def create_module(module_name, expression_name_tuples, directory):
"""Generates a cython module that can be imported."""
routines = []
for name, expression, args in expression_name_tuples:
try:
routine = make_routine(name, [expression], args)
except CodeGenArgumentListError as e:
new_args = []
for missing in e.missing_args:
if not isinstance(missing, OutputArgument):
raise
new_args.append(missing.name)
routine = make_routine(name, expression, list(args) + new_args)
routines.append(routine)
if not os.path.exists(directory):
os.makedirs(directory)
cg = CCodeGen()
[(cf, cs), (hf, hs)] = cg.write(routines, module_name + '_code')
with open(directory + '/' + cf, "w") as text_file:
text_file.write(cs)
with open(directory + '/' + hf, "w") as text_file:
text_file.write(hs)
ccw = CythonCodeWrapper(cg)
with open(directory + '/' + module_name + '.pyx', "w") as text_file:
ccw.dump_pyx(routines, text_file, module_name + '_code')
create_setup(module_name + '.pyx', module_name + '_code.c', directory,
module_name)
open(directory + '/__init__.py', 'w').close()
oldwork = os.getcwd()
os.chdir(directory)
workdir = os.getcwd()
command = [sys.executable, "setup.py", "build_ext", "--inplace"]
try:
sys.path.append(workdir)
retoutput = check_output(command, stderr=STDOUT)
except CalledProcessError as e:
raise CodeWrapError(
"Error while executing command: %s. Command output is:\n%s" %
(" ".join(command), e.output.decode()))
finally:
sys.path.remove(workdir)
os.chdir(oldwork)
def __init__(self, model, with_jacobian=False, cleanup=True, _logger=None):
super(CythonRhsBuilder, self).__init__(model, with_jacobian, cleanup,
_logger)
routine_names = ["kinetics"]
if with_jacobian:
routine_names += ["kinetics_jacobian_y", "kinetics_jacobian_o"]
# We want more control over various details of code generation and
# wrapper module creation than sympy's autowrap provides, so we'll use
# the lower-level building blocks directly.
routines = {name: self._build_routine(name) for name in routine_names}
code_gen = C99CodeGen()
extra_compile_args = [
# The RHS evaluation is such a tiny part of overall integration
# time, even for huge models, that compiler optimization actually
# takes more time than it will ever yield back. Since Cython sets
# -O2 by default we need to override it.
"-O0",
]
# Opt in to the newer numpy C API which is only supported in Cython 3+.
import Cython
if not Cython.__version__.startswith("0."):
extra_compile_args.append(
"-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION")
code_wrapper = CythonCodeWrapper(
code_gen,
filepath=self.work_path,
extra_compile_args=extra_compile_args,
)
# Build a module-name-safe string that identifies the model as uniquely
# as possible to assist in debugging.
escaped_name = re.sub(
r"[^A-Za-z0-9]",
"_",
self.model_name.encode("unicode_escape").decode(),
)
base_name = "pysb_" + escaped_name + "_kinetics"
code_wrapper._filename = base_name
code_wrapper._module_basename = base_name + "_wrapper"
self._logger.debug("Running code generation and Cython compilation")
functions = {
name: code_wrapper.wrap_code(routine)
for name, routine in routines.items()
}
# Grab specs for the Cython-compiled modules for reloading later.
self.module_specs = {
name: inspect.getmodule(function).__spec__
for name, function in functions.items()
}
def test_cython_wrapper_scalar_function():
x, y, z = symbols('xyz')
expr = (x + y) * z
routine = Routine("test", expr)
code_gen = CythonCodeWrapper(CCodeGen())
source = get_string(code_gen.dump_pyx, [routine])
expected = ('cdef extern from "file.h":\n'
' double test(double x, double y, double z)\n'
'def test_c(double x, double y, double z):\n'
' return test(x, y, z)\n')
assert source == expected
def test_cython_wrapper_inoutarg():
from sympy import Equality
x, y, z = symbols('xyz')
code_gen = CythonCodeWrapper(CCodeGen())
routine = Routine("test", Equality(z, x + y + z))
source = get_string(code_gen.dump_pyx, [routine])
expected = ('cdef extern from "file.h":\n'
' void test(double x, double y, double &z)\n'
'def test_c(double x, double y, double z):\n'
' test(x, y, z)\n'
' return z\n')
assert source == expected
def test_cython_wrapper_scalar_function():
x, y, z = symbols('x,y,z')
expr = (x + y) * z
routine = make_routine("test", expr)
code_gen = CythonCodeWrapper(CCodeGen())
source = get_string(code_gen.dump_pyx, [routine])
expected = ("cdef extern from 'file.h':\n"
" double test(double x, double y, double z)\n"
"\n"
"def test_c(double x, double y, double z):\n"
"\n"
" return test(x, y, z)")
assert source == expected
def test_cython_wrapper_inoutarg():
from sympy import Equality
x, y, z = symbols('x,y,z')
code_gen = CythonCodeWrapper(C99CodeGen())
routine = make_routine("test", Equality(z, x + y + z))
source = get_string(code_gen.dump_pyx, [routine])
expected = ("cdef extern from 'file.h':\n"
" void test(double x, double y, double *z)\n"
"\n"
"def test_c(double x, double y, double z):\n"
"\n"
" test(x, y, &z)\n"
" return z")
assert source == expected
def test_cython_wrapper_scalar_function():
x, y, z = symbols('x,y,z')
expr = (x + y) * z
routine = make_routine("test", expr)
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=SymPyDeprecationWarning)
code_gen = CythonCodeWrapper(CCodeGen())
source = get_string(code_gen.dump_pyx, [routine])
expected = ("cdef extern from 'file.h':\n"
" double test(double x, double y, double z)\n"
"\n"
"def test_c(double x, double y, double z):\n"
"\n"
" return test(x, y, z)")
assert source == expected
def test_cython_wrapper_unique_dummyvars():
from sympy import Dummy, Equality
x, y, z = Dummy('x'), Dummy('y'), Dummy('z')
x_id, y_id, z_id = [str(d.dummy_index) for d in [x, y, z]]
expr = Equality(z, x + y)
routine = make_routine("test", expr)
code_gen = CythonCodeWrapper(CCodeGen())
source = get_string(code_gen.dump_pyx, [routine])
expected_template = (
"cdef extern from 'file.h':\n"
" void test(double x_{x_id}, double y_{y_id}, double *z_{z_id})\n"
"\n"
"def test_c(double x_{x_id}, double y_{y_id}):\n"
"\n"
" cdef double z_{z_id} = 0\n"
" test(x_{x_id}, y_{y_id}, &z_{z_id})\n"
" return z_{z_id}")
expected = expected_template.format(x_id=x_id, y_id=y_id, z_id=z_id)
assert source == expected
def test_cython_wrapper_compile_flags():
from sympy import Equality
x, y, z = symbols('x,y,z')
routine = make_routine("test", Equality(z, x + y))
code_gen = CythonCodeWrapper(CCodeGen())
expected = """\
try:
from setuptools import setup
from setuptools import Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
cy_opts = {}
ext_mods = [Extension(
'wrapper_module_0', ['wrapper_module_0.pyx', 'wrapped_code_0.c'],
include_dirs=[],
library_dirs=[],
libraries=[],
extra_compile_args=['-std=c99'],
extra_link_args=[]
)]
setup(ext_modules=cythonize(ext_mods, **cy_opts))
"""
temp_dir = tempfile.mkdtemp()
setup_file_path = os.path.join(temp_dir, 'setup.py')
code_gen._prepare_files(routine, build_dir=temp_dir)
with open(setup_file_path) as f:
setup_text = f.read()
assert setup_text == expected
code_gen = CythonCodeWrapper(
CCodeGen(),
include_dirs=['/usr/local/include', '/opt/booger/include'],
library_dirs=['/user/local/lib'],
libraries=['thelib', 'nilib'],
extra_compile_args=['-slow-math'],
extra_link_args=['-lswamp', '-ltrident'],
cythonize_options={'compiler_directives': {
'boundscheck': False
}})
expected = """\
try:
from setuptools import setup
from setuptools import Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
cy_opts = {'compiler_directives': {'boundscheck': False}}
ext_mods = [Extension(
'wrapper_module_0', ['wrapper_module_0.pyx', 'wrapped_code_0.c'],
include_dirs=['/usr/local/include', '/opt/booger/include'],
library_dirs=['/user/local/lib'],
libraries=['thelib', 'nilib'],
extra_compile_args=['-slow-math', '-std=c99'],
extra_link_args=['-lswamp', '-ltrident']
)]
setup(ext_modules=cythonize(ext_mods, **cy_opts))
"""
code_gen._prepare_files(routine, build_dir=temp_dir)
with open(setup_file_path) as f:
setup_text = f.read()
assert setup_text == expected
expected = """\
try:
from setuptools import setup
from setuptools import Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
cy_opts = {'compiler_directives': {'boundscheck': False}}
import numpy as np
ext_mods = [Extension(
'wrapper_module_0', ['wrapper_module_0.pyx', 'wrapped_code_0.c'],
include_dirs=['/usr/local/include', '/opt/booger/include', np.get_include()],
library_dirs=['/user/local/lib'],
libraries=['thelib', 'nilib'],
extra_compile_args=['-slow-math', '-std=c99'],
extra_link_args=['-lswamp', '-ltrident']
)]
setup(ext_modules=cythonize(ext_mods, **cy_opts))
"""
code_gen._need_numpy = True
code_gen._prepare_files(routine, build_dir=temp_dir)
with open(setup_file_path) as f:
setup_text = f.read()
assert setup_text == expected
def test_cython_wrapper_compile_flags():
from sympy import Equality
x, y, z = symbols('x,y,z')
routine = make_routine("test", Equality(z, x + y))
code_gen = CythonCodeWrapper(CCodeGen())
expected = """\
try:
from setuptools import setup
from setuptools import Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
cy_opts = {}
ext_mods = [Extension(
'wrapper_module_%(num)s', ['wrapper_module_%(num)s.pyx', 'wrapped_code_%(num)s.c'],
include_dirs=[],
library_dirs=[],
libraries=[],
extra_compile_args=['-std=c99'],
extra_link_args=[]
)]
setup(ext_modules=cythonize(ext_mods, **cy_opts))
""" % {'num': CodeWrapper._module_counter}
temp_dir = tempfile.mkdtemp()
setup_file_path = os.path.join(temp_dir, 'setup.py')
code_gen._prepare_files(routine, build_dir=temp_dir)
with open(setup_file_path) as f:
setup_text = f.read()
assert setup_text == expected
code_gen = CythonCodeWrapper(CCodeGen(),
include_dirs=['/usr/local/include', '/opt/booger/include'],
library_dirs=['/user/local/lib'],
libraries=['thelib', 'nilib'],
extra_compile_args=['-slow-math'],
extra_link_args=['-lswamp', '-ltrident'],
cythonize_options={'compiler_directives': {'boundscheck': False}}
)
expected = """\
try:
from setuptools import setup
from setuptools import Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
cy_opts = {'compiler_directives': {'boundscheck': False}}
ext_mods = [Extension(
'wrapper_module_%(num)s', ['wrapper_module_%(num)s.pyx', 'wrapped_code_%(num)s.c'],
include_dirs=['/usr/local/include', '/opt/booger/include'],
library_dirs=['/user/local/lib'],
libraries=['thelib', 'nilib'],
extra_compile_args=['-slow-math', '-std=c99'],
extra_link_args=['-lswamp', '-ltrident']
)]
setup(ext_modules=cythonize(ext_mods, **cy_opts))
""" % {'num': CodeWrapper._module_counter}
code_gen._prepare_files(routine, build_dir=temp_dir)
with open(setup_file_path) as f:
setup_text = f.read()
assert setup_text == expected
expected = """\
try:
from setuptools import setup
from setuptools import Extension
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
cy_opts = {'compiler_directives': {'boundscheck': False}}
import numpy as np
ext_mods = [Extension(
'wrapper_module_%(num)s', ['wrapper_module_%(num)s.pyx', 'wrapped_code_%(num)s.c'],
include_dirs=['/usr/local/include', '/opt/booger/include', np.get_include()],
library_dirs=['/user/local/lib'],
libraries=['thelib', 'nilib'],
extra_compile_args=['-slow-math', '-std=c99'],
extra_link_args=['-lswamp', '-ltrident']
)]
setup(ext_modules=cythonize(ext_mods, **cy_opts))
""" % {'num': CodeWrapper._module_counter}
code_gen._need_numpy = True
code_gen._prepare_files(routine, build_dir=temp_dir)
with open(setup_file_path) as f:
setup_text = f.read()
assert setup_text == expected
# Use codegen and autowrap to write c code and wrappers
from sympy.utilities.autowrap import CythonCodeWrapper
from sympy.utilities.codegen import CCodeGen
from sympy.utilities.codegen import Routine
routines = []
for ds, args in [(derivs, symbols('st dms sf1 f sf2')), (derivs_sfc, symbols('st dms sfc f sf2')),
(derivs_sfs, symbols('st dms sfc f sfs')),
(derivs_sfc_calib, symbols('st stm dms sfco sfcs f sf2o sf2s')),
(derivs_sfs_calib, symbols('st stm dms sfco sfcs f sfso sfss'))]:
for name, expr in ds.iteritems():
routines.append(Routine(name, expr, argument_sequence = args))
cgen = CCodeGen(project = 'P2VV')
with open(os.path.join(install_dir, "dilution_impl.c"), "w") as c_file:
cgen.dump_c(routines, c_file, 'dilution')
with open(os.path.join(install_dir, "dilution.h"), "w") as h_file:
cgen.dump_h(routines, h_file, 'dilution')
wrapper = CythonCodeWrapper(cgen)
with open(os.path.join(install_dir, "dilution.pyx"), "w") as wrapper_file:
wrapper.dump_pyx(routines, wrapper_file, 'dilution')
# Call cython to create the python wrapper c file.
import subprocess
pwd = os.path.realpath('.')
wd = os.chdir(install_dir)
subprocess.call(['cython', 'dilution.pyx'])
os.chdir(pwd)
