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Merge pull request #162 from MHKiT-Software/develop
Release MHKiT-MATLAB Version 0.6.0
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‎.github/workflows/build_release.yml‎

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name: Build Production and Development Release
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on:
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push:
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branches:
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- master
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- develop
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jobs:
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build-toolbox:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Verify Version Numbers
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run: |
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# Extract version from pyproject.toml
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PYPROJECT_VERSION=$(grep -Po '(?<=version = ")[^"]*' pyproject.toml)
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# Extract version from __init__.py
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INIT_PY_VERSION=$(grep -Po '(?<=__version__ = ")[^"]*' mhkit_python_utils/__init__.py)
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# Extract version from build_release.m
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MATLAB_VERSION=$(grep -Po "(?<=project_version = ')[^']*" scripts/build_release.m)
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echo "Versions found:"
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echo "pyproject.toml: $PYPROJECT_VERSION"
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echo "__init__.py: $INIT_PY_VERSION"
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echo "build_release.m: $MATLAB_VERSION"
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# Verify all versions match
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if [ "$PYPROJECT_VERSION" != "$INIT_PY_VERSION" ] || [ "$PYPROJECT_VERSION" != "$MATLAB_VERSION" ]; then
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echo "Error: Version numbers do not match across files!"
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echo "Please ensure versions are consistent in:"
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echo "- pyproject.toml ($PYPROJECT_VERSION)"
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echo "- mhkit_python_utils/__init__.py ($INIT_PY_VERSION)"
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echo "- scripts/build_release.m ($MATLAB_VERSION)"
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exit 1
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fi
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# Set version as environment variable for later use
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echo "MHKIT_MATLAB_VERSION=$MATLAB_VERSION" >> $GITHUB_ENV
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- name: Check for existing version tag
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run: |
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if git ls-remote --exit-code --tags origin "refs/tags/v${MHKIT_MATLAB_VERSION}" >/dev/null 2>&1; then
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echo "Error: Version v${MHKIT_MATLAB_VERSION} already exists as a tag!"
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echo "Please update the version number in:"
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echo "- pyproject.toml"
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echo "- mhkit_python_utils/__init__.py"
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echo "- scripts/build_release.m"
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exit 1
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fi
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- name: Set environment variables
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run: |
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echo "SHORT_SHA=$(echo ${{ github.sha }} | cut -c1-7)" >> $GITHUB_ENV
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- name: Set up MATLAB
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uses: matlab-actions/setup-matlab@v2
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with:
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release: R2024a
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- name: Build Toolbox
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uses: matlab-actions/run-command@v2
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with:
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command: addpath('scripts'); build_release
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- name: Rename files for develop branch
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if: github.ref != 'refs/heads/master'
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run: |
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for f in mhkit_v*.mltbx; do
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mv "$f" "${f/.mltbx/-dev-${SHORT_SHA}.mltbx}"
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done
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for f in mhkit_examples_v*.zip; do
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mv "$f" "${f/.zip/-dev-${SHORT_SHA}.zip}"
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done
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for f in mhkit_python_utils*.zip; do
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mv "$f" "${f/.zip/-dev-${SHORT_SHA}.zip}"
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done
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- name: Upload MATLAB Toolbox
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uses: actions/upload-artifact@v4
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with:
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name: mhkit-toolbox
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path: mhkit_v*.mltbx
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if-no-files-found: error
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- name: Upload Examples
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uses: actions/upload-artifact@v4
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with:
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name: mhkit-examples
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path: mhkit_examples_v*.zip
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if-no-files-found: error
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- name: Upload mhkit_python_utils
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uses: actions/upload-artifact@v4
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with:
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name: mhkit-python-utils
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path: mhkit_python_utils_v*.zip
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if-no-files-found: error
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- name: Create Release
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uses: softprops/action-gh-release@v1
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if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop'
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with:
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files: |
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mhkit_v*.mltbx
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mhkit_examples_v*.zip
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mhkit_python_utils_v*.zip
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name: ${{ github.ref == 'refs/heads/master' && format('MHKiT-MATLAB v{0} Release', env.MHKIT_MATLAB_VERSION) || format('MHKiT-MATLAB v{0} Development Build ({1})', env.MHKIT_MATLAB_VERSION, env.SHORT_SHA) }}
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tag_name: ${{ github.ref == 'refs/heads/master' && format('v{0}', env.MHKIT_MATLAB_VERSION) || format('v{0}-dev-{1}', env.MHKIT_MATLAB_VERSION, env.SHORT_SHA) }}
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# Release visibility settings:
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# - For master branch: Creates a public production release (draft=false)
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# - For other branches: Creates a draft release (draft=true) visible only to repository contributors
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# This allows the development team to test new builds before making them public.
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draft: ${{ github.ref != 'refs/heads/master' }}
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prerelease: false
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/unix_unit_tests.yml‎

