Commit 674b8c7c authored by van den Berg's avatar van den Berg
Browse files

Fix packaging

parent c6f39403
Pipeline #2944 failed with stage
in 22 seconds
include vtools/*.pyx
\ No newline at end of file
[metadata]
license_file=LICENSE
......@@ -7,69 +7,35 @@ setup.py
:license: MIT
"""
from os.path import abspath, dirname, join
import sys
import pkg_resources
import subprocess
from setuptools import setup, find_packages
# Temporarily install dependencies required by setup.py before trying to
# import them. From https://bitbucket.org/dholth/setup-requires
sys.path[0:0] = ['setup-requires']
pkg_resources.working_set.add_entry('setup-requires')
def missing_requirements(specifiers):
for specifier in specifiers:
try:
pkg_resources.require(specifier)
except pkg_resources.DistributionNotFound:
yield specifier
def install_requirements(specifiers):
to_install = list(specifiers)
if to_install:
cmd = [sys.executable, "-m", "pip", "install",
"-t", "setup-requires"] + to_install
subprocess.call(cmd)
requires = ['cython', 'numpy']
install_requirements(missing_requirements(requires))
from Cython.Build import cythonize
import numpy as np
from setuptools import setup, find_packages, Extension
readme_file = join(abspath(dirname(__file__)), "README.md")
with open(readme_file) as desc_handle:
long_desc = desc_handle.read()
# create extensions and add numpy includes to all of them.
cython_extensions = cythonize("vtools/*.pyx")
for ext in cython_extensions:
ext.include_dirs.append(np.get_include())
setup(
name="v-tools",
version="1.0.0",
version="1.0.0-dev",
description="Various tools operating over VCF files",
long_description=long_desc,
author="Sander Bollen",
author_email="a.h.b.bollen@lumc.nl",
url="https://git.lumc.nl/klinische-genetica/capture-lumc/vtools",
license="MIT",
packages=find_packages(),
package_dir={"": "src"},
packages=find_packages("src"),
package_data={
'vtools': ['vtools/*.pyx']
},
python_requires=">=3.6",
zip_safe=False,
include_package_data=True,
setup_requires=["cython"],
install_requires=[
"click",
"cyvcf2",
"numpy",
"cython",
"tqdm"
],
entry_points={
......@@ -87,5 +53,5 @@ setup(
"Programming Language :: Python :: 3.7",
"Topic :: Scientific/Engineering :: Bio-Informatics"
],
ext_modules=cython_extensions
ext_modules=[Extension("vtools.optimized", ["src/vtools/optimized.pyx"])]
)
"""
vtools
~~~~~~
:copyright: (c) 2018 Sander Bollen
:copyright: (c) 2018 Leiden University Medical Center
:license: MIT
"""
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