pIMZ/setup.py at master · mjoppich/pIMZ · GitHub

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'''
pySRM: Statistical Region Merging for python3 (C++ backend)

Note that "python setup.py test" invokes pytest on the package. With appropriately
configured setup.cfg, this will check both xxx_test modules and docstrings.

Copyright 2019, Markus Joppich.
Licensed under MIT.
'''
import sys, os
from setuptools import setup, find_packages, Extension

ext_lib_path = 'rectangle'
include_dir = os.path.join(ext_lib_path, 'include')

curBaseFolder = os.path.relpath(os.path.abspath(os.path.dirname(__file__)), os.getcwd())

print(curBaseFolder, file=sys.stderr)

segment_sources = [os.path.join(curBaseFolder, 'cIMZ/segment.cpp')]
imageregion_sources = [os.path.join(curBaseFolder, 'cIMZ/src/imageregion.cpp')]
srm_sources = [os.path.join(curBaseFolder, 'cIMZ/src/srm.cpp')]

print(segment_sources, file=sys.stderr)

compileArgs = ["-std=c++1z", "-Wall", "-fopenmp", "-fPIC", "-std=gnu++17",'-O3']

libPIMZ=Extension('pIMZ.libPIMZ',
 sources=srm_sources+imageregion_sources+segment_sources,
 language='c++',
 libraries=['z', 'gomp'],
 extra_compile_args=compileArgs,
 extra_objects=[],

 )

version = "1.0a"
import pathlib


setup(name="pIMZ",
      version=version,
      description="pIMZ: an integrative framework for imaging mass spectrometry analysis",
      long_description=open("README.md").read(),
      long_description_content_type='text/markdown',
      classifiers=[ # Get strings from http://pypi.python.org/pypi?%3Aaction=list_classifiers
 'Development Status :: 3 - Alpha',
 'Intended Audience :: Developers',
 'Programming Language :: Python',
 'Programming Language :: Python :: 3 :: Only',
 'Programming Language :: Python :: 3.6',
 'Programming Language :: Python :: 3.7',
 'Programming Language :: Python :: 3.8',
 'Programming Language :: Python :: 3.9',
 'Topic :: Scientific/Engineering :: Bio-Informatics',
 'Topic :: Scientific/Engineering :: Medical Science Apps.'
      ],
      keywords="IMS MSI imaging mass-spectrometry interactive integrative", # Separate with spaces
      author="Markus Joppich",
      author_email="pIMZ@compbio.cc",
      url="https://github.com/mjoppich/pIMZ",
      license="MIT",
      packages=find_packages(exclude=['examples']),
      include_package_data=True,
      zip_safe=False,
      tests_require=[],
      cmdclass={},
      python_requires='>=3.6',
      # TODO: List of packages that this one depends upon:
      install_requires=[
            'numpy>=1.17.5', 'joblib', 'tqdm', 'h5py', "networkx~=2.3", "hnswlib", "pronto", "upsetplot", 'matplotlib', "joblib", 'pandas', 'scipy', 'scikit-image', 'scikit-learn<1.7',  "pybaselines", 'dill',  'pathos', 'ms_peak_picker',  'globus_sdk',  'progressbar',  'anndata',  'diffxpy',  'pyimzml', 'natsort', 'seaborn', 'llvmlite', 'pykeops', 'imageio', 'umap-learn', 'jinja2', 'hdbscan', 'regex','Pillow', 'adjustText', 'intervaltree'
            ], #dabest, 'fuzzy-c-means'
      # TODO: List executable scripts, provided by the package (this is just an example)
      entry_points={
 'console_scripts':
     []
      },
      ext_modules=[libPIMZ]
)