def get_ext_modules():
ext = ".pyx" if HAVE_CYTHON else ".c"
src_files = glob.glob(
os.path.join(os.path.dirname(__file__), "pairtools", "lib", "*" + ext)
)
ext_modules = []
for src_file in src_files:
name = "pairtools.lib." + os.path.splitext(os.path.basename(src_file))[0]
if not "pysam" in name and not "regions" in name:
ext_modules.append(Extension(name, [src_file]))
elif "regions" in name:
ext_modules.append(Extension(
name, [src_file],
language="c++",
))
else:
import pysam
ext_modules.append(
Extension(
name,
[src_file],
extra_link_args=pysam.get_libraries(),
include_dirs=pysam.get_include(),
define_macros=pysam.get_defines(),
)
)
if HAVE_CYTHON:
# .pyx to .c
ext_modules = cythonize(ext_modules) # , annotate=True
return ext_modules
def test_package_tests_pass_if_ld_library_path_set(self):
pysam_libraries = pysam.get_libraries()
pysam_libdirs, pysam_libs = zip(
*[os.path.split(x) for x in pysam_libraries])
pysam_libdir = pysam_libdirs[0]
self.assertTrue(
check_tests_pass(
"export LD_LIBRARY_PATH={}:$PATH && cd {} && python test_module.py"
.format(pysam_libdir, os.path.join(self.workdir, "tests"))))
def test_package_tests_pass_if_ld_library_path_set(self):
pysam_libraries = pysam.get_libraries()
pysam_libdirs, pysam_libs = zip(
*[os.path.split(x) for x in pysam_libraries])
pysam_libdir = pysam_libdirs[0]
self.assertTrue(check_pass(
"export LD_LIBRARY_PATH={}:$PATH && cd {} && python test_module.py".format(
pysam_libdir,
os.path.join(self.workdir, "tests"))))
License :: OSI Approved
Programming Language :: Python
Topic :: Software Development
Topic :: Scientific/Engineering
Operating System :: POSIX
Operating System :: Unix
Operating System :: MacOS
"""
##########################################################
# Cython Extensions
conda_includes = [os.path.dirname(sysconfig.get_paths()["include"])]
conda_libdirs = [os.path.dirname(sysconfig.get_paths()["stdlib"])]
# Connected components cython extension
pysam_libraries = pysam.get_libraries()
pysam_libdirs = list(set(os.path.dirname(x)
for x in pysam_libraries)) + conda_libdirs
# remove lib and .so and add htslib
pysam_libs = ["hts"] + list(
[os.path.basename(x)[3:-3] for x in pysam_libraries])
pysam_dirname = os.path.dirname(pysam.__file__)
if IS_OSX:
# linking against bundles does no work (and apparently is not needed)
# within OS X
extra_link_args = []
else:
extra_link_args = [
os.path.join(pysam_dirname, x) for x in pysam.get_libraries()
import os
import glob
import numpy
from setuptools import setup, Extension
import pysam
src_list = glob.glob("src/*.c")
pyx_list = glob.glob("dnaUtilsPy/*.pyx")
include_dirs = pysam.get_include() + ["src", numpy.get_include()]
extra_link_args = pysam.get_libraries()
extensions = []
for pyx in pyx_list:
assert pyx.endswith(".pyx")
submodule = os.path.basename(pyx)[:-len(".pyx")]
extensions.append(
Extension("dnaUtilsPy." + submodule,
sources=[pyx] + src_list,
include_dirs=include_dirs,
extra_link_args=extra_link_args))
setup(name="dnaUtilsPy",
packages=["dnaUtilsPy"],
ext_modules=extensions,
install_requires=['numpy', 'pysam'],
setup_requires=['numpy', 'pysam', 'cython'])
import glob
import sys
import os
from setuptools import setup, find_packages, Extension
from Cython.Distutils import build_ext
import pysam
test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(
os.sep)[-1]
test_module_name = "PysamTestModule_{}".format(test_module_suffix)
pysam_libraries = pysam.get_libraries()
pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in pysam_libraries])
pysam_libdir = pysam_libdirs[0]
