def get_extension() -> Extension:
"""Get distutils extension object for this AMICI model package"""
cxx_flags = []
linker_flags = []
if compiledWithOpenMP():
# Only build model with OpenMP support if AMICI base packages was built
# that way
add_openmp_flags(cxx_flags=cxx_flags, ldflags=linker_flags)
add_coverage_flags_if_required(cxx_flags, linker_flags)
add_debug_flags_if_required(cxx_flags, linker_flags)
h5pkgcfg = get_hdf5_config()
blaspkgcfg = get_blas_config()
linker_flags.extend(blaspkgcfg.get('extra_link_args', []))
libraries = [*get_amici_libs(), *blaspkgcfg['libraries']]
if hdf5_enabled:
libraries.extend(['hdf5_hl_cpp', 'hdf5_hl', 'hdf5_cpp', 'hdf5'])
sources = [
os.path.join("swig", "Boehm_JProteomeRes2014.i"), *get_model_sources()
]
# compiler and linker flags for libamici
if 'AMICI_CXXFLAGS' in os.environ:
cxx_flags.extend(os.environ['AMICI_CXXFLAGS'].split(' '))
if 'AMICI_LDFLAGS' in os.environ:
linker_flags.extend(os.environ['AMICI_LDFLAGS'].split(' '))
ext_include_dirs = [
os.getcwd(),
os.path.join(amici_path, 'include'),
os.path.join(amici_path, "ThirdParty", "gsl"),
os.path.join(amici_path, "ThirdParty", "sundials", "include"),
os.path.join(amici_path, "ThirdParty", "SuiteSparse", "include"),
*h5pkgcfg['include_dirs'], *blaspkgcfg['include_dirs']
]
ext_library_dirs = [
*h5pkgcfg['library_dirs'], *blaspkgcfg['library_dirs'],
os.path.join(amici_path, 'libs')
]
# Build shared object
ext = Extension('Boehm_JProteomeRes2014._Boehm_JProteomeRes2014',
sources=sources,
include_dirs=ext_include_dirs,
libraries=libraries,
library_dirs=ext_library_dirs,
swig_opts=[
'-c++',
'-modern',
'-outdir',
'Boehm_JProteomeRes2014',
'-I%s' % os.path.join(amici_path, 'swig'),
'-I%s' % os.path.join(amici_path, 'include'),
],
extra_compile_args=cxx_flags,
extra_link_args=linker_flags)
# see `set_compiler_specific_extension_options`
ext.extra_compile_args_mingw32 = ['-std=c++14']
ext.extra_compile_args_unix = ['-std=c++14']
ext.extra_compile_args_msvc = ['/std:c++14']
return ext
def main():
# Extra compiler flags
cxx_flags = []
amici_module_linker_flags = []
define_macros = []
add_openmp_flags(cxx_flags=cxx_flags, ldflags=amici_module_linker_flags)
blaspkgcfg = get_blas_config()
amici_module_linker_flags.extend(blaspkgcfg['extra_link_args'])
amici_module_linker_flags.extend(f'-l{lib}'
for lib in blaspkgcfg['libraries'])
define_macros.extend(blaspkgcfg['define_macros'])
extension_sources = [
'amici/amici_wrap.cxx', # swig interface
]
h5pkgcfg = get_hdf5_config()
if h5pkgcfg['found']:
# Manually add linker flags. The libraries passed to Extension will
# end up in front of the clibs in the linker line and not after, where
# they are required.
print("HDF5 library found. Building AMICI with HDF5 support.")
amici_module_linker_flags.extend([
f'-l{lib}'
for lib in ['hdf5_hl_cpp', 'hdf5_hl', 'hdf5_cpp', 'hdf5']
])
define_macros.extend(h5pkgcfg['define_macros'])
else:
print("HDF5 library NOT found. Building AMICI WITHOUT HDF5 support.")
