Merge branch 'develop' into avg-profile-bugfixes

Author: akeeste

.github/workflows/main.yml

@@ -10,10 +10,6 @@ on:
       - main
       - develop
 
-concurrency:
-  group: ${{ github.event.pull_request.number }}  # Use the pull request number as the concurrency group
-  cancel-in-progress: true # Cancel any in-progress jobs for the same group. Prevents duplicate workflows on PRs from develop into main or from main into develop.
-
 jobs:
   set-os:
     runs-on: ubuntu-latest
@@ -286,12 +282,20 @@ jobs:
           name: data
           path: ~/.cache/mhkit
 
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y libhdf5-dev libnetcdf-dev
+
       - name: Update and install packages
         shell: bash -l {0}
         run: |
           python -m pip install --upgrade pip wheel
           pip install -e  ".[all,dev]"
 
+      - name: Reinstall h5py and netCDF4 with system libraries
+        if: runner.os == 'Linux'
+        run: "pip install --force-reinstall --no-binary=:all: h5py netCDF4"
+
       - name: Install setuptools for Python 3.12
         if: matrix.python-version == '3.12'
         run: pip install setuptools
@@ -394,10 +398,67 @@ jobs:
           parallel: true
           path-to-lcov: ./coverage.lcov
 
+  test-wheel-packaging:
+    name: Test Built Wheel
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install build dependencies
+        run: python -m pip install build --user
+
+      - name: Build wheel
+        run: python -m build --wheel --outdir dist/ .
+
+      - name: Install MHKiT from built wheel
+        run: |
+          # Install from build wheel in dist/ directory, not from PyPI
+           # -f, --find-links <url>      If a URL or path to an html file, then parse for links to archives such as sdist (.tar.gz) or wheel (.whl) files.
+             # If a local path or file:// URL that's a directory, then look for archives in the directory listing.
+          pip install 'mhkit[all]' --find-links dist/
+
+      - name: Test mhkit submodule imports
+        run: |
+          python -c "
+          import mhkit
+          print(f'Version: {mhkit.__version__}')
+
+          # Test all submodules can be imported
+          modules = ['wave', 'river', 'tidal', 'dolfyn', 'power', 'loads', 'mooring', 'acoustics', 'qc', 'utils']
+          for mod in modules:
+              exec(f'from mhkit import {mod}')
+              print(f'Successfully imported mhkit.{mod}')
+
+          print('All submodules imported successfully!')
+          "
+
+      - name: Verify mhkit package structure
+        run: |
+          python -c "
+          import mhkit
+          import os
+
+          mhkit_path = os.path.dirname(mhkit.__file__)
+          expected_dirs = ['wave', 'river', 'tidal', 'dolfyn', 'power', 'loads', 'mooring', 'acoustics', 'qc', 'utils']
+
+          for d in expected_dirs:
+              dir_path = os.path.join(mhkit_path, d)
+              assert os.path.isdir(dir_path), f'Missing submodule directory: {d}'
+              init_file = os.path.join(dir_path, '__init__.py')
+              assert os.path.isfile(init_file), f'Missing __init__.py in {d}'
+
+          print('Package structure verified!')
+          "
+
   test-optional-pip-dependencies:
     needs: [set-os, prepare-nonhindcast-cache]
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         module:
           [wave, tidal, river, dolfyn, power, loads, mooring, acoustics, utils]
@@ -417,12 +478,20 @@ jobs:
           name: data
           path: ~/.cache/mhkit
 
+      - name: Install system dependencies
+        if: matrix.module != 'river' || matrix.module != 'power' || matrix.module != 'utils' || matrix.module != 'loads'
+        run: sudo apt-get install -y libhdf5-dev libnetcdf-dev
+
       - name: Install MHKiT with optional dependency
         run: |
           python -m pip install --upgrade pip
-          pip install "mhkit[${{ matrix.module }}]"
+          pip install -e ".[${{ matrix.module }}]"
           pip install pytest
 
