| modules = ['wave', 'river', 'tidal', 'dolfyn', 'power', 'loads', 'mooring', 'acoustics', 'qc', 'utils'] | |
| for mod in modules: | |
| exec(f'from mhkit import {mod}') | |
| print(f'Successfully imported mhkit.{mod}') | |
| print('All submodules imported successfully!') | |
| " | |
| - name: Verify mhkit package structure | |
| run: | | |
| python -c " | |
| import mhkit | |
| import os | |
| mhkit_path = os.path.dirname(mhkit.__file__) | |
| expected_dirs = ['wave', 'river', 'tidal', 'dolfyn', 'power', 'loads', 'mooring', 'acoustics', 'qc', 'utils'] | |
| for d in expected_dirs: | |
| dir_path = os.path.join(mhkit_path, d) | |
| assert os.path.isdir(dir_path), f'Missing submodule directory: {d}' | |
| init_file = os.path.join(dir_path, '__init__.py') | |
| assert os.path.isfile(init_file), f'Missing __init__.py in {d}' | |
| print('Package structure verified!') | |
| " | |
| test-optional-pip-dependencies: | |
| needs: [set-os, prepare-nonhindcast-cache] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| module: | |
| [wave, tidal, river, dolfyn, power, loads, mooring, acoustics, utils] | |
| python-version: ['3.12'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Download non-hindcast data | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: data | |
| path: ~/.cache/mhkit | |
| - name: Install system dependencies | |
| run: sudo apt-get install -y libhdf5-dev libnetcdf-dev | |
| - name: Install MHKiT with optional dependency | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install "mhkit[${{ matrix.module }}]" | |
| pip install pytest | |
| - name: Reinstall h5py and netCDF4 with system libraries | |
| run: "pip install --force-reinstall --no-binary=:all: h5py netCDF4" | |
| - name: Run tests for ${{ matrix.module }} | |
| env: | |
| MPLBACKEND: Agg | |
| run: | | |
| python -m pytest -c .github/workflows/pytest.ini mhkit/tests/${{ matrix.module }}/ | |
| 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: '3.12' | |
| channels: conda-forge | |
| activate-environment: TESTconda | |
| use-only-tar-bz2: false | |
| - name: Create MHKiT Conda environment | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -f environment.yml | |
| conda activate mhkit-env | |
| - name: Install notebook testing dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| conda install -y pytest coverage coveralls nbval jupyter utm folium | |
| - name: Install mhkit | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit-env | |
| pip install -e ".[all,dev]" --no-deps | |
| - 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: | | |
| conda activate mhkit-env | |
| 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 }} |