text: from setuptools import setup
  from setuptools import find_packages
  import numpy
  from distutils.extension import Extension
  from Cython.Distutils import build_ext
  peaks = Extension("clipper.src.peaks", sources = ['clipper/src/peaksmodule.cc'],
  #for debugging
  #                  extra_compile_args = ['-O0'] 
  )                 
  
  readsToWiggle = Extension("clipper.src.readsToWiggle", ['clipper/src/readsToWiggle.pyx'], 
                            #include_dirs=[numpy.get_include()]
                            )
  
  long_description = "CLIPPER - clip peak enrichment"
  setup(
      name = "clipper",
      long_description = long_description,
      version = "2.1.2",
      packages = find_packages(),
      cmdclass = {'build_ext' : build_ext},
      ext_modules = [readsToWiggle, peaks],
  
      package_data = {
          'clipper' : ['data/*', 'data/regions/*', 'test/data/*']
          },
  
      install_requires = ['setuptools', 
                          'pysam >= 0.15.3',
                          'numpy >= 1.18.5 ',
                          'scipy >= 1.5.0',
                          'matplotlib >= 3.2.2',
                          'pybedtools >= 0.8.1',
                          'scikit-learn >= 0.23.1',
                          'HTSeq >= 0.11.3'
                          ],
        
      setup_requires = ["setuptools_git >= 0.3",],
      
      entry_points = {
                      'console_scripts': [
                                          'clipper = clipper.src.main:call_main',
                                          ],
                      },
  
      #metadata for upload to PyPI
      author = "Michael Lovci and Gabriel Pratt",
      author_email = "mlovci@ucsd.edu",
      description = "A set of scripts for calling peaks on CLIP-seq data",
      license = "GPL2",
      keywords = "CLIP-seq, peaks, bioinformatics",
      url = "https://github.com/YeoLab/clipper",
      
      #Other stuff I feel like including here
      #include_package_data = True
      #zip_safe = True #True I think
  )
  