Modernize Package Configuration

.github/workflows/main.yml

@@ -83,7 +83,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Prepare non-hindcast API data
         shell: bash -l {0}
@@ -134,7 +134,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Prepare Wave Hindcast data
         shell: bash -l {0}
@@ -183,7 +183,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Prepare Wind Hindcast data
         shell: bash -l {0}
@@ -286,7 +286,7 @@ jobs:
         shell: bash -l {0}
         run: |
           python -m pip install --upgrade pip wheel
-          pip install coverage pytest coveralls .
+          pip install -e  ".[all,dev]"
 
       - name: Install setuptools for Python 3.12
         if: matrix.python-version == '3.12'
@@ -354,7 +354,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Download Wave Hindcast data from artifact
         uses: actions/download-artifact@v4
@@ -390,6 +390,39 @@ jobs:
           parallel: true
           path-to-lcov: ./coverage.lcov
 
+  test-optional-pip-dependencies:
+    needs: [set-os, prepare-nonhindcast-cache]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        module:
+          [wave, tidal, river, dolfyn, power, loads, mooring, acoustics, utils]
+        python-version: ['3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Download non-hindcast data
+        uses: actions/download-artifact@v4
+        with:
+          name: data
+          path: ~/.cache/mhkit
+
+      - name: Install MHKiT with optional dependency
+        run: |
+          python -m pip install --upgrade pip
+          pip install "mhkit[${{ matrix.module }}]"
+          pip install pytest
+
+      - name: Run tests for ${{ matrix.module }}
+        run: |
+          python -m pytest -c .github/workflows/pytest.ini mhkit/tests/${{ matrix.module }}/
+
   notebook-matrix:
     runs-on: ubuntu-latest
     needs:
@@ -476,7 +509,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Download non-hindcast data
         uses: actions/download-artifact@v4

.github/workflows/pylint.yml

@@ -18,8 +18,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip wheel
-          pip install pylint
-          pip install .
+          pip install ".[all,dev]"
 
       - name: Run Pylint on mhkit/loads/
         run: |

mhkit/__init__.py

@@ -1,14 +1,5 @@
 import warnings as _warn
-from mhkit import wave
-from mhkit import river
-from mhkit import tidal
-from mhkit import qc
-from mhkit import utils
-from mhkit import power
-from mhkit import loads
-from mhkit import dolfyn
-from mhkit import mooring
-from mhkit import acoustics
+import importlib
 
 # Register datetime converter for a matplotlib plotting methods
 from pandas.plotting import register_matplotlib_converters as _rmc
@@ -28,3 +19,33 @@
 retains certain rights in this software."""
 
 __license__ = "Revised BSD License"
+
+
+def __getattr__(name):
+    """Lazy import modules to handle pip optional dependencies."""
+    known_modules = [
+        "wave",
+        "river",
+        "tidal",
+        "qc",
+        "utils",
+        "power",
+        "loads",
+        "dolfyn",
+        "mooring",
+        "acoustics",
+    ]
+
+    if name in known_modules:
+        try:
+            return importlib.import_module(f"mhkit.{name}")
+        except ModuleNotFoundError:
+            error_msg = "Module dependencies not found.\n"
+            error_msg += f"To install the {name} module, run:\n"
+            error_msg += f"  pip install mhkit[{name}]\n\n"
+            error_msg += "Or install all modules with:\n"
+            error_msg += "  pip install mhkit[all]"
+    else:
+        error_msg = f"module 'mhkit' has no attribute '{name}'"
+
+    raise AttributeError(error_msg)

mhkit/acoustics/graphics.py

@@ -33,7 +33,7 @@ def plot_spectrogram(
     fmax: int = 100000,
     fig: plt.figure = None,
     ax: plt.Axes = None,
-    **kwargs
+    **kwargs,
 ) -> Tuple[plt.figure, plt.Axes]:
     """
     Plots the spectrogram of the sound pressure spectral density level.
@@ -86,7 +86,7 @@ def plot_spectrogram(
         spsdl[freq].values,
         spsdl.transpose(freq, time),
         shading="nearest",
-        **kwargs
+        **kwargs,
     )
     fig.colorbar(h, ax=ax, label=getattr(spsdl, "units", None))
     ax.set(ylim=(fmin, fmax), xlabel="Time", ylabel="Frequency [Hz]")
@@ -100,7 +100,7 @@ def plot_spectra(
     fmax: int = 100000,
     fig: plt.figure = None,
     ax: plt.Axes = None,
-    **kwargs
+    **kwargs,
 ) -> Tuple[plt.figure, plt.Axes]:
     """
     Plots spectral density. X axis is log-transformed.

