Merge pull request #184 from MHKiT-Software/develop

v1.0.0 Release

Author: simmsa

.github/workflows/code_compatibility_report.yml

@@ -13,9 +13,8 @@ jobs:
 
       matrix:
         # os: [macos-13, ubuntu-latest, windows-latest]
-        os: [ubuntu-latest]
-        python-version: [3.8, 3.9, "3.10", 3.11]
-        matlab-version: [R2021b, R2022a, R2022b, R2023a, R2023b]
+        os: ["ubuntu-22.04"]
+        matlab-version: [R2022b, R2023a, R2023b, R2024a, R2024b, R2025a, latest]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/unix_unit_tests.yml

@@ -1,20 +1,29 @@
 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-latest]
-        python-version: ["3.10"]
-        matlab-version: [R2022b]
+        os: ["ubuntu-22.04"]
+        python-version: ["3.11"]
+        matlab-version: [R2023b]
 
     runs-on: ${{ matrix.os }}
 
@@ -37,6 +46,12 @@ jobs:
           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++
+          echo "LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6:/lib/x86_64-linux-gnu/libstdc++.so.6" >> "$GITHUB_ENV"
+
       - name: Check out MHKiT-MATLAB
         uses: actions/checkout@v4
 
@@ -122,15 +137,15 @@ jobs:
       fail-fast: false
 
       matrix:
-        os: [macos-13, ubuntu-latest]
+        os: [macos-13, "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'
         matlab-version: [R2022b, R2023a, R2023b, R2024a, R2024b]
         mhkit-python-version: ["0.9.0"]
         exclude:
           - python-version: "3.10" # cache_population job
             matlab-version: R2022b
-            os: ubuntu-latest
+            os: "ubuntu-22.04"
           # Python 3.12 + MATLAB incompatability
           - matlab-version: R2024a
             python-version: 3.12
@@ -153,6 +168,10 @@ jobs:
           - matlab-version: R2024b
             python-version: 3.12
             os: macos-13
+          # 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 }}
 
@@ -179,9 +198,15 @@ jobs:
           conda activate mhkit_conda_env
           conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4
 
-      - 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: Fix libstdc++ compatibility
+        if: matrix.os == 'ubuntu-22.04'
+        run: |
+          # Force MATLAB to use system libstdc++
+          echo "LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6:/lib/x86_64-linux-gnu/libstdc++.so.6" >> "$GITHUB_ENV"
+
+      # - name: Setup MATLAB Path on Ubuntu
+      #   if: ${{ matrix.os == '"ubuntu-22.04"' }}
+      #   run: echo "LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6" >> "$GITHUB_ENV"
 
       - name: Print Python executable
         shell: bash -l {0}

.github/workflows/windows_unit_tests.yml

@@ -1,18 +1,27 @@
 name: MHKiT-MATLAB Windows 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/windows_unit_tests.yml'
   pull_request:
     branches: [ master, develop ]
+    paths:
+      - 'mhkit/**/*.m'
+      - 'examples/**/*.m'
+      - '.github/workflows/windows_unit_tests.yml'
 
 jobs:
   cache_population:
     strategy:
       fail-fast: false
       matrix:
         os: [windows-latest]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
         matlab-version: [R2023b]
     runs-on: ${{ matrix.os }}
 
@@ -80,6 +89,14 @@ jobs:
         with:
           release: ${{ matrix.matlab-version }}
 
+      - name: Set PYBIND11 GIL workaround
+        # if: ${{ matrix.matlab-version == 'R2025a' }}
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit_conda_env
+          export PYBIND11_NO_ASSERT_GIL_HELD_INCREF_DECREF=1
+          echo "PYBIND11_NO_ASSERT_GIL_HELD_INCREF_DECREF=1" >> $GITHUB_ENV
+
       - name: Configure MATLAB pyenv Version and ExecutionMode
         if: ${{ matrix.os == 'windows-latest' }}
         shell: pwsh
@@ -128,7 +145,8 @@ jobs:
       matrix:
         os: [windows-latest]
         python-version: ["3.10", 3.11, 3.12]
-        matlab-version: [R2022b, R2023a, R2023b, R2024a, R2024b]
+        # matlab-version: [R2022b, R2023a, R2023b, R2024a, R2024b]
+        matlab-version: [R2023a, R2023b, R2024a, R2024b]
         mhkit-python-version: ["0.9.0"]
         exclude:
           # Cache population job
@@ -150,6 +168,11 @@ jobs:
             python-version: 3.11
           - matlab-version: R2022b
             python-version: 3.11
+          # Failing Job
+          # Python Error: ImportError: DLL load failed while importing pyexpat: The operating system cannot run %1
+          - matlab-version: R2023a
+            python-version: "3.10"
+
     runs-on: ${{ matrix.os }}
 
