# -*- 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``. Usage ===== To enable the magics below, execute ``%load_ext cython``. ``%%cython`` {CYTHON_DOC} ``%%cython_inline`` {CYTHON_INLINE_DOC} ``%%cython_pyximport`` {CYTHON_PYXIMPORT_DOC} Author: * 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 try: reload except NameError: # Python 3 from imp import reload try: 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 try: 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 PGO_CONFIG = { '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'] @magics_class 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__'] else: keys = [k for k in mdict if not k.startswith('_')] for k in keys: try: self.shell.push({k: mdict[k]}) except KeyError: msg = "'module' object has no attribute '%s'" % k raise AttributeError(msg) @cell_magic 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:: %%cython_inline return a+b For most purposes, we recommend the usage of the `%%cython` magic. """ locs = self.shell.user_global_ns globs = self.shell.user_ns return cython_inline(cell, locals=locs, globals=globs) @cell_magic 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 io.open(fname, 'w', encoding='utf-8') as f: f.write(cell) if 'pyximport' not in sys.modules or not self._pyximport_installed: import pyximport pyximport.install(reload_support=True) self._pyximport_installed = True if module_name in self._reloads: module = self._reloads[module_name] reload(module) else: __import__(module_name) module = sys.modules[module_name] self._reloads[module_name] = module self._import_all(module) @magic_arguments.magic_arguments() @magic_arguments.argument( '-a', '--annotate', action='store_true', default=False, help="Produce a colorized HTML version of the source." ) @magic_arguments.argument( '-+', '--cplus', action='store_true', default=False, help="Output a C++ rather than C file." ) @magic_arguments.argument( '-3', dest='language_level', action='store_const', const=3, default=None, help="Select Python 3 syntax." ) @magic_arguments.argument( '-2', dest='language_level', action='store_const', const=2, default=None, help="Select Python 2 syntax." ) @magic_arguments.argument( '-f', '--force', action='store_true', default=False, help="Force the compilation of a new module, even if the source has been " "previously compiled." ) @magic_arguments.argument( '-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)." ) @magic_arguments.argument( '--link-args', action='append', default=[], help="Extra flags to pass to linker via the `extra_link_args` " "Extension flag (can be specified multiple times)." ) @magic_arguments.argument( '-l', '--lib', action='append', default=[], help="Add a library to link the extension against (can be specified " "multiple times)." ) @magic_arguments.argument( '-n', '--name', help="Specify a name for the Cython module." ) @magic_arguments.argument( '-L', dest='library_dirs', metavar='dir', action='append', default=[], help="Add a path to the list of library directories (can be specified " "multiple times)." ) @magic_arguments.argument( '-I', '--include', action='append', default=[], help="Add a path to the list of include directories (can be specified " "multiple times)." ) @magic_arguments.argument( '-S', '--src', action='append', default=[], help="Add a path to the list of src files (can be specified " "multiple times)." ) @magic_arguments.argument( '--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.") ) @magic_arguments.argument( '--verbose', dest='quiet', action='store_false', default=True, help=("Print debug information like generated .c/.cpp file location " "and exact gcc/g++ command invoked.") ) @cell_magic 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:: %%cython 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): critical_function(some_typical_data) 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): os.makedirs(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(),) if args.name: module_name = py3compat.unicode_to_str(args.name) else: 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, quiet=args.quiet) 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 = 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 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 = 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 @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('

Raw output: (.*)') 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__), )