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# -*- coding: utf-8 -*-
Cython related magics
Magic command interface for interactive work with Cython
.. note::
The ``Cython`` package needs to be installed separately. It
can be obtained using ``easy_install`` or ``pip``.
To enable the magics below, execute ``%load_ext cython``.
* Brian Granger
Code moved from IPython and adapted by:
* Martín Gaitán
Parts of this code were taken from Cython.inline.
# Copyright (C) 2010-2011, IPython Development Team.
# Distributed under the terms of the Modified BSD License.
# The full license is in the file ipython-COPYING.rst, distributed with this software.
from __future__ import absolute_import, print_function
import imp
import io
import os
import re
import sys
import time
import copy
import distutils.log
import textwrap
except NameError: # Python 3
from imp import reload
import hashlib
except ImportError:
import md5 as hashlib
from distutils.core import Distribution, Extension
from distutils.command.build_ext import build_ext
from IPython.core import display
from IPython.core import magic_arguments
from IPython.core.magic import Magics, magics_class, cell_magic
from IPython.utils import py3compat
from IPython.paths import get_ipython_cache_dir
except ImportError:
# older IPython version
from IPython.utils.path import get_ipython_cache_dir
from IPython.utils.text import dedent
from ..Shadow import __version__ as cython_version
from ..Compiler.Errors import CompileError
from .Inline import cython_inline
from .Dependencies import cythonize
'gcc': {
'gen': ['-fprofile-generate', '-fprofile-dir={TEMPDIR}'],
'use': ['-fprofile-use', '-fprofile-correction', '-fprofile-dir={TEMPDIR}'],
# blind copy from 'configure' script in CPython 3.7
'icc': {
'gen': ['-prof-gen'],
'use': ['-prof-use'],
PGO_CONFIG['mingw32'] = PGO_CONFIG['gcc']
class CythonMagics(Magics):
def __init__(self, shell):
super(CythonMagics, self).__init__(shell)
self._reloads = {}
self._code_cache = {}
self._pyximport_installed = False
def _import_all(self, module):
mdict = module.__dict__
if '__all__' in mdict:
keys = mdict['__all__']
keys = [k for k in mdict if not k.startswith('_')]
for k in keys:
try:{k: mdict[k]})
except KeyError:
msg = "'module' object has no attribute '%s'" % k
raise AttributeError(msg)
def cython_inline(self, line, cell):
"""Compile and run a Cython code cell using Cython.inline.
This magic simply passes the body of the cell to Cython.inline
and returns the result. If the variables `a` and `b` are defined
in the user's namespace, here is a simple example that returns
their sum::
return a+b
For most purposes, we recommend the usage of the `%%cython` magic.
locs =
globs =
return cython_inline(cell, locals=locs, globals=globs)
def cython_pyximport(self, line, cell):
"""Compile and import a Cython code cell using pyximport.
The contents of the cell are written to a `.pyx` file in the current
working directory, which is then imported using `pyximport`. This
magic requires a module name to be passed::
%%cython_pyximport modulename
def f(x):
return 2.0*x
The compiled module is then imported and all of its symbols are
injected into the user's namespace. For most purposes, we recommend
the usage of the `%%cython` magic.
module_name = line.strip()
if not module_name:
raise ValueError('module name must be given')
fname = module_name + '.pyx'
with, 'w', encoding='utf-8') as f:
if 'pyximport' not in sys.modules or not self._pyximport_installed:
import pyximport
self._pyximport_installed = True
if module_name in self._reloads:
module = self._reloads[module_name]
# Note: reloading extension modules is not actually supported
# (requires PEP-489 reinitialisation support).
# Don't know why this should ever have worked as it reads here.
# All we really need to do is to update the globals below.
module = sys.modules[module_name]
self._reloads[module_name] = module
'-a', '--annotate', action='store_true', default=False,
help="Produce a colorized HTML version of the source."
'-+', '--cplus', action='store_true', default=False,
help="Output a C++ rather than C file."
'-3', dest='language_level', action='store_const', const=3, default=None,
help="Select Python 3 syntax."
'-2', dest='language_level', action='store_const', const=2, default=None,
help="Select Python 2 syntax."
'-f', '--force', action='store_true', default=False,
help="Force the compilation of a new module, even if the source has been "
"previously compiled."
'-c', '--compile-args', action='append', default=[],
help="Extra flags to pass to compiler via the `extra_compile_args` "
"Extension flag (can be specified multiple times)."
'--link-args', action='append', default=[],
help="Extra flags to pass to linker via the `extra_link_args` "
"Extension flag (can be specified multiple times)."
'-l', '--lib', action='append', default=[],
help="Add a library to link the extension against (can be specified "
"multiple times)."
'-n', '--name',
help="Specify a name for the Cython module."
'-L', dest='library_dirs', metavar='dir', action='append', default=[],
help="Add a path to the list of library directories (can be specified "
"multiple times)."
'-I', '--include', action='append', default=[],
help="Add a path to the list of include directories (can be specified "
"multiple times)."
'-S', '--src', action='append', default=[],
help="Add a path to the list of src files (can be specified "
"multiple times)."
'--pgo', dest='pgo', action='store_true', default=False,
help=("Enable profile guided optimisation in the C compiler. "
"Compiles the cell twice and executes it in between to generate a runtime profile.")
'--verbose', dest='quiet', action='store_false', default=True,
help=("Print debug information like generated .c/.cpp file location "
"and exact gcc/g++ command invoked.")
def cython(self, line, cell):
"""Compile and import everything from a Cython code cell.
The contents of the cell are written to a `.pyx` file in the
directory `IPYTHONDIR/cython` using a filename with the hash of the
code. This file is then cythonized and compiled. The resulting module
is imported and all of its symbols are injected into the user's
namespace. The usage is similar to that of `%%cython_pyximport` but
you don't have to pass a module name::
def f(x):
return 2.0*x
To compile OpenMP codes, pass the required `--compile-args`
and `--link-args`. For example with gcc::
%%cython --compile-args=-fopenmp --link-args=-fopenmp
To enable profile guided optimisation, pass the ``--pgo`` option.
Note that the cell itself needs to take care of establishing a suitable
profile when executed. This can be done by implementing the functions to
optimise, and then calling them directly in the same cell on some realistic
training data like this::
%%cython --pgo
def critical_function(data):
for item in data:
# execute function several times to build profile
from somewhere import some_typical_data
for _ in range(100):
In Python 3.5 and later, you can distinguish between the profile and
non-profile runs as follows::
if "_pgo_" in __name__:
... # execute critical code here
args = magic_arguments.parse_argstring(self.cython, line)
code = cell if cell.endswith('\n') else cell + '\n'
lib_dir = os.path.join(get_ipython_cache_dir(), 'cython')
key = (code, line, sys.version_info, sys.executable, cython_version)
if not os.path.exists(lib_dir):
if args.pgo:
key += ('pgo',)
if args.force:
# Force a new module name by adding the current time to the
# key which is hashed to determine the module name.
key += (time.time(),)
module_name = py3compat.unicode_to_str(
module_name = "_cython_magic_" + hashlib.md5(str(key).encode('utf-8')).hexdigest()
html_file = os.path.join(lib_dir, module_name + '.html')
module_path = os.path.join(lib_dir, module_name + self.so_ext)
have_module = os.path.isfile(module_path)
need_cythonize = args.pgo or not have_module
if args.annotate:
if not os.path.isfile(html_file):
need_cythonize = True
extension = None
if need_cythonize:
extensions = self._cythonize(module_name, code, lib_dir, args, quiet=args.quiet)
assert len(extensions) == 1
extension = extensions[0]
self._code_cache[key] = module_name
if args.pgo:
self._profile_pgo_wrapper(extension, lib_dir)
self._build_extension(extension, lib_dir, pgo_step_name='use' if args.pgo else None,
module = imp.load_dynamic(module_name, module_path)
if args.annotate:
with, encoding='utf-8') as f:
annotated_html =
except IOError as e:
# File could not be opened. Most likely the user has a version
# of Cython before 0.15.1 (when `cythonize` learned the
# `force` keyword argument) and has already compiled this
# exact source without annotation.
print('Cython completed successfully but the annotated '
'source could not be read.', file=sys.stderr)
print(e, file=sys.stderr)
return display.HTML(self.clean_annotated_html(annotated_html))
def _profile_pgo_wrapper(self, extension, lib_dir):
Generate a .c file for a separate extension module that calls the
module init function of the original module. This makes sure that the
PGO profiler sees the correct .o file of the final module, but it still
allows us to import the module under a different name for profiling,
before recompiling it into the PGO optimised module. Overwriting and
reimporting the same shared library is not portable.
extension = copy.copy(extension) # shallow copy, do not modify sources in place!
module_name =
pgo_module_name = '_pgo_' + module_name
pgo_wrapper_c_file = os.path.join(lib_dir, pgo_module_name + '.c')
with, 'w', encoding='utf-8') as f:
#include "Python.h"
extern PyMODINIT_FUNC init%(module_name)s(void);
PyMODINIT_FUNC init%(pgo_module_name)s(void); /*proto*/
PyMODINIT_FUNC init%(pgo_module_name)s(void) {
PyObject *sys_modules;
init%(module_name)s(); if (PyErr_Occurred()) return;
sys_modules = PyImport_GetModuleDict(); /* borrowed, no exception, "never" fails */
if (sys_modules) {
PyObject *module = PyDict_GetItemString(sys_modules, "%(module_name)s"); if (!module) return;
PyDict_SetItemString(sys_modules, "%(pgo_module_name)s", module);
extern PyMODINIT_FUNC PyInit_%(module_name)s(void);
PyMODINIT_FUNC PyInit_%(pgo_module_name)s(void); /*proto*/
PyMODINIT_FUNC PyInit_%(pgo_module_name)s(void) {
return PyInit_%(module_name)s();
""" % {'module_name': module_name, 'pgo_module_name': pgo_module_name}))
extension.sources = extension.sources + [pgo_wrapper_c_file] # do not modify in place! = pgo_module_name
self._build_extension(extension, lib_dir, pgo_step_name='gen')
# import and execute module code to generate profile
so_module_path = os.path.join(lib_dir, pgo_module_name + self.so_ext)
imp.load_dynamic(pgo_module_name, so_module_path)
def _cythonize(self, module_name, code, lib_dir, args, quiet=True):
pyx_file = os.path.join(lib_dir, module_name + '.pyx')
pyx_file = py3compat.cast_bytes_py2(pyx_file, encoding=sys.getfilesystemencoding())
c_include_dirs = args.include
c_src_files = list(map(str, args.src))
if 'numpy' in code:
import numpy
with, 'w', encoding='utf-8') as f:
extension = Extension(
sources=[pyx_file] + c_src_files,
language='c++' if args.cplus else 'c',
opts = dict(
if args.language_level is not None:
assert args.language_level in (2, 3)
opts['language_level'] = args.language_level
elif sys.version_info[0] >= 3:
opts['language_level'] = 3
return cythonize([extension], **opts)
except CompileError:
return None
def _build_extension(self, extension, lib_dir, temp_dir=None, pgo_step_name=None, quiet=True):
build_extension = self._get_build_extension(
extension, lib_dir=lib_dir, temp_dir=temp_dir, pgo_step_name=pgo_step_name)
old_threshold = None
if not quiet:
old_threshold = distutils.log.set_threshold(distutils.log.DEBUG)
if not quiet and old_threshold is not None:
def _add_pgo_flags(self, build_extension, step_name, temp_dir):
compiler_type = build_extension.compiler.compiler_type
if compiler_type == 'unix':
compiler_cmd = build_extension.compiler.compiler_so
# TODO: we could try to call "[cmd] --version" for better insights
if not compiler_cmd:
elif 'clang' in compiler_cmd or 'clang' in compiler_cmd[0]:
compiler_type = 'clang'
elif 'icc' in compiler_cmd or 'icc' in compiler_cmd[0]:
compiler_type = 'icc'
elif 'gcc' in compiler_cmd or 'gcc' in compiler_cmd[0]:
compiler_type = 'gcc'
elif 'g++' in compiler_cmd or 'g++' in compiler_cmd[0]:
compiler_type = 'gcc'
config = PGO_CONFIG.get(compiler_type)
orig_flags = []
if config and step_name in config:
flags = [f.format(TEMPDIR=temp_dir) for f in config[step_name]]
for extension in build_extension.extensions:
orig_flags.append((extension.extra_compile_args, extension.extra_link_args))
extension.extra_compile_args = extension.extra_compile_args + flags
extension.extra_link_args = extension.extra_link_args + flags
print("No PGO %s configuration known for C compiler type '%s'" % (step_name, compiler_type),
return orig_flags
def so_ext(self):
"""The extension suffix for compiled modules."""
return self._so_ext
except AttributeError:
self._so_ext = self._get_build_extension().get_ext_filename('')
return self._so_ext
def _clear_distutils_mkpath_cache(self):
"""clear distutils mkpath cache
prevents distutils from skipping re-creation of dirs that have been removed
from distutils.dir_util import _path_created
except ImportError:
def _get_build_extension(self, extension=None, lib_dir=None, temp_dir=None,
pgo_step_name=None, _build_ext=build_ext):
dist = Distribution()
config_files = dist.find_config_files()
except ValueError:
if not temp_dir:
temp_dir = lib_dir
add_pgo_flags = self._add_pgo_flags
if pgo_step_name:
base_build_ext = _build_ext
class _build_ext(_build_ext):
def build_extensions(self):
add_pgo_flags(self, pgo_step_name, temp_dir)
build_extension = _build_ext(dist)
if temp_dir:
temp_dir = py3compat.cast_bytes_py2(temp_dir, encoding=sys.getfilesystemencoding())
build_extension.build_temp = temp_dir
if lib_dir:
lib_dir = py3compat.cast_bytes_py2(lib_dir, encoding=sys.getfilesystemencoding())
build_extension.build_lib = lib_dir
if extension is not None:
build_extension.extensions = [extension]
return build_extension
def clean_annotated_html(html):
"""Clean up the annotated HTML source.
Strips the link to the generated C or C++ file, which we do not
present to the user.
r = re.compile('<p>Raw output: <a href="(.*)">(.*)</a>')
html = '\n'.join(l for l in html.splitlines() if not r.match(l))
return html
__doc__ = __doc__.format(
# rST doesn't see the -+ flag as part of an option list, so we
# hide it from the module-level docstring.
.replace('-+, --cplus', '--cplus ')),