Actions: Migrate to newer versions of macos #475
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| name: MHKiT-MATLAB Unix Unit Tests | |
| # Only run tests when MATLAB files or this workflow file changes | |
| on: | |
| push: | |
| branches: [ master, develop ] | |
| paths: | |
| - 'mhkit/**/*.m' | |
| - 'examples/**/*.m' | |
| - '.github/workflows/unix_unit_tests.yml' | |
| pull_request: | |
| branches: [ master, develop ] | |
| paths: | |
| - 'mhkit/**/*.m' | |
| - 'examples/**/*.m' | |
| - '.github/workflows/unix_unit_tests.yml' | |
| jobs: | |
| cache_population: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-22.04"] | |
| python-version: ["3.11"] | |
| matlab-version: [R2023b] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| mhkit-python-dir: "MHKiT-Python" | |
| MHKIT_PYTHON_VERSION: '1.0.1' | |
| steps: | |
| - name: Install & Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: latest | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: mhkit_conda_env | |
| channels: conda-forge,defaults | |
| # - name: "Conda install netcdf4, hdf5" | |
| # shell: bash -l {0} | |
| # run: | | |
| # conda activate mhkit_conda_env | |
| # conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4 | |
| # | |
| # - name: Fix libstdc++ compatibility | |
| # if: matrix.os == 'ubuntu-22.04' | |
| # run: | | |
| # # Force MATLAB to use system libstdc++ instead of its bundled (older) version | |
| # # LD_PRELOAD forces the library to be loaded first | |
| # # LD_LIBRARY_PATH ensures symbol resolution finds the system library | |
| # echo "LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6" >> "$GITHUB_ENV" | |
| # echo "LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH" >> "$GITHUB_ENV" | |
| - name: Check out MHKiT-MATLAB | |
| uses: actions/checkout@v4 | |
| - name: Conda install mhkit | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| conda install -c conda-forge 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==1.14.0 | |
| - 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 }} | |
| # Generate run.m using Python to match Windows workflow approach | |
| # Using InProcess mode for cache_population job | |
| - name: Generate run.m | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| python -c " | |
| import sys | |
| python_exe = sys.executable | |
| content = f'''pyenv(Version='{python_exe}', ExecutionMode='InProcess') | |
| % Verify Python environment | |
| pe = pyenv; | |
| disp(pe); | |
| % Warm up numpy - must call function to force resolution | |
| py.importlib.import_module('numpy'); | |
| dummy = py.numpy.array([1,2,3]); | |
| disp(class(dummy)); | |
| clear dummy; | |
| disp('py.numpy.array: resolved'); | |
| % Warm up mhkit submodules - force resolution by calling functions | |
| py.importlib.import_module('mhkit'); | |
| py.importlib.import_module('mhkit.wave.io.ndbc'); | |
| py.importlib.import_module('mhkit.wave.io.swan'); | |
| py.importlib.import_module('mhkit.river.resource'); | |
| disp('mhkit submodules: imported'); | |
| version | |
| pyenv | |
| 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) | |
| ''' | |
| with open('run.m', 'w', encoding='utf-8', newline='\\n') as f: | |
| f.write(content) | |
| " | |
| - 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 | |
| matrix: | |
| os: [macos-15, macos-15-intel, "ubuntu-22.04"] | |
| python-version: ["3.10", 3.11, 3.12] | |
| # Note: It is preferred to use an actual release name as opposed to 'latest' | |
| # macos-15 is ARM (Apple Silicon) - R2023b+ run natively | |
| # macos-15-intel is x64 - R2022b/R2023a run natively (no Rosetta needed) | |
| matlab-version: [R2022b, R2023a, R2023b, R2024a, R2024b, R2025a] | |
| mhkit-python-version: ["1.0.1"] | |
| exclude: | |
| # Python 3.12 + MATLAB incompatibility | |
| - matlab-version: R2024a | |
| python-version: 3.12 | |
| - matlab-version: R2023b | |
| python-version: 3.12 | |
| - matlab-version: R2023a | |
| python-version: 3.12 | |
| - matlab-version: R2022b | |
| python-version: 3.12 | |
| - matlab-version: R2025a | |
| python-version: 3.12 | |
| # Python 3.11 + MATLAB incompatibility | |
| - matlab-version: R2023a | |
| python-version: 3.11 | |
| - matlab-version: R2022b | |
| python-version: 3.11 | |
| # Architecture-specific macOS exclusions | |
| # Intel MATLAB (R2022b, R2023a) should only run on macos-15-intel | |
| - matlab-version: R2022b | |
| os: macos-15 | |
| - matlab-version: R2023a | |
| os: macos-15 | |
| # ARM MATLAB (R2023b+) should only run on macos-15 (ARM) | |
| - matlab-version: R2023b | |
| os: macos-15-intel | |
| - matlab-version: R2024a | |
| os: macos-15-intel | |
| - matlab-version: R2024b | |
| os: macos-15-intel | |
| - matlab-version: R2025a | |
| os: macos-15-intel | |
| # Specific MATLAB/Python/OS Errors | |
| # Error using _cythonized_array_utils>init | |
| # scipy.linalg._cythonized_array_utils (line 1) | |
| # Python Error: ValueError: numpy.dtype size changed, may indicate binary | |
| # incompatibility. Expected 96 from C header, got 88 from PyObject | |
| # - matlab-version: R2024b | |
| # python-version: 3.12 | |
| # os: macos-15 | |
| # Unable to resolve the name 'py.mhkit.wave.resource.jonswap_spectrum' | |
| # - matlab-version: R2023a | |
| # python-version: 3.10 | |
| # os: "ubuntu-22.04" | |
