Package and testing updates and fixes

.github/workflows/black.yml

@@ -8,10 +8,10 @@ jobs:
 
     steps:
       - name: Check out code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
 

.github/workflows/main.yml

@@ -31,7 +31,7 @@ jobs:
       should-run-hindcast: ${{ steps.hindcast-logic.outputs.should-run-hindcast }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Check for changes in wave/io/hindcast
         id: changes
@@ -56,12 +56,12 @@ jobs:
       PYTHON_VER: 3.11
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniconda-version: 'latest'
+          miniconda-version: "latest"
           auto-update-conda: true
           python-version: ${{ env.PYTHON_VER }}
           activate-environment: TESTconda
@@ -83,7 +83,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e  ".[all,dev]" --no-deps
+          pip install -e ".[all,dev]"
 
       - name: Prepare non-hindcast API data
         shell: bash -l {0}
@@ -107,12 +107,12 @@ jobs:
     if: (needs.check-changes.outputs.should-run-hindcast == 'true')
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniconda-version: 'latest'
+          miniconda-version: "latest"
           auto-update-conda: true
           activate-environment: TEST
           python-version: ${{ env.PYTHON_VER }}
@@ -134,7 +134,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e  ".[all,dev]" --no-deps
+          pip install -e ".[all,dev]"
 
       - name: Prepare Wave Hindcast data
         shell: bash -l {0}
@@ -156,12 +156,12 @@ jobs:
     if: (needs.check-changes.outputs.should-run-hindcast == 'true')
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniconda-version: 'latest'
+          miniconda-version: "latest"
           auto-update-conda: true
           activate-environment: TEST
           python-version: ${{ env.PYTHON_VER }}
@@ -183,7 +183,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e  ".[all,dev]" --no-deps
+          pip install -e ".[all,dev]"
 
       - name: Prepare Wind Hindcast data
         shell: bash -l {0}
@@ -205,27 +205,27 @@ jobs:
       fail-fast: false
       matrix:
         os: ${{fromJson(needs.set-os.outputs.matrix_os)}}
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ["3.10", "3.11", "3.12"]
     env:
       PYTHON_VER: ${{ matrix.python-version }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniconda-version: 'latest'
+          miniconda-version: "latest"
           auto-update-conda: true
-          environment-file: environment.yml
+          environment-file: mhkit/tests/conda-forge/environment.yml
           activate-environment: TEST
           python-version: ${{ matrix.python-version }}
           use-only-tar-bz2: false
 
       - name: Create MHKiT Conda environment
         shell: bash -l {0}
         run: |
-          conda env create -f environment.yml
+          conda env create -f mhkit/tests/conda-forge/environment.yml
           conda activate mhkit-env
 
       - name: Install testing dependencies
@@ -238,7 +238,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e ".[all,dev]" --no-deps
 
       - name: Run pytest & generate coverage report
         shell: bash -l {0}
@@ -263,18 +263,18 @@ jobs:
       fail-fast: false
       matrix:
         os: ${{fromJson(needs.set-os.outputs.matrix_os)}}
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: conda-incubator/setup-miniconda@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Set up Git repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Download data from artifact
         uses: actions/download-artifact@v4
@@ -290,7 +290,7 @@ jobs:
         shell: bash -l {0}
         run: |
           python -m pip install --upgrade pip wheel
-          pip install -e  ".[all,dev]"
+          pip install -e ".[all,dev]"
 
       - name: Reinstall h5py and netCDF4 with system libraries
         if: runner.os == 'Linux'
@@ -331,15 +331,15 @@ jobs:
       fail-fast: false
       matrix:
         os: ${{fromJson(needs.set-os.outputs.matrix_os)}}
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniconda-version: 'latest'
+          miniconda-version: "latest"
           auto-update-conda: true
           environment-file: environment.yml
           activate-environment: TEST
@@ -362,7 +362,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e  ".[all,dev]" --no-deps
+          pip install -e ".[all,dev]" --no-deps
 
       - name: Download Wave Hindcast data from artifact
         uses: actions/download-artifact@v4
@@ -402,11 +402,11 @@ jobs:
     name: Test Built Wheel
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: '3.11'
+          python-version: "3.11"
 
       - name: Install build dependencies
         run: python -m pip install build --user
@@ -462,13 +462,13 @@ jobs:
       matrix:
         module:
           [wave, tidal, river, dolfyn, power, loads, mooring, acoustics, utils]
-        python-version: ['3.12']
+        python-version: ["3.12"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -514,7 +514,7 @@ jobs:
           needs.prepare-nonhindcast-cache.result == 'success' &&
           needs.prepare-wave-hindcast-cache.result == 'skipped' &&
           needs.prepare-wind-hindcast-cache.result == 'skipped' &&
-          needs.check-changes.outputs.should-run-hindcast == 'false'    
+          needs.check-changes.outputs.should-run-hindcast == 'false'
         ) ||
         (
           needs.prepare-nonhindcast-cache.result == 'success' &&
@@ -527,12 +527,12 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v6
         with:
-          python-version: '3.11'
+          python-version: "3.11"
 
       - name: Generate matrix
         id: set-matrix
@@ -556,14 +556,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniconda-version: 'latest'
+          miniconda-version: "latest"
           auto-update-conda: true
-          python-version: '3.12'
+          python-version: "3.12"
           channels: conda-forge
           activate-environment: TESTconda
           use-only-tar-bz2: false
@@ -584,7 +584,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e  ".[all,dev]" --no-deps
+          pip install -e ".[all,dev]"
 
       - name: Download non-hindcast data
         uses: actions/download-artifact@v4

.github/workflows/pylint.yml

@@ -8,12 +8,12 @@ jobs:
 
     steps:
       - name: Check out code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v6
         with:
-          python-version: '3.11'
+          python-version: "3.11"
 
       - name: Install dependencies
         run: |

.github/workflows/pypi.yml

@@ -19,13 +19,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - run: python -m pip install build --user
       - run: python -m build --sdist --wheel --outdir dist/ .

.github/workflows/test-wheel-build.yml

@@ -16,14 +16,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.12']
+        python-version: ["3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 

LICENSE.md

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2019, Alliance for Energy Innovation, LLC under the terms of Contract DE-AC36-08GO28308, Battelle Memorial Institute under the terms of Contract DE-AC05-76RL01830, and National Technology & Engineering Solutions of Sandia, LLC under the terms of Contract DE-NA0003525. The U.S. Government retains certain rights in this software. 
+Copyright (c) 2026, Alliance for Energy Innovation, LLC under the terms of Contract DE-AC36-08GO28308, Battelle Memorial Institute under the terms of Contract DE-AC05-76RL01830, and National Technology & Engineering Solutions of Sandia, LLC under the terms of Contract DE-NA0003525. The U.S. Government retains certain rights in this software. 
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

environment.yml

@@ -5,24 +5,4 @@ channels:
 dependencies:
   - python>=3.10,<3.13
   - pip
-  - numpy>=2.0.0
-  - pandas>=2.2.2
-  - scipy>=1.14.0
-  - xarray>=2024.6.0
-  - scikit-learn>=1.5.1
-  - h5py>=3.11.0
-  - h5pyd>=0.18.0
-  - netCDF4>=1.6.5
   - hdf5>=1.14.3,<1.14.5.0a0
-  - statsmodels>=0.14.2
-  - requests
-  - beautifulsoup4
-  - numexpr>=2.10.0
-  - lxml
-  - bottleneck
-  - pecos>=0.3.0
-  - notebook
-  - matplotlib>=3.9.1
-  - fatpack
-  - nrel-rex
-  - cartopy