setup.py

#!/usr/bin/env python

from setuptools import setup, find_packages

version = '8.0.0'

setup(name='Cogent',
      version=version,
      description='COding GENome reconstruction Tool using transcript sequences',
      author='Elizabeth Tseng',
      author_email='etseng@pacb.com',
      install_requires=[
          'matplotlib',
          'numpy',
          'scipy',
          'networkx>=2.5',
          'scikit-image',
          'pulp',
          'biopython',
          'bx-python>=0.7.3'     ],
      packages=['Cogent', 'Cogent.test'],
      package_dir = {'Cogent':'Cogent'},
      zip_safe=False,
      test_suite = "Cogent.test.test_cogent",
      scripts=['Cogent/run_mash.py',
               'Cogent/process_kmer_to_graph.py',
               'Cogent/gff3_to_collapsed.py',
               'Cogent/reconstruct_contig.py',
               'Cogent/generate_batch_cmd_for_Cogent_reconstruction.py',
               'Cogent/generate_batch_cmd_for_Cogent_family_finding.py'
     ])