| 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: ${{ matrix.python-version }} | |
| activate-environment: mhkit_conda_env | |
| channels: conda-forge,defaults | |
| # This is necessary to fix any issues with netcdf4 and hdf5 headers | |
| - name: "Conda install netcdf4, hdf5" | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4 | |
| - name: Fix libstdc++ compatibility | |
| if: matrix.os == 'ubuntu-22.04' | |
| run: | | |
| # Force MATLAB to use system libstdc++ instead of its bundled (older) version | |
| # LD_PRELOAD forces the library to be loaded first | |
| # LD_LIBRARY_PATH ensures symbol resolution finds the system library | |
| echo "LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6" >> "$GITHUB_ENV" | |
| echo "LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH" >> "$GITHUB_ENV" | |
| # Pin compatible ICU version based on MATLAB's bundled libstdc++ capabilities | |
| # Older MATLAB versions bundle older libstdc++ missing newer GLIBCXX symbols | |
| - name: Pin compatible ICU version for MATLAB | |
| if: matrix.os == 'ubuntu-22.04' | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| # Lookup table: MATLAB version -> max compatible ICU version | |
| # Based on GLIBCXX symbols available in MATLAB's bundled libstdc++ | |
| declare -A ICU_COMPAT=( | |
| ["R2022a"]="70" | |
| ["R2022b"]="70" | |
| ["R2023a"]="70" | |
| ["R2023b"]="" # empty = use latest (has modern libstdc++) | |
| ["R2024a"]="" | |
| ["R2024b"]="" | |
| ["R2025a"]="" | |
| ) | |
| MATLAB_VERSION="${{ matrix.matlab-version }}" | |
| ICU_VERSION="${ICU_COMPAT[$MATLAB_VERSION]}" | |
| if [ -n "$ICU_VERSION" ]; then | |
| echo "MATLAB $MATLAB_VERSION requires older ICU. Installing icu=$ICU_VERSION" | |
| conda install -y "icu<=$ICU_VERSION" | |
| else | |
| echo "MATLAB $MATLAB_VERSION has modern libstdc++, using default ICU" | |
| fi | |
| # Diagnostic: Check what GLIBC symbols are required by key libraries | |
| - name: Diagnose library dependencies (Ubuntu) | |
| if: matrix.os == 'ubuntu-22.04' | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| echo "=== System libstdc++ GLIBCXX versions ===" | |
| strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX | tail -10 | |
| echo "" | |
| echo "=== Conda libicuuc location and GLIBCXX requirements ===" | |
| ICUUC=$(find $CONDA_PREFIX -name "libicuuc.so*" 2>/dev/null | head -1) | |
| if [ -n "$ICUUC" ]; then | |
| echo "Found: $ICUUC" | |
| strings "$ICUUC" | grep GLIBCXX || echo "No GLIBCXX requirements" | |
| else | |
| echo "libicuuc not found in conda env" | |
| fi | |
| echo "" | |
| echo "=== MATLAB libstdc++ location (if accessible) ===" | |
| ls -la /opt/hostedtoolcache/MATLAB/*/x64/sys/os/glnxa64/libstdc++.so.6 2>/dev/null || echo "MATLAB libstdc++ not found" | |
| - 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:$PATH" # so setup.py finds nc-config | |
| pip install --upgrade netcdf4 | |
| - name: pip install mhkit-python-utils module from source | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip install -e . | |
| - name: Pin scipy version | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip uninstall -y scipy | |
| pip install scipy==1.14.0 | |
| - name: List installed pip modules | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| pip freeze | |
| - name: Print MHKiT-Python Version | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| python -c "import mhkit; print(mhkit.__version__)" | |
| - name: Verify MHKiT-Python Operation | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| python -c "import mhkit; [ED, AP] = mhkit.river.performance.circular(30); print(ED); print(AP);" | |
| - name: Download mhkit_webread_cache artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: mhkit_webread_cache | |
| path: mhkit_webread_cache | |
| - name: Display structure mhkit_webread_cache | |
| run: ls -R | |
| working-directory: . | |
| - name: Install Amazon Corretto 11 for ARM MATLAB | |
| if: runner.os == 'macOS' | |
| run: | | |
| # ARM MATLAB (R2023b+) requires Java 11 | |
| brew install --cask corretto@11 | |
| echo "JAVA_HOME=$(/usr/libexec/java_home -v 11)" >> $GITHUB_ENV | |
| - name: Set up MATLAB | |
| uses: matlab-actions/setup-matlab@v2 | |
| with: | |
| release: ${{ matrix.matlab-version }} | |
| - name: Configure OpenSSL for MacOS/MATLAB | |
| if: runner.os == 'macOS' | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mhkit_conda_env | |
| conda install openssl=="3.0.*" | |
| CONDA_LIB_PATH=$(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 "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 | |
| # Note: LD_PRELOAD and LD_LIBRARY_PATH are set via GITHUB_ENV earlier for Linux | |
| - 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 | |
| # Warm up Python OutOfProcess worker to prevent intermittent "Unable to resolve" errors | |
| - name: Add Python environment verification | |
| shell: bash | |
| run: | | |
| echo "% Verify Python environment and warm up OutOfProcess worker" >> run.m | |
| echo "pe = pyenv;" >> run.m | |
| echo "disp(pe);" >> run.m | |
| echo "py.importlib.import_module('numpy');" >> run.m | |
| echo "py.importlib.import_module('mhkit');" >> run.m | |
| echo "disp('Python environment verified: numpy and mhkit imported successfully');" >> 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 | |
| # 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 |