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import platform
import sys
from glob import glob
from setuptools import (
Extension,
setup,
)
from setuptools.command.sdist import sdist
def main():
metadata = {"scripts": glob("scripts/*.py"), "cmdclass": command_classes}
if len(sys.argv) >= 2 and (
"--help" in sys.argv[1:] or sys.argv[1] in ("--help-commands", "egg_info", "--version", "clean")
):
# For these actions, NumPy is not required.
#
# They are required to succeed without Numpy for example when
# pip is used to install when Numpy is not yet present in
# the system.
pass
else:
try:
import numpy
# Suppress numpy tests
numpy.test = None
except Exception as e:
raise Exception(f"numpy must be installed to build: {e}")
metadata["ext_modules"] = get_extension_modules(numpy_include=numpy.get_include())
setup(**metadata)
# ---- Commands -------------------------------------------------------------
# Use build_ext from Cython if found
command_classes = {}
try:
import Cython.Distutils
command_classes["build_ext"] = Cython.Distutils.build_ext
class build_ext_sdist(sdist):
def run(self):
# Make sure the compiled Cython files in the distribution are up-to-date
self.run_command("build_ext")
super().run()
command_classes["sdist"] = build_ext_sdist
except ImportError:
pass
# ---- Extension Modules ----------------------------------------------------
# # suppress C++ #warning, e.g., to silence NumPy deprecation warnings:
# from functools import partial
# _Extension = Extension
# Extension = partial(_Extension, extra_compile_args=["-Wno-cpp"])
def get_extension_modules(numpy_include=None):
extensions = []
# Bitsets
extensions.append(
Extension(
"bx.bitset",
["lib/bx/bitset.pyx", "src/binBits.c", "src/kent/bits.c", "src/kent/common.c"],
include_dirs=["src/kent", "src"],
)
)
# Interval intersection
extensions.append(Extension("bx.intervals.intersection", ["lib/bx/intervals/intersection.pyx"]))
# Alignment object speedups
extensions.append(Extension("bx.align._core", ["lib/bx/align/_core.pyx"]))
# NIB reading speedups
extensions.append(Extension("bx.seq._nib", ["lib/bx/seq/_nib.pyx"]))
# 2bit reading speedups
extensions.append(Extension("bx.seq._twobit", ["lib/bx/seq/_twobit.pyx"]))
# Translation if character / integer strings
extensions.append(Extension("bx._seqmapping", ["lib/bx/_seqmapping.pyx"]))
# BGZF
extensions.append(
Extension(
"bx.misc.bgzf",
["lib/bx/misc/bgzf.pyx", "src/samtools/bgzf.c"],
include_dirs=["src/samtools"],
libraries=["z"],
)
)
# The following extensions won't (currently) compile on windows
if platform.system() not in ("Microsoft", "Windows"):
# Interval clustering
extensions.append(
Extension("bx.intervals.cluster", ["lib/bx/intervals/cluster.pyx", "src/cluster.c"], include_dirs=["src"])
)
# Position weight matrices
extensions.append(
Extension(
"bx.pwm._position_weight_matrix",
["lib/bx/pwm/_position_weight_matrix.pyx", "src/pwm_utils.c"],
include_dirs=["src"],
)
)
extensions.append(Extension("bx.motif._pwm", ["lib/bx/motif/_pwm.pyx"], include_dirs=[numpy_include]))
# Sparse arrays with summaries organized as trees on disk
extensions.append(
Extension("bx.arrays.array_tree", ["lib/bx/arrays/array_tree.pyx"], include_dirs=[numpy_include])
)
# Reading UCSC "big binary index" files
extensions.append(Extension("bx.bbi.bpt_file", ["lib/bx/bbi/bpt_file.pyx"]))
extensions.append(Extension("bx.bbi.cirtree_file", ["lib/bx/bbi/cirtree_file.pyx"]))
extensions.append(Extension("bx.bbi.bbi_file", ["lib/bx/bbi/bbi_file.pyx"], include_dirs=[numpy_include]))
extensions.append(Extension("bx.bbi.bigwig_file", ["lib/bx/bbi/bigwig_file.pyx"], include_dirs=[numpy_include]))
extensions.append(Extension("bx.bbi.bigbed_file", ["lib/bx/bbi/bigbed_file.pyx"], include_dirs=[numpy_include]))
# EPO and Chain arithmetics and IO speedups
extensions.append(Extension("bx.align._epo", ["lib/bx/align/_epo.pyx"], include_dirs=[numpy_include]))
# Reading UCSC bed and wiggle formats
extensions.append(Extension("bx.arrays.bed", ["lib/bx/arrays/bed.pyx"]))
extensions.append(Extension("bx.arrays.wiggle", ["lib/bx/arrays/wiggle.pyx"]))
# CpG masking
extensions.append(
Extension("bx.align.sitemask._cpg", ["lib/bx/align/sitemask/_cpg.pyx", "lib/bx/align/sitemask/find_cpg.c"])
)
# Counting n-grams in integer strings
extensions.append(Extension("bx.intseq.ngramcount", ["lib/bx/intseq/ngramcount.pyx"], include_dirs=["src"]))
# Seekable access to bzip2 files
extensions.append(
Extension(
"bx.misc._seekbzip2",
["lib/bx/misc/_seekbzip2.pyx", "src/bunzip/micro-bunzip.c"],
include_dirs=["src/bunzip"],
)
)
return extensions
if __name__ == "__main__":
main()
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