unix_unit_tests.yml

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
          # conda install netcdf4 hdf5
          # export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config

      - name: Check out MHKiT-MATLAB
        uses: actions/checkout@v4

      # - name: Check out MHKiT-Python
      #   uses: actions/checkout@v4
      #   with:
      #     repository: "MHKiT-Software/MHKiT-Python"
      #     path: ${{env.mhkit-python-dir}}

      # - name: pip install mhkit module from source
      #   shell: bash -l {0}
      #   run: |
      #     conda activate mhkit_conda_env
      #     pip install -e .
      #   working-directory: ${{env.mhkit-python-dir}}

      - 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: Check out MHKiT-Python
      #   uses: actions/checkout@v4
      #   with:
      #     repository: "MHKiT-Software/MHKiT-Python"
      #     path: ${{env.mhkit-python-dir}}

      - 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
          # conda install netcdf4 hdf5
          # export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config

      # - name: Setup Python ${{ matrix.python-version }}
        # shell: bash -l {0}
        # run: |
        #   conda create --name mhkit_conda_env python=${{ matrix.python-version }} numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4 --strict-channel-priority
        #   conda activate mhkit_conda_env
        #   export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
        #   pip install -e . --no-deps --force-reinstall

      # - name: Setup MHKiT Dependencies on macOS
      #   if: ${{ matrix.os == 'macos-13' }}
      #   run: brew install hdf5 netcdf

      # - name: Setup MHKiT Dependencies on ubuntu
      #   run: sudo apt install libhdf5-serial-dev libnetcdf-dev
      #   if: ${{ matrix.os == 'ubuntu-latest' }}

      # - name: Setup MHKiT Dependencies on ubuntu
      #   if: ${{ matrix.os == 'ubuntu-latest' }}
      #   run: |
      #     sudo apt update
      #     sudo apt upgrade
      #     sudo apt install build-essential

      # - name: Print GCC Version
      #   if: ${{ matrix.os == 'ubuntu-latest' }}
      #   run: |
      #     gcc --version
      #     g++ --version

      # - name: Setup MATLAB Path on Ubuntu
      #   if: ${{ matrix.os == 'ubuntu-latest' }}
      #   run: echo "export LD_LIBRARY_PATH=/usr/local/MATLAB/${{ matrix.matlab-version }}/sys/os/glnxa64" >> "$GITHUB_ENV"

      - 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 module from source
      #   working-directory: ${{env.mhkit-python-dir}}
      #   shell: bash -l {0}
      #   run: |
      #     conda activate mhkit_conda_env
      #     export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
      #     pip install -e .

      - 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: 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

      - 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