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import fnmatch
import os
import re
import subprocess
from distutils.command.build import build
from setuptools import setup
def find_package_data_files(directory):
for root, dirs, files in os.walk(directory):
for basename in files:
if fnmatch.fnmatch(basename, "*"):
filename = os.path.join(root, basename)
yield filename.replace("cf/", "", 1)
def find_test_files():
"""Yield the data files in cf/test/"""
for filename in os.listdir("cf/test"):
if (
fnmatch.fnmatch(filename, "*.sh")
or fnmatch.fnmatch(filename, "*.nc")
or fnmatch.fnmatch(filename, "*.pp")
or fnmatch.fnmatch(filename, "*.cdl")
):
filename = os.path.join("test", filename)
yield filename
def _read(fname):
"""Returns content of a file."""
fpath = os.path.dirname(__file__)
fpath = os.path.join(fpath, fname)
with open(fpath, "r") as file_:
return file_.read()
def _get_version():
"""Returns library version by inspecting __init__.py file."""
return re.search(
r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
_read("cf/__init__.py"),
re.MULTILINE,
).group(1)
version = _get_version()
packages = ["cf"]
etc_files = [f for f in find_package_data_files("cf/etc")]
umread_files = [f for f in find_package_data_files("cf/umread_lib/c-lib")]
test_files = [f for f in find_test_files()]
package_data = etc_files + umread_files + test_files
class build_umread(build):
"""Adpated from https://github.com/Turbo87/py-
xcsoar/blob/master/setup.py."""
def run(self):
# Run original build code
build.run(self)
# Build umread
print("Running build_umread")
build_dir = os.path.join(
os.path.abspath(self.build_lib), "cf/umread_lib/c-lib"
)
cmd = ["make", "-C", build_dir]
def compile():
print("*" * 80)
print("Running:", " ".join(cmd), "\n")
try:
rc = subprocess.call(cmd)
except Exception as error:
print(error)
rc = 40
print("\n", "-" * 80)
if not rc:
print("SUCCESSFULLY built UM read C library")
else:
print("WARNING: Failed to build the UM read C library.")
print(
" Attempting to read UKMO PP and UM format files "
"will result in failure."
)
print(
" This will not affect any other cf functionality."
)
print(
" In particular, netCDF file processing is "
"unaffected."
)
print("-" * 80)
print("\n", "*" * 80)
print()
print("cf build successful")
print()
self.execute(compile, [], "compiling umread")
long_description = """
CF Python
=========
The Python cf package is an Earth science data analysis library that
is built on a complete implementation of the `CF data
model <https://cfconventions.org/cf-conventions/cf-conventions.html#appendix-CF-data-model>`_.
Documentation
=============
http://ncas-cms.github.io/cf-python
Dask
====
From version 3.14.0, the ``cf`` package uses `Dask
<https://docs.dask.org>`_ for all of its data manipulations.
Recipes
=======
https://ncas-cms.github.io/cf-python/recipes
Tutorial
========
https://ncas-cms.github.io/cf-python/tutorial
Installation
============
http://ncas-cms.github.io/cf-python/installation
Command line utilities
======================
During installation the ``cfa`` command line utility is also
installed, which
* generates text descriptions of field constructs contained in files,
and
* creates new datasets aggregated from existing files.
Visualization
=============
Powerful, flexible, and very simple to produce visualizations of field
constructs are available with the
[cfplot](http://ajheaps.github.io/cf-plot) package, that needs to be
installed seprately to the ``cf`` package.
See the `cfplot gallery
<http://ajheaps.github.io/cf-plot/gallery.html>`_ for the full range
of plotting possibilities with example code.
Functionality
=============
The ``cf`` package implements the `CF data model
<https://cfconventions.org/cf-conventions/cf-conventions.html#appendix-CF-data-model>`_
for its internal data structures and so is able to process any
CF-compliant dataset. It is not strict about CF-compliance, however,
so that partially conformant datasets may be ingested from existing
datasets and written to new datasets. This is so that datasets which
are partially conformant may nonetheless be modified in memory.
