refactor: modernize build with pyproject.toml

refactor: pyTMD updates to definition files and database

pyproject.toml

@@ -0,0 +1,102 @@
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "Grounding-Zones"
+description = "Python Tools for Estimating Ice Sheet Grounding Zone Locations with ICESat-2"
+keywords = [
+    "ICESat-2 laser altimetry",
+    "Elastic Bending",
+    "Grounding Zones",
+    "Ice Shelves",
+    "Ice Sheets",
+]
+authors = [
+    {name = "Tyler Sutterley"},
+    {name = "Karen Alley"},
+    {name = "Kelly Brunt"},
+    {name = "Susan Howard"},
+    {name = "Laurie Padman"},
+    {name = "Matt Siegfried"},
+    {email = "[email protected]"}
+]
+maintainers = [{ name = "Grounding-Zones contributors" }]
+license = {file = "LICENSE"}
+readme = "README.rst"
+version = "1.0.0"
+
+requires-python = "~=3.6"
+dependencies = [
+    "lxml",
+    "numpy",
+    "pyproj",
+    "python-dateutil",
+    "pyTMD",
+    "scipy>=1.10.1",
+    "timescale>=0.0.3",
+]
+
+
+classifiers=[
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "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",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+
+[project.urls]
+Homepage = "https://grounding-zones.readthedocs.io"
+Documentation = "https://grounding-zones.readthedocs.io"
+Repository = "https://github.com/tsutterley/Grounding-Zones"
+Issues = "https://github.com/tsutterley/Grounding-Zones/issues"
+
+[project.optional-dependencies]
+doc = ["docutils", "fontconfig", "freetype", "graphviz", "numpydoc", "sphinx", "sphinx-argparse>=0.4", "sphinx_rtd_theme"]
+all = ["cartopy", "earthengine-api", "gdal", "h5py", "matplotlib", "mpi4py", "notebook", "pyyaml", "scikit-learn", "shapely", "ATM1b-QFIT", "geoid-toolkit", "icesat2-toolkit", "spatial-interpolators"]
+dev = ["flake8", "pytest>=4.6", "pytest-cov"]
+
+[tool.setuptools.packages.find]
+exclude = ["test*", "run*"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+norecursedirs = ".git"
+python_files = [
+    "test*.py"
+]
+testpaths = [
+    "test"
+]
+
+[tool.coverage.run]
+branch = true
+source = [
+    "Grounding-Zones",
+    "test",
+]
+omit = [
+    "setup.py",
+    "conf.py",
+    "DAC/*",
+    "DEM/*",
+    "geoid/*",
+    "GZ/*",
+    "SL/*",
+    "scripts/*",
+    "subset/*",
+    "tides/*",
+]
+
+[tool.coverage.report]
+show_missing = true
+precision = 2

setup.py

@@ -1,84 +1,12 @@
 import os
-import sys
-import logging
-import subprocess
-from setuptools import setup, find_packages
-
-logging.basicConfig(stream=sys.stderr, level=logging.INFO)
-log = logging.getLogger()
-
-# package description and keywords
-description = 'Python Tools for Estimating Ice Sheet Grounding Zone Locations with ICESat-2'
-keywords = 'ICESat-2 laser altimetry, Elastic Bending, Grounding Zones, Ice Shelves, Ice Sheets'
-# get long_description from README.rst
-with open('README.rst', 'r', encoding='utf8') as fh:
-    long_description = fh.read()
-long_description_content_type = "text/x-rst"
-
-# install requirements and dependencies
-on_rtd = os.environ.get('READTHEDOCS') == 'True'
-if on_rtd:
-    install_requires = []
-else:
-    # get install requirements
-    with open('requirements.txt', 'r', encoding='utf8') as fh:
-        install_requires = [line.split().pop(0) for line in fh.read().splitlines()]
-
-# get version
-with open('version.txt', 'r', encoding='utf8') as fh:
-    version = fh.read()
+from setuptools import setup
 
 # list of all scripts to be included with package
 scripts=[]
 for s in ['scripts','subset','DAC','DEM','geoid','GZ','SL','tides']:
     scripts.extend([os.path.join(s,f) for f in os.listdir(s) if f.endswith('.py')])
 
-# run cmd from the command line
-def check_output(cmd):
-    return subprocess.check_output(cmd).decode('utf')
-
-# check if GDAL is installed
-gdal_output = [None] * 4
-try:
-    for i, flag in enumerate(("--cflags", "--libs", "--datadir", "--version")):
-        gdal_output[i] = check_output(['gdal-config', flag]).strip()
-except:
-    log.warning('Failed to get options via gdal-config')
-else:
-    log.info(f"GDAL version from via gdal-config: {gdal_output[3]}")
-# if setting GDAL version from via gdal-config
-if gdal_output[3] and ('gdal' in install_requires):
-    # add version information to gdal in install_requires
-    gdal_index = install_requires.index('gdal')
-    install_requires[gdal_index] = f'gdal=={gdal_output[3]}'
-elif any(install_requires) and ('gdal' in install_requires):
-    # gdal version not found
-    gdal_index = install_requires.index('gdal')
-    install_requires.pop(gdal_index)
-
 setup(
     name='grounding-zones',
-    version=version,
-    description=description,
-    long_description=long_description,
-    long_description_content_type=long_description_content_type,
-    url='https://github.com/tsutterley/Grounding-Zones',
-    author='Tyler Sutterley',
-    author_email='[email protected]',
-    license='MIT',
-    classifiers=[
-        'Development Status :: 3 - Alpha',
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering :: Physics',
-        'License :: OSI Approved :: MIT License',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-    ],
-    keywords=keywords,
-    packages=find_packages(),
-    install_requires=install_requires,
     scripts=scripts,
-    include_package_data=True,
 )

tides/adjust_tides_ICESat2_ATL11.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 adjust_tides_ICESat2_ATL11.py
-Written by Tyler Sutterley (08/2024)
+Written by Tyler Sutterley (09/2024)
 Applies interpolated tidal adjustment scale factors to
     ICESat-2 ATL11 annual land ice height data within
     ice sheet grounding zones
@@ -34,6 +34,8 @@
     io/ATL11.py: reads ICESat-2 annual land ice height data files
 
 UPDATE HISTORY:
+    Updated 09/2024: use JSON database for known model parameters
+        drop support for the ascii definition file format
     Updated 08/2024: option for automatic detection of definition format
     Updated 07/2024: added option to use JSON format definition files
     Updated 05/2024: use wrapper to importlib for optional dependencies
@@ -67,7 +69,6 @@ def adjust_tides_ICESat2_ATL11(adjustment_file, INPUT_FILE,
         OUTPUT_DIRECTORY=None,
         TIDE_MODEL=None,
         DEFINITION_FILE=None,
-        DEFINITION_FORMAT='auto',
         VERBOSE=False,
         MODE=0o775
     ):
@@ -78,8 +79,7 @@ def adjust_tides_ICESat2_ATL11(adjustment_file, INPUT_FILE,
 
     # get tide model parameters
     if DEFINITION_FILE is not None:
-        model = pyTMD.io.model(None, verify=False).from_file(DEFINITION_FILE,
-            format=DEFINITION_FORMAT)
+        model = pyTMD.io.model(None, verify=False).from_file(DEFINITION_FILE)
     else:
         model = pyTMD.io.model(None, verify=False).elevation(TIDE_MODEL)
     # source of tide model
@@ -745,9 +745,6 @@ def arguments():
     group.add_argument('--definition-file',
         type=pathlib.Path,
         help='Tide model definition file')
-    parser.add_argument('--definition-format',
-        type=str, default='auto', choices=('ascii','json','auto'),
-        help='Format for model definition file')
     # verbosity settings
     # verbose will output information about each output file
     parser.add_argument('--verbose','-V',
@@ -772,7 +769,6 @@ def main():
             OUTPUT_DIRECTORY=args.output_directory,
             TIDE_MODEL=args.tide,
             DEFINITION_FILE=args.definition_file,
-            DEFINITION_FORMAT=args.definition_format,
             VERBOSE=args.verbose,
             MODE=args.mode)
 