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env:
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mhkit-python-dir: "MHKiT-Python"
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MHKIT_PYTHON_VERSION: '0.7.0'
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MHKIT_PYTHON_VERSION: '0.9.0'
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steps:
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- name: Install & Setup Miniconda
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uses: conda-incubator/setup-miniconda@v3
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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activate-environment: mhkit_conda_env
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channels: conda-forge
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channels: conda-forge,defaults
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- name: "Conda install netcdf4, hdf5"
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shell: bash -l {0}
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run: |
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conda activate mhkit_conda_env
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conda install numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4
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# conda install netcdf4 hdf5
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# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
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conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4
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- name: Check out MHKiT-MATLAB
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uses: actions/checkout@v4
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# - name: Check out MHKiT-Python
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# uses: actions/checkout@v4
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# with:
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# repository: "MHKiT-Software/MHKiT-Python"
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# path: ${{env.mhkit-python-dir}}
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# - name: pip install mhkit module from source
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# shell: bash -l {0}
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# run: |
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# conda activate mhkit_conda_env
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# pip install -e .
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# working-directory: ${{env.mhkit-python-dir}}
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- name: pip install mhkit from pypi
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shell: bash -l {0}
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run: |
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run: |
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conda activate mhkit_conda_env
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pip uninstall -y scipy
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pip install scipy==1.10.1
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pip install scipy==1.12.0
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- name: List installed pip modules
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shell: bash -l {0}
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strategy:
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fail-fast: false
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# Expecting 2 * 4 * 7 - (13 * 2) = 30 jobs
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matrix:
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os: [macos-13, ubuntu-latest]
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python-version: [3.8, 3.9, "3.10", 3.11]
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python-version: ["3.10", 3.11, 3.12]
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# Note: It is preferred to use an actual release name as opposed to 'latest'
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matlab-version: [R2021b, R2022a, R2022b, R2023a, R2023b, R2024a]
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mhkit-python-version: ["0.7.0"]
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matlab-version: [R2022b, R2023a, R2023b, R2024a, R2024b]
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mhkit-python-version: ["0.9.0"]
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exclude:
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- python-version: "3.10" # cache_population job
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matlab-version: R2022b
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os: ubuntu-latest
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- matlab-version: R2024a # Non compatiable versions of Python and MATLAB
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python-version: 3.8
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# Python 3.12 + MATLAB incompatability
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- matlab-version: R2024a
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python-version: 3.12
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- matlab-version: R2023b
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python-version: 3.8
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python-version: 3.12
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- matlab-version: R2023a
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python-version: 3.11
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python-version: 3.12
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- matlab-version: R2022b
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python-version: 3.12
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# Python 3.11 + MATLAB incompatability
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- matlab-version: R2023a
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python-version: 3.11
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- matlab-version: R2022a
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python-version: 3.11
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- matlab-version: R2022a
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python-version: "3.10"
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- matlab-version: R2021b
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python-version: 3.11
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- matlab-version: R2021b
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python-version: "3.10"
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- matlab-version: R2021a
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python-version: 3.11
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- matlab-version: R2021a
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python-version: "3.10"
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- matlab-version: R2021a
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python-version: 3.9
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- matlab-version: R2020b
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- matlab-version: R2022b
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python-version: 3.11
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- matlab-version: R2020b
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python-version: "3.10"
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- matlab-version: R2020b
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python-version: 3.9
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# Specific versions of tests that fail consistently. Most likely due to the GitHub actions environment
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# - matlab-version: R2024a # Python netcdf4 pip build error: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123413351
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# python-version: 3.11
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# os: macos-13
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# - matlab-version: R2024a # Working!
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# python-version: "3.10"
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# os: macos-13
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# - matlab-version: R2024a # Java Segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123411604
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# python-version: 3.9
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# os: macos-13
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# - matlab-version: R2023b # Python netcd4 pip build error: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123412889
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# python-version: 3.11
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# os: macos-13
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# - matlab-version: R2023b # Java segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123412352
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# python-version: "3.10"
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# os: macos-13
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# - matlab-version: R2023b # Java segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123411335
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# python-version: 3.9
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# os: macos-13
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# Specific MATLAB/Python/OS Errors
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# Error using _cythonized_array_utils>init
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# scipy.linalg._cythonized_array_utils (line 1)
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# Python Error: ValueError: numpy.dtype size changed, may indicate binary
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# incompatibility. Expected 96 from C header, got 88 from PyObject
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- matlab-version: R2024b
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python-version: 3.12
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os: macos-13
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runs-on: ${{ matrix.os }}
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- name: Check out MHKiT-MATLAB
205164
uses: actions/checkout@v4
206165

