566 lines
21 KiB
Python
566 lines
21 KiB
Python
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# -*- coding: utf-8 -*-
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"""
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=====================
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Cython related magics
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=====================
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Magic command interface for interactive work with Cython
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.. note::
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The ``Cython`` package needs to be installed separately. It
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can be obtained using ``easy_install`` or ``pip``.
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Usage
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=====
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To enable the magics below, execute ``%load_ext cython``.
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``%%cython``
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{CYTHON_DOC}
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``%%cython_inline``
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{CYTHON_INLINE_DOC}
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``%%cython_pyximport``
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{CYTHON_PYXIMPORT_DOC}
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Author:
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* Brian Granger
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Code moved from IPython and adapted by:
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* Martín Gaitán
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Parts of this code were taken from Cython.inline.
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"""
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#-----------------------------------------------------------------------------
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# Copyright (C) 2010-2011, IPython Development Team.
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#
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# Distributed under the terms of the Modified BSD License.
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#
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# The full license is in the file ipython-COPYING.rst, distributed with this software.
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#-----------------------------------------------------------------------------
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from __future__ import absolute_import, print_function
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import imp
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import io
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import os
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import re
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import sys
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import time
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import copy
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import distutils.log
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import textwrap
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IO_ENCODING = sys.getfilesystemencoding()
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IS_PY2 = sys.version_info[0] < 3
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try:
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reload
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except NameError: # Python 3
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from imp import reload
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try:
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import hashlib
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except ImportError:
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import md5 as hashlib
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from distutils.core import Distribution, Extension
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from distutils.command.build_ext import build_ext
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from IPython.core import display
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from IPython.core import magic_arguments
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from IPython.core.magic import Magics, magics_class, cell_magic
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try:
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from IPython.paths import get_ipython_cache_dir
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except ImportError:
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# older IPython version
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from IPython.utils.path import get_ipython_cache_dir
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from IPython.utils.text import dedent
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from ..Shadow import __version__ as cython_version
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from ..Compiler.Errors import CompileError
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from .Inline import cython_inline
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from .Dependencies import cythonize
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PGO_CONFIG = {
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'gcc': {
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'gen': ['-fprofile-generate', '-fprofile-dir={TEMPDIR}'],
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'use': ['-fprofile-use', '-fprofile-correction', '-fprofile-dir={TEMPDIR}'],
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},
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# blind copy from 'configure' script in CPython 3.7
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'icc': {
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'gen': ['-prof-gen'],
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'use': ['-prof-use'],
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}
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}
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PGO_CONFIG['mingw32'] = PGO_CONFIG['gcc']
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if IS_PY2:
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def encode_fs(name):
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return name if isinstance(name, bytes) else name.encode(IO_ENCODING)
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else:
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def encode_fs(name):
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return name
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@magics_class
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class CythonMagics(Magics):
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def __init__(self, shell):
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super(CythonMagics, self).__init__(shell)
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self._reloads = {}
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self._code_cache = {}
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self._pyximport_installed = False
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def _import_all(self, module):
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mdict = module.__dict__
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if '__all__' in mdict:
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keys = mdict['__all__']
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else:
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keys = [k for k in mdict if not k.startswith('_')]
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for k in keys:
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try:
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self.shell.push({k: mdict[k]})
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except KeyError:
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msg = "'module' object has no attribute '%s'" % k
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raise AttributeError(msg)
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@cell_magic
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def cython_inline(self, line, cell):
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"""Compile and run a Cython code cell using Cython.inline.
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This magic simply passes the body of the cell to Cython.inline
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and returns the result. If the variables `a` and `b` are defined
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in the user's namespace, here is a simple example that returns
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their sum::
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%%cython_inline
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return a+b
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For most purposes, we recommend the usage of the `%%cython` magic.
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"""
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locs = self.shell.user_global_ns
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globs = self.shell.user_ns
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return cython_inline(cell, locals=locs, globals=globs)
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@cell_magic
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def cython_pyximport(self, line, cell):
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"""Compile and import a Cython code cell using pyximport.
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The contents of the cell are written to a `.pyx` file in the current
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working directory, which is then imported using `pyximport`. This
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magic requires a module name to be passed::
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%%cython_pyximport modulename
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def f(x):
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return 2.0*x
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The compiled module is then imported and all of its symbols are
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injected into the user's namespace. For most purposes, we recommend
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the usage of the `%%cython` magic.
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"""
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module_name = line.strip()
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if not module_name:
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raise ValueError('module name must be given')
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fname = module_name + '.pyx'
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with io.open(fname, 'w', encoding='utf-8') as f:
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f.write(cell)
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if 'pyximport' not in sys.modules or not self._pyximport_installed:
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import pyximport
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pyximport.install()
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self._pyximport_installed = True
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if module_name in self._reloads:
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module = self._reloads[module_name]
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# Note: reloading extension modules is not actually supported
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# (requires PEP-489 reinitialisation support).
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# Don't know why this should ever have worked as it reads here.
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# All we really need to do is to update the globals below.
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#reload(module)
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else:
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__import__(module_name)
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module = sys.modules[module_name]
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self._reloads[module_name] = module
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self._import_all(module)
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@magic_arguments.magic_arguments()
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@magic_arguments.argument(
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'-a', '--annotate', action='store_true', default=False,
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help="Produce a colorized HTML version of the source."
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)
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@magic_arguments.argument(
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'-+', '--cplus', action='store_true', default=False,
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help="Output a C++ rather than C file."
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)
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@magic_arguments.argument(
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'-3', dest='language_level', action='store_const', const=3, default=None,
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help="Select Python 3 syntax."
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)
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@magic_arguments.argument(
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'-2', dest='language_level', action='store_const', const=2, default=None,
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help="Select Python 2 syntax."
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)
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@magic_arguments.argument(
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'-f', '--force', action='store_true', default=False,
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help="Force the compilation of a new module, even if the source has been "
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"previously compiled."
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)
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@magic_arguments.argument(
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'-c', '--compile-args', action='append', default=[],
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help="Extra flags to pass to compiler via the `extra_compile_args` "
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"Extension flag (can be specified multiple times)."
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)
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@magic_arguments.argument(
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'--link-args', action='append', default=[],
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help="Extra flags to pass to linker via the `extra_link_args` "
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"Extension flag (can be specified multiple times)."
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)
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@magic_arguments.argument(
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'-l', '--lib', action='append', default=[],
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help="Add a library to link the extension against (can be specified "
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"multiple times)."
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)
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@magic_arguments.argument(
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'-n', '--name',
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help="Specify a name for the Cython module."
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)
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@magic_arguments.argument(
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'-L', dest='library_dirs', metavar='dir', action='append', default=[],
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help="Add a path to the list of library directories (can be specified "
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"multiple times)."
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)
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@magic_arguments.argument(
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'-I', '--include', action='append', default=[],
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help="Add a path to the list of include directories (can be specified "
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"multiple times)."
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)
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@magic_arguments.argument(
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'-S', '--src', action='append', default=[],
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help="Add a path to the list of src files (can be specified "
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"multiple times)."
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)
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@magic_arguments.argument(
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'--pgo', dest='pgo', action='store_true', default=False,
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help=("Enable profile guided optimisation in the C compiler. "
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"Compiles the cell twice and executes it in between to generate a runtime profile.")
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)
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@magic_arguments.argument(
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'--verbose', dest='quiet', action='store_false', default=True,
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help=("Print debug information like generated .c/.cpp file location "
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"and exact gcc/g++ command invoked.")
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)
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@cell_magic
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def cython(self, line, cell):
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"""Compile and import everything from a Cython code cell.
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The contents of the cell are written to a `.pyx` file in the
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directory `IPYTHONDIR/cython` using a filename with the hash of the
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code. This file is then cythonized and compiled. The resulting module
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is imported and all of its symbols are injected into the user's
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namespace. The usage is similar to that of `%%cython_pyximport` but
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you don't have to pass a module name::
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%%cython
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def f(x):
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return 2.0*x
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To compile OpenMP codes, pass the required `--compile-args`
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and `--link-args`. For example with gcc::
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%%cython --compile-args=-fopenmp --link-args=-fopenmp
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...
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To enable profile guided optimisation, pass the ``--pgo`` option.
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Note that the cell itself needs to take care of establishing a suitable
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profile when executed. This can be done by implementing the functions to
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optimise, and then calling them directly in the same cell on some realistic
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training data like this::
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%%cython --pgo
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def critical_function(data):
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for item in data:
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...
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# execute function several times to build profile
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from somewhere import some_typical_data
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for _ in range(100):
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critical_function(some_typical_data)
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In Python 3.5 and later, you can distinguish between the profile and
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non-profile runs as follows::
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if "_pgo_" in __name__:
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... # execute critical code here
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"""
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args = magic_arguments.parse_argstring(self.cython, line)
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code = cell if cell.endswith('\n') else cell + '\n'
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lib_dir = os.path.join(get_ipython_cache_dir(), 'cython')
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key = (code, line, sys.version_info, sys.executable, cython_version)
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if not os.path.exists(lib_dir):
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os.makedirs(lib_dir)
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if args.pgo:
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key += ('pgo',)
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if args.force:
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# Force a new module name by adding the current time to the
|
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# key which is hashed to determine the module name.
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key += (time.time(),)
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if args.name:
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module_name = str(args.name) # no-op in Py3
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else:
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module_name = "_cython_magic_" + hashlib.md5(str(key).encode('utf-8')).hexdigest()
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html_file = os.path.join(lib_dir, module_name + '.html')
|
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module_path = os.path.join(lib_dir, module_name + self.so_ext)
|
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|
|
|
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have_module = os.path.isfile(module_path)
|
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need_cythonize = args.pgo or not have_module
|
||
|
|
|
||
|
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if args.annotate:
|
||
|
|
if not os.path.isfile(html_file):
|
||
|
|
need_cythonize = True
|
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|
|
|
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|
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extension = None
|
||
|
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if need_cythonize:
|
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|
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extensions = self._cythonize(module_name, code, lib_dir, args, quiet=args.quiet)
|
||
|
|
if extensions is None:
|
||
|
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# Compilation failed and printed error message
|
||
|
|
return None
|
||
|
|
assert len(extensions) == 1
|
||
|
|
extension = extensions[0]
|
||
|
|
self._code_cache[key] = module_name
|
||
|
|
|
||
|
|
if args.pgo:
|
||
|
|
self._profile_pgo_wrapper(extension, lib_dir)
|
||
|
|
|
||
|
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try:
|
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self._build_extension(extension, lib_dir, pgo_step_name='use' if args.pgo else None,
|
||
|
|
quiet=args.quiet)
|
||
|
|
except distutils.errors.CompileError:
|
||
|
|
# Build failed and printed error message
|
||
|
|
return None
|
||
|
|
|
||
|
|
module = imp.load_dynamic(module_name, module_path)
|
||
|
|
self._import_all(module)
|
||
|
|
|
||
|
|
if args.annotate:
|
||
|
|
try:
|
||
|
|
with io.open(html_file, encoding='utf-8') as f:
|
||
|
|
annotated_html = f.read()
|
||
|
|
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)
|
||
|
|
else:
|
||
|
|
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 = extension.name
|
||
|
|
pgo_module_name = '_pgo_' + module_name
|
||
|
|
pgo_wrapper_c_file = os.path.join(lib_dir, pgo_module_name + '.c')
|
||
|
|
with io.open(pgo_wrapper_c_file, 'w', encoding='utf-8') as f:
|
||
|
|
f.write(textwrap.dedent(u"""
|
||
|
|
#include "Python.h"
|
||
|
|
#if PY_MAJOR_VERSION < 3
|
||
|
|
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);
|
||
|
|
Py_DECREF(module);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
#else
|
||
|
|
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();
|
||
|
|
}
|
||
|
|
#endif
|
||
|
|
""" % {'module_name': module_name, 'pgo_module_name': pgo_module_name}))
|
||
|
|
|
||
|
|
extension.sources = extension.sources + [pgo_wrapper_c_file] # do not modify in place!
|
||
|
|
extension.name = 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 = encode_fs(pyx_file)
|
||
|
|
|
||
|
|
c_include_dirs = args.include
|
||
|
|
c_src_files = list(map(str, args.src))
|
||
|
|
if 'numpy' in code:
|
||
|
|
import numpy
|
||
|
|
c_include_dirs.append(numpy.get_include())
|
||
|
|
with io.open(pyx_file, 'w', encoding='utf-8') as f:
|
||
|
|
f.write(code)
|
||
|
|
extension = Extension(
|
||
|
|
name=module_name,
|
||
|
|
sources=[pyx_file] + c_src_files,
|
||
|
|
include_dirs=c_include_dirs,
|
||
|
|
library_dirs=args.library_dirs,
|
||
|
|
extra_compile_args=args.compile_args,
|
||
|
|
extra_link_args=args.link_args,
|
||
|
|
libraries=args.lib,
|
||
|
|
language='c++' if args.cplus else 'c',
|
||
|
|
)
|
||
|
|
try:
|
||
|
|
opts = dict(
|
||
|
|
quiet=quiet,
|
||
|
|
annotate=args.annotate,
|
||
|
|
force=True,
|
||
|
|
)
|
||
|
|
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
|
||
|
|
try:
|
||
|
|
if not quiet:
|
||
|
|
old_threshold = distutils.log.set_threshold(distutils.log.DEBUG)
|
||
|
|
build_extension.run()
|
||
|
|
finally:
|
||
|
|
if not quiet and old_threshold is not None:
|
||
|
|
distutils.log.set_threshold(old_threshold)
|
||
|
|
|
||
|
|
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:
|
||
|
|
pass
|
||
|
|
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
|
||
|
|
else:
|
||
|
|
print("No PGO %s configuration known for C compiler type '%s'" % (step_name, compiler_type),
|
||
|
|
file=sys.stderr)
|
||
|
|
return orig_flags
|
||
|
|
|
||
|
|
@property
|
||
|
|
def so_ext(self):
|
||
|
|
"""The extension suffix for compiled modules."""
|
||
|
|
try:
|
||
|
|
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
|
||
|
|
"""
|
||
|
|
try:
|
||
|
|
from distutils.dir_util import _path_created
|
||
|
|
except ImportError:
|
||
|
|
pass
|
||
|
|
else:
|
||
|
|
_path_created.clear()
|
||
|
|
|
||
|
|
def _get_build_extension(self, extension=None, lib_dir=None, temp_dir=None,
|
||
|
|
pgo_step_name=None, _build_ext=build_ext):
|
||
|
|
self._clear_distutils_mkpath_cache()
|
||
|
|
dist = Distribution()
|
||
|
|
config_files = dist.find_config_files()
|
||
|
|
try:
|
||
|
|
config_files.remove('setup.cfg')
|
||
|
|
except ValueError:
|
||
|
|
pass
|
||
|
|
dist.parse_config_files(config_files)
|
||
|
|
|
||
|
|
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)
|
||
|
|
base_build_ext.build_extensions(self)
|
||
|
|
|
||
|
|
build_extension = _build_ext(dist)
|
||
|
|
build_extension.finalize_options()
|
||
|
|
if temp_dir:
|
||
|
|
temp_dir = encode_fs(temp_dir)
|
||
|
|
build_extension.build_temp = temp_dir
|
||
|
|
if lib_dir:
|
||
|
|
lib_dir = encode_fs(lib_dir)
|
||
|
|
build_extension.build_lib = lib_dir
|
||
|
|
if extension is not None:
|
||
|
|
build_extension.extensions = [extension]
|
||
|
|
return build_extension
|
||
|
|
|
||
|
|
@staticmethod
|
||
|
|
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.
|
||
|
|
CYTHON_DOC=dedent(CythonMagics.cython.__doc__\
|
||
|
|
.replace('-+, --cplus', '--cplus ')),
|
||
|
|
CYTHON_INLINE_DOC=dedent(CythonMagics.cython_inline.__doc__),
|
||
|
|
CYTHON_PYXIMPORT_DOC=dedent(CythonMagics.cython_pyximport.__doc__),
|
||
|
|
)
|