From 435e44d33d8996f839fb8d838843dfd05bb99a47 Mon Sep 17 00:00:00 2001
From: Max Levine <mflevine@optonline.net>
Date: Wed, 22 May 2019 11:57:53 -0400
Subject: [PATCH] =?UTF-8?q?=F0=9F=92=8E=20properly=20package=20cython=20fi?=
 =?UTF-8?q?les=20and=20bump?=
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---
 setup.py | 110 +++++++++++++++++++++++++++++++------------------------
 1 file changed, 63 insertions(+), 47 deletions(-)

diff --git a/setup.py b/setup.py
index 0632235..52523aa 100644
--- a/setup.py
+++ b/setup.py
@@ -1,68 +1,84 @@
 # based on https://github.com/pypa/sampleproject
-from setuptools import setup, find_packages
 from codecs import open
+from distutils.command.sdist import sdist as _sdist
+from distutils.core import setup
+from distutils.extension import Extension
 from os import path
 
+from setuptools import find_packages, setup
+
 here = path.abspath(path.dirname(__file__))
 
+try:
+    from Cython.Distutils import build_ext
+    from Cython.Build import cythonize
+except ImportError:
+    use_cython = False
+else:
+    use_cython = True
+
+cmdclass = {}
+
+if use_cython:
+    ext_modules = cythonize("mergesvvcf/*pyx")
+    cmdclass.update({"build_ext": build_ext})
+else:
+    ext_modules = [
+        Extension("mergesvvcf.locations", ["mergesvvcf/locations.c"]),
+        Extension("mergesvvcf.variantdict", ["mergesvvcf/variantdict.c"]),
+        Extension("mergesvvcf.vcftobreakpoints", ["mergesvvcf/vcftobreakpoints.c"]),
+    ]
+
+
+class sdist(_sdist):
+    def run(self):
+        # Make sure the compiled Cython files in the distribution are up-to-date
+        from Cython.Build import cythonize
+
+        cythonize(["mergesvvcf/*.pyx"])
+        _sdist.run(self)
+
+
+cmdclass["sdist"] = sdist
+
 # Get the long description from the relevant file
-with open(path.join(here, 'DESCRIPTION.md'), encoding='utf-8') as f:
+with open(path.join(here, "DESCRIPTION.md"), encoding="utf-8") as f:
     long_description = f.read()
 
 setup(
-    name='mergesvvcf',
-
-    version='1.0.1',
-
-    description='Merge SV VCF calls. Fork of https://github.com/ljdursi/mergevcf by Jonathan Dursi (Jonathan.Dursi@oicr.on.ca)',
+    name="mergesvvcf",
+    version="1.0.2",
+    description="Merge SV VCF calls. Fork of https://github.com/ljdursi/mergevcf by Jonathan Dursi (Jonathan.Dursi@oicr.on.ca)",
     long_description=long_description,
-
     # The project's main homepage.
-    url='https://github.com/papaemmelab/mergeSVvcf',
-
+    url="https://github.com/papaemmelab/mergeSVvcf",
     # Author details
-    author='Max Levine',
-    author_email='levinem1@mskcc.org',
-
+    author="Max Levine",
+    author_email="levinem1@mskcc.org",
     # Choose your license
-    license='GPL',
-
+    license="GPL",
     classifiers=[
         #   5 - Production/Stable
-        'Development Status :: 5 - Production/Stable',
-
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering',
-
-        'License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)',
-
-        'Programming Language :: Python :: 2',
-        'Programming Language :: Python :: 3',
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering",
+        "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
+        "Programming Language :: Python :: 2",
+        "Programming Language :: Python :: 3",
     ],
-
-    keywords='merge sv vcfs',
-
-    packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
-
-    install_requires=['pysam>=0.15.2','Cython>=0.29.7'],
-
-    test_suite='tests',
-
-    extras_require={
-        'dev': ['check-manifest'],
-        'test': ['coverage'],
-    },
-
+    keywords="merge sv vcfs",
+    packages=find_packages(exclude=["contrib", "docs", "tests*"]),
+    install_requires=["pysam>=0.15.2", "Cython>=0.29.7"],
+    # ext_modules=[],
+    test_suite="tests",
+    extras_require={"dev": ["check-manifest"], "test": ["coverage"]},
     # If there are data files included in your packages that need to be
     # installed, specify them here.  If using Python 2.6 or less, then these
     # have to be included in MANIFEST.in as well.
-#    package_data={
-#        'sample': ['package_data.dat'],
-#    },
-
-    entry_points={
-        'console_scripts': [
-            'mergesvvcf=mergesvvcf:main',
-        ],
-    },
+    #    package_data={
+    #        'sample': ['package_data.dat'],
+    #    },
+    entry_points={"console_scripts": ["mergesvvcf=mergesvvcf:main"]},
+    ext_modules=ext_modules,
+    cmdclass={"sdist": sdist},
 )