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@@ -1,312 +1,313 b''
1 # -*- coding: utf-8 -*-
1 # -*- coding: utf-8 -*-
2 """
2 """
3 =====================
3 =====================
4 Cython related magics
4 Cython related magics
5 =====================
5 =====================
6
6
7 Usage
7 Usage
8 =====
8 =====
9
9
10 ``%%cython``
10 ``%%cython``
11
11
12 {CYTHON_DOC}
12 {CYTHON_DOC}
13
13
14 ``%%cython_inline``
14 ``%%cython_inline``
15
15
16 {CYTHON_INLINE_DOC}
16 {CYTHON_INLINE_DOC}
17
17
18 ``%%cython_pyximport``
18 ``%%cython_pyximport``
19
19
20 {CYTHON_PYXIMPORT_DOC}
20 {CYTHON_PYXIMPORT_DOC}
21
21
22 Author:
22 Author:
23 * Brian Granger
23 * Brian Granger
24
24
25 Parts of this code were taken from Cython.inline.
25 Parts of this code were taken from Cython.inline.
26 """
26 """
27 #-----------------------------------------------------------------------------
27 #-----------------------------------------------------------------------------
28 # Copyright (C) 2010-2011, IPython Development Team.
28 # Copyright (C) 2010-2011, IPython Development Team.
29 #
29 #
30 # Distributed under the terms of the Modified BSD License.
30 # Distributed under the terms of the Modified BSD License.
31 #
31 #
32 # The full license is in the file COPYING.txt, distributed with this software.
32 # The full license is in the file COPYING.txt, distributed with this software.
33 #-----------------------------------------------------------------------------
33 #-----------------------------------------------------------------------------
34
34
35 from __future__ import print_function
35 from __future__ import print_function
36
36
37 import imp
37 import imp
38 import io
38 import io
39 import os
39 import os
40 import re
40 import re
41 import sys
41 import sys
42 import time
42 import time
43
43
44 try:
44 try:
45 reload
45 reload
46 except NameError: # Python 3
46 except NameError: # Python 3
47 from imp import reload
47 from imp import reload
48
48
49 try:
49 try:
50 import hashlib
50 import hashlib
51 except ImportError:
51 except ImportError:
52 import md5 as hashlib
52 import md5 as hashlib
53
53
54 from distutils.core import Distribution, Extension
54 from distutils.core import Distribution, Extension
55 from distutils.command.build_ext import build_ext
55 from distutils.command.build_ext import build_ext
56
56
57 from IPython.core import display
57 from IPython.core import display
58 from IPython.core import magic_arguments
58 from IPython.core import magic_arguments
59 from IPython.core.magic import Magics, magics_class, cell_magic
59 from IPython.core.magic import Magics, magics_class, cell_magic
60 from IPython.testing.skipdoctest import skip_doctest
60 from IPython.testing.skipdoctest import skip_doctest
61 from IPython.utils import py3compat
61 from IPython.utils import py3compat
62 from IPython.utils.path import get_ipython_cache_dir
62
63
63 import Cython
64 import Cython
64 from Cython.Compiler.Errors import CompileError
65 from Cython.Compiler.Errors import CompileError
65 from Cython.Build.Dependencies import cythonize
66 from Cython.Build.Dependencies import cythonize
66
67
67
68
68 @magics_class
69 @magics_class
69 class CythonMagics(Magics):
70 class CythonMagics(Magics):
70
71
71 def __init__(self, shell):
72 def __init__(self, shell):
72 super(CythonMagics,self).__init__(shell)
73 super(CythonMagics,self).__init__(shell)
73 self._reloads = {}
74 self._reloads = {}
74 self._code_cache = {}
75 self._code_cache = {}
75
76
76 def _import_all(self, module):
77 def _import_all(self, module):
77 for k,v in module.__dict__.items():
78 for k,v in module.__dict__.items():
78 if not k.startswith('__'):
79 if not k.startswith('__'):
79 self.shell.push({k:v})
80 self.shell.push({k:v})
80
81
81 @cell_magic
82 @cell_magic
82 def cython_inline(self, line, cell):
83 def cython_inline(self, line, cell):
83 """Compile and run a Cython code cell using Cython.inline.
84 """Compile and run a Cython code cell using Cython.inline.
84
85
85 This magic simply passes the body of the cell to Cython.inline
86 This magic simply passes the body of the cell to Cython.inline
86 and returns the result. If the variables `a` and `b` are defined
87 and returns the result. If the variables `a` and `b` are defined
87 in the user's namespace, here is a simple example that returns
88 in the user's namespace, here is a simple example that returns
88 their sum::
89 their sum::
89
90
90 %%cython_inline
91 %%cython_inline
91 return a+b
92 return a+b
92
93
93 For most purposes, we recommend the usage of the `%%cython` magic.
94 For most purposes, we recommend the usage of the `%%cython` magic.
94 """
95 """
95 locs = self.shell.user_global_ns
96 locs = self.shell.user_global_ns
96 globs = self.shell.user_ns
97 globs = self.shell.user_ns
97 return Cython.inline(cell, locals=locs, globals=globs)
98 return Cython.inline(cell, locals=locs, globals=globs)
98
99
99 @cell_magic
100 @cell_magic
100 def cython_pyximport(self, line, cell):
101 def cython_pyximport(self, line, cell):
101 """Compile and import a Cython code cell using pyximport.
102 """Compile and import a Cython code cell using pyximport.
102
103
103 The contents of the cell are written to a `.pyx` file in the current
104 The contents of the cell are written to a `.pyx` file in the current
104 working directory, which is then imported using `pyximport`. This
105 working directory, which is then imported using `pyximport`. This
105 magic requires a module name to be passed::
106 magic requires a module name to be passed::
106
107
107 %%cython_pyximport modulename
108 %%cython_pyximport modulename
108 def f(x):
109 def f(x):
109 return 2.0*x
110 return 2.0*x
110
111
111 The compiled module is then imported and all of its symbols are
112 The compiled module is then imported and all of its symbols are
112 injected into the user's namespace. For most purposes, we recommend
113 injected into the user's namespace. For most purposes, we recommend
113 the usage of the `%%cython` magic.
114 the usage of the `%%cython` magic.
114 """
115 """
115 module_name = line.strip()
116 module_name = line.strip()
116 if not module_name:
117 if not module_name:
117 raise ValueError('module name must be given')
118 raise ValueError('module name must be given')
118 fname = module_name + '.pyx'
119 fname = module_name + '.pyx'
119 with io.open(fname, 'w', encoding='utf-8') as f:
120 with io.open(fname, 'w', encoding='utf-8') as f:
120 f.write(cell)
121 f.write(cell)
121 if 'pyximport' not in sys.modules:
122 if 'pyximport' not in sys.modules:
122 import pyximport
123 import pyximport
123 pyximport.install(reload_support=True)
124 pyximport.install(reload_support=True)
124 if module_name in self._reloads:
125 if module_name in self._reloads:
125 module = self._reloads[module_name]
126 module = self._reloads[module_name]
126 reload(module)
127 reload(module)
127 else:
128 else:
128 __import__(module_name)
129 __import__(module_name)
129 module = sys.modules[module_name]
130 module = sys.modules[module_name]
130 self._reloads[module_name] = module
131 self._reloads[module_name] = module
131 self._import_all(module)
132 self._import_all(module)
132
133
133 @magic_arguments.magic_arguments()
134 @magic_arguments.magic_arguments()
134 @magic_arguments.argument(
135 @magic_arguments.argument(
135 '-c', '--compile-args', action='append', default=[],
136 '-c', '--compile-args', action='append', default=[],
136 help="Extra flags to pass to compiler via the `extra_compile_args` "
137 help="Extra flags to pass to compiler via the `extra_compile_args` "
137 "Extension flag (can be specified multiple times)."
138 "Extension flag (can be specified multiple times)."
138 )
139 )
139 @magic_arguments.argument(
140 @magic_arguments.argument(
140 '--link-args', action='append', default=[],
141 '--link-args', action='append', default=[],
141 help="Extra flags to pass to linker via the `extra_link_args` "
142 help="Extra flags to pass to linker via the `extra_link_args` "
142 "Extension flag (can be specified multiple times)."
143 "Extension flag (can be specified multiple times)."
143 )
144 )
144 @magic_arguments.argument(
145 @magic_arguments.argument(
145 '-l', '--lib', action='append', default=[],
146 '-l', '--lib', action='append', default=[],
146 help="Add a library to link the extension against (can be specified "
147 help="Add a library to link the extension against (can be specified "
147 "multiple times)."
148 "multiple times)."
148 )
149 )
149 @magic_arguments.argument(
150 @magic_arguments.argument(
150 '-L', dest='library_dirs', metavar='dir', action='append', default=[],
151 '-L', dest='library_dirs', metavar='dir', action='append', default=[],
151 help="Add a path to the list of libary directories (can be specified "
152 help="Add a path to the list of libary directories (can be specified "
152 "multiple times)."
153 "multiple times)."
153 )
154 )
154 @magic_arguments.argument(
155 @magic_arguments.argument(
155 '-I', '--include', action='append', default=[],
156 '-I', '--include', action='append', default=[],
156 help="Add a path to the list of include directories (can be specified "
157 help="Add a path to the list of include directories (can be specified "
157 "multiple times)."
158 "multiple times)."
158 )
159 )
159 @magic_arguments.argument(
160 @magic_arguments.argument(
160 '-+', '--cplus', action='store_true', default=False,
161 '-+', '--cplus', action='store_true', default=False,
161 help="Output a C++ rather than C file."
162 help="Output a C++ rather than C file."
162 )
163 )
163 @magic_arguments.argument(
164 @magic_arguments.argument(
164 '-f', '--force', action='store_true', default=False,
165 '-f', '--force', action='store_true', default=False,
165 help="Force the compilation of a new module, even if the source has been "
166 help="Force the compilation of a new module, even if the source has been "
166 "previously compiled."
167 "previously compiled."
167 )
168 )
168 @magic_arguments.argument(
169 @magic_arguments.argument(
169 '-a', '--annotate', action='store_true', default=False,
170 '-a', '--annotate', action='store_true', default=False,
170 help="Produce a colorized HTML version of the source."
171 help="Produce a colorized HTML version of the source."
171 )
172 )
172 @cell_magic
173 @cell_magic
173 def cython(self, line, cell):
174 def cython(self, line, cell):
174 """Compile and import everything from a Cython code cell.
175 """Compile and import everything from a Cython code cell.
175
176
176 The contents of the cell are written to a `.pyx` file in the
177 The contents of the cell are written to a `.pyx` file in the
177 directory `IPYTHONDIR/cython` using a filename with the hash of the
178 directory `IPYTHONDIR/cython` using a filename with the hash of the
178 code. This file is then cythonized and compiled. The resulting module
179 code. This file is then cythonized and compiled. The resulting module
179 is imported and all of its symbols are injected into the user's
180 is imported and all of its symbols are injected into the user's
180 namespace. The usage is similar to that of `%%cython_pyximport` but
181 namespace. The usage is similar to that of `%%cython_pyximport` but
181 you don't have to pass a module name::
182 you don't have to pass a module name::
182
183
183 %%cython
184 %%cython
184 def f(x):
185 def f(x):
185 return 2.0*x
186 return 2.0*x
186
187
187 To compile OpenMP codes, pass the required `--compile-args`
188 To compile OpenMP codes, pass the required `--compile-args`
188 and `--link-args`. For example with gcc::
189 and `--link-args`. For example with gcc::
189
190
190 %%cython --compile-args=-fopenmp --link-args=-fopenmp
191 %%cython --compile-args=-fopenmp --link-args=-fopenmp
191 ...
192 ...
192 """
193 """
193 args = magic_arguments.parse_argstring(self.cython, line)
194 args = magic_arguments.parse_argstring(self.cython, line)
194 code = cell if cell.endswith('\n') else cell+'\n'
195 code = cell if cell.endswith('\n') else cell+'\n'
195 lib_dir = os.path.join(self.shell.ipython_dir, 'cython')
196 lib_dir = os.path.join(get_ipython_cache_dir(), 'cython')
196 quiet = True
197 quiet = True
197 key = code, sys.version_info, sys.executable, Cython.__version__
198 key = code, sys.version_info, sys.executable, Cython.__version__
198
199
199 if not os.path.exists(lib_dir):
200 if not os.path.exists(lib_dir):
200 os.makedirs(lib_dir)
201 os.makedirs(lib_dir)
201
202
202 if args.force:
203 if args.force:
203 # Force a new module name by adding the current time to the
204 # Force a new module name by adding the current time to the
204 # key which is hashed to determine the module name.
205 # key which is hashed to determine the module name.
205 key += time.time(),
206 key += time.time(),
206
207
207 module_name = "_cython_magic_" + hashlib.md5(str(key).encode('utf-8')).hexdigest()
208 module_name = "_cython_magic_" + hashlib.md5(str(key).encode('utf-8')).hexdigest()
208 module_path = os.path.join(lib_dir, module_name + self.so_ext)
209 module_path = os.path.join(lib_dir, module_name + self.so_ext)
209
210
210 have_module = os.path.isfile(module_path)
211 have_module = os.path.isfile(module_path)
211 need_cythonize = not have_module
212 need_cythonize = not have_module
212
213
213 if args.annotate:
214 if args.annotate:
214 html_file = os.path.join(lib_dir, module_name + '.html')
215 html_file = os.path.join(lib_dir, module_name + '.html')
215 if not os.path.isfile(html_file):
216 if not os.path.isfile(html_file):
216 need_cythonize = True
217 need_cythonize = True
217
218
218 if need_cythonize:
219 if need_cythonize:
219 c_include_dirs = args.include
220 c_include_dirs = args.include
220 if 'numpy' in code:
221 if 'numpy' in code:
221 import numpy
222 import numpy
222 c_include_dirs.append(numpy.get_include())
223 c_include_dirs.append(numpy.get_include())
223 pyx_file = os.path.join(lib_dir, module_name + '.pyx')
224 pyx_file = os.path.join(lib_dir, module_name + '.pyx')
224 pyx_file = py3compat.cast_bytes_py2(pyx_file, encoding=sys.getfilesystemencoding())
225 pyx_file = py3compat.cast_bytes_py2(pyx_file, encoding=sys.getfilesystemencoding())
225 with io.open(pyx_file, 'w', encoding='utf-8') as f:
226 with io.open(pyx_file, 'w', encoding='utf-8') as f:
226 f.write(code)
227 f.write(code)
227 extension = Extension(
228 extension = Extension(
228 name = module_name,
229 name = module_name,
229 sources = [pyx_file],
230 sources = [pyx_file],
230 include_dirs = c_include_dirs,
231 include_dirs = c_include_dirs,
231 library_dirs = args.library_dirs,
232 library_dirs = args.library_dirs,
232 extra_compile_args = args.compile_args,
233 extra_compile_args = args.compile_args,
233 extra_link_args = args.link_args,
234 extra_link_args = args.link_args,
234 libraries = args.lib,
235 libraries = args.lib,
235 language = 'c++' if args.cplus else 'c',
236 language = 'c++' if args.cplus else 'c',
236 )
237 )
237 build_extension = self._get_build_extension()
238 build_extension = self._get_build_extension()
238 try:
239 try:
239 opts = dict(
240 opts = dict(
240 quiet=quiet,
241 quiet=quiet,
241 annotate = args.annotate,
242 annotate = args.annotate,
242 force = True,
243 force = True,
243 )
244 )
244 build_extension.extensions = cythonize([extension], **opts)
245 build_extension.extensions = cythonize([extension], **opts)
245 except CompileError:
246 except CompileError:
246 return
247 return
247
248
248 if not have_module:
249 if not have_module:
249 build_extension.build_temp = os.path.dirname(pyx_file)
250 build_extension.build_temp = os.path.dirname(pyx_file)
250 build_extension.build_lib = lib_dir
251 build_extension.build_lib = lib_dir
251 build_extension.run()
252 build_extension.run()
252 self._code_cache[key] = module_name
253 self._code_cache[key] = module_name
253
254
254 module = imp.load_dynamic(module_name, module_path)
255 module = imp.load_dynamic(module_name, module_path)
255 self._import_all(module)
256 self._import_all(module)
256
257
257 if args.annotate:
258 if args.annotate:
258 try:
259 try:
259 with io.open(html_file, encoding='utf-8') as f:
260 with io.open(html_file, encoding='utf-8') as f:
260 annotated_html = f.read()
261 annotated_html = f.read()
261 except IOError as e:
262 except IOError as e:
262 # File could not be opened. Most likely the user has a version
263 # File could not be opened. Most likely the user has a version
263 # of Cython before 0.15.1 (when `cythonize` learned the
264 # of Cython before 0.15.1 (when `cythonize` learned the
264 # `force` keyword argument) and has already compiled this
265 # `force` keyword argument) and has already compiled this
265 # exact source without annotation.
266 # exact source without annotation.
266 print('Cython completed successfully but the annotated '
267 print('Cython completed successfully but the annotated '
267 'source could not be read.', file=sys.stderr)
268 'source could not be read.', file=sys.stderr)
268 print(e, file=sys.stderr)
269 print(e, file=sys.stderr)
269 else:
270 else:
270 return display.HTML(self.clean_annotated_html(annotated_html))
271 return display.HTML(self.clean_annotated_html(annotated_html))
271
272
272 @property
273 @property
273 def so_ext(self):
274 def so_ext(self):
274 """The extension suffix for compiled modules."""
275 """The extension suffix for compiled modules."""
275 try:
276 try:
276 return self._so_ext
277 return self._so_ext
277 except AttributeError:
278 except AttributeError:
278 self._so_ext = self._get_build_extension().get_ext_filename('')
279 self._so_ext = self._get_build_extension().get_ext_filename('')
279 return self._so_ext
280 return self._so_ext
280
281
281 def _get_build_extension(self):
282 def _get_build_extension(self):
282 dist = Distribution()
283 dist = Distribution()
283 config_files = dist.find_config_files()
284 config_files = dist.find_config_files()
284 try:
285 try:
285 config_files.remove('setup.cfg')
286 config_files.remove('setup.cfg')
286 except ValueError:
287 except ValueError:
287 pass
288 pass
288 dist.parse_config_files(config_files)
289 dist.parse_config_files(config_files)
289 build_extension = build_ext(dist)
290 build_extension = build_ext(dist)
290 build_extension.finalize_options()
291 build_extension.finalize_options()
291 return build_extension
292 return build_extension
292
293
293 @staticmethod
294 @staticmethod
294 def clean_annotated_html(html):
295 def clean_annotated_html(html):
295 """Clean up the annotated HTML source.
296 """Clean up the annotated HTML source.
296
297
297 Strips the link to the generated C or C++ file, which we do not
298 Strips the link to the generated C or C++ file, which we do not
298 present to the user.
299 present to the user.
299 """
300 """
300 r = re.compile('<p>Raw output: <a href="(.*)">(.*)</a>')
301 r = re.compile('<p>Raw output: <a href="(.*)">(.*)</a>')
301 html = '\n'.join(l for l in html.splitlines() if not r.match(l))
302 html = '\n'.join(l for l in html.splitlines() if not r.match(l))
302 return html
303 return html
303
304
304 __doc__ = __doc__.format(
305 __doc__ = __doc__.format(
305 CYTHON_DOC = ' '*8 + CythonMagics.cython.__doc__,
306 CYTHON_DOC = ' '*8 + CythonMagics.cython.__doc__,
306 CYTHON_INLINE_DOC = ' '*8 + CythonMagics.cython_inline.__doc__,
307 CYTHON_INLINE_DOC = ' '*8 + CythonMagics.cython_inline.__doc__,
307 CYTHON_PYXIMPORT_DOC = ' '*8 + CythonMagics.cython_pyximport.__doc__,
308 CYTHON_PYXIMPORT_DOC = ' '*8 + CythonMagics.cython_pyximport.__doc__,
308 )
309 )
309
310
310 def load_ipython_extension(ip):
311 def load_ipython_extension(ip):
311 """Load the extension in IPython."""
312 """Load the extension in IPython."""
312 ip.register_magics(CythonMagics)
313 ip.register_magics(CythonMagics)
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