mhkit/dolfyn/adp/discharge.py

@@ -1,6 +1,5 @@
 import numpy as np
 import xarray as xr
-import cartopy.crs as ccrs
 
 
 def discharge(ds, water_depth, rho, mu=None, surface_offset=0, utm_zone=10):
@@ -54,6 +53,9 @@ def discharge(ds, water_depth, rho, mu=None, surface_offset=0, utm_zone=10):
          - `reynolds_number`: (1) Reynolds number, unitless
     """
 
+    # Lazy import cartopy
+    import cartopy.crs as ccrs
+
     def _extrapolate_to_bottom(vel, bottom, rng):
         """
         Linearly extrapolate velocity values from the deepest valid bin down to zero at the seafloor.

mhkit/river/io/usgs.py

@@ -199,8 +199,23 @@ def request_usgs_data(
 
     print("Data request URL: ", data_url + api_query)
 
-    response = requests.get(url=data_url + api_query, proxies=proxy, timeout=timeout)
-    text = json.loads(response.text)
+    max_retries = 3
+    retry_count = 0
+    while retry_count < max_retries:
+        try:
+            response = requests.get(
+                url=data_url + api_query, proxies=proxy, timeout=timeout, verify=True
+            )
+            text = json.loads(response.text)
+            break
+        except requests.exceptions.SSLError as e:
+            retry_count += 1
+            if retry_count == max_retries:
+                raise e
+            print(
+                f"SSL Error occurred, retrying... (Attempt {retry_count}/{max_retries})"
+            )
+            continue
 
     # handle_caching is only set-up for pandas, so force this data to output as pandas for now
     data = _read_usgs_json(text, True)

pyproject.toml

@@ -0,0 +1,135 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "mhkit"
+# `version` is read from `[tools.setuptools.dynamic] version` during build: https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#dynamic-metadata
+dynamic = ["version"]
+description = "Marine and Hydrokinetic Toolkit"
+readme = "README.md"
+authors = [
+    {name = "MHKiT developers"}
+]
+license = {text = "Revised BSD"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+]
+requires-python = ">=3.10"
+dependencies = [
+    "numpy>=2.0.0",
+    "pandas>=2.2.2",
+    "scipy>=1.14.0",
+    "xarray>=2024.6.0",
+    "matplotlib>=3.9.1",
+    "pecos>=0.3.0",
+]
+
+[project.optional-dependencies]
+# Core dependencies for each module
+wave = [
+    "scikit-learn>=1.5.1",
+    "statsmodels>=0.14.2",
+    "netCDF4>=1.7.1.post1",
+    "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",
+]
+
+dolfyn = [
+    "h5py>=3.11.0",
+    "h5pyd>=0.18.0",
+    "netCDF4>=1.7.1.post1",
+    "cartopy",
+]
+
+power = [
+]
+
+loads = [
+ "fatpack"
+]
+
+mooring = [
+]
+
+acoustics = [
+
+]
+
+qc = [
+
+]
+
+utils = [
+
+]
+
+# Development dependencies
+dev = [
+    "pytest",
+    "pylint",
+    "pytest-cov",
+    "pre-commit",
+    "coverage",
+    "coveralls"
+]
+
+
+
+# Install all optional dependencies
+all = [
+    "mhkit[wave]",
+    "mhkit[tidal]",
+    "mhkit[river]",
+    "mhkit[dolfyn]",
+    "mhkit[power]",
+    "mhkit[loads]",
+    "mhkit[mooring]",
+    "mhkit[acoustics]",
+    "mhkit[qc]",
+    "mhkit[utils]",
+]
+
+# Examples dependencies
+examples = [
+    "jupyter",
+    "notebook",
+    "ipykernel",
+    "nbval",
+    "utm",
+    "folium",
+    "mhkit[all]",
+
+]
+
+[project.urls]
+Homepage = "https://github.com/MHKiT-Software/mhkit-python"
+Documentation = "https://mhkit-software.github.io/MHKiT"
+
+[tool.setuptools]
+packages = ["mhkit"]
+zip-safe = false
+include-package-data = true
+
+[tool.setuptools.dynamic]
+version = {attr = "mhkit.__version__"}