setup.py

import os
from setuptools import setup, find_packages, Extension
import versioneer

try:
    from Cython.Build import cythonize
    USE_CYTHON = True
except ImportError:
    USE_CYTHON = False

ext = ".pyx" if USE_CYTHON else ".c"
module_names = [
    "mockinbird.ivtree.ivtree",
    "mockinbird.ivtree.ivtreenode",
    "mockinbird.ivtree.ivnode",
    "mockinbird.ivtree.tests.node_utils",
    "mockinbird.ivtree.tests.tree_utils",
]

extensions = []
for module_name in module_names:
    file_name = module_name.replace(".", os.sep) + ext
    extension = Extension(module_name, [file_name])
    extensions.append(extension)
if USE_CYTHON:
    extensions = cythonize(extensions)


setup(
    name='mockinbird',
    version=versioneer.get_version(),
    cmdclass=versioneer.get_cmdclass(),
    description='PAR-CLIP data analysis pipeline',
    author='Christian Roth, Phillipp Torkler',
    author_email='christan.roth@mpibpc.mpg.de',
    license='GPLv3',
    entry_points={
        'console_scripts': [

            # general
            'mockinbird = mockinbird.scripts.mockinbird:main',
            'mb-preprocess = mockinbird.scripts.preprocess:main',
            'mb-postprocess = mockinbird.scripts.postprocess:main',

            # mockinbird model
            'mb-extract-sites = mockinbird.scripts.extract_sites:main',
            'mb-pileup2sites = mockinbird.scripts.pileup2sites:main',
            'mb-site-merger = mockinbird.scripts.site_merger_full:main',
            'mb-create-bam-statistics = mockinbird.scripts.estimate_bam_statistics:main',
            'mb-calculate-posterior = mockinbird.scripts.calculate_posterior:main',
            'mb-mockinbird2table = mockinbird.scripts.mockinbird2table:main',
            'mb-learn-mock = mockinbird.scripts.learn_model:main',

            # preprocessing
            'mb-remove-duplicates = mockinbird.scripts.removePCRduplicates:run',
            'mb-adapter-clipper = mockinbird.scripts.clipper53:main',
            'mb-bam-postprocess = mockinbird.scripts.bam_postprocessing:main',
            'mb-softclip-analyzer = mockinbird.scripts.clipped_seq:main',
            'mb-bsfinder = mockinbird.scripts.bsfinder:run',
            'mb-naive-bsfinder = mockinbird.scripts.naive_bsfinder:run',
            'mb-normalize = mockinbird.scripts.normalize:run',
            'mb-cap-occupancy = mockinbird.scripts.convert2quantile:run',
            'mb-table2fasta = mockinbird.utils.table2fasta:main',
            'mb-upgrade-table = mockinbird.utils.update_table:main',

            # postprocessing
            'mb-plot-metagene-nobs = mockinbird.plots.makeCenterBothEnds:run',
            'mb-plot-metagene = mockinbird.plots.makeCenterBothEnds_bs:main',
            'mb-plot-kmer-enrichment = mockinbird.plots.makeKmerPerPosition:run',
            'mb-generate-negative-set = mockinbird.scripts.makeNegSets:run',
            'mb-plot-kmer-logodds = mockinbird.plots.makeKmerLogOdds:run',
            'mb-xxmotif = mockinbird.scripts.xxmotif:run',
            'mb-plot-transition-frequencies = mockinbird.plots.makeNucleotideProbabilities:run',
            'mb-plot-heatmap = mockinbird.plots.makeHeatMap:run',
            'mb-plot-heatmap-small = mockinbird.plots.makeHeatMapSmall:run',
            'mb-filter-sites = mockinbird.scripts.filter_sites:main',
            'mb-annotate-table = mockinbird.scripts.annotate_table:main',
        ]
    },
    packages=find_packages(),
    ext_modules=extensions,
    include_package_data=True,
    test_suite='nose.collector',
    zip_safe=False
)