setup.py

# -*- coding: utf-8 -*-

from __future__ import division
from __future__ import absolute_import
from __future__ import print_function

import warnings

from setuptools import find_packages
from setuptools import setup
from setuptools import Extension

# Try to use Cython to compile .pyx files.
# If Cython it not available then try to compile .c related files.
# So be sure to always have the .c version for each .pyx files.
# You can generate .c files with python setup.py build_ext --inplace
try:
    import numpy as np
except ImportError as e:
    raise ImportError("Numpy is needed to compile .pyx extensions. Use : pip install numpy")

try:
    from Cython.Distutils import build_ext
except ImportError as e:
    from setuptools.command.build_ext import build_ext
    warnings.warn("Cython is not present. .pyx extensions will be build against .c files.")

extensions = [Extension("sktracker.tracker.lapjv._lapjv",
                        ["sktracker/tracker/lapjv/_lapjv.pyx"],
                        include_dirs=[np.get_include()]),

              Extension("sktracker.io._tifffile",
                        ["sktracker/io/_tifffile.c"],
                        include_dirs=[np.get_include()]),
              ]

# Get version number
import sys
sys.path.append('.')
import sktracker

# Fill project desciption fields
DISTNAME = 'scikit-tracker'
DESCRIPTION = 'Object detection and tracking for cell biology'
LONG_DESCRIPTION = """scikit-tracker aims to be a robust Python library to work with cell biology
microscopy images. OME XML and OME Tiff are supported to handle input/output to the lib. The two
main goals of the library is to implement detection and tracking algorithms relevant to analyse
biological microscopy dataset.

Several algorithms are featured and it is planned to add others:

- Gaussian peak detection by deflation loop : Segré et al. Nature Methods (2008)
- Cell boundary detection with bright field depth fitting : Julou, T., PNAS, (2013)
- Cell nucleus segmentation : by Guillaume Gay
- Lap Tracker, a robust single-particle tracking : K. Jaqaman and G. Danuser, Nature Methods, 2008.
  The version implemented in scikit-tracker is a slightly modified version from the original to allow
  easy, flexible and yet powerfull parameters adjustements with custom cost function.

For more details, please visit : http://scikit-tracker.org/
"""
MAINTAINER = 'Guillaume Gay and Hadrien Mary'
MAINTAINER_EMAIL = 'gllm.gay@gmail.com'
URL = 'http://scikit-tracker.org/'
LICENSE = 'BSD 3-Clause'
DOWNLOAD_URL = 'https://github.com/bnoi/scikit-tracker'
VERSION = sktracker.__version__
DEPENDENCIES = ["numpy >= 1.8",
                "scipy >= 0.12",
                "pandas >= 0.13",
                "scikit-image >= 0.9",
                "scikit-learn >= 0.13",
                "matplotlib >= 1.3",
                ]

if VERSION.endswith('dev'):
    DEPENDENCIES += ["nose >= 1.3",
                     "sphinx >= 1.2",
                     "coverage >= 3.7"
                     ]

if __name__ == "__main__":

    setup(
        name=DISTNAME,
        description=DESCRIPTION,
        long_description=LONG_DESCRIPTION,
        maintainer=MAINTAINER,
        maintainer_email=MAINTAINER_EMAIL,
        url=URL,
        license=LICENSE,
        download_url=DOWNLOAD_URL,
        version=VERSION,

        classifiers=["Development Status :: 4 - Beta",
                     "Intended Audience :: Science/Research",
                     "License :: OSI Approved :: BSD License",
                     "Natural Language :: English",
                     "Operating System :: MacOS",
                     "Operating System :: Microsoft",
                     "Operating System :: POSIX :: Linux",
                     "Programming Language :: Python :: 2.7",
                     "Programming Language :: Python :: 3.3",
                     "Programming Language :: Python :: 3.4",
                     "Programming Language :: Python :: Implementation :: CPython",
                     "Topic :: Scientific/Engineering :: Artificial Intelligence",
                     "Topic :: Scientific/Engineering :: Bio-Informatics",
                     "Topic :: Scientific/Engineering :: Image Recognition",
                     "Topic :: Scientific/Engineering :: Medical Science Apps",
                     ],

        packages=find_packages(),
        package_data={
            '': ['data/*.h5', 'data/*.xml', 'data/*.tif', 'data/stack_list/*.tif', 'data/stack_list/*.h5'],
        },

        tests_require='nose',
        test_suite='nose.collector',

        # Should DEPENDENCIES need to be included or let the user install them himself ?
        install_requires=[],
        # install_requires=DEPENDENCIES,
        setup_requires=['numpy'],

        cmdclass={"build_ext": build_ext},
        ext_modules=extensions,
    )