     env:
@@ -197,6 +220,21 @@ jobs:
       #     pip uninstall -y scipy
       #     pip install scipy==1.10.1
       #
+
+      # Some tests fail with:
+      # Python Error: ImportError: DLL load failed while importing pyexpat: The operating system cannot run %1.
+      # One potential fix is to install expat and lxml
+      - name: Install Windows XML dependencies
+        if: ${{ matrix.os == 'windows-latest' }}
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit_conda_env
+          # Simple single package install to avoid solver issues
+          conda install expat -y
+          # Alternative: use pip for XML parsing
+          pip install lxml
+
+
       - name: List installed pip modules
         shell: bash -l {0}
         run: |
@@ -227,6 +265,14 @@ jobs:
         with:
           release: ${{ matrix.matlab-version }}
 
+      - name: Set PYBIND11 GIL workaround
+        # if: ${{ matrix.matlab-version == 'R2025a' }}
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit_conda_env
+          export PYBIND11_NO_ASSERT_GIL_HELD_INCREF_DECREF=1
+          echo "PYBIND11_NO_ASSERT_GIL_HELD_INCREF_DECREF=1" >> $GITHUB_ENV
+
       - name: Add Python Dir to Path
         shell: bash -l {0}
         run: |

changelog.md

@@ -1,3 +1,68 @@
+# Version 1.0.0
+
+## Release Highlights
+
+- New acoustics, and mooring modules
+- Improvements to Wave, WDRT, and DOLFYN modules
+- New examples for acoustics, mooring, and WEC-sim, and improved examples for DOLFYN and wave modules
+- Multiple bug fixes and performance improvements
+
+## PR #174 - Acoustics Module
+
+- Authors: @hivanov-nrel, @simmsa
+- Addition of acoustics module:
+  - Reading and standardization of of OceanSonics icListen and OceanInstruments Soundtrap hydrophone files
+  - Implementation of numerical computation sections IEC 62600-40 "Acoustic characterization of marine energy converters" standard
+  - Spectrogram data visualizations using `plot_spectrogram`
+  - Sound exposure level calculations with auditory weighting functions for 5 groups of marine mammals
+  - Complete example livescript in examples/acoustics_example.mlx
+
+## PR 176 - Wave Module Native MATLAB Implementation
+
+- Authors: @MShabara, @simmsa
+- Convert wave module functions to native MATLAB code:
+  - wave/resource/standardize_wave_spectra_frequency.m:
+  - wave/resource/frequency_moment.m:
+  - wave/resource/energy_period.m:
+  - wave/resource/significant_wave_height.m:
+  - wave/resource/jonswap_spectrum.m:
+  - wave/resource/pierson_moskowitz_spectrum.m:
+  - wave/resource/surface_elevation.m:
+
+## PR 153 - Mooring Module
+
+- Author: @hivanov-nrel
+- Addition of the mooring module, which includes
+  - Read in MoorDyn files into MATLAB
+  - Function to calculate mooring line lay length
+  - Functions to visualize mooring line dynamics in 2D or 3D.
+  - Example LiveScript demonstrating the functionality of the mooring module
+
+## PR #173 - Dolfyn Turbulence Functionality
+
+- Author: @simmsa, @browniea
+- Addition of turbulence calculations for acoustic doppler instruments
+  - Turbulence intensity, noise, and reynolds stress calculations
+  - Updates to examples/adcp_example.mlx live script
+
+## PR 170 - WDRT leftovers
+
+- Author: @hivanov-nrel
+- Expanded WDRT functionality by adding `automatic_hs_threshold` and `return_year_value` functions
+
+## PR 169 - Code Compatibility Improvements
+
+- Author: @simmsa
+- Fix code compatibility issues detailed in issues #115, #116, #117, #118, #119, #120, #121, and #122
+
+## Bug Fixes
+
+- Issue #172 - Fix Failing MLER Test - @hivanov-nrel
+- Issue #152 - Fix dimensionality differences in environmental_contours_example - @simmsa
+- Issue #146, #74 - Finish WDRT Parity - @hivanov-nrel
+- Issue #145 - Fix build errors in documentation - @simmsa
+- Issue #114, #115, #116, #117, #118, #119, #121, #122 - MATLAB code compatibility issues
+
 # MHKiT-MATLAB v0.6.0
 
 ## Release Highlights