setup.py

#!/usr/bin/env python

import glob
import sys
import subprocess
import setuptools

from distutils.core import setup
from distutils.extension import Extension

# check if cython exists
try:
    from Cython.Distutils import build_ext
except:
    print """Cython not installed. Please install cython from
    http://cython.org.
"""
    sys.exit(1)

# check if lfasta exitst
retcode = subprocess.call("which lfasta",
                          shell=True)
if retcode != 0:
    print """WARNING: could not find lfasta in your path.

Please download the source code of W.R. Pearson's fasta package and
build lfasta using the following commands:

mkdir fasta2
cd fasta2
wget http://faculty.virginia.edu/wrpearson/fasta/fasta2/fasta2.shar.Z
gunzip fasta2.shar.Z
sh fasta2.shar
make lfasta

Copy the lfasta executable somewhere into your path.
"""

c_sources = [x for x in glob.glob("src/*.c") if x not in "src/main.c"]

# build the interface
pyradar = Extension(
    "pyradar",                   # name of extension
    ["pyradar/pyradar.pyx", ] + c_sources,
    library_dirs=[],
    libraries=[],
    language="c",
)

setup(name='Radar',
      version='1.3',
      description='RADAR - Rapid Automatic Detection and Alignment of Repeats',
      author='Andreas Heger & Liisa Holm',
      author_email='andreas.heger@gmail.com',
      url='https://github.com/AndreasHeger/radar',
      package_dir={},
      packages=[],
      scripts=['scripts/radar.py', ],
      ext_modules=[pyradar],
      cmdclass={'build_ext': build_ext}
      )