# remove lib and .so
pysam_libs = [x[3:-3] for x in pysam_libs]
TestModule = Extension(
"{}.BuildRead".format(test_module_name),
["{}/BuildRead.pyx".format(test_module_name)],
include_dirs=pysam.get_include(),
library_dirs=[pysam_libdir],
libraries=pysam_libs,
language="C",
)
setup(
name=test_module_name,
version='0.1',
language="c++",
extra_compile_args=compile_options,
extra_link_args=link_options),
# Extension("epic2.src.differential",
# ["epic2/src/differential.pyx"], language="c++",
# extra_compile_args=compile_options),
Extension("epic2.src.find_islands", ["epic2/src/find_islands.pyx"],
language="c++",
extra_compile_args=compile_options,
extra_link_args=link_options),
Extension("epic2.src.read_bam", ["epic2/src/read_bam.pyx"],
language="c++",
include_dirs=conda_include + pysam.get_include(),
library_dirs=conda_lib,
extra_compile_args=compile_options,
extra_link_args=link_options + pysam.get_libraries(),
define_macros=pysam.get_defines(),
libraries=["z"]),
Extension("epic2.src.genome_info", ["epic2/src/genome_info.pyx"],
language="c++",
extra_compile_args=compile_options,
extra_link_args=link_options)
]
setup(
name="epic2",
packages=find_packages(),
ext_modules=cythonize(extensions, annotate=True, language_level='2'),
scripts=["bin/epic2", "bin/epic2-df", "bin/epic2-bw"],
package_data={
'epic2': [
language="c",
)
# automatically build pyximport script extensions
pyx_files = glob.glob("scripts/*.pyx")
script_extensions = []
pysam_dirname = os.path.dirname(pysam.__file__)
include_dirs = [numpy.get_include()] + pysam.get_include()
if IS_OSX:
# linking against bundles does no work (and apparently is not needed)
# within OS X
extra_link_args = []
else:
extra_link_args = [os.path.join(pysam_dirname, x) for x in
pysam.get_libraries()]
for pyx_file in pyx_files:
script_name = os.path.basename(pyx_file)
script_prefix = script_name[:-4]
script_extensions.append(
Extension("CGAT.%s" % (script_prefix),
sources=[pyx_file],
extra_link_args=extra_link_args,
include_dirs=include_dirs,
define_macros=pysam.get_defines())
)
ext_modules = [Components, NCL, Timeseries] + script_extensions
import glob
import sys
import os
from setuptools import setup, find_packages, Extension
from cy_build import CyExtension as Extension, cy_build_ext as build_ext
import pysam
test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1]
test_module_name = "PysamTestModule_{}".format(test_module_suffix)
TestModule = Extension(
"{}.BuildRead".format(test_module_name),
["{}/BuildRead.pyx".format(test_module_name)],
include_dirs=pysam.get_include(),
extra_link_args=pysam.get_libraries(),
define_macros=pysam.get_defines(),
)
setup(
name=test_module_name,
version='0.1',
packages=find_packages(),
package_dir={test_module_name: test_module_name},
ext_modules=[TestModule],
cmdclass={'build_ext': build_ext},
)
import glob
import sys
import os
from setuptools import setup, find_packages, Extension
from Cython.Distutils import build_ext
import pysam
test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1]
test_module_name = "PysamTestModule_{}".format(test_module_suffix)
pysam_libraries = pysam.get_libraries()
pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in pysam_libraries])
pysam_libdir = pysam_libdirs[0]
# remove lib and .so
pysam_libs = [x[3:-3] for x in pysam_libs]
TestModule = Extension(
"{}.BuildRead".format(test_module_name),
["{}/BuildRead.pyx".format(test_module_name)],
include_dirs=pysam.get_include(),
library_dirs=[pysam_libdir],
libraries=pysam_libs,
language="C",
)
setup(
name=test_module_name,
version='0.1',
packages=find_packages(),