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setup.py
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setup.py
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import sys
import os
import platform
from setuptools import setup
from setuptools.extension import Extension
# Ensure Cython is installed before we even attempt to install Ripser.py
try:
from Cython.Build import cythonize
from Cython.Distutils import build_ext
except:
print("You don't seem to have Cython installed. Please get a")
print("copy from www.cython.org or install it with `pip install Cython`")
sys.exit(1)
## Get version information from _version.py
import re
VERSIONFILE = "ripser/_version.py"
verstrline = open(VERSIONFILE, "rt").read()
VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(VSRE, verstrline, re.M)
if mo:
verstr = mo.group(1)
else:
raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,))
# Use README.md as the package long description
with open("README.md") as f:
long_description = f.read()
class CustomBuildExtCommand(build_ext):
"""This extension command lets us not require numpy be installed before running pip install ripser
build_ext command for use when numpy headers are needed.
"""
def run(self):
# Import numpy here, only when headers are needed
import numpy
# Add numpy headers to include_dirs
self.include_dirs.append(numpy.get_include())
# Call original build_ext command
build_ext.run(self)
extra_compile_args = ["-Ofast", "-D_hypot=hypot"]
extra_link_args = []
if platform.system() == "Windows":
extra_compile_args.extend(
[
# Supported by Visual C++ >=14.1
"/std:c++14"
]
)
elif platform.system() == "Darwin":
extra_compile_args.extend(["-std=c++11", "-mmacosx-version-min=10.9"])
extra_link_args.extend(["-stdlib=libc++", "-mmacosx-version-min=10.9"])
else:
extra_compile_args.extend(["-std=c++11"])
macros = [("USE_COEFFICIENTS", 1), ("NDEBUG", 1), ("ASSEMBLE_REDUCTION_MATRIX", 1)]
# Robinhood
robinhood_path = os.path.join("ripser", "robinhood")
if os.path.isdir(robinhood_path):
macros.extend([("USE_ROBINHOOD_HASHMAP", 1)])
robinhood_include_path = os.path.join("src", "include")
if platform.system() == "Windows":
extra_compile_args.extend(
["/I" + os.path.join(robinhood_path, robinhood_include_path)]
)
else:
extra_compile_args.extend(
["-I" + os.path.join(robinhood_path, robinhood_include_path)]
)
ext_modules = Extension(
"pyRipser",
sources=["ripser/pyRipser.pyx"],
define_macros=macros,
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
language="c++",
)
setup(
name="ripser",
version=verstr,
description="A Lean Persistent Homology Library for Python",
long_description=long_description,
long_description_content_type="text/markdown",
author="Chris Tralie, Nathaniel Saul",
author_email="chris.tralie@gmail.com, nat@riverasaul.com",
url="https://ripser.scikit-tda.org",
license="MIT",
packages=["ripser"],
ext_modules=cythonize(ext_modules),
install_requires=["Cython", "numpy", "scipy", "scikit-learn", "persim"],
extras_require={
"testing": [ # `pip install -e ".[testing]"``
"pytest"
],
"docs": [ # `pip install -e ".[docs]"`
"sktda_docs_config"
],
"examples": ["persim", "tadasets", "jupyter", "pillow"],
},
cmdclass={"build_ext": CustomBuildExtCommand},
python_requires=">=3.6",
classifiers=[
"Intended Audience :: Science/Research",
"Intended Audience :: Education",
"Intended Audience :: Financial and Insurance Industry",
"Intended Audience :: Healthcare Industry",
"Topic :: Scientific/Engineering :: Information Analysis",
"Topic :: Scientific/Engineering :: Mathematics",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
],
keywords="persistent homology, rips filtration, persistence diagrams, topology data analysis, algebraic topology, unsupervised learning",
)