+      - name: Reinstall h5py and netCDF4 with system libraries
+        if: matrix.module != 'river' || matrix.module != 'power' || matrix.module != 'utils' || matrix.module != 'loads'
+        run: "pip install --force-reinstall --no-binary=:all: h5py netCDF4"
+
       - name: Run tests for ${{ matrix.module }}
         env:
           MPLBACKEND: Agg

.github/workflows/pypi.yml

@@ -7,6 +7,9 @@ on:
   push:
     branches:
       - main
+  pull_request:
+    branches:
+      - main
   release:
     types: [published]
 
@@ -16,19 +19,28 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: '3.10'
 
       - run: python -m pip install build --user
       - run: python -m build --sdist --wheel --outdir dist/ .
 
-      - name: Upload to Test PyPI
-        if: github.event_name != 'release' && github.repository_owner == 'MHKiT-Software'
+      - name: Test wheel contents before upload
+        run: |
+          # Install the built wheel from dist/ to verify it was packaged correctly before upload
+          # --find-links dist/ tells pip to look in dist/ directory first and prefer the wheel
+          # Dependencies (numpy, pandas, etc.) are fetched from PyPI as normal
+          # This verifies the wheel contains all necessary files and can be installed successfully
+          pip install 'mhkit[all]' --find-links dist/
+          python -c "from mhkit import wave, river, tidal, dolfyn, power, loads, mooring, acoustics, qc, utils; print('All modules imported successfully')"
+
+      - name: Upload to Test PyPI (commits to main only)
+        if: github.event_name == 'push' && github.repository_owner == 'MHKiT-Software'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__

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

@@ -0,0 +1,43 @@
+# Tests that the package can be built and installed from a wheel
+# Runs on PRs to catch build issues before merging to main
+# Does NOT publish to PyPI
+
+name: Test PIP Package Build
+
+on:
+  pull_request:
+    branches:
+      - main
+      - develop
+
+jobs:
+  test-build:
+    name: Test wheel build
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install build tools
+        run: python -m pip install build --user
+
+      - name: Build wheel and source distribution
+        run: python -m build --sdist --wheel --outdir dist/ .
+
+      - name: Test wheel installation
+        run: |
+          # Install the built wheel from dist/ to verify it was packaged correctly
+          # --find-links dist/ tells pip to look in dist/ directory first and prefer the wheel
+          # Dependencies (numpy, pandas, etc.) are fetched from PyPI as normal
+          # This verifies the wheel contains all necessary files and can be installed successfully
+          pip install 'mhkit[all]' --find-links dist/
+          python -c "from mhkit import wave, river, tidal, dolfyn, power, loads, mooring, acoustics, qc, utils; print('All modules imported successfully')"

LICENSE.md

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2025, Alliance for Sustainable Energy, 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) 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. 
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -84,7 +84,7 @@ See [installation instructions](https://mhkit-software.github.io/MHKiT/installat
 
 ## Copyright and license
 
-MHKiT-Python is copyright through the National Renewable Energy Laboratory,
+MHKiT-Python is copyright through the National Laboratory of the Rockies,
 Pacific Northwest National Laboratory, and Sandia National Laboratories.
 The software is distributed under the Revised BSD License.
 See [copyright and license](LICENSE.md) for more information.

mhkit/__init__.py

@@ -11,10 +11,10 @@
 
 configure_warnings()
 
-__version__ = "v1.0.0"
+__version__ = "v1.0.1"
 
 __copyright__ = """
-Copyright 2019, Alliance for Sustainable Energy, LLC under the terms of 
+Copyright 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 

mhkit/dolfyn/velocity.py

@@ -421,10 +421,10 @@ def E_coh(
         """
         Coherent turbulent energy
 
-        Niel Kelley's 'coherent turbulence energy', which is the
+        Neil Kelley's 'coherent turbulence energy', which is the
         root-mean-square of the Reynold's stresses.
 
