Fixes bugs with the short_term_extremes_example.mlx #235
Workflow file for this run
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| name: MHKiT-MATLAB Unix Unit Tests | |
| on: | |
| push: | |
| branches: [ master, develop ] | |
| pull_request: | |
| branches: [ master, develop ] | |
| jobs: | |
| cache_population: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.10"] | |
| matlab-version: [R2022b] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| mhkit-python-dir: "MHKiT-Python" | |
| MHKIT_PYTHON_VERSION: '0.7.0' | |
| steps: | |
| - name: Install & Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: latest | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: mhkit_conda_env | |
| channels: conda-forge | |
| - name: "Conda install netcdf4, hdf5" | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| conda install numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4 | |
| - name: Check out MHKiT-MATLAB | |
| uses: actions/checkout@v4 | |
| - name: pip install mhkit from pypi | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip install mhkit==$MHKIT_PYTHON_VERSION | |
| - name: pip install mhkit-python-utils module from source | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip install -e . | |
| - name: Pin scipy version | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip uninstall -y scipy | |
| pip install scipy==1.10.1 | |
| - name: List installed pip modules | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip freeze | |
| # Create the cache and add a dummy file | |
| # The dummy file ensures that the artifact download | |
| - name: Setup mhkit_webread_cache | |
| shell: bash -l {0} | |
| run: | | |
| mkdir mhkit_webread_cache | |
| touch mhkit_webread_cache/test.txt | |
| echo "Hello World" > mhkit_webread_cache/test.txt | |
| - name: Set up MATLAB | |
| uses: matlab-actions/setup-matlab@v2 | |
| with: | |
| release: ${{ matrix.matlab-version }} | |
| # OutOfProcess is required to properly call netcdf/hdf5 and works reliably on macos and ubuntu | |
| - name: Configure MATLAB Python Environment | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| printf 'pyenv(Version="%s", ExecutionMode="OutOfProcess")\n' $(python -c "import sys; print(sys.executable)") > run.m | |
| - name: Add MATLAB test commands | |
| shell: bash | |
| run: echo "version, | |
| addpath(genpath('mhkit')), | |
| import matlab.unittest.TestSuite, | |
| import matlab.unittest.TestRunner, | |
| testFolder = ['mhkit' filesep 'tests'], | |
| suite = TestSuite.fromFolder(testFolder), | |
| runner = TestRunner.withTextOutput, | |
| results = runner.run(suite), | |
| assertSuccess(results)" >> run.m | |
| - name: Output run.m | |
| shell: bash | |
| run: cat run.m | |
| - name: Run MATLAB Unit Tests | |
| uses: matlab-actions/run-command@v2 | |
| with: | |
| command: run | |
| startup-options: -noFigureWindows | |
| - name: Save mhkit_webread_cache directory as an artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| # GitHub Action "Name" of artifact | |
| name: mhkit_webread_cache | |
| # Filesystem path of directory | |
| path: mhkit_webread_cache | |
| main: | |
| needs: cache_population | |
| strategy: | |
| fail-fast: false | |
| # Expecting 2 * 4 * 7 - (13 * 2) = 30 jobs | |
| matrix: | |
| os: [macos-13, ubuntu-latest] | |
| python-version: [3.8, 3.9, "3.10", 3.11] | |
| # Note: It is preferred to use an actual release name as opposed to 'latest' | |
| matlab-version: [R2021b, R2022a, R2022b, R2023a, R2023b, R2024a] | |
| mhkit-python-version: ["0.7.0"] | |
| exclude: | |
| - python-version: "3.10" # cache_population job | |
| matlab-version: R2022b | |
| os: ubuntu-latest | |
| - matlab-version: R2024a # Non compatiable versions of Python and MATLAB | |
| python-version: 3.8 | |
| - matlab-version: R2023b | |
| python-version: 3.8 | |
| - matlab-version: R2023a | |
| python-version: 3.11 | |
| - matlab-version: R2022b | |
| python-version: 3.11 | |
| - matlab-version: R2022a | |
| python-version: 3.11 | |
| - matlab-version: R2022a | |
| python-version: "3.10" | |
| - matlab-version: R2021b | |
| python-version: 3.11 | |
| - matlab-version: R2021b | |
| python-version: "3.10" | |
| - matlab-version: R2021a | |
| python-version: 3.11 | |
| - matlab-version: R2021a | |
| python-version: "3.10" | |
| - matlab-version: R2021a | |
| python-version: 3.9 | |
| - matlab-version: R2020b | |
| python-version: 3.11 | |
| - matlab-version: R2020b | |
| python-version: "3.10" | |
| - matlab-version: R2020b | |
| python-version: 3.9 | |
| # Specific versions of tests that fail consistently. Most likely due to the GitHub actions environment | |
| # - matlab-version: R2024a # Python netcdf4 pip build error: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123413351 | |
| # python-version: 3.11 | |
| # os: macos-13 | |
| # - matlab-version: R2024a # Working! | |
| # python-version: "3.10" | |
| # os: macos-13 | |
| # - matlab-version: R2024a # Java Segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123411604 | |
| # python-version: 3.9 | |
