Update develop with master branch changes

.github/workflows/unix_unit_tests.yml

@@ -35,7 +35,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit_conda_env
-          conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4
+          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
 
@@ -67,6 +67,19 @@ jobs:
           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
@@ -163,24 +176,24 @@ jobs:
           - 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 # 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
+          # - 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 }}
 
@@ -211,14 +224,14 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit_conda_env
-          conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4
+          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 cython pip pytest hdf5 libnetcdf cftime netcdf4 --strict-channel-priority
+        #   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
@@ -292,6 +305,13 @@ jobs:
           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: |

.github/workflows/windows_unit_tests.yml

@@ -33,7 +33,7 @@ jobs:
       - name: "Conda install netcdf4, hdf5"
         run: |
           conda activate mhkit_conda_env
-          conda install netcdf4 hdf5
+          conda install numpy==1.24.4 netcdf4 hdf5
       - name: Check out MHKiT-MATLAB
         uses: actions/checkout@v4
 
@@ -54,10 +54,19 @@ jobs:
         run: |
           conda activate mhkit_conda_env
           pip install mhkit==$MHKIT_PYTHON_VERSION
+
       - name: pip install mhkit-python-utils module from source
         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
+
       # Create the cache and add a dummy file
       # The dummy file ensures that the artifact download
       - name: Setup mhkit_webread_cache
@@ -120,6 +129,7 @@ jobs:
         matlab-version: [R2021b, R2022a, R2022b, R2023a, R2023b, R2024a]
         mhkit-python-version: ["0.7.0"]
         exclude:
+          # Cache population job
           - matlab-version: R2022a
             python-version: 3.9
           - matlab-version: R2023b
@@ -170,7 +180,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit_conda_env
-          conda install netcdf4 hdf5
+          conda install numpy==1.24.4 netcdf4 hdf5
       - name: Output python executable
         shell: bash -l {0}
         run: |
@@ -206,6 +216,14 @@ jobs:
         run: |
           conda activate mhkit_conda_env
           pip3 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: |

.gitignore

@@ -1,40 +1,78 @@
-*.xlsm
-*.xlsx
-*.pyc
-test.egg-info/*
-*.exe
-*.spec
-**/build
-**./dist/
-**/cache/
-**/static/
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
-*.log
-*.sql
-*.sqlite
-*.7z
-*.dmg
-*.gz
-*.iso
-*.jar
-*.rar
-*.tar
-*.zip
-*~
-*.json
-*egg-info
-*build
-.gitignore
-
+# MHKiT-MATLAB Specific Files
 # Test results
 mhkit/tests/test_results/*
 
-# MHKiT-MATLAB Specific Files
 # Hindcast data cache
 mhkit_webread_cache
+
+# MATLAB
+
+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Packaged app and toolbox files
+*.mlappinstall
+# *.mltbx
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Simulink code generation folders
+slprj/
+sccprj/
+
+# Matlab code generation folders
+codegen/
+
+# Simulink autosave extension
+*.autosave
+
+# Simulink cache files
+*.slxc
+
+# Octave session info
+octave-workspace
+
+# Python
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+eggs/
+.eggs/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# MacOS
+
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent