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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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Usage
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=====
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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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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 COPYING.txt, distributed with this software.
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#-----------------------------------------------------------------------------
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from __future__ 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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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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from IPython.utils import py3compat
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from IPython.utils.path import get_ipython_cache_dir
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import Cython
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from Cython.Compiler.Errors import CompileError
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from Cython.Build.Dependencies import cythonize
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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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def _import_all(self, module):
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for k,v in module.__dict__.items():
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if not k.startswith('__'):
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self.shell.push({k:v})
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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:
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import pyximport
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pyximport.install(reload_support=True)
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if module_name in self._reloads:
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module = self._reloads[module_name]
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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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'-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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'-L', dest='library_dirs', metavar='dir', action='append', default=[],
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help="Add a path to the list of libary 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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'-+', '--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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'-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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'-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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@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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"""
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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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quiet = True
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key = code, 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.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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module_name = "_cython_magic_" + hashlib.md5(str(key).encode('utf-8')).hexdigest()
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module_path = os.path.join(lib_dir, module_name + self.so_ext)
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have_module = os.path.isfile(module_path)
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need_cythonize = not have_module
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if args.annotate:
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html_file = os.path.join(lib_dir, module_name + '.html')
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if not os.path.isfile(html_file):
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need_cythonize = True
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if need_cythonize:
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c_include_dirs = args.include
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if 'numpy' in code:
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import numpy
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c_include_dirs.append(numpy.get_include())
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pyx_file = os.path.join(lib_dir, module_name + '.pyx')
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pyx_file = py3compat.cast_bytes_py2(pyx_file, encoding=sys.getfilesystemencoding())
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with io.open(pyx_file, 'w', encoding='utf-8') as f:
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f.write(code)
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extension = Extension(
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name = module_name,
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sources = [pyx_file],
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include_dirs = c_include_dirs,
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library_dirs = args.library_dirs,
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extra_compile_args = args.compile_args,
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extra_link_args = args.link_args,
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libraries = args.lib,
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language = 'c++' if args.cplus else 'c',
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)
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build_extension = self._get_build_extension()
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try:
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opts = dict(
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quiet=quiet,
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annotate = args.annotate,
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force = True,
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)
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build_extension.extensions = cythonize([extension], **opts)
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except CompileError:
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return
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if not have_module:
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build_extension.build_temp = os.path.dirname(pyx_file)
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build_extension.build_lib = lib_dir
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build_extension.run()
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self._code_cache[key] = module_name
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module = imp.load_dynamic(module_name, module_path)
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self._import_all(module)
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if args.annotate:
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try:
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with io.open(html_file, encoding='utf-8') as f:
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annotated_html = f.read()
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except IOError as e:
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# File could not be opened. Most likely the user has a version
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# of Cython before 0.15.1 (when `cythonize` learned the
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# `force` keyword argument) and has already compiled this
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# exact source without annotation.
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print('Cython completed successfully but the annotated '
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'source could not be read.', file=sys.stderr)
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print(e, file=sys.stderr)
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else:
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return display.HTML(self.clean_annotated_html(annotated_html))
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@property
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def so_ext(self):
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"""The extension suffix for compiled modules."""
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try:
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return self._so_ext
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except AttributeError:
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self._so_ext = self._get_build_extension().get_ext_filename('')
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return self._so_ext
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def _clear_distutils_mkpath_cache(self):
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"""clear distutils mkpath cache
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prevents distutils from skipping re-creation of dirs that have been removed
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"""
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try:
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from distutils.dir_util import _path_created
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except ImportError:
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pass
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else:
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_path_created.clear()
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def _get_build_extension(self):
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self._clear_distutils_mkpath_cache()
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dist = Distribution()
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config_files = dist.find_config_files()
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try:
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config_files.remove('setup.cfg')
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except ValueError:
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pass
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dist.parse_config_files(config_files)
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build_extension = build_ext(dist)
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build_extension.finalize_options()
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return build_extension
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@staticmethod
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def clean_annotated_html(html):
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"""Clean up the annotated HTML source.
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Strips the link to the generated C or C++ file, which we do not
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present to the user.
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"""
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r = re.compile('<p>Raw output: <a href="(.*)">(.*)</a>')
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html = '\n'.join(l for l in html.splitlines() if not r.match(l))
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return html
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__doc__ = __doc__.format(
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CYTHON_DOC = ' '*8 + CythonMagics.cython.__doc__,
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CYTHON_INLINE_DOC = ' '*8 + CythonMagics.cython_inline.__doc__,
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CYTHON_PYXIMPORT_DOC = ' '*8 + CythonMagics.cython_pyximport.__doc__,
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)
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def load_ipython_extension(ip):
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"""Load the extension in IPython."""
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ip.register_magics(CythonMagics)
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