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setup.py
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setup.py
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import sys
import os
import re
import traceback
from setuptools import setup, find_packages, Extension as _Extension
from distutils.command.build_ext import build_ext
from distutils.errors import (CCompilerError, DistutilsExecError,
DistutilsPlatformError)
def has_option(name):
try:
sys.argv.remove('--%s' % name)
return True
except ValueError:
pass
# allow passing all cmd line options also as environment variables
env_val = os.getenv(name.upper().replace('-', '_'), 'false').lower()
if env_val == "true":
return True
return False
include_diagnostics = has_option("include-diagnostics")
force_cythonize = has_option("force-cythonize")
def Extension(*args, **kwargs):
ext = _Extension(*args, **kwargs)
ext.include_dirs.append("src/glycopeptidepy/_c")
return ext
def make_extensions():
is_ci = bool(os.getenv("CI", ""))
macros = []
try:
from Cython.Build import cythonize
cython_directives = {
'embedsignature': True,
"profile": include_diagnostics
}
if include_diagnostics:
macros.append(("CYTHON_TRACE_NOGIL", "1"))
if is_ci and include_diagnostics:
cython_directives['linetrace'] = True
extensions = cythonize([
Extension("glycopeptidepy._c.collectiontools", sources=['src/glycopeptidepy/_c/collectiontools.pyx']),
Extension("glycopeptidepy._c.count_table", sources=[
'src/glycopeptidepy/_c/count_table.pyx']),
Extension("glycopeptidepy._c.parser", sources=[
'src/glycopeptidepy/_c/parser.pyx']),
Extension("glycopeptidepy._c.structure.base", sources=[
'src/glycopeptidepy/_c/structure/base.pyx']),
Extension("glycopeptidepy._c.structure.fragment",
sources=['src/glycopeptidepy/_c/structure/fragment.pyx']
),
Extension("glycopeptidepy._c.structure.constants", sources=[
'src/glycopeptidepy/_c/structure/constants.pyx']),
Extension("glycopeptidepy._c.structure.glycan", sources=[
'src/glycopeptidepy/_c/structure/glycan.pyx']),
Extension("glycopeptidepy._c.structure.sequence_methods",
sources=['src/glycopeptidepy/_c/structure/sequence_methods.pyx']),
Extension("glycopeptidepy._c.structure.modification.rule",
sources=['src/glycopeptidepy/_c/structure/modification/rule.pyx']),
Extension("glycopeptidepy._c.structure.modification.modification",
sources=['src/glycopeptidepy/_c/structure/modification/modification.pyx']),
Extension("glycopeptidepy._c.structure.modification.source",
sources=['src/glycopeptidepy/_c/structure/modification/source.pyx']),
Extension("glycopeptidepy._c.structure.fragmentation_strategy.base",
sources=["src/glycopeptidepy/_c/structure/fragmentation_strategy/base.pyx"]),
Extension("glycopeptidepy._c.structure.fragmentation_strategy.peptide",
sources=["src/glycopeptidepy/_c/structure/fragmentation_strategy/peptide.pyx"]),
Extension("glycopeptidepy._c.structure.fragmentation_strategy.glycan",
sources=["src/glycopeptidepy/_c/structure/fragmentation_strategy/glycan.pyx"]),
Extension("glycopeptidepy._c.algorithm",
sources=['src/glycopeptidepy/_c/algorithm.pyx']),
], compiler_directives=cython_directives, force=force_cythonize)
except ImportError:
extensions = [
Extension("glycopeptidepy._c.collectiontools", sources=['src/glycopeptidepy/_c/collectiontools.c']),
Extension("glycopeptidepy._c.count_table", sources=['src/glycopeptidepy/_c/count_table.c']),
Extension("glycopeptidepy._c.parser", sources=['src/glycopeptidepy/_c/parser.c']),
