Merge remote-tracking branch 'origin/develop' into upcrossing

MHKiT-Software · Dec 16, 2024 · 0605d34 · 0605d34
2 parents 3a7662d + caf8263
commit 0605d34
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diff --git a/.github/workflows/unix_unit_tests.yml b/.github/workflows/unix_unit_tests.yml
@@ -36,25 +36,10 @@ jobs:
         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: |
@@ -204,12 +189,6 @@ jobs:
       - 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: ${{env.mhkit-python-dir}}
-
       - name: Install & Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -225,41 +204,6 @@ jobs:
         run: |
           conda activate mhkit_conda_env
           conda install numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4
-          # conda install netcdf4 hdf5
-          # export PATH="${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' }}
@@ -277,14 +221,6 @@ jobs:
           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: |
@@ -345,6 +281,16 @@ jobs:
         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: |
@@ -357,6 +303,10 @@ jobs:
         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

diff --git a/.github/workflows/windows_unit_tests.yml b/.github/workflows/windows_unit_tests.yml
@@ -37,18 +37,6 @@ jobs:
       - 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 from source
-      #   working-directory: ${{env.mhkit-python-dir}}
-      #   run: |
-      #     conda activate mhkit_conda_env
-      #     pip3 install -e .
-
       - name: pip install mhkit from pypi
         shell: bash -l {0}
         run: |
@@ -194,18 +182,6 @@ jobs:
       - 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 from source
-      #   working-directory: ${{env.mhkit-python-dir}}
-      #   run: |
-      #     conda activate mhkit_conda_env
-      #     pip3 install -e .
-
       - name: pip install mhkit from pypi
         shell: bash -l {0}
         run: |

diff --git a/mhkit/river/IO/delft_3d/delft_3d_get_all_time.m b/mhkit/river/IO/delft_3d/delft_3d_get_all_time.m
@@ -16,12 +16,24 @@
 %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-    if ~isa(delft_3d_py_object, 'py.netCDF4._netCDF4.Dataset')
-        error('MATLAB:delft_3d_get_all_time:InvalidInput', ...
-              'Invalid input Delft3D data type: `delft_3d_get_all_time` expects a `py.netCDF4._netCDF4.Dataset` object. Please use the `delft_3d_open_netcdf` function to convert Delft3D netCDF files for use with this function.');
-    end
+if ~isa(delft_3d_py_object, 'py.netCDF4._netCDF4.Dataset')
+    error('MATLAB:delft_3d_get_all_time:InvalidInput', ...
+        'Invalid input Delft3D data type: `delft_3d_get_all_time` expects a `py.netCDF4._netCDF4.Dataset` object. Please use the `delft_3d_open_netcdf` function to convert Delft3D netCDF files for use with this function.');
+end
 
     python_result = py.mhkit.river.io.d3d.get_all_time(delft_3d_py_object);
 
-    result = double(python_result);
+    % Handle masked arrays using numpy.ma.getdata
+    if isa(python_result, 'py.numpy.ma.MaskedArray')
+        % Extract the underlying data
+        data_array = py.numpy.ma.getdata(python_result);
+    else
+        % Convert directly if not masked
+        data_array = py.numpy.array(python_result);
+    end
+
+    % Ensure data is of type float
+    float_array = data_array.astype('float');
+
+    result = double(float_array);
 end