| # os: macos-13 | |
| # - matlab-version: R2023b # Python netcd4 pip build error: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123412889 | |
| # python-version: 3.11 | |
| # os: macos-13 | |
| # - matlab-version: R2023b # Java segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123412352 | |
| # python-version: "3.10" | |
| # os: macos-13 | |
| # - matlab-version: R2023b # Java segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123411335 | |
| # python-version: 3.9 | |
| # os: macos-13 | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| mhkit-python-dir: "MHKiT-Python" | |
| MHKIT_PYTHON_VERSION: ${{ matrix.mhkit-python-version }} | |
| steps: | |
| - name: Check out MHKiT-MATLAB | |
| uses: actions/checkout@v4 | |
| - name: Install & Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: latest | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: mhkit_conda_env | |
| channels: conda-forge | |
| # This is necessary to fix any issues with netcdf4 and hdf5 headers | |
| - name: "Conda install netcdf4, hdf5" | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| conda install numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4 | |
| - name: Setup MATLAB Path on Ubuntu | |
| if: ${{ matrix.os == 'ubuntu-latest' }} | |
| run: echo "LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6" >> "$GITHUB_ENV" | |
| - name: Print Python executable | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| python -c "import sys; print(sys.executable)" | |
| - name: Print Python Version | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| python --version | |
| - name: pip install mhkit from pypi | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config | |
| pip install mhkit==$MHKIT_PYTHON_VERSION | |
| - name: pip upgrade netcdf4 | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config | |
| pip install --upgrade netcdf4 | |
| - name: pip install mhkit-python-utils module from source | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip install -e . | |
| - name: Pin scipy version | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip uninstall -y scipy | |
| pip install scipy==1.10.1 | |
| - name: List installed pip modules | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip freeze | |
| - name: Print MHKiT-Python Version | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| python -c "import mhkit; print(mhkit.__version__)" | |
| - name: Verify MHKiT-Python Operation | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| python -c "import mhkit; [ED, AP] = mhkit.river.performance.circular(30); print(ED); print(AP);" | |
| - name: Download mhkit_webread_cache artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: mhkit_webread_cache | |
| path: mhkit_webread_cache | |
| - name: Display structure mhkit_webread_cache | |
| run: ls -R | |
| working-directory: . | |
| - name: Set up MATLAB | |
| uses: matlab-actions/setup-matlab@v2 | |
| with: | |
| release: ${{ matrix.matlab-version }} | |
| - name: Configure OpenSSL for MacOS/MATLAB | |
| if: matrix.os == 'macos-13' | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| conda install openssl=="3.0.*" | |
| CONDA_LIB_PATH=$(python -c "import sys; import os; print(os.path.join(os.path.dirname(sys.executable), 'lib'))") | |
| export DYLD_LIBRARY_PATH="$CONDA_LIB_PATH:$DYLD_LIBRARY_PATH" | |
| echo "export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH" >> $GITHUB_ENV | |
| - name: Add Python Dir to Path | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| printf "getenv('path')\nsetenv('path', ['%s;', getenv('path')])\ngetenv('path')\n" $(python -c "import sys; import os; print(os.path.dirname(sys.executable))") >> run.m | |
| # OutOfProcess is required to properly call netcdf/hdf5 and works reliably on macos and ubuntu | |
| - name: Configure MATLAB Python Environment | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| printf 'pyenv(Version="%s", ExecutionMode="OutOfProcess")\n' $(python -c "import sys; print(sys.executable)") >> run.m | |
| # Pass dynamic library paths to MATLAB only on macOS | |
| if [[ $OSTYPE == "darwin"* ]]; then | |
| echo "setenv('DYLD_LIBRARY_PATH', getenv('DYLD_LIBRARY_PATH'));" >> run.m | |
| fi | |
| - name: Add MATLAB test commands | |
| shell: bash | |
| run: echo "version, | |
| addpath(genpath('mhkit')), | |
| import matlab.unittest.TestSuite, | |
| import matlab.unittest.TestRunner, | |
| testFolder = ['mhkit' filesep 'tests'], | |
| suite = TestSuite.fromFolder(testFolder), | |
| runner = TestRunner.withTextOutput, | |
| results = runner.run(suite), | |
| assertSuccess(results)" >> run.m | |
| - name: Output run.m | |
| shell: bash | |
| run: cat run.m | |
| # This is a good idea but does not work because you cannot explicitly set the python execution mode | |
| # - name: Run MHKiT-MATLAB Unit Tests | |
| # uses: matlab-actions/run-tests@v1 | |
| # with: | |
| # select-by-folder: mhkit/tests | |
| - name: Run MATLAB Unit Tests | |
| uses: matlab-actions/run-command@v2 | |
| with: | |
| command: run | |
| startup-options: -noFigureWindows |