tides/compute_tides_ICESat2_ATL03.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 compute_tides_ICESat2_ATL03.py
-Written by Tyler Sutterley (08/2024)
+Written by Tyler Sutterley (09/2024)
 Calculates tidal elevations for correcting ICESat-2 photon height data
 Calculated at ATL03 segment level using reference photon geolocation and time
 Segment level corrections can be applied to the individual photon events (PEs)
@@ -17,7 +17,6 @@
     -D X, --directory X: Working data directory
     -O X, --output-directory X: input/output data directory
     -T X, --tide X: Tide model to use in correction
-    --atlas-format X: ATLAS tide model format (OTIS, netcdf)
     --gzip, -G: Tide model files are gzip compressed
     --definition-file X: Model definition file for use as correction
     -I X, --interpolate X: Interpolation method
@@ -67,6 +66,8 @@
     predict.py: predict tidal values using harmonic constants
 
 UPDATE HISTORY:
+    Updated 09/2024: use JSON database for known model parameters
+        drop support for the ascii definition file format
     Updated 08/2024: project bounds for cropping non-geographic OTIS models
         added option to allow inferring only specific minor constituents
         added option to try automatic detection of definition file format
@@ -144,10 +145,8 @@
 def compute_tides_ICESat2(tide_dir, INPUT_FILE,
         OUTPUT_DIRECTORY=None,
         TIDE_MODEL=None,
-        ATLAS_FORMAT=None,
         GZIP=True,
         DEFINITION_FILE=None,
-        DEFINITION_FORMAT='auto',
         CROP=False,
         METHOD='spline',
         EXTRAPOLATE=False,
@@ -165,11 +164,9 @@ def compute_tides_ICESat2(tide_dir, INPUT_FILE,
 
     # get parameters for tide model
     if DEFINITION_FILE is not None:
-        model = pyTMD.io.model(tide_dir).from_file(DEFINITION_FILE,
-            format=DEFINITION_FORMAT)
+        model = pyTMD.io.model(tide_dir).from_file(DEFINITION_FILE)
     else:
-        model = pyTMD.io.model(tide_dir, format=ATLAS_FORMAT,
-            compressed=GZIP).elevation(TIDE_MODEL)
+        model = pyTMD.io.model(tide_dir, compressed=GZIP).elevation(TIDE_MODEL)
 
     # log input file
     logging.info(f'{str(INPUT_FILE)} -->')
@@ -652,20 +649,13 @@ def arguments():
         metavar='TIDE', type=str,
         choices=get_available_models(),
         help='Tide model to use in correction')
-    parser.add_argument('--atlas-format',
-        type=str, choices=('OTIS','ATLAS-netcdf'),
-        default='ATLAS-netcdf',
-        help='ATLAS tide model format')
     parser.add_argument('--gzip','-G',
         default=False, action='store_true',
         help='Tide model files are gzip compressed')
     # tide model definition file to set an undefined model
     group.add_argument('--definition-file',
         type=pathlib.Path,
         help='Tide model definition file')
-    parser.add_argument('--definition-format',
-        type=str, default='auto', choices=('ascii','json','auto'),
-        help='Format for model definition file')
     # crop tide model to (buffered) bounds of data
     parser.add_argument('--crop',
         default=False, action='store_true',
@@ -719,10 +709,8 @@ def main():
         compute_tides_ICESat2(args.directory, FILE,
             OUTPUT_DIRECTORY=args.output_directory,
             TIDE_MODEL=args.tide,
-            ATLAS_FORMAT=args.atlas_format,
             GZIP=args.gzip,
             DEFINITION_FILE=args.definition_file,
-            DEFINITION_FORMAT=args.definition_format,
             CROP=args.crop,
             METHOD=args.interpolate,
             EXTRAPOLATE=args.extrapolate,