Refactor to standard Python package structure

MANIFEST.in

@@ -0,0 +1,12 @@
+include README.md
+include License.md
+include CONTRIBUTING.md
+include CHANGES_SUMMARY.md
+include TESTING.md
+include requirements.txt
+include pytest.ini
+recursive-include examples *.ipynb
+recursive-include tests *.py
+global-exclude __pycache__
+global-exclude *.py[co]
+global-exclude .DS_Store

README.md

@@ -16,20 +16,20 @@ Converted from: https://github.com/metocean/diwasp
 
 ## Installation
 
-### Basic Installation
+### From Source
 
 ```bash
 # Clone the repository
 git clone https://github.com/SBFRF/pyDIWASP.git
 cd pyDIWASP
 
-# Install dependencies
-pip install numpy scipy matplotlib
+# Install the package
+pip install -e .
 ```
 
 ### Requirements
 
-- Python 3.6+
+- Python 3.8+
 - NumPy
 - SciPy
 - Matplotlib
@@ -38,7 +38,7 @@ pip install numpy scipy matplotlib
 
 ```python
 import numpy as np
-from dirspec import dirspec
+from pydiwasp import dirspec
 
 # Define instrument data structure
 ID = {

examples/pyDIWASP_example.ipynb

@@ -45,17 +45,9 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "# Add pyDIWASP to Python path\n",
-    "# This assumes you're running the notebook from the examples/ directory\n",
-    "# The parent directory (..) contains the pyDIWASP modules\n",
-    "if os.getcwd().endswith('examples'):\n",
-    "    sys.path.insert(0, '..')\n",
-    "elif os.path.basename(os.getcwd()) != 'pyDIWASP':\n",
-    "    print('Warning: Notebook should be run from examples/ directory or repo root')\n",
-    "\n",
-    "from dirspec import dirspec\n",
-    "from infospec import infospec\n",
-    "from plotspec import plotspec\n",
+    "# Import pyDIWASP functions\n",
+    "# If the package is installed (pip install -e .), you can import directly\n",
+    "from pydiwasp import dirspec, infospec, plotspec\n",
     "\n",
     "# Set random seed for reproducibility\n",
     "np.random.seed(42)\n",

pydiwasp/__init__.py

@@ -0,0 +1,30 @@
+"""
+pyDIWASP - DIrectional WAve SPectrum analysis in Python
+
+Python conversion of the DIWASP package (DIrectional WAve SPectrum analysis Version 1.4)
+
+Main Functions:
+- dirspec: Main directional wave spectrum estimation
+- infospec: Calculate wave statistics from spectrum
+- plotspec: Plot directional spectrum
+- interpspec: Interpolate spectrum to different grid
+- writespec: Write spectrum to file
+"""
+
+__version__ = "0.1.0"
+
+# Import main API functions
+from .dirspec import dirspec
+from .infospec import infospec, compangle
+from .plotspec import plotspec
+from .interpspec import interpspec
+from .writespec import writespec
+
+__all__ = [
+    'dirspec',
+    'infospec',
+    'compangle',
+    'plotspec',
+    'interpspec',
+    'writespec',
+]

dirspec.py → pydiwasp/dirspec.py

@@ -2,22 +2,22 @@
 import numpy as np
 import matplotlib.pyplot as plt
 from scipy.signal import detrend
-from interpspec import interpspec
-from infospec import infospec
-from writespec import writespec
-from plotspec import plotspec
-from private.velx import velx
-from private.vely import vely
-from private.pres import pres
-from private.elev import elev
-from private.vels import vels
-from private.accs import accs, accz
-from private.wavenumber import wavenumber
-from private.IMLM import IMLM
-from private.EMEP import EMEP
-from private.smoothspec import smoothspec
-from private.diwasp_csd import diwasp_csd
-from private.check_data import check_data
+from .interpspec import interpspec
+from .infospec import infospec
+from .writespec import writespec
+from .plotspec import plotspec
+from .private.velx import velx
+from .private.vely import vely
+from .private.pres import pres
+from .private.elev import elev
+from .private.vels import vels
+from .private.accs import accs, accz
+from .private.wavenumber import wavenumber
+from .private.IMLM import IMLM
+from .private.EMEP import EMEP
+from .private.smoothspec import smoothspec
+from .private.diwasp_csd import diwasp_csd
+from .private.check_data import check_data
 
 def dirspec(ID, SM, EP, Options_=None):
     """

infospec.py → pydiwasp/infospec.py

@@ -1,5 +1,5 @@
 import numpy as np
-from private.hsig import hsig
+from .private.hsig import hsig
 
