old_contents: from setuptools import setup, find_packages
  from distutils.extension import Extension
  from Cython.Build import cythonize
  import numpy
  
  #directive_defaults['linetrace'] = True
  #directive_defaults['binding'] = True
  
  extensions = [
          Extension('uncurl.nolips', ['uncurl/nolips.pyx'],
              extra_compile_args=['-O3', '-ffast-math']),
          Extension('uncurl.sparse_utils', ['uncurl/sparse_utils.pyx'],
              extra_compile_args=['-O3', '-ffast-math'])
          ]
  
  parallel_extensions = [
          Extension('uncurl.nolips_parallel', ['uncurl/nolips_parallel.pyx'],
              extra_compile_args=['-O3', '-ffast-math', '-fopenmp'],
              extra_link_args=['-fopenmp'])
          ]
  
  long_description = ''
  with open('README.rst') as f:
      long_description = f.read()
  
  setup(name='uncurl_seq',
        version='0.2.12',
        description='Tool for pre-processing single-cell RNASeq data',
        long_description=long_description,
        long_description_content_type='text/x-rst',
        url='https://github.com/yjzhang/uncurl_python',
        author='Yue Zhang',
        author_email='yjzhang@cs.washington.edu',
        license='MIT',
        include_dirs=[numpy.get_include()],
        ext_modules = cythonize(extensions + parallel_extensions),
        packages=find_packages("."),
        install_requires=[
            'numpy',
            'scipy',
            'cython',
            'scikit-learn',
        ],
        test_suite='nose.collector',
        tests_require=['nose', 'flaky'],
        classifiers=[
            'Development Status :: 3 - Alpha',
            'Topic :: Scientific/Engineering :: Bio-Informatics',
            'License :: OSI Approved :: MIT License',
            'Programming Language :: Python :: 2.7',
            'Programming Language :: Python :: 3.5',
        ],
        zip_safe=False)
  
new_contents: from setuptools import setup, find_packages
  from distutils.extension import Extension
  from Cython.Build import cythonize
  import numpy
  
  #directive_defaults['linetrace'] = True
  #directive_defaults['binding'] = True
  
  extensions = [
          Extension('uncurl.nolips', ['uncurl/nolips.pyx'],
              extra_compile_args=['-O3', '-ffast-math']),
          Extension('uncurl.sparse_utils', ['uncurl/sparse_utils.pyx'],
              extra_compile_args=['-O3', '-ffast-math'])
          ]
  
  parallel_extensions = [
          Extension('uncurl.nolips_parallel', ['uncurl/nolips_parallel.pyx'],
              extra_compile_args=['-O3', '-ffast-math', '-fopenmp'],
              extra_link_args=['-fopenmp'])
          ]
  
  long_description = ''
  with open('README.rst') as f:
      long_description = f.read()
  
  setup(name='uncurl_seq',
        version='0.2.13',
        description='Tool for pre-processing single-cell RNASeq data',
        long_description=long_description,
        long_description_content_type='text/x-rst',
        url='https://github.com/yjzhang/uncurl_python',
        author='Yue Zhang',
        author_email='yjzhang@cs.washington.edu',
        license='MIT',
        include_dirs=[numpy.get_include()],
        ext_modules = cythonize(extensions + parallel_extensions),
        packages=find_packages("."),
        install_requires=[
            'numpy',
            'scipy',
            'cython',
            'scikit-learn',
        ],
        test_suite='nose.collector',
        tests_require=['nose', 'flaky'],
        classifiers=[
            'Development Status :: 3 - Alpha',
            'Topic :: Scientific/Engineering :: Bio-Informatics',
            'License :: OSI Approved :: MIT License',
            'Programming Language :: Python :: 2.7',
            'Programming Language :: Python :: 3.5',
        ],
        zip_safe=False)
  
subject: bump version