unix_unit_tests.yml

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: 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==1.14.0

      - 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 }}

      # 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

      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