Extension("glycopeptidepy._c.structure.base", sources=['src/glycopeptidepy/_c/structure/base.c']),
Extension("glycopeptidepy._c.structure.fragment", sources=['src/glycopeptidepy/_c/structure/fragment.c']),
Extension("glycopeptidepy._c.structure.constants", sources=['src/glycopeptidepy/_c/structure/constants.c']),
Extension("glycopeptidepy._c.structure.glycan", sources=[
'src/glycopeptidepy/_c/structure/glycan.c']),
Extension("glycopeptidepy._c.structure.sequence_methods",
sources=['src/glycopeptidepy/_c/structure/sequence_methods.c']),
Extension("glycopeptidepy._c.structure.modification.rule",
sources=['src/glycopeptidepy/_c/structure/modification/rule.c']),
Extension("glycopeptidepy._c.structure.modification.modification",
sources=['src/glycopeptidepy/_c/structure/modification/modification.c']),
Extension("glycopeptidepy._c.structure.modification.source",
sources=['src/glycopeptidepy/_c/structure/modification/source.c']),
Extension("glycopeptidepy._c.structure.fragmentation_strategy.base",
sources=["src/glycopeptidepy/_c/structure/fragmentation_strategy/base.c"]),
Extension("glycopeptidepy._c.structure.fragmentation_strategy.peptide",
sources=["src/glycopeptidepy/_c/structure/fragmentation_strategy/peptide.c"]),
Extension("glycopeptidepy._c.structure.fragmentation_strategy.glycan",
sources=["src/glycopeptidepy/_c/structure/fragmentation_strategy/glycan.c"]),
Extension("glycopeptidepy._c.algorithm", sources=['src/glycopeptidepy/_c/algorithm.c']),
]
return extensions
ext_errors = (CCompilerError, DistutilsExecError, DistutilsPlatformError)
if sys.platform == 'win32':
# 2.6's distutils.msvc9compiler can raise an IOError when failing to
# find the compiler
ext_errors += (IOError,)
class BuildFailed(Exception):
def __init__(self):
self.cause = sys.exc_info()[1] # work around py 2/3 different syntax
def __str__(self):
return str(self.cause)
class ve_build_ext(build_ext):
# This class allows C extension building to fail.
def run(self):
try:
build_ext.run(self)
except DistutilsPlatformError:
traceback.print_exc()
raise BuildFailed()
def build_extension(self, ext):
try:
build_ext.build_extension(self, ext)
except ext_errors:
traceback.print_exc()
raise BuildFailed()
except ValueError:
# this can happen on Windows 64 bit, see Python issue 7511
traceback.print_exc()
if "'path'" in str(sys.exc_info()[1]): # works with both py 2/3
raise BuildFailed()
raise
cmdclass = {}
cmdclass['build_ext'] = ve_build_ext
def status_msgs(*msgs):
print('*' * 75)
for msg in msgs:
print(msg)
print('*' * 75)
def version():
return re.sub(
r'[\s\'"\n]',
'',
open("src/glycopeptidepy/version.py").readline().split("=")[1]
)
required = []
with open('requirements.txt') as f:
required = f.read().splitlines()
def run_setup(include_cext=True):
setup(
name='glycopeptidepy',
version=version(),
packages=find_packages(where='src', include='glycopeptidepy*'),
install_requires=required,
include_package_data=True,
package_dir={"": "src"},
ext_modules=make_extensions() if include_cext else None,
cmdclass=cmdclass,
zip_safe=False,
package_data={
'src/glycopeptidepy': ["*.csv", "*.xml", "*.json", "data/*.csv"],
'src/glycopeptidepy/structure': [
"structure/modification/data/*.csv",
"structure/modification/data/*.json"]
},
)
run_setup(True)
# try:
# run_setup(True)
# except Exception as exc:
# run_setup(False)
# status_msgs(
# "WARNING: The C extension could not be compiled, " +
# "speedups are not enabled.",
# "Plain-Python build succeeded."
# )