define_macros.append(('AMICI_SWIG_WITHOUT_HDF5', None))
add_coverage_flags_if_required(
cxx_flags,
amici_module_linker_flags,
)
add_debug_flags_if_required(
cxx_flags,
amici_module_linker_flags,
)
# compiler and linker flags for libamici
if 'AMICI_CXXFLAGS' in os.environ:
cxx_flags.extend(os.environ['AMICI_CXXFLAGS'].split(' '))
if 'AMICI_LDFLAGS' in os.environ:
amici_module_linker_flags.extend(
os.environ['AMICI_LDFLAGS'].split(' '))
libamici = setup_clibs.get_lib_amici(h5pkgcfg=h5pkgcfg,
blaspkgcfg=blaspkgcfg,
extra_compiler_flags=cxx_flags)
libsundials = setup_clibs.get_lib_sundials(extra_compiler_flags=cxx_flags)
libsuitesparse = setup_clibs.get_lib_suite_sparse(
extra_compiler_flags=cxx_flags + ['-DDLONG'])
# Readme as long package description to go on PyPi
# (https://pypi.org/project/amici/)
with open(os.path.join(os.path.dirname(__file__), "README.md"),
"r",
encoding="utf-8") as fh:
long_description = fh.read()
# Build shared object
amici_module = Extension(
name='amici._amici',
sources=extension_sources,
include_dirs=[
'amici/include', 'amici/ThirdParty/gsl/',
*libsundials[1]['include_dirs'],
*libsuitesparse[1]['include_dirs'], *h5pkgcfg['include_dirs'],
*blaspkgcfg['include_dirs'],
np.get_include()
],
# Cannot use here, see above
# libraries=[
# 'hdf5_hl_cpp', 'hdf5_hl', 'hdf5_cpp', 'hdf5'
# ],
define_macros=define_macros,
library_dirs=[
*h5pkgcfg['library_dirs'],
*blaspkgcfg['library_dirs'],
'amici/libs', # clib target directory
],
extra_compile_args=cxx_flags,
extra_link_args=amici_module_linker_flags)
# Monkey-patch extension (see
# `custom_commands.set_compiler_specific_extension_options`)
amici_module.extra_compile_args_mingw32 = ['-std=c++14']
amici_module.extra_compile_args_unix = ['-std=c++14']
amici_module.extra_compile_args_msvc = ['/std:c++14']
# Install
setup(
name='amici',
cmdclass={
'install': AmiciInstall,
'sdist': AmiciSDist,
'build_ext': AmiciBuildExt,
'build_clib': AmiciBuildCLib,
'install_lib': AmiciInstallLib,
'develop': AmiciDevelop,
},
version=__version__,
description='Advanced multi-language Interface to CVODES and IDAS',
long_description=long_description,
long_description_content_type="text/markdown",
url='https://github.com/AMICI-dev/AMICI',
author='Fabian Froehlich, Jan Hasenauer, Daniel Weindl and '
'Paul Stapor',
author_email='*****@*****.**',
license='BSD',
libraries=[libamici, libsundials, libsuitesparse],
ext_modules=[amici_module],
py_modules=[
# the swig interface
'amici/amici',
],
packages=find_packages(),
package_dir={'amici': 'amici'},
entry_points={
'console_scripts': [
'amici_import_petab = amici.petab_import:main',
# for backwards compatibility
'amici_import_petab.py = amici.petab_import:main'
]
},
install_requires=[
'sympy>=1.6.0', 'python-libsbml', 'h5py', 'pandas', 'pkgconfig',
'wurlitzer'
],
setup_requires=['setuptools>=40.6.3'],
python_requires='>=3.6',
extras_require={
'petab': ['petab==0.1.7'],
'pysb': ['pysb>=1.11.0']
},
package_data={
'amici': [
'amici/include/amici/*',
'src/*template*',
'swig/*',
'libs/*',
'amici.py',
'setup.py.template',
],
},
zip_safe=False,
include_package_data=True,
exclude_package_data={
'': ['README.txt'],
},
test_suite="tests",
classifiers=[
'Development Status :: 5 - Production/Stable',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Operating System :: POSIX :: Linux',
'Operating System :: MacOS :: MacOS X',
'Programming Language :: Python',
'Programming Language :: C++',
'Topic :: Scientific/Engineering :: Bio-Informatics',
],
)
def main():
# Extra compiler flags
cxx_flags = []
amici_module_linker_flags = []
define_macros = []
add_openmp_flags(cxx_flags=cxx_flags, ldflags=amici_module_linker_flags)
blaspkgcfg = get_blas_config()
amici_module_linker_flags.extend(blaspkgcfg['extra_link_args'])
amici_module_linker_flags.extend(f'-l{lib}'
for lib in blaspkgcfg['libraries'])
define_macros.extend(blaspkgcfg['define_macros'])
extension_sources = [
'amici/amici_wrap.cxx', # swig interface
]
h5pkgcfg = get_hdf5_config()
if h5pkgcfg['found']:
# Manually add linker flags. The libraries passed to Extension will
# end up in front of the clibs in the linker line and not after, where
# they are required.
print("HDF5 library found. Building AMICI with HDF5 support.")
amici_module_linker_flags.extend([
f'-l{lib}'
for lib in ['hdf5_hl_cpp', 'hdf5_hl', 'hdf5_cpp', 'hdf5']
])
define_macros.extend(h5pkgcfg['define_macros'])
else:
print("HDF5 library NOT found. Building AMICI WITHOUT HDF5 support.")
define_macros.append(('AMICI_SWIG_WITHOUT_HDF5', None))
add_coverage_flags_if_required(
cxx_flags,
amici_module_linker_flags,
)
add_debug_flags_if_required(
cxx_flags,
amici_module_linker_flags,
)
# compiler and linker flags for libamici
if 'AMICI_CXXFLAGS' in os.environ:
cxx_flags.extend(os.environ['AMICI_CXXFLAGS'].split(' '))
if 'AMICI_LDFLAGS' in os.environ:
amici_module_linker_flags.extend(
os.environ['AMICI_LDFLAGS'].split(' '))
libamici = setup_clibs.get_lib_amici(h5pkgcfg=h5pkgcfg,
blaspkgcfg=blaspkgcfg,
extra_compiler_flags=cxx_flags)
libsundials = setup_clibs.get_lib_sundials(extra_compiler_flags=cxx_flags)
libsuitesparse = setup_clibs.get_lib_suite_sparse(
extra_compiler_flags=cxx_flags + ['-DDLONG'])
# Readme as long package description to go on PyPi
# (https://pypi.org/project/amici/)
with open(os.path.join(os.path.dirname(__file__), "README.md"),
"r",
encoding="utf-8") as fh:
long_description = fh.read()
# Build shared object
amici_module = Extension(
name='amici._amici',
sources=extension_sources,
include_dirs=[
'amici/include', 'amici/ThirdParty/gsl/',
*libsundials[1]['include_dirs'],
*libsuitesparse[1]['include_dirs'], *h5pkgcfg['include_dirs'],
*blaspkgcfg['include_dirs'],
np.get_include()
],
# Cannot use here, see above
# libraries=[
# 'hdf5_hl_cpp', 'hdf5_hl', 'hdf5_cpp', 'hdf5'
# ],
define_macros=define_macros,
library_dirs=[
*h5pkgcfg['library_dirs'],
*blaspkgcfg['library_dirs'],
'amici/libs', # clib target directory
],
extra_compile_args=cxx_flags,
extra_link_args=amici_module_linker_flags)
# Monkey-patch extension (see
# `custom_commands.set_compiler_specific_extension_options`)
amici_module.extra_compile_args_mingw32 = ['-std=c++14']
amici_module.extra_compile_args_unix = ['-std=c++14']
amici_module.extra_compile_args_msvc = ['/std:c++14']
# Install
setup(
cmdclass={
'install': AmiciInstall,
'sdist': AmiciSDist,
'build_ext': AmiciBuildExt,
'build_clib': AmiciBuildCLib,
'install_lib': AmiciInstallLib,
'develop': AmiciDevelop,
},
long_description=long_description,
long_description_content_type="text/markdown",
libraries=[libamici, libsundials, libsuitesparse],
ext_modules=[amici_module],
)