-        See: NREL Technical Report TP-500-52353
+        See: NLR Technical Report TP-500-52353
         """
         E_coh = (self.upwp_**2 + self.upvp_**2 + self.vpwp_**2) ** (0.5)
 

mhkit/wave/__init__.py

@@ -1,5 +1,37 @@
+import importlib
+
 from mhkit.wave import resource
-from mhkit.wave import io
 from mhkit.wave import graphics
 from mhkit.wave import performance
 from mhkit.wave import contours
+
+
+def __getattr__(name):
+    """
+    Lazy load the wave.io submodule using PEP 562 module-level __getattr__.
+
+    This defers importing heavy wave.io dependencies (rex, netCDF4, etc,) until
+    they are actually accessed, improving import time for users who don't need
+    all wave submodules, and avoiding import errors for users who have specified
+    module level installs that need wave module functions, but not wave.io functions.
+    """
+    if name == "io":
+        # This uses importlib.import_module() here, not "from mhkit.wave import io"
+        # because when Python executes getattr(), it looks for 'io' as an attribute of
+        # mhkit.wave. At this point in the module loading code 'io' doesn't exist yet and
+        # Python calls __getattr__('io') again. This triggers the same "from" statement,
+        # which calls __getattr__('io') again yielding a RecursionError.
+        #
+        # To fix this uses importlib.import_module("mhkit.wave.io") which loads the module directly
+        # using the  absolute path without doing attribute lookup on the parent.
+        #
+        # The statement "from mhkit.wave import io" is equivalent to:
+        #   io = getattr(mhkit.wave, 'io')
+        #
+        io = importlib.import_module("mhkit.wave.io")
+
+        # Cache the module so subsequent accesses bypass __getattr__ entirely
+        globals()[name] = io
+        return io
+
+    raise AttributeError(f"module '{__name__}' has no attribute '{name}'")

pyproject.toml

@@ -27,6 +27,7 @@ dependencies = [
     "xarray>=2024.6.0",
     "matplotlib>=3.9.1",
     "pecos>=0.3.0",
+    "requests",
 ]
 
 [project.optional-dependencies]
@@ -38,20 +39,17 @@ wave = [
     "pytz",
     "NREL-rex>=0.2.63",
     "beautifulsoup4",
-    "requests",
     "bottleneck",
     "lxml"
 ]
 
 tidal = [
     "netCDF4>=1.7.1.post1",
-    "requests",
     "bottleneck"
 ]
 
 river = [
     "netCDF4>=1.7.1.post1",
-    "requests",
     "bottleneck",
 ]
 
@@ -66,7 +64,9 @@ power = [
 ]
 
 loads = [
- "fatpack"
+    "fatpack",
+    "statsmodels>=0.14.2",
+    "scikit-learn>=1.5.1",
 ]
 
 mooring = [
@@ -126,8 +126,22 @@ examples = [
 Homepage = "https://github.com/MHKiT-Software/mhkit-python"
 Documentation = "https://mhkit-software.github.io/MHKiT"
 
+[tool.setuptools.packages.find]
+# This section controls how this python package is built for pip installations
+# Getting this section wrong results in an incomplete package that is missing submodules
+# This can be tested by simply running python -m build in the root directory
+# and then inspecting the generated .tar.gz and .whl files in the dist/ directory
+#
+# https://setuptools.pypa.io/en/latest/userguide/package_discovery.html#finding-simple-packages
+# What this does: (per the above docs):
+# - `where = ["."]`: Search for packages starting from the root directory
+# - `include = ["mhkit*"]`: Only include packages that match the pattern `mhkit*`
+#     - this includes `mhkit`, `mhkit.wave`, `mhkit.river`, etc.
+# - Setuptools will automatically discover all directories containing `__init__.py` files
+where = ["."]
+include = ["mhkit*"]
+
 [tool.setuptools]
-packages = ["mhkit"]
 zip-safe = false
 include-package-data = true