The ``cf`` package can:
* read field constructs from netCDF, CDL, PP and UM datasets,
* create new field constructs in memory,
* write and append field constructs to netCDF datasets on disk,
* read, write, and create coordinates defined by geometry cells,
* read netCDF and CDL datasets containing hierarchical groups,
* inspect field constructs,
* test whether two field constructs are the same,
* modify field construct metadata and data,
* create subspaces of field constructs,
* write field constructs to netCDF datasets on disk,
* incorporate, and create, metadata stored in external files,
* read, write, and create data that have been compressed by convention
(i.e. ragged or gathered arrays, or coordinate arrays compressed by
subsampling), whilst presenting a view of the data in its
uncompressed form,
* combine field constructs arithmetically,
* manipulate field construct data by arithmetical and trigonometrical
operations,
* perform statistical collapses on field constructs,
* perform histogram, percentile and binning operations on field
constructs,
* regrid structured grid, mesh and DSG field constructs with
(multi-)linear, nearest neighbour, first- and second-order
conservative and higher order patch recovery methods, including 3-d
regridding,
* apply convolution filters to field constructs,
* create running means from field constructs,
* apply differential operators to field constructs,
* create derived quantities (such as relative vorticity).
"""
# Get dependencies
requirements = open("requirements.txt", "r")
install_requires = requirements.read().splitlines()
tests_require = (
[
"pytest",
"pycodestyle",
"coverage",
],
)
extras_require = {
"required C libraries": ["udunits2==2.2.25"],
"regridding": ["esmpy", "ESMF>=8.0"],
"convolution filters, derivatives, relative vorticity": ["scipy>=1.1.0"],
"subspacing with multi-dimensional construct cells": ["matplotlib>=3.0.0"],
"documentation": [
"sphinx==2.4.5",
"sphinx-copybutton",
"sphinx-toggleprompt",
"sphinxcontrib-spelling",
],
"pre-commit hooks": [
"pre-commit",
"black",
"docformatter",
"flake8",
],
}
setup(
name="cf-python",
long_description=long_description,
long_description_content_type="text/x-rst",
version=version,
description="A CF-compliant earth science data analysis library",
author="David Hassell",
maintainer="David Hassell, Sadie Bartholomew",
maintainer_email="david.hassell@ncas.ac.uk, sadie.bartholomew@ncas.ac.uk",
author_email="david.hassell@ncas.ac.uk",
url="https://ncas-cms.github.io/cf-python",
platforms=["Linux", "MacOS"],
license="MIT",
keywords=[
"cf",
"netcdf",
"UM",
"data",
"science",
"oceanography",
"meteorology",
"climate",
],
classifiers=[
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Topic :: Scientific/Engineering :: Mathematics",
"Topic :: Scientific/Engineering :: Physics",
"Topic :: Scientific/Engineering :: Atmospheric Science",
"Topic :: Utilities",
"Operating System :: POSIX :: Linux",
"Operating System :: MacOS",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"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",
],
packages=[
"cf",
"cf.mixin",
"cf.mixin2",
"cf.data",
"cf.data.array",
"cf.data.array.abstract",
"cf.data.array.mixin",
"cf.data.collapse",
"cf.data.fragment",
"cf.data.fragment.mixin",
"cf.data.mixin",
"cf.docstring",
"cf.read_write",
"cf.read_write.um",
"cf.read_write.netcdf",
"cf.regrid",
"cf.umread_lib",
"cf.test",
],
package_data={"cf": package_data},
scripts=["scripts/cfa"],
python_requires=">=3.8",
install_requires=install_requires,
tests_require=tests_require,
extras_require=extras_require,
include_package_data=True,
# install_requires=[
# 'netCDF4>=1.5.3',
# 'cftime>=1.1.3',
# 'numpy>=1.15',
# 'cfdm>=1.8.5, <1.9',
# 'psutil>=0.6.0',
# 'cfunits>=3.2.7'
# 'scipy>=1.1.0',
# 'matplotlib>=3.0.0',
# 'mpi4py>=3.0.0',
# 'ESMF>=8.0',
# 'udunits2==2.2.25',
# ],
#
# https://docs.python.org/2/distutils/apiref.html:
cmdclass={"build": build_umread},
)
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