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# - name: Check out MHKiT-Python
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# uses: actions/checkout@v4
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# with:
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# repository: "MHKiT-Software/MHKiT-Python"
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# path: ${{env.mhkit-python-dir}}
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213166
- name: Install & Setup Miniconda
214167
uses: conda-incubator/setup-miniconda@v3
215168
with:
216169
miniconda-version: latest
217170
auto-update-conda: true
218171
python-version: ${{ matrix.python-version }}
219172
activate-environment: mhkit_conda_env
220-
channels: conda-forge
173+
channels: conda-forge,defaults
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222175
# This is necessary to fix any issues with netcdf4 and hdf5 headers
223176
- name: "Conda install netcdf4, hdf5"
224177
shell: bash -l {0}
225178
run: |
226179
conda activate mhkit_conda_env
227-
conda install numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4
228-
# conda install netcdf4 hdf5
229-
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
230-
231-
# - name: Setup Python ${{ matrix.python-version }}
232-
# shell: bash -l {0}
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# run: |
234-
# conda create --name mhkit_conda_env python=${{ matrix.python-version }} numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4 --strict-channel-priority
235-
# conda activate mhkit_conda_env
236-
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
237-
# pip install -e . --no-deps --force-reinstall
238-
239-
# - name: Setup MHKiT Dependencies on macOS
240-
# if: ${{ matrix.os == 'macos-13' }}
241-
# run: brew install hdf5 netcdf
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# - name: Setup MHKiT Dependencies on ubuntu
244-
# run: sudo apt install libhdf5-serial-dev libnetcdf-dev
245-
# if: ${{ matrix.os == 'ubuntu-latest' }}
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247-
# - name: Setup MHKiT Dependencies on ubuntu
248-
# if: ${{ matrix.os == 'ubuntu-latest' }}
249-
# run: |
250-
# sudo apt update
251-
# sudo apt upgrade
252-
# sudo apt install build-essential
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254-
# - name: Print GCC Version
255-
# if: ${{ matrix.os == 'ubuntu-latest' }}
256-
# run: |
257-
# gcc --version
258-
# g++ --version
259-
260-
# - name: Setup MATLAB Path on Ubuntu
261-
# if: ${{ matrix.os == 'ubuntu-latest' }}
262-
# run: echo "export LD_LIBRARY_PATH=/usr/local/MATLAB/${{ matrix.matlab-version }}/sys/os/glnxa64" >> "$GITHUB_ENV"
180+
conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4
263181
264182
- name: Setup MATLAB Path on Ubuntu
265183
if: ${{ matrix.os == 'ubuntu-latest' }}
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277195
conda activate mhkit_conda_env
278196
python --version
279197
280-
# - name: pip install mhkit module from source
281-
# working-directory: ${{env.mhkit-python-dir}}
282-
# shell: bash -l {0}
283-
# run: |
284-
# conda activate mhkit_conda_env
285-
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
286-
# pip install -e .
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288198
- name: pip install mhkit from pypi
289199
shell: bash -l {0}
290200
run: |
@@ -310,7 +220,7 @@ jobs:
310220
run: |
311221
conda activate mhkit_conda_env
312222
pip uninstall -y scipy
313-
pip install scipy==1.10.1
223+
pip install scipy==1.12.0
314224
315225
- name: List installed pip modules
316226
shell: bash -l {0}
@@ -345,6 +255,16 @@ jobs:
345255
with:
346256
release: ${{ matrix.matlab-version }}
347257

258+
- name: Configure OpenSSL for MacOS/MATLAB
259+
if: matrix.os == 'macos-13'
260+
shell: bash -l {0}
261+
run: |
262+
conda activate mhkit_conda_env
263+
conda install openssl=="3.0.*"
264+
CONDA_LIB_PATH=$(python -c "import sys; import os; print(os.path.join(os.path.dirname(sys.executable), 'lib'))")
265+
export DYLD_LIBRARY_PATH="$CONDA_LIB_PATH:$DYLD_LIBRARY_PATH"
266+
echo "export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
267+
348268
- name: Add Python Dir to Path
349269
shell: bash -l {0}
350270
run: |
@@ -357,6 +277,10 @@ jobs:
357277
run: |
358278
conda activate mhkit_conda_env
359279
printf 'pyenv(Version="%s", ExecutionMode="OutOfProcess")\n' $(python -c "import sys; print(sys.executable)") >> run.m
280+
# Pass dynamic library paths to MATLAB only on macOS
281+
if [[ $OSTYPE == "darwin"* ]]; then
282+
echo "setenv('DYLD_LIBRARY_PATH', getenv('DYLD_LIBRARY_PATH'));" >> run.m
283+
fi
360284
361285
- name: Add MATLAB test commands
362286
shell: bash

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