return modelSources
def getAmiciLibs():
"""Get list of libraries for the amici base library"""
return [
'amici', 'sundials', 'suitesparse'
#'sundials_nvecserial', 'sundials_cvodes', 'sundials_idas',
#'klu', 'colamd', 'btf', 'amd', 'suitesparseconfig'
]
cxx_flags = ['-std=c++11']
linker_flags = []
addCoverageFlagsIfRequired(cxx_flags, linker_flags)
addDebugFlagsIfRequired(cxx_flags, linker_flags)
h5pkgcfg = getHdf5Config()
blaspkgcfg = getBlasConfig()
linker_flags.extend(blaspkgcfg.get('extra_link_args', []))
libraries = [*getAmiciLibs(), *blaspkgcfg['libraries']]
if hdf5_enabled:
libraries.extend(['hdf5_hl_cpp', 'hdf5_hl', 'hdf5_cpp', 'hdf5'])
sources = ['swig/SPARCED_Brep.i', *getModelSources()]
# Remove the "-Wstrict-prototypes" compiler option, which isn't valid for
# C++ to fix warnings.
def main():
# Extra compiler flags
cxx_flags = []
amici_module_linker_flags = []
define_macros = []
blaspkgcfg = getBlasConfig()
amici_module_linker_flags.extend('-l%s' % l
for l in blaspkgcfg['libraries'])
h5pkgcfg = getHdf5Config()
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([
'-l%s' % l for l in ['hdf5_hl_cpp', 'hdf5_hl', 'hdf5_cpp', 'hdf5']
])
extension_sources = [
'amici/amici_wrap.cxx', # swig interface
]
else:
print("HDF5 library NOT found. Building AMICI WITHOUT HDF5 support.")
extension_sources = [
'amici/amici_wrap_without_hdf5.cxx', # swig interface
]
addCoverageFlagsIfRequired(
cxx_flags,
amici_module_linker_flags,
)
addDebugFlagsIfRequired(
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.getLibAmici(h5pkgcfg=h5pkgcfg,
blaspkgcfg=blaspkgcfg,
extra_compiler_flags=cxx_flags)
libsundials = setup_clibs.getLibSundials(extra_compiler_flags=cxx_flags)
libsuitesparse = setup_clibs.getLibSuiteSparse(
extra_compiler_flags=cxx_flags + ['-DDLONG'])
# Build shared object
amici_module = Extension(
name='amici._amici',
sources=extension_sources,
include_dirs=[
'amici/include', *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=['-std=c++11', *cxx_flags],
extra_link_args=amici_module_linker_flags)
# Readme as long package description to go on PyPi
# (https://pypi.org/project/amici/)
with open("README.md", "r") as fh:
long_description = fh.read()
# Remove the "-Wstrict-prototypes" compiler option, which isn't valid for
# C++ to fix warnings.
cfg_vars = sysconfig.get_config_vars()
for key, value in cfg_vars.items():
if type(value) == str:
cfg_vars[key] = value.replace("-Wstrict-prototypes", "")
# Install
setup(
name='amici',
cmdclass={
'install': my_install,
'sdist': my_sdist,
'build_ext': my_build_ext,
'build_clib': my_build_clib,
'install_lib': my_install_lib,
'develop': my_develop,
},
version=__version__,
description='Advanced multi-language Interface to CVODES and IDAS (%s)',
long_description=long_description,
long_description_content_type="text/markdown",
url='https://github.com/ICB-DCM/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=[
'amici/amici', # the swig interface
'amici/amici_without_hdf5', # the swig interface
],
packages=find_packages(),
package_dir={'amici': 'amici'},
scripts=['bin/amici_import_petab.py'],
install_requires=[
'sympy', 'python-libsbml', 'h5py', 'pandas', 'setuptools>=40.6.3'
],
python_requires='>=3.6',
extras_require={'wurlitzer': ['wurlitzer']},
package_data={
'amici': [
'amici/include/amici/*',
'src/*template*',
'swig/*',
'libs/*',
'amici.py',
'amici_without_hdf5.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',
],
)
# 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(
['-l%s' % l for l in ['hdf5_hl_cpp', 'hdf5_hl', 'hdf5_cpp', 'hdf5']])
extension_sources = [
'amici/amici_wrap.cxx', # swig interface
]
else:
print("HDF5 library NOT found. Building AMICI WITHOUT HDF5 support.")
extension_sources = [
'amici/amici_wrap_without_hdf5.cxx', # swig interface
]
addCoverageFlagsIfRequired(
cxx_flags,
amici_module_linker_flags,
)
addDebugFlagsIfRequired(
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.getLibAmici(h5pkgcfg=h5pkgcfg,
blaspkgcfg=blaspkgcfg,