 def infospec(SM):
     """

interpspec.py → pydiwasp/interpspec.py

@@ -1,8 +1,8 @@
 import numpy as np
 from warnings import warn
 from scipy.interpolate import griddata
-from private.hsig import hsig
-from private.spectobasis import spectobasis
+from .private.hsig import hsig
+from .private.spectobasis import spectobasis
 
 def interpspec(SMin, SMout, method='linear'):
     """

plotspec.py → pydiwasp/plotspec.py

@@ -1,6 +1,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
-from private.spectobasis import spectobasis
+from .private.spectobasis import spectobasis
 
 def plotspec(SM, ptype):
     """

pydiwasp/private/__init__.py

@@ -0,0 +1,6 @@
+"""
+Private internal functions for pyDIWASP.
+
+This module contains internal functions used by the main analysis routines.
+These are not part of the public API and may change without notice.
+"""

private/vels.py → pydiwasp/private/vels.py

@@ -1,4 +1,4 @@
-from private.velz import velz
+from .velz import velz
 
 def vels(ffreqs, dirs, wns, z, depth):
     """

pyproject.toml

@@ -0,0 +1,38 @@
+[build-system]
+requires = ["setuptools>=45", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyDIWASP"
+version = "0.1.0"
+description = "Python conversion of DIWASP: DIrectional WAve SPectrum analysis"
+readme = "README.md"
+authors = [
+    {name = "SBFRF", email = "support@sbfrf.org"}
+]
+license = {text = "GPL-3.0"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+requires-python = ">=3.8"
+dependencies = [
+    "numpy>=1.20.0,<2.0",
+    "scipy>=1.7.0,<2.0",
+    "matplotlib>=3.3.0,<4.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/SBFRF/pyDIWASP"
+Repository = "https://github.com/SBFRF/pyDIWASP"
+
+[tool.setuptools.packages.find]
+include = ["pydiwasp*"]

setup.py

@@ -15,7 +15,7 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/SBFRF/pyDIWASP",
-    packages=find_packages(),
+    packages=find_packages(include=['pydiwasp', 'pydiwasp.*']),
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Science/Research",

tests/test_api.py

@@ -10,9 +10,7 @@
 import os
 from contextlib import redirect_stdout
 
-from infospec import infospec
-from interpspec import interpspec
-from writespec import writespec
+from pydiwasp import infospec, interpspec, writespec
 
 
 class TestInfospec:
@@ -106,7 +104,7 @@ def test_interpspec_basic(self):
 
     def test_interpspec_preserves_energy(self):
         """Test that interpolation approximately preserves energy."""
-        from private.hsig import hsig
+        from pydiwasp.private.hsig import hsig
 
         # Create a peaked spectrum
         freqs_in = np.linspace(0.05, 0.5, 15)

tests/test_core.py

@@ -7,18 +7,15 @@
 
 
 import unittest
-import numpy as np
-from infospec import compangle
-from private.hsig import hsig
-from private.check_data import check_data
-
 import numpy as np
 import pytest
 
+from pydiwasp.infospec import compangle
+
 try:
-    from private.wavenumber import wavenumber
-    from private.hsig import hsig
-    from private.check_data import check_data
+    from pydiwasp.private.wavenumber import wavenumber
+    from pydiwasp.private.hsig import hsig
+    from pydiwasp.private.check_data import check_data
 except ImportError as exc:
     raise ImportError(
         "Could not import pyDIWASP modules. Ensure the package is installed, "
@@ -182,7 +179,7 @@ class TestTransferFunctions:
 
     def test_elev_transfer_function(self):
         """Test elevation transfer function."""
-        from private.elev import elev
+        from pydiwasp.private.elev import elev
 
         # Test parameters
         w = 2 * np.pi * np.array([0.1, 0.2])  # Angular frequencies
@@ -198,7 +195,7 @@ def test_elev_transfer_function(self):
 
     def test_pres_transfer_function(self):
         """Test pressure transfer function."""
-        from private.pres import pres
+        from pydiwasp.private.pres import pres
 
         w = 2 * np.pi * np.array([0.1, 0.2])
         dirs = np.array([0, np.pi/4, np.pi/2])

tests/test_integration.py

@@ -10,7 +10,7 @@
 import os
 from contextlib import redirect_stdout
 
-from dirspec import dirspec
+from pydiwasp import dirspec
 
 
 class TestDirspecIntegration: