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@@ -1,325 +1,334 b'' | |||||
1 | # -*- coding: utf-8 -*- |
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1 | # -*- coding: utf-8 -*- | |
2 | """ |
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2 | """ | |
3 | ===================== |
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3 | ===================== | |
4 | Cython related magics |
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4 | Cython related magics | |
5 | ===================== |
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5 | ===================== | |
6 |
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6 | |||
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7 | Magic command interface for interactive work with Cython | |||
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8 | ||||
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9 | .. note:: | |||
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10 | ||||
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11 | The ``Cython`` package needs to be installed separately. It | |||
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12 | can be obtained using ``easy_install`` or ``pip``. | |||
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13 | ||||
7 | Usage |
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14 | Usage | |
8 | ===== |
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15 | ===== | |
9 |
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16 | |||
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17 | To enable the magics below, execute ``%load_ext cythonmagic``. | |||
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18 | ||||
10 | ``%%cython`` |
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19 | ``%%cython`` | |
11 |
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20 | |||
12 | {CYTHON_DOC} |
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21 | {CYTHON_DOC} | |
13 |
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22 | |||
14 | ``%%cython_inline`` |
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23 | ``%%cython_inline`` | |
15 |
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24 | |||
16 | {CYTHON_INLINE_DOC} |
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25 | {CYTHON_INLINE_DOC} | |
17 |
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26 | |||
18 | ``%%cython_pyximport`` |
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27 | ``%%cython_pyximport`` | |
19 |
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28 | |||
20 | {CYTHON_PYXIMPORT_DOC} |
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29 | {CYTHON_PYXIMPORT_DOC} | |
21 |
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30 | |||
22 | Author: |
|
31 | Author: | |
23 | * Brian Granger |
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32 | * Brian Granger | |
24 |
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33 | |||
25 | Parts of this code were taken from Cython.inline. |
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34 | Parts of this code were taken from Cython.inline. | |
26 | """ |
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35 | """ | |
27 | #----------------------------------------------------------------------------- |
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36 | #----------------------------------------------------------------------------- | |
28 | # Copyright (C) 2010-2011, IPython Development Team. |
|
37 | # Copyright (C) 2010-2011, IPython Development Team. | |
29 | # |
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38 | # | |
30 | # Distributed under the terms of the Modified BSD License. |
|
39 | # Distributed under the terms of the Modified BSD License. | |
31 | # |
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40 | # | |
32 | # The full license is in the file COPYING.txt, distributed with this software. |
|
41 | # The full license is in the file COPYING.txt, distributed with this software. | |
33 | #----------------------------------------------------------------------------- |
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42 | #----------------------------------------------------------------------------- | |
34 |
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43 | |||
35 | from __future__ import print_function |
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44 | from __future__ import print_function | |
36 |
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45 | |||
37 | import imp |
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46 | import imp | |
38 | import io |
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47 | import io | |
39 | import os |
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48 | import os | |
40 | import re |
|
49 | import re | |
41 | import sys |
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50 | import sys | |
42 | import time |
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51 | import time | |
43 |
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52 | |||
44 | try: |
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53 | try: | |
45 | reload |
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54 | reload | |
46 | except NameError: # Python 3 |
|
55 | except NameError: # Python 3 | |
47 | from imp import reload |
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56 | from imp import reload | |
48 |
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57 | |||
49 | try: |
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58 | try: | |
50 | import hashlib |
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59 | import hashlib | |
51 | except ImportError: |
|
60 | except ImportError: | |
52 | import md5 as hashlib |
|
61 | import md5 as hashlib | |
53 |
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62 | |||
54 | from distutils.core import Distribution, Extension |
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63 | from distutils.core import Distribution, Extension | |
55 | from distutils.command.build_ext import build_ext |
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64 | from distutils.command.build_ext import build_ext | |
56 |
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65 | |||
57 | from IPython.core import display |
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66 | from IPython.core import display | |
58 | from IPython.core import magic_arguments |
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67 | from IPython.core import magic_arguments | |
59 | from IPython.core.magic import Magics, magics_class, cell_magic |
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68 | from IPython.core.magic import Magics, magics_class, cell_magic | |
60 | from IPython.utils import py3compat |
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69 | from IPython.utils import py3compat | |
61 | from IPython.utils.path import get_ipython_cache_dir |
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70 | from IPython.utils.path import get_ipython_cache_dir | |
62 |
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71 | |||
63 | import Cython |
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72 | import Cython | |
64 | from Cython.Compiler.Errors import CompileError |
|
73 | from Cython.Compiler.Errors import CompileError | |
65 | from Cython.Build.Dependencies import cythonize |
|
74 | from Cython.Build.Dependencies import cythonize | |
66 |
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75 | |||
67 |
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76 | |||
68 | @magics_class |
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77 | @magics_class | |
69 | class CythonMagics(Magics): |
|
78 | class CythonMagics(Magics): | |
70 |
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79 | |||
71 | def __init__(self, shell): |
|
80 | def __init__(self, shell): | |
72 | super(CythonMagics,self).__init__(shell) |
|
81 | super(CythonMagics,self).__init__(shell) | |
73 | self._reloads = {} |
|
82 | self._reloads = {} | |
74 | self._code_cache = {} |
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83 | self._code_cache = {} | |
75 |
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84 | |||
76 | def _import_all(self, module): |
|
85 | def _import_all(self, module): | |
77 | for k,v in module.__dict__.items(): |
|
86 | for k,v in module.__dict__.items(): | |
78 | if not k.startswith('__'): |
|
87 | if not k.startswith('__'): | |
79 | self.shell.push({k:v}) |
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88 | self.shell.push({k:v}) | |
80 |
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89 | |||
81 | @cell_magic |
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90 | @cell_magic | |
82 | def cython_inline(self, line, cell): |
|
91 | def cython_inline(self, line, cell): | |
83 | """Compile and run a Cython code cell using Cython.inline. |
|
92 | """Compile and run a Cython code cell using Cython.inline. | |
84 |
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93 | |||
85 | This magic simply passes the body of the cell to Cython.inline |
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94 | 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 |
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95 | 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 |
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96 | in the user's namespace, here is a simple example that returns | |
88 | their sum:: |
|
97 | their sum:: | |
89 |
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98 | |||
90 | %%cython_inline |
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99 | %%cython_inline | |
91 | return a+b |
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100 | return a+b | |
92 |
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101 | |||
93 | For most purposes, we recommend the usage of the `%%cython` magic. |
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102 | For most purposes, we recommend the usage of the `%%cython` magic. | |
94 | """ |
|
103 | """ | |
95 | locs = self.shell.user_global_ns |
|
104 | locs = self.shell.user_global_ns | |
96 | globs = self.shell.user_ns |
|
105 | globs = self.shell.user_ns | |
97 | return Cython.inline(cell, locals=locs, globals=globs) |
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106 | return Cython.inline(cell, locals=locs, globals=globs) | |
98 |
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107 | |||
99 | @cell_magic |
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108 | @cell_magic | |
100 | def cython_pyximport(self, line, cell): |
|
109 | def cython_pyximport(self, line, cell): | |
101 | """Compile and import a Cython code cell using pyximport. |
|
110 | """Compile and import a Cython code cell using pyximport. | |
102 |
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111 | |||
103 | The contents of the cell are written to a `.pyx` file in the current |
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112 | The contents of the cell are written to a `.pyx` file in the current | |
104 | working directory, which is then imported using `pyximport`. This |
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113 | working directory, which is then imported using `pyximport`. This | |
105 | magic requires a module name to be passed:: |
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114 | magic requires a module name to be passed:: | |
106 |
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115 | |||
107 | %%cython_pyximport modulename |
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116 | %%cython_pyximport modulename | |
108 | def f(x): |
|
117 | def f(x): | |
109 | return 2.0*x |
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118 | return 2.0*x | |
110 |
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119 | |||
111 | The compiled module is then imported and all of its symbols are |
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120 | The compiled module is then imported and all of its symbols are | |
112 | injected into the user's namespace. For most purposes, we recommend |
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121 | injected into the user's namespace. For most purposes, we recommend | |
113 | the usage of the `%%cython` magic. |
|
122 | the usage of the `%%cython` magic. | |
114 | """ |
|
123 | """ | |
115 | module_name = line.strip() |
|
124 | module_name = line.strip() | |
116 | if not module_name: |
|
125 | if not module_name: | |
117 | raise ValueError('module name must be given') |
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126 | raise ValueError('module name must be given') | |
118 | fname = module_name + '.pyx' |
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127 | fname = module_name + '.pyx' | |
119 | with io.open(fname, 'w', encoding='utf-8') as f: |
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128 | with io.open(fname, 'w', encoding='utf-8') as f: | |
120 | f.write(cell) |
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129 | f.write(cell) | |
121 | if 'pyximport' not in sys.modules: |
|
130 | if 'pyximport' not in sys.modules: | |
122 | import pyximport |
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131 | import pyximport | |
123 | pyximport.install(reload_support=True) |
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132 | pyximport.install(reload_support=True) | |
124 | if module_name in self._reloads: |
|
133 | if module_name in self._reloads: | |
125 | module = self._reloads[module_name] |
|
134 | module = self._reloads[module_name] | |
126 | reload(module) |
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135 | reload(module) | |
127 | else: |
|
136 | else: | |
128 | __import__(module_name) |
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137 | __import__(module_name) | |
129 | module = sys.modules[module_name] |
|
138 | module = sys.modules[module_name] | |
130 | self._reloads[module_name] = module |
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139 | self._reloads[module_name] = module | |
131 | self._import_all(module) |
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140 | self._import_all(module) | |
132 |
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141 | |||
133 | @magic_arguments.magic_arguments() |
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142 | @magic_arguments.magic_arguments() | |
134 | @magic_arguments.argument( |
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143 | @magic_arguments.argument( | |
135 | '-c', '--compile-args', action='append', default=[], |
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144 | '-c', '--compile-args', action='append', default=[], | |
136 | help="Extra flags to pass to compiler via the `extra_compile_args` " |
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145 | help="Extra flags to pass to compiler via the `extra_compile_args` " | |
137 | "Extension flag (can be specified multiple times)." |
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146 | "Extension flag (can be specified multiple times)." | |
138 | ) |
|
147 | ) | |
139 | @magic_arguments.argument( |
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148 | @magic_arguments.argument( | |
140 | '--link-args', action='append', default=[], |
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149 | '--link-args', action='append', default=[], | |
141 | help="Extra flags to pass to linker via the `extra_link_args` " |
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150 | help="Extra flags to pass to linker via the `extra_link_args` " | |
142 | "Extension flag (can be specified multiple times)." |
|
151 | "Extension flag (can be specified multiple times)." | |
143 | ) |
|
152 | ) | |
144 | @magic_arguments.argument( |
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153 | @magic_arguments.argument( | |
145 | '-l', '--lib', action='append', default=[], |
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154 | '-l', '--lib', action='append', default=[], | |
146 | help="Add a library to link the extension against (can be specified " |
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155 | help="Add a library to link the extension against (can be specified " | |
147 | "multiple times)." |
|
156 | "multiple times)." | |
148 | ) |
|
157 | ) | |
149 | @magic_arguments.argument( |
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158 | @magic_arguments.argument( | |
150 | '-L', dest='library_dirs', metavar='dir', action='append', default=[], |
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159 | '-L', dest='library_dirs', metavar='dir', action='append', default=[], | |
151 | help="Add a path to the list of libary directories (can be specified " |
|
160 | help="Add a path to the list of libary directories (can be specified " | |
152 | "multiple times)." |
|
161 | "multiple times)." | |
153 | ) |
|
162 | ) | |
154 | @magic_arguments.argument( |
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163 | @magic_arguments.argument( | |
155 | '-I', '--include', action='append', default=[], |
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164 | '-I', '--include', action='append', default=[], | |
156 | help="Add a path to the list of include directories (can be specified " |
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165 | help="Add a path to the list of include directories (can be specified " | |
157 | "multiple times)." |
|
166 | "multiple times)." | |
158 | ) |
|
167 | ) | |
159 | @magic_arguments.argument( |
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168 | @magic_arguments.argument( | |
160 | '-+', '--cplus', action='store_true', default=False, |
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169 | '-+', '--cplus', action='store_true', default=False, | |
161 | help="Output a C++ rather than C file." |
|
170 | help="Output a C++ rather than C file." | |
162 | ) |
|
171 | ) | |
163 | @magic_arguments.argument( |
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172 | @magic_arguments.argument( | |
164 | '-f', '--force', action='store_true', default=False, |
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173 | '-f', '--force', action='store_true', default=False, | |
165 | help="Force the compilation of a new module, even if the source has been " |
|
174 | help="Force the compilation of a new module, even if the source has been " | |
166 | "previously compiled." |
|
175 | "previously compiled." | |
167 | ) |
|
176 | ) | |
168 | @magic_arguments.argument( |
|
177 | @magic_arguments.argument( | |
169 | '-a', '--annotate', action='store_true', default=False, |
|
178 | '-a', '--annotate', action='store_true', default=False, | |
170 | help="Produce a colorized HTML version of the source." |
|
179 | help="Produce a colorized HTML version of the source." | |
171 | ) |
|
180 | ) | |
172 | @cell_magic |
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181 | @cell_magic | |
173 | def cython(self, line, cell): |
|
182 | def cython(self, line, cell): | |
174 | """Compile and import everything from a Cython code cell. |
|
183 | """Compile and import everything from a Cython code cell. | |
175 |
|
184 | |||
176 | The contents of the cell are written to a `.pyx` file in the |
|
185 | 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 |
|
186 | directory `IPYTHONDIR/cython` using a filename with the hash of the | |
178 | code. This file is then cythonized and compiled. The resulting module |
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187 | 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 |
|
188 | 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 |
|
189 | namespace. The usage is similar to that of `%%cython_pyximport` but | |
181 | you don't have to pass a module name:: |
|
190 | you don't have to pass a module name:: | |
182 |
|
191 | |||
183 | %%cython |
|
192 | %%cython | |
184 | def f(x): |
|
193 | def f(x): | |
185 | return 2.0*x |
|
194 | return 2.0*x | |
186 |
|
195 | |||
187 | To compile OpenMP codes, pass the required `--compile-args` |
|
196 | To compile OpenMP codes, pass the required `--compile-args` | |
188 | and `--link-args`. For example with gcc:: |
|
197 | and `--link-args`. For example with gcc:: | |
189 |
|
198 | |||
190 | %%cython --compile-args=-fopenmp --link-args=-fopenmp |
|
199 | %%cython --compile-args=-fopenmp --link-args=-fopenmp | |
191 | ... |
|
200 | ... | |
192 | """ |
|
201 | """ | |
193 | args = magic_arguments.parse_argstring(self.cython, line) |
|
202 | args = magic_arguments.parse_argstring(self.cython, line) | |
194 | code = cell if cell.endswith('\n') else cell+'\n' |
|
203 | code = cell if cell.endswith('\n') else cell+'\n' | |
195 | lib_dir = os.path.join(get_ipython_cache_dir(), 'cython') |
|
204 | lib_dir = os.path.join(get_ipython_cache_dir(), 'cython') | |
196 | quiet = True |
|
205 | quiet = True | |
197 | key = code, sys.version_info, sys.executable, Cython.__version__ |
|
206 | key = code, sys.version_info, sys.executable, Cython.__version__ | |
198 |
|
207 | |||
199 | if not os.path.exists(lib_dir): |
|
208 | if not os.path.exists(lib_dir): | |
200 | os.makedirs(lib_dir) |
|
209 | os.makedirs(lib_dir) | |
201 |
|
210 | |||
202 | if args.force: |
|
211 | if args.force: | |
203 | # Force a new module name by adding the current time to the |
|
212 | # Force a new module name by adding the current time to the | |
204 | # key which is hashed to determine the module name. |
|
213 | # key which is hashed to determine the module name. | |
205 | key += time.time(), |
|
214 | key += time.time(), | |
206 |
|
215 | |||
207 | module_name = "_cython_magic_" + hashlib.md5(str(key).encode('utf-8')).hexdigest() |
|
216 | 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) |
|
217 | module_path = os.path.join(lib_dir, module_name + self.so_ext) | |
209 |
|
218 | |||
210 | have_module = os.path.isfile(module_path) |
|
219 | have_module = os.path.isfile(module_path) | |
211 | need_cythonize = not have_module |
|
220 | need_cythonize = not have_module | |
212 |
|
221 | |||
213 | if args.annotate: |
|
222 | if args.annotate: | |
214 | html_file = os.path.join(lib_dir, module_name + '.html') |
|
223 | html_file = os.path.join(lib_dir, module_name + '.html') | |
215 | if not os.path.isfile(html_file): |
|
224 | if not os.path.isfile(html_file): | |
216 | need_cythonize = True |
|
225 | need_cythonize = True | |
217 |
|
226 | |||
218 | if need_cythonize: |
|
227 | if need_cythonize: | |
219 | c_include_dirs = args.include |
|
228 | c_include_dirs = args.include | |
220 | if 'numpy' in code: |
|
229 | if 'numpy' in code: | |
221 | import numpy |
|
230 | import numpy | |
222 | c_include_dirs.append(numpy.get_include()) |
|
231 | c_include_dirs.append(numpy.get_include()) | |
223 | pyx_file = os.path.join(lib_dir, module_name + '.pyx') |
|
232 | pyx_file = os.path.join(lib_dir, module_name + '.pyx') | |
224 | pyx_file = py3compat.cast_bytes_py2(pyx_file, encoding=sys.getfilesystemencoding()) |
|
233 | pyx_file = py3compat.cast_bytes_py2(pyx_file, encoding=sys.getfilesystemencoding()) | |
225 | with io.open(pyx_file, 'w', encoding='utf-8') as f: |
|
234 | with io.open(pyx_file, 'w', encoding='utf-8') as f: | |
226 | f.write(code) |
|
235 | f.write(code) | |
227 | extension = Extension( |
|
236 | extension = Extension( | |
228 | name = module_name, |
|
237 | name = module_name, | |
229 | sources = [pyx_file], |
|
238 | sources = [pyx_file], | |
230 | include_dirs = c_include_dirs, |
|
239 | include_dirs = c_include_dirs, | |
231 | library_dirs = args.library_dirs, |
|
240 | library_dirs = args.library_dirs, | |
232 | extra_compile_args = args.compile_args, |
|
241 | extra_compile_args = args.compile_args, | |
233 | extra_link_args = args.link_args, |
|
242 | extra_link_args = args.link_args, | |
234 | libraries = args.lib, |
|
243 | libraries = args.lib, | |
235 | language = 'c++' if args.cplus else 'c', |
|
244 | language = 'c++' if args.cplus else 'c', | |
236 | ) |
|
245 | ) | |
237 | build_extension = self._get_build_extension() |
|
246 | build_extension = self._get_build_extension() | |
238 | try: |
|
247 | try: | |
239 | opts = dict( |
|
248 | opts = dict( | |
240 | quiet=quiet, |
|
249 | quiet=quiet, | |
241 | annotate = args.annotate, |
|
250 | annotate = args.annotate, | |
242 | force = True, |
|
251 | force = True, | |
243 | ) |
|
252 | ) | |
244 | build_extension.extensions = cythonize([extension], **opts) |
|
253 | build_extension.extensions = cythonize([extension], **opts) | |
245 | except CompileError: |
|
254 | except CompileError: | |
246 | return |
|
255 | return | |
247 |
|
256 | |||
248 | if not have_module: |
|
257 | if not have_module: | |
249 | build_extension.build_temp = os.path.dirname(pyx_file) |
|
258 | build_extension.build_temp = os.path.dirname(pyx_file) | |
250 | build_extension.build_lib = lib_dir |
|
259 | build_extension.build_lib = lib_dir | |
251 | build_extension.run() |
|
260 | build_extension.run() | |
252 | self._code_cache[key] = module_name |
|
261 | self._code_cache[key] = module_name | |
253 |
|
262 | |||
254 | module = imp.load_dynamic(module_name, module_path) |
|
263 | module = imp.load_dynamic(module_name, module_path) | |
255 | self._import_all(module) |
|
264 | self._import_all(module) | |
256 |
|
265 | |||
257 | if args.annotate: |
|
266 | if args.annotate: | |
258 | try: |
|
267 | try: | |
259 | with io.open(html_file, encoding='utf-8') as f: |
|
268 | with io.open(html_file, encoding='utf-8') as f: | |
260 | annotated_html = f.read() |
|
269 | annotated_html = f.read() | |
261 | except IOError as e: |
|
270 | except IOError as e: | |
262 | # File could not be opened. Most likely the user has a version |
|
271 | # File could not be opened. Most likely the user has a version | |
263 | # of Cython before 0.15.1 (when `cythonize` learned the |
|
272 | # of Cython before 0.15.1 (when `cythonize` learned the | |
264 | # `force` keyword argument) and has already compiled this |
|
273 | # `force` keyword argument) and has already compiled this | |
265 | # exact source without annotation. |
|
274 | # exact source without annotation. | |
266 | print('Cython completed successfully but the annotated ' |
|
275 | print('Cython completed successfully but the annotated ' | |
267 | 'source could not be read.', file=sys.stderr) |
|
276 | 'source could not be read.', file=sys.stderr) | |
268 | print(e, file=sys.stderr) |
|
277 | print(e, file=sys.stderr) | |
269 | else: |
|
278 | else: | |
270 | return display.HTML(self.clean_annotated_html(annotated_html)) |
|
279 | return display.HTML(self.clean_annotated_html(annotated_html)) | |
271 |
|
280 | |||
272 | @property |
|
281 | @property | |
273 | def so_ext(self): |
|
282 | def so_ext(self): | |
274 | """The extension suffix for compiled modules.""" |
|
283 | """The extension suffix for compiled modules.""" | |
275 | try: |
|
284 | try: | |
276 | return self._so_ext |
|
285 | return self._so_ext | |
277 | except AttributeError: |
|
286 | except AttributeError: | |
278 | self._so_ext = self._get_build_extension().get_ext_filename('') |
|
287 | self._so_ext = self._get_build_extension().get_ext_filename('') | |
279 | return self._so_ext |
|
288 | return self._so_ext | |
280 |
|
289 | |||
281 | def _clear_distutils_mkpath_cache(self): |
|
290 | def _clear_distutils_mkpath_cache(self): | |
282 | """clear distutils mkpath cache |
|
291 | """clear distutils mkpath cache | |
283 |
|
292 | |||
284 | prevents distutils from skipping re-creation of dirs that have been removed |
|
293 | prevents distutils from skipping re-creation of dirs that have been removed | |
285 | """ |
|
294 | """ | |
286 | try: |
|
295 | try: | |
287 | from distutils.dir_util import _path_created |
|
296 | from distutils.dir_util import _path_created | |
288 | except ImportError: |
|
297 | except ImportError: | |
289 | pass |
|
298 | pass | |
290 | else: |
|
299 | else: | |
291 | _path_created.clear() |
|
300 | _path_created.clear() | |
292 |
|
301 | |||
293 | def _get_build_extension(self): |
|
302 | def _get_build_extension(self): | |
294 | self._clear_distutils_mkpath_cache() |
|
303 | self._clear_distutils_mkpath_cache() | |
295 | dist = Distribution() |
|
304 | dist = Distribution() | |
296 | config_files = dist.find_config_files() |
|
305 | config_files = dist.find_config_files() | |
297 | try: |
|
306 | try: | |
298 | config_files.remove('setup.cfg') |
|
307 | config_files.remove('setup.cfg') | |
299 | except ValueError: |
|
308 | except ValueError: | |
300 | pass |
|
309 | pass | |
301 | dist.parse_config_files(config_files) |
|
310 | dist.parse_config_files(config_files) | |
302 | build_extension = build_ext(dist) |
|
311 | build_extension = build_ext(dist) | |
303 | build_extension.finalize_options() |
|
312 | build_extension.finalize_options() | |
304 | return build_extension |
|
313 | return build_extension | |
305 |
|
314 | |||
306 | @staticmethod |
|
315 | @staticmethod | |
307 | def clean_annotated_html(html): |
|
316 | def clean_annotated_html(html): | |
308 | """Clean up the annotated HTML source. |
|
317 | """Clean up the annotated HTML source. | |
309 |
|
318 | |||
310 | Strips the link to the generated C or C++ file, which we do not |
|
319 | Strips the link to the generated C or C++ file, which we do not | |
311 | present to the user. |
|
320 | present to the user. | |
312 | """ |
|
321 | """ | |
313 | r = re.compile('<p>Raw output: <a href="(.*)">(.*)</a>') |
|
322 | r = re.compile('<p>Raw output: <a href="(.*)">(.*)</a>') | |
314 | html = '\n'.join(l for l in html.splitlines() if not r.match(l)) |
|
323 | html = '\n'.join(l for l in html.splitlines() if not r.match(l)) | |
315 | return html |
|
324 | return html | |
316 |
|
325 | |||
317 | __doc__ = __doc__.format( |
|
326 | __doc__ = __doc__.format( | |
318 | CYTHON_DOC = ' '*8 + CythonMagics.cython.__doc__, |
|
327 | CYTHON_DOC = ' '*8 + CythonMagics.cython.__doc__, | |
319 | CYTHON_INLINE_DOC = ' '*8 + CythonMagics.cython_inline.__doc__, |
|
328 | CYTHON_INLINE_DOC = ' '*8 + CythonMagics.cython_inline.__doc__, | |
320 | CYTHON_PYXIMPORT_DOC = ' '*8 + CythonMagics.cython_pyximport.__doc__, |
|
329 | CYTHON_PYXIMPORT_DOC = ' '*8 + CythonMagics.cython_pyximport.__doc__, | |
321 | ) |
|
330 | ) | |
322 |
|
331 | |||
323 | def load_ipython_extension(ip): |
|
332 | def load_ipython_extension(ip): | |
324 | """Load the extension in IPython.""" |
|
333 | """Load the extension in IPython.""" | |
325 | ip.register_magics(CythonMagics) |
|
334 | ip.register_magics(CythonMagics) |
@@ -1,367 +1,371 b'' | |||||
1 | # -*- coding: utf-8 -*- |
|
1 | # -*- coding: utf-8 -*- | |
2 | """ |
|
2 | """ | |
3 | =========== |
|
3 | =========== | |
4 | octavemagic |
|
4 | octavemagic | |
5 | =========== |
|
5 | =========== | |
6 |
|
6 | |||
7 | Magics for interacting with Octave via oct2py. |
|
7 | Magics for interacting with Octave via oct2py. | |
8 |
|
8 | |||
9 | .. note:: |
|
9 | .. note:: | |
10 |
|
10 | |||
11 | The ``oct2py`` module needs to be installed separately and |
|
11 | The ``oct2py`` module needs to be installed separately and | |
12 | can be obtained using ``easy_install`` or ``pip``. |
|
12 | can be obtained using ``easy_install`` or ``pip``. | |
13 |
|
13 | |||
|
14 | You will also need a working copy of GNU Octave. | |||
|
15 | ||||
14 | Usage |
|
16 | Usage | |
15 | ===== |
|
17 | ===== | |
16 |
|
18 | |||
|
19 | To enable the magics below, execute ``%load_ext octavemagic``. | |||
|
20 | ||||
17 | ``%octave`` |
|
21 | ``%octave`` | |
18 |
|
22 | |||
19 | {OCTAVE_DOC} |
|
23 | {OCTAVE_DOC} | |
20 |
|
24 | |||
21 | ``%octave_push`` |
|
25 | ``%octave_push`` | |
22 |
|
26 | |||
23 | {OCTAVE_PUSH_DOC} |
|
27 | {OCTAVE_PUSH_DOC} | |
24 |
|
28 | |||
25 | ``%octave_pull`` |
|
29 | ``%octave_pull`` | |
26 |
|
30 | |||
27 | {OCTAVE_PULL_DOC} |
|
31 | {OCTAVE_PULL_DOC} | |
28 |
|
32 | |||
29 | """ |
|
33 | """ | |
30 |
|
34 | |||
31 | #----------------------------------------------------------------------------- |
|
35 | #----------------------------------------------------------------------------- | |
32 | # Copyright (C) 2012 The IPython Development Team |
|
36 | # Copyright (C) 2012 The IPython Development Team | |
33 | # |
|
37 | # | |
34 | # Distributed under the terms of the BSD License. The full license is in |
|
38 | # Distributed under the terms of the BSD License. The full license is in | |
35 | # the file COPYING, distributed as part of this software. |
|
39 | # the file COPYING, distributed as part of this software. | |
36 | #----------------------------------------------------------------------------- |
|
40 | #----------------------------------------------------------------------------- | |
37 |
|
41 | |||
38 | import tempfile |
|
42 | import tempfile | |
39 | from glob import glob |
|
43 | from glob import glob | |
40 | from shutil import rmtree |
|
44 | from shutil import rmtree | |
41 |
|
45 | |||
42 | import numpy as np |
|
46 | import numpy as np | |
43 | import oct2py |
|
47 | import oct2py | |
44 | from xml.dom import minidom |
|
48 | from xml.dom import minidom | |
45 |
|
49 | |||
46 | from IPython.core.displaypub import publish_display_data |
|
50 | from IPython.core.displaypub import publish_display_data | |
47 | from IPython.core.magic import (Magics, magics_class, line_magic, |
|
51 | from IPython.core.magic import (Magics, magics_class, line_magic, | |
48 | line_cell_magic, needs_local_scope) |
|
52 | line_cell_magic, needs_local_scope) | |
49 | from IPython.testing.skipdoctest import skip_doctest |
|
53 | from IPython.testing.skipdoctest import skip_doctest | |
50 | from IPython.core.magic_arguments import ( |
|
54 | from IPython.core.magic_arguments import ( | |
51 | argument, magic_arguments, parse_argstring |
|
55 | argument, magic_arguments, parse_argstring | |
52 | ) |
|
56 | ) | |
53 | from IPython.utils.py3compat import unicode_to_str |
|
57 | from IPython.utils.py3compat import unicode_to_str | |
54 |
|
58 | |||
55 | class OctaveMagicError(oct2py.Oct2PyError): |
|
59 | class OctaveMagicError(oct2py.Oct2PyError): | |
56 | pass |
|
60 | pass | |
57 |
|
61 | |||
58 | _mimetypes = {'png' : 'image/png', |
|
62 | _mimetypes = {'png' : 'image/png', | |
59 | 'svg' : 'image/svg+xml', |
|
63 | 'svg' : 'image/svg+xml', | |
60 | 'jpg' : 'image/jpeg', |
|
64 | 'jpg' : 'image/jpeg', | |
61 | 'jpeg': 'image/jpeg'} |
|
65 | 'jpeg': 'image/jpeg'} | |
62 |
|
66 | |||
63 | @magics_class |
|
67 | @magics_class | |
64 | class OctaveMagics(Magics): |
|
68 | class OctaveMagics(Magics): | |
65 | """A set of magics useful for interactive work with Octave via oct2py. |
|
69 | """A set of magics useful for interactive work with Octave via oct2py. | |
66 | """ |
|
70 | """ | |
67 | def __init__(self, shell): |
|
71 | def __init__(self, shell): | |
68 | """ |
|
72 | """ | |
69 | Parameters |
|
73 | Parameters | |
70 | ---------- |
|
74 | ---------- | |
71 | shell : IPython shell |
|
75 | shell : IPython shell | |
72 |
|
76 | |||
73 | """ |
|
77 | """ | |
74 | super(OctaveMagics, self).__init__(shell) |
|
78 | super(OctaveMagics, self).__init__(shell) | |
75 | self._oct = oct2py.Oct2Py() |
|
79 | self._oct = oct2py.Oct2Py() | |
76 | self._plot_format = 'png' |
|
80 | self._plot_format = 'png' | |
77 |
|
81 | |||
78 | # Allow publish_display_data to be overridden for |
|
82 | # Allow publish_display_data to be overridden for | |
79 | # testing purposes. |
|
83 | # testing purposes. | |
80 | self._publish_display_data = publish_display_data |
|
84 | self._publish_display_data = publish_display_data | |
81 |
|
85 | |||
82 |
|
86 | |||
83 | def _fix_gnuplot_svg_size(self, image, size=None): |
|
87 | def _fix_gnuplot_svg_size(self, image, size=None): | |
84 | """ |
|
88 | """ | |
85 | GnuPlot SVGs do not have height/width attributes. Set |
|
89 | GnuPlot SVGs do not have height/width attributes. Set | |
86 | these to be the same as the viewBox, so that the browser |
|
90 | these to be the same as the viewBox, so that the browser | |
87 | scales the image correctly. |
|
91 | scales the image correctly. | |
88 |
|
92 | |||
89 | Parameters |
|
93 | Parameters | |
90 | ---------- |
|
94 | ---------- | |
91 | image : str |
|
95 | image : str | |
92 | SVG data. |
|
96 | SVG data. | |
93 | size : tuple of int |
|
97 | size : tuple of int | |
94 | Image width, height. |
|
98 | Image width, height. | |
95 |
|
99 | |||
96 | """ |
|
100 | """ | |
97 | (svg,) = minidom.parseString(image).getElementsByTagName('svg') |
|
101 | (svg,) = minidom.parseString(image).getElementsByTagName('svg') | |
98 | viewbox = svg.getAttribute('viewBox').split(' ') |
|
102 | viewbox = svg.getAttribute('viewBox').split(' ') | |
99 |
|
103 | |||
100 | if size is not None: |
|
104 | if size is not None: | |
101 | width, height = size |
|
105 | width, height = size | |
102 | else: |
|
106 | else: | |
103 | width, height = viewbox[2:] |
|
107 | width, height = viewbox[2:] | |
104 |
|
108 | |||
105 | svg.setAttribute('width', '%dpx' % width) |
|
109 | svg.setAttribute('width', '%dpx' % width) | |
106 | svg.setAttribute('height', '%dpx' % height) |
|
110 | svg.setAttribute('height', '%dpx' % height) | |
107 | return svg.toxml() |
|
111 | return svg.toxml() | |
108 |
|
112 | |||
109 |
|
113 | |||
110 | @skip_doctest |
|
114 | @skip_doctest | |
111 | @line_magic |
|
115 | @line_magic | |
112 | def octave_push(self, line): |
|
116 | def octave_push(self, line): | |
113 | ''' |
|
117 | ''' | |
114 | Line-level magic that pushes a variable to Octave. |
|
118 | Line-level magic that pushes a variable to Octave. | |
115 |
|
119 | |||
116 | `line` should be made up of whitespace separated variable names in the |
|
120 | `line` should be made up of whitespace separated variable names in the | |
117 | IPython namespace:: |
|
121 | IPython namespace:: | |
118 |
|
122 | |||
119 | In [7]: import numpy as np |
|
123 | In [7]: import numpy as np | |
120 |
|
124 | |||
121 | In [8]: X = np.arange(5) |
|
125 | In [8]: X = np.arange(5) | |
122 |
|
126 | |||
123 | In [9]: X.mean() |
|
127 | In [9]: X.mean() | |
124 | Out[9]: 2.0 |
|
128 | Out[9]: 2.0 | |
125 |
|
129 | |||
126 | In [10]: %octave_push X |
|
130 | In [10]: %octave_push X | |
127 |
|
131 | |||
128 | In [11]: %octave mean(X) |
|
132 | In [11]: %octave mean(X) | |
129 | Out[11]: 2.0 |
|
133 | Out[11]: 2.0 | |
130 |
|
134 | |||
131 | ''' |
|
135 | ''' | |
132 | inputs = line.split(' ') |
|
136 | inputs = line.split(' ') | |
133 | for input in inputs: |
|
137 | for input in inputs: | |
134 | input = unicode_to_str(input) |
|
138 | input = unicode_to_str(input) | |
135 | self._oct.put(input, self.shell.user_ns[input]) |
|
139 | self._oct.put(input, self.shell.user_ns[input]) | |
136 |
|
140 | |||
137 |
|
141 | |||
138 | @skip_doctest |
|
142 | @skip_doctest | |
139 | @line_magic |
|
143 | @line_magic | |
140 | def octave_pull(self, line): |
|
144 | def octave_pull(self, line): | |
141 | ''' |
|
145 | ''' | |
142 | Line-level magic that pulls a variable from Octave. |
|
146 | Line-level magic that pulls a variable from Octave. | |
143 |
|
147 | |||
144 | In [18]: _ = %octave x = [1 2; 3 4]; y = 'hello' |
|
148 | In [18]: _ = %octave x = [1 2; 3 4]; y = 'hello' | |
145 |
|
149 | |||
146 | In [19]: %octave_pull x y |
|
150 | In [19]: %octave_pull x y | |
147 |
|
151 | |||
148 | In [20]: x |
|
152 | In [20]: x | |
149 | Out[20]: |
|
153 | Out[20]: | |
150 | array([[ 1., 2.], |
|
154 | array([[ 1., 2.], | |
151 | [ 3., 4.]]) |
|
155 | [ 3., 4.]]) | |
152 |
|
156 | |||
153 | In [21]: y |
|
157 | In [21]: y | |
154 | Out[21]: 'hello' |
|
158 | Out[21]: 'hello' | |
155 |
|
159 | |||
156 | ''' |
|
160 | ''' | |
157 | outputs = line.split(' ') |
|
161 | outputs = line.split(' ') | |
158 | for output in outputs: |
|
162 | for output in outputs: | |
159 | output = unicode_to_str(output) |
|
163 | output = unicode_to_str(output) | |
160 | self.shell.push({output: self._oct.get(output)}) |
|
164 | self.shell.push({output: self._oct.get(output)}) | |
161 |
|
165 | |||
162 |
|
166 | |||
163 | @skip_doctest |
|
167 | @skip_doctest | |
164 | @magic_arguments() |
|
168 | @magic_arguments() | |
165 | @argument( |
|
169 | @argument( | |
166 | '-i', '--input', action='append', |
|
170 | '-i', '--input', action='append', | |
167 | help='Names of input variables to be pushed to Octave. Multiple names ' |
|
171 | help='Names of input variables to be pushed to Octave. Multiple names ' | |
168 | 'can be passed, separated by commas with no whitespace.' |
|
172 | 'can be passed, separated by commas with no whitespace.' | |
169 | ) |
|
173 | ) | |
170 | @argument( |
|
174 | @argument( | |
171 | '-o', '--output', action='append', |
|
175 | '-o', '--output', action='append', | |
172 | help='Names of variables to be pulled from Octave after executing cell ' |
|
176 | help='Names of variables to be pulled from Octave after executing cell ' | |
173 | 'body. Multiple names can be passed, separated by commas with no ' |
|
177 | 'body. Multiple names can be passed, separated by commas with no ' | |
174 | 'whitespace.' |
|
178 | 'whitespace.' | |
175 | ) |
|
179 | ) | |
176 | @argument( |
|
180 | @argument( | |
177 | '-s', '--size', action='store', |
|
181 | '-s', '--size', action='store', | |
178 | help='Pixel size of plots, "width,height". Default is "-s 400,250".' |
|
182 | help='Pixel size of plots, "width,height". Default is "-s 400,250".' | |
179 | ) |
|
183 | ) | |
180 | @argument( |
|
184 | @argument( | |
181 | '-f', '--format', action='store', |
|
185 | '-f', '--format', action='store', | |
182 | help='Plot format (png, svg or jpg).' |
|
186 | help='Plot format (png, svg or jpg).' | |
183 | ) |
|
187 | ) | |
184 |
|
188 | |||
185 | @needs_local_scope |
|
189 | @needs_local_scope | |
186 | @argument( |
|
190 | @argument( | |
187 | 'code', |
|
191 | 'code', | |
188 | nargs='*', |
|
192 | nargs='*', | |
189 | ) |
|
193 | ) | |
190 | @line_cell_magic |
|
194 | @line_cell_magic | |
191 | def octave(self, line, cell=None, local_ns=None): |
|
195 | def octave(self, line, cell=None, local_ns=None): | |
192 | ''' |
|
196 | ''' | |
193 | Execute code in Octave, and pull some of the results back into the |
|
197 | Execute code in Octave, and pull some of the results back into the | |
194 | Python namespace. |
|
198 | Python namespace. | |
195 |
|
199 | |||
196 | In [9]: %octave X = [1 2; 3 4]; mean(X) |
|
200 | In [9]: %octave X = [1 2; 3 4]; mean(X) | |
197 | Out[9]: array([[ 2., 3.]]) |
|
201 | Out[9]: array([[ 2., 3.]]) | |
198 |
|
202 | |||
199 | As a cell, this will run a block of Octave code, without returning any |
|
203 | As a cell, this will run a block of Octave code, without returning any | |
200 | value:: |
|
204 | value:: | |
201 |
|
205 | |||
202 | In [10]: %%octave |
|
206 | In [10]: %%octave | |
203 | ....: p = [-2, -1, 0, 1, 2] |
|
207 | ....: p = [-2, -1, 0, 1, 2] | |
204 | ....: polyout(p, 'x') |
|
208 | ....: polyout(p, 'x') | |
205 |
|
209 | |||
206 | -2*x^4 - 1*x^3 + 0*x^2 + 1*x^1 + 2 |
|
210 | -2*x^4 - 1*x^3 + 0*x^2 + 1*x^1 + 2 | |
207 |
|
211 | |||
208 | In the notebook, plots are published as the output of the cell, e.g. |
|
212 | In the notebook, plots are published as the output of the cell, e.g. | |
209 |
|
213 | |||
210 | %octave plot([1 2 3], [4 5 6]) |
|
214 | %octave plot([1 2 3], [4 5 6]) | |
211 |
|
215 | |||
212 | will create a line plot. |
|
216 | will create a line plot. | |
213 |
|
217 | |||
214 | Objects can be passed back and forth between Octave and IPython via the |
|
218 | Objects can be passed back and forth between Octave and IPython via the | |
215 | -i and -o flags in line:: |
|
219 | -i and -o flags in line:: | |
216 |
|
220 | |||
217 | In [14]: Z = np.array([1, 4, 5, 10]) |
|
221 | In [14]: Z = np.array([1, 4, 5, 10]) | |
218 |
|
222 | |||
219 | In [15]: %octave -i Z mean(Z) |
|
223 | In [15]: %octave -i Z mean(Z) | |
220 | Out[15]: array([ 5.]) |
|
224 | Out[15]: array([ 5.]) | |
221 |
|
225 | |||
222 |
|
226 | |||
223 | In [16]: %octave -o W W = Z * mean(Z) |
|
227 | In [16]: %octave -o W W = Z * mean(Z) | |
224 | Out[16]: array([ 5., 20., 25., 50.]) |
|
228 | Out[16]: array([ 5., 20., 25., 50.]) | |
225 |
|
229 | |||
226 | In [17]: W |
|
230 | In [17]: W | |
227 | Out[17]: array([ 5., 20., 25., 50.]) |
|
231 | Out[17]: array([ 5., 20., 25., 50.]) | |
228 |
|
232 | |||
229 | The size and format of output plots can be specified:: |
|
233 | The size and format of output plots can be specified:: | |
230 |
|
234 | |||
231 | In [18]: %%octave -s 600,800 -f svg |
|
235 | In [18]: %%octave -s 600,800 -f svg | |
232 | ...: plot([1, 2, 3]); |
|
236 | ...: plot([1, 2, 3]); | |
233 |
|
237 | |||
234 | ''' |
|
238 | ''' | |
235 | args = parse_argstring(self.octave, line) |
|
239 | args = parse_argstring(self.octave, line) | |
236 |
|
240 | |||
237 | # arguments 'code' in line are prepended to the cell lines |
|
241 | # arguments 'code' in line are prepended to the cell lines | |
238 | if cell is None: |
|
242 | if cell is None: | |
239 | code = '' |
|
243 | code = '' | |
240 | return_output = True |
|
244 | return_output = True | |
241 | else: |
|
245 | else: | |
242 | code = cell |
|
246 | code = cell | |
243 | return_output = False |
|
247 | return_output = False | |
244 |
|
248 | |||
245 | code = ' '.join(args.code) + code |
|
249 | code = ' '.join(args.code) + code | |
246 |
|
250 | |||
247 | # if there is no local namespace then default to an empty dict |
|
251 | # if there is no local namespace then default to an empty dict | |
248 | if local_ns is None: |
|
252 | if local_ns is None: | |
249 | local_ns = {} |
|
253 | local_ns = {} | |
250 |
|
254 | |||
251 | if args.input: |
|
255 | if args.input: | |
252 | for input in ','.join(args.input).split(','): |
|
256 | for input in ','.join(args.input).split(','): | |
253 | input = unicode_to_str(input) |
|
257 | input = unicode_to_str(input) | |
254 | try: |
|
258 | try: | |
255 | val = local_ns[input] |
|
259 | val = local_ns[input] | |
256 | except KeyError: |
|
260 | except KeyError: | |
257 | val = self.shell.user_ns[input] |
|
261 | val = self.shell.user_ns[input] | |
258 | self._oct.put(input, val) |
|
262 | self._oct.put(input, val) | |
259 |
|
263 | |||
260 | # generate plots in a temporary directory |
|
264 | # generate plots in a temporary directory | |
261 | plot_dir = tempfile.mkdtemp().replace('\\', '/') |
|
265 | plot_dir = tempfile.mkdtemp().replace('\\', '/') | |
262 | if args.size is not None: |
|
266 | if args.size is not None: | |
263 | size = args.size |
|
267 | size = args.size | |
264 | else: |
|
268 | else: | |
265 | size = '400,240' |
|
269 | size = '400,240' | |
266 |
|
270 | |||
267 | if args.format is not None: |
|
271 | if args.format is not None: | |
268 | plot_format = args.format |
|
272 | plot_format = args.format | |
269 | else: |
|
273 | else: | |
270 | plot_format = 'png' |
|
274 | plot_format = 'png' | |
271 |
|
275 | |||
272 | pre_call = ''' |
|
276 | pre_call = ''' | |
273 | global __ipy_figures = []; |
|
277 | global __ipy_figures = []; | |
274 | page_screen_output(0); |
|
278 | page_screen_output(0); | |
275 |
|
279 | |||
276 | function fig_create(src, event) |
|
280 | function fig_create(src, event) | |
277 | global __ipy_figures; |
|
281 | global __ipy_figures; | |
278 | __ipy_figures(size(__ipy_figures) + 1) = src; |
|
282 | __ipy_figures(size(__ipy_figures) + 1) = src; | |
279 | set(src, "visible", "off"); |
|
283 | set(src, "visible", "off"); | |
280 | end |
|
284 | end | |
281 |
|
285 | |||
282 | set(0, 'DefaultFigureCreateFcn', @fig_create); |
|
286 | set(0, 'DefaultFigureCreateFcn', @fig_create); | |
283 |
|
287 | |||
284 | close all; |
|
288 | close all; | |
285 | clear ans; |
|
289 | clear ans; | |
286 |
|
290 | |||
287 | # ___<end_pre_call>___ # |
|
291 | # ___<end_pre_call>___ # | |
288 | ''' |
|
292 | ''' | |
289 |
|
293 | |||
290 | post_call = ''' |
|
294 | post_call = ''' | |
291 | # ___<start_post_call>___ # |
|
295 | # ___<start_post_call>___ # | |
292 |
|
296 | |||
293 | # Save output of the last execution |
|
297 | # Save output of the last execution | |
294 | if exist("ans") == 1 |
|
298 | if exist("ans") == 1 | |
295 | _ = ans; |
|
299 | _ = ans; | |
296 | else |
|
300 | else | |
297 | _ = nan; |
|
301 | _ = nan; | |
298 | end |
|
302 | end | |
299 |
|
303 | |||
300 | for f = __ipy_figures |
|
304 | for f = __ipy_figures | |
301 | outfile = sprintf('%(plot_dir)s/__ipy_oct_fig_%%03d.png', f); |
|
305 | outfile = sprintf('%(plot_dir)s/__ipy_oct_fig_%%03d.png', f); | |
302 | try |
|
306 | try | |
303 | print(f, outfile, '-d%(plot_format)s', '-tight', '-S%(size)s'); |
|
307 | print(f, outfile, '-d%(plot_format)s', '-tight', '-S%(size)s'); | |
304 | end |
|
308 | end | |
305 | end |
|
309 | end | |
306 |
|
310 | |||
307 | ''' % locals() |
|
311 | ''' % locals() | |
308 |
|
312 | |||
309 | code = ' '.join((pre_call, code, post_call)) |
|
313 | code = ' '.join((pre_call, code, post_call)) | |
310 | try: |
|
314 | try: | |
311 | text_output = self._oct.run(code, verbose=False) |
|
315 | text_output = self._oct.run(code, verbose=False) | |
312 | except (oct2py.Oct2PyError) as exception: |
|
316 | except (oct2py.Oct2PyError) as exception: | |
313 | msg = exception.message |
|
317 | msg = exception.message | |
314 | msg = msg.split('# ___<end_pre_call>___ #')[1] |
|
318 | msg = msg.split('# ___<end_pre_call>___ #')[1] | |
315 | msg = msg.split('# ___<start_post_call>___ #')[0] |
|
319 | msg = msg.split('# ___<start_post_call>___ #')[0] | |
316 | raise OctaveMagicError('Octave could not complete execution. ' |
|
320 | raise OctaveMagicError('Octave could not complete execution. ' | |
317 | 'Traceback (currently broken in oct2py): %s' |
|
321 | 'Traceback (currently broken in oct2py): %s' | |
318 | % msg) |
|
322 | % msg) | |
319 |
|
323 | |||
320 | key = 'OctaveMagic.Octave' |
|
324 | key = 'OctaveMagic.Octave' | |
321 | display_data = [] |
|
325 | display_data = [] | |
322 |
|
326 | |||
323 | # Publish text output |
|
327 | # Publish text output | |
324 | if text_output: |
|
328 | if text_output: | |
325 | display_data.append((key, {'text/plain': text_output})) |
|
329 | display_data.append((key, {'text/plain': text_output})) | |
326 |
|
330 | |||
327 | # Publish images |
|
331 | # Publish images | |
328 | images = [open(imgfile, 'rb').read() for imgfile in \ |
|
332 | images = [open(imgfile, 'rb').read() for imgfile in \ | |
329 | glob("%s/*" % plot_dir)] |
|
333 | glob("%s/*" % plot_dir)] | |
330 | rmtree(plot_dir) |
|
334 | rmtree(plot_dir) | |
331 |
|
335 | |||
332 | plot_mime_type = _mimetypes.get(plot_format, 'image/png') |
|
336 | plot_mime_type = _mimetypes.get(plot_format, 'image/png') | |
333 | width, height = [int(s) for s in size.split(',')] |
|
337 | width, height = [int(s) for s in size.split(',')] | |
334 | for image in images: |
|
338 | for image in images: | |
335 | if plot_format == 'svg': |
|
339 | if plot_format == 'svg': | |
336 | image = self._fix_gnuplot_svg_size(image, size=(width, height)) |
|
340 | image = self._fix_gnuplot_svg_size(image, size=(width, height)) | |
337 | display_data.append((key, {plot_mime_type: image})) |
|
341 | display_data.append((key, {plot_mime_type: image})) | |
338 |
|
342 | |||
339 | if args.output: |
|
343 | if args.output: | |
340 | for output in ','.join(args.output).split(','): |
|
344 | for output in ','.join(args.output).split(','): | |
341 | output = unicode_to_str(output) |
|
345 | output = unicode_to_str(output) | |
342 | self.shell.push({output: self._oct.get(output)}) |
|
346 | self.shell.push({output: self._oct.get(output)}) | |
343 |
|
347 | |||
344 | for source, data in display_data: |
|
348 | for source, data in display_data: | |
345 | self._publish_display_data(source, data) |
|
349 | self._publish_display_data(source, data) | |
346 |
|
350 | |||
347 | if return_output: |
|
351 | if return_output: | |
348 | ans = self._oct.get('_') |
|
352 | ans = self._oct.get('_') | |
349 |
|
353 | |||
350 | # Unfortunately, Octave doesn't have a "None" object, |
|
354 | # Unfortunately, Octave doesn't have a "None" object, | |
351 | # so we can't return any NaN outputs |
|
355 | # so we can't return any NaN outputs | |
352 | if np.isscalar(ans) and np.isnan(ans): |
|
356 | if np.isscalar(ans) and np.isnan(ans): | |
353 | ans = None |
|
357 | ans = None | |
354 |
|
358 | |||
355 | return ans |
|
359 | return ans | |
356 |
|
360 | |||
357 |
|
361 | |||
358 | __doc__ = __doc__.format( |
|
362 | __doc__ = __doc__.format( | |
359 | OCTAVE_DOC = ' '*8 + OctaveMagics.octave.__doc__, |
|
363 | OCTAVE_DOC = ' '*8 + OctaveMagics.octave.__doc__, | |
360 | OCTAVE_PUSH_DOC = ' '*8 + OctaveMagics.octave_push.__doc__, |
|
364 | OCTAVE_PUSH_DOC = ' '*8 + OctaveMagics.octave_push.__doc__, | |
361 | OCTAVE_PULL_DOC = ' '*8 + OctaveMagics.octave_pull.__doc__ |
|
365 | OCTAVE_PULL_DOC = ' '*8 + OctaveMagics.octave_pull.__doc__ | |
362 | ) |
|
366 | ) | |
363 |
|
367 | |||
364 |
|
368 | |||
365 | def load_ipython_extension(ip): |
|
369 | def load_ipython_extension(ip): | |
366 | """Load the extension in IPython.""" |
|
370 | """Load the extension in IPython.""" | |
367 | ip.register_magics(OctaveMagics) |
|
371 | ip.register_magics(OctaveMagics) |
@@ -1,667 +1,676 b'' | |||||
1 | # -*- coding: utf-8 -*- |
|
1 | # -*- coding: utf-8 -*- | |
2 | """ |
|
2 | """ | |
3 | ====== |
|
3 | ====== | |
4 | Rmagic |
|
4 | Rmagic | |
5 | ====== |
|
5 | ====== | |
6 |
|
6 | |||
7 | Magic command interface for interactive work with R via rpy2 |
|
7 | Magic command interface for interactive work with R via rpy2 | |
8 |
|
8 | |||
|
9 | .. note:: | |||
|
10 | ||||
|
11 | The ``rpy2`` package needs to be installed separately. It | |||
|
12 | can be obtained using ``easy_install`` or ``pip``. | |||
|
13 | ||||
|
14 | You will also need a working copy of R. | |||
|
15 | ||||
9 | Usage |
|
16 | Usage | |
10 | ===== |
|
17 | ===== | |
11 |
|
18 | |||
|
19 | To enable the magics below, execute ``%load_ext rmagic``. | |||
|
20 | ||||
12 | ``%R`` |
|
21 | ``%R`` | |
13 |
|
22 | |||
14 | {R_DOC} |
|
23 | {R_DOC} | |
15 |
|
24 | |||
16 | ``%Rpush`` |
|
25 | ``%Rpush`` | |
17 |
|
26 | |||
18 | {RPUSH_DOC} |
|
27 | {RPUSH_DOC} | |
19 |
|
28 | |||
20 | ``%Rpull`` |
|
29 | ``%Rpull`` | |
21 |
|
30 | |||
22 | {RPULL_DOC} |
|
31 | {RPULL_DOC} | |
23 |
|
32 | |||
24 | ``%Rget`` |
|
33 | ``%Rget`` | |
25 |
|
34 | |||
26 | {RGET_DOC} |
|
35 | {RGET_DOC} | |
27 |
|
36 | |||
28 | """ |
|
37 | """ | |
29 |
|
38 | |||
30 | #----------------------------------------------------------------------------- |
|
39 | #----------------------------------------------------------------------------- | |
31 | # Copyright (C) 2012 The IPython Development Team |
|
40 | # Copyright (C) 2012 The IPython Development Team | |
32 | # |
|
41 | # | |
33 | # Distributed under the terms of the BSD License. The full license is in |
|
42 | # Distributed under the terms of the BSD License. The full license is in | |
34 | # the file COPYING, distributed as part of this software. |
|
43 | # the file COPYING, distributed as part of this software. | |
35 | #----------------------------------------------------------------------------- |
|
44 | #----------------------------------------------------------------------------- | |
36 |
|
45 | |||
37 | import sys |
|
46 | import sys | |
38 | import tempfile |
|
47 | import tempfile | |
39 | from glob import glob |
|
48 | from glob import glob | |
40 | from shutil import rmtree |
|
49 | from shutil import rmtree | |
41 |
|
50 | |||
42 | # numpy and rpy2 imports |
|
51 | # numpy and rpy2 imports | |
43 |
|
52 | |||
44 | import numpy as np |
|
53 | import numpy as np | |
45 |
|
54 | |||
46 | import rpy2.rinterface as ri |
|
55 | import rpy2.rinterface as ri | |
47 | import rpy2.robjects as ro |
|
56 | import rpy2.robjects as ro | |
48 | try: |
|
57 | try: | |
49 | from rpy2.robjects import pandas2ri |
|
58 | from rpy2.robjects import pandas2ri | |
50 | pandas2ri.activate() |
|
59 | pandas2ri.activate() | |
51 | except ImportError: |
|
60 | except ImportError: | |
52 | pandas2ri = None |
|
61 | pandas2ri = None | |
53 | from rpy2.robjects import numpy2ri |
|
62 | from rpy2.robjects import numpy2ri | |
54 | numpy2ri.activate() |
|
63 | numpy2ri.activate() | |
55 |
|
64 | |||
56 | # IPython imports |
|
65 | # IPython imports | |
57 |
|
66 | |||
58 | from IPython.core.displaypub import publish_display_data |
|
67 | from IPython.core.displaypub import publish_display_data | |
59 | from IPython.core.magic import (Magics, magics_class, line_magic, |
|
68 | from IPython.core.magic import (Magics, magics_class, line_magic, | |
60 | line_cell_magic, needs_local_scope) |
|
69 | line_cell_magic, needs_local_scope) | |
61 | from IPython.testing.skipdoctest import skip_doctest |
|
70 | from IPython.testing.skipdoctest import skip_doctest | |
62 | from IPython.core.magic_arguments import ( |
|
71 | from IPython.core.magic_arguments import ( | |
63 | argument, magic_arguments, parse_argstring |
|
72 | argument, magic_arguments, parse_argstring | |
64 | ) |
|
73 | ) | |
65 | from IPython.external.simplegeneric import generic |
|
74 | from IPython.external.simplegeneric import generic | |
66 | from IPython.utils.py3compat import str_to_unicode, unicode_to_str, PY3 |
|
75 | from IPython.utils.py3compat import str_to_unicode, unicode_to_str, PY3 | |
67 |
|
76 | |||
68 | class RInterpreterError(ri.RRuntimeError): |
|
77 | class RInterpreterError(ri.RRuntimeError): | |
69 | """An error when running R code in a %%R magic cell.""" |
|
78 | """An error when running R code in a %%R magic cell.""" | |
70 | def __init__(self, line, err, stdout): |
|
79 | def __init__(self, line, err, stdout): | |
71 | self.line = line |
|
80 | self.line = line | |
72 | self.err = err.rstrip() |
|
81 | self.err = err.rstrip() | |
73 | self.stdout = stdout.rstrip() |
|
82 | self.stdout = stdout.rstrip() | |
74 |
|
83 | |||
75 | def __unicode__(self): |
|
84 | def __unicode__(self): | |
76 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ |
|
85 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ | |
77 | (self.line, self.err) |
|
86 | (self.line, self.err) | |
78 | if self.stdout and (self.stdout != self.err): |
|
87 | if self.stdout and (self.stdout != self.err): | |
79 | s += '\nR stdout:\n' + self.stdout |
|
88 | s += '\nR stdout:\n' + self.stdout | |
80 | return s |
|
89 | return s | |
81 |
|
90 | |||
82 | if PY3: |
|
91 | if PY3: | |
83 | __str__ = __unicode__ |
|
92 | __str__ = __unicode__ | |
84 | else: |
|
93 | else: | |
85 | def __str__(self): |
|
94 | def __str__(self): | |
86 | return unicode_to_str(unicode(self), 'utf-8') |
|
95 | return unicode_to_str(unicode(self), 'utf-8') | |
87 |
|
96 | |||
88 | def Rconverter(Robj, dataframe=False): |
|
97 | def Rconverter(Robj, dataframe=False): | |
89 | """ |
|
98 | """ | |
90 | Convert an object in R's namespace to one suitable |
|
99 | Convert an object in R's namespace to one suitable | |
91 | for ipython's namespace. |
|
100 | for ipython's namespace. | |
92 |
|
101 | |||
93 | For a data.frame, it tries to return a structured array. |
|
102 | For a data.frame, it tries to return a structured array. | |
94 | It first checks for colnames, then names. |
|
103 | It first checks for colnames, then names. | |
95 | If all are NULL, it returns np.asarray(Robj), else |
|
104 | If all are NULL, it returns np.asarray(Robj), else | |
96 | it tries to construct a recarray |
|
105 | it tries to construct a recarray | |
97 |
|
106 | |||
98 | Parameters |
|
107 | Parameters | |
99 | ---------- |
|
108 | ---------- | |
100 |
|
109 | |||
101 | Robj: an R object returned from rpy2 |
|
110 | Robj: an R object returned from rpy2 | |
102 | """ |
|
111 | """ | |
103 | is_data_frame = ro.r('is.data.frame') |
|
112 | is_data_frame = ro.r('is.data.frame') | |
104 | colnames = ro.r('colnames') |
|
113 | colnames = ro.r('colnames') | |
105 | rownames = ro.r('rownames') # with pandas, these could be used for the index |
|
114 | rownames = ro.r('rownames') # with pandas, these could be used for the index | |
106 | names = ro.r('names') |
|
115 | names = ro.r('names') | |
107 |
|
116 | |||
108 | if dataframe: |
|
117 | if dataframe: | |
109 | as_data_frame = ro.r('as.data.frame') |
|
118 | as_data_frame = ro.r('as.data.frame') | |
110 | cols = colnames(Robj) |
|
119 | cols = colnames(Robj) | |
111 | _names = names(Robj) |
|
120 | _names = names(Robj) | |
112 | if cols != ri.NULL: |
|
121 | if cols != ri.NULL: | |
113 | Robj = as_data_frame(Robj) |
|
122 | Robj = as_data_frame(Robj) | |
114 | names = tuple(np.array(cols)) |
|
123 | names = tuple(np.array(cols)) | |
115 | elif _names != ri.NULL: |
|
124 | elif _names != ri.NULL: | |
116 | names = tuple(np.array(_names)) |
|
125 | names = tuple(np.array(_names)) | |
117 | else: # failed to find names |
|
126 | else: # failed to find names | |
118 | return np.asarray(Robj) |
|
127 | return np.asarray(Robj) | |
119 | Robj = np.rec.fromarrays(Robj, names = names) |
|
128 | Robj = np.rec.fromarrays(Robj, names = names) | |
120 | return np.asarray(Robj) |
|
129 | return np.asarray(Robj) | |
121 |
|
130 | |||
122 | @generic |
|
131 | @generic | |
123 | def pyconverter(pyobj): |
|
132 | def pyconverter(pyobj): | |
124 | """Convert Python objects to R objects. Add types using the decorator: |
|
133 | """Convert Python objects to R objects. Add types using the decorator: | |
125 |
|
134 | |||
126 | @pyconverter.when_type |
|
135 | @pyconverter.when_type | |
127 | """ |
|
136 | """ | |
128 | return pyobj |
|
137 | return pyobj | |
129 |
|
138 | |||
130 | # The default conversion for lists seems to make them a nested list. That has |
|
139 | # The default conversion for lists seems to make them a nested list. That has | |
131 | # some advantages, but is rarely convenient, so for interactive use, we convert |
|
140 | # some advantages, but is rarely convenient, so for interactive use, we convert | |
132 | # lists to a numpy array, which becomes an R vector. |
|
141 | # lists to a numpy array, which becomes an R vector. | |
133 | @pyconverter.when_type(list) |
|
142 | @pyconverter.when_type(list) | |
134 | def pyconverter_list(pyobj): |
|
143 | def pyconverter_list(pyobj): | |
135 | return np.asarray(pyobj) |
|
144 | return np.asarray(pyobj) | |
136 |
|
145 | |||
137 | if pandas2ri is None: |
|
146 | if pandas2ri is None: | |
138 | # pandas2ri was new in rpy2 2.3.3, so for now we'll fallback to pandas' |
|
147 | # pandas2ri was new in rpy2 2.3.3, so for now we'll fallback to pandas' | |
139 | # conversion function. |
|
148 | # conversion function. | |
140 | try: |
|
149 | try: | |
141 | from pandas import DataFrame |
|
150 | from pandas import DataFrame | |
142 | from pandas.rpy.common import convert_to_r_dataframe |
|
151 | from pandas.rpy.common import convert_to_r_dataframe | |
143 | @pyconverter.when_type(DataFrame) |
|
152 | @pyconverter.when_type(DataFrame) | |
144 | def pyconverter_dataframe(pyobj): |
|
153 | def pyconverter_dataframe(pyobj): | |
145 | return convert_to_r_dataframe(pyobj, strings_as_factors=True) |
|
154 | return convert_to_r_dataframe(pyobj, strings_as_factors=True) | |
146 | except ImportError: |
|
155 | except ImportError: | |
147 | pass |
|
156 | pass | |
148 |
|
157 | |||
149 | @magics_class |
|
158 | @magics_class | |
150 | class RMagics(Magics): |
|
159 | class RMagics(Magics): | |
151 | """A set of magics useful for interactive work with R via rpy2. |
|
160 | """A set of magics useful for interactive work with R via rpy2. | |
152 | """ |
|
161 | """ | |
153 |
|
162 | |||
154 | def __init__(self, shell, Rconverter=Rconverter, |
|
163 | def __init__(self, shell, Rconverter=Rconverter, | |
155 | pyconverter=pyconverter, |
|
164 | pyconverter=pyconverter, | |
156 | cache_display_data=False): |
|
165 | cache_display_data=False): | |
157 | """ |
|
166 | """ | |
158 | Parameters |
|
167 | Parameters | |
159 | ---------- |
|
168 | ---------- | |
160 |
|
169 | |||
161 | shell : IPython shell |
|
170 | shell : IPython shell | |
162 |
|
171 | |||
163 | Rconverter : callable |
|
172 | Rconverter : callable | |
164 | To be called on values taken from R before putting them in the |
|
173 | To be called on values taken from R before putting them in the | |
165 | IPython namespace. |
|
174 | IPython namespace. | |
166 |
|
175 | |||
167 | pyconverter : callable |
|
176 | pyconverter : callable | |
168 | To be called on values in ipython namespace before |
|
177 | To be called on values in ipython namespace before | |
169 | assigning to variables in rpy2. |
|
178 | assigning to variables in rpy2. | |
170 |
|
179 | |||
171 | cache_display_data : bool |
|
180 | cache_display_data : bool | |
172 | If True, the published results of the final call to R are |
|
181 | If True, the published results of the final call to R are | |
173 | cached in the variable 'display_cache'. |
|
182 | cached in the variable 'display_cache'. | |
174 |
|
183 | |||
175 | """ |
|
184 | """ | |
176 | super(RMagics, self).__init__(shell) |
|
185 | super(RMagics, self).__init__(shell) | |
177 | self.cache_display_data = cache_display_data |
|
186 | self.cache_display_data = cache_display_data | |
178 |
|
187 | |||
179 | self.r = ro.R() |
|
188 | self.r = ro.R() | |
180 |
|
189 | |||
181 | self.Rstdout_cache = [] |
|
190 | self.Rstdout_cache = [] | |
182 | self.pyconverter = pyconverter |
|
191 | self.pyconverter = pyconverter | |
183 | self.Rconverter = Rconverter |
|
192 | self.Rconverter = Rconverter | |
184 |
|
193 | |||
185 | def eval(self, line): |
|
194 | def eval(self, line): | |
186 | ''' |
|
195 | ''' | |
187 | Parse and evaluate a line with rpy2. |
|
196 | Parse and evaluate a line with rpy2. | |
188 | Returns the output to R's stdout() connection |
|
197 | Returns the output to R's stdout() connection | |
189 | and the value of eval(parse(line)). |
|
198 | and the value of eval(parse(line)). | |
190 | ''' |
|
199 | ''' | |
191 | old_writeconsole = ri.get_writeconsole() |
|
200 | old_writeconsole = ri.get_writeconsole() | |
192 | ri.set_writeconsole(self.write_console) |
|
201 | ri.set_writeconsole(self.write_console) | |
193 | try: |
|
202 | try: | |
194 | value = ri.baseenv['eval'](ri.parse(line)) |
|
203 | value = ri.baseenv['eval'](ri.parse(line)) | |
195 | except (ri.RRuntimeError, ValueError) as exception: |
|
204 | except (ri.RRuntimeError, ValueError) as exception: | |
196 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error |
|
205 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error | |
197 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) |
|
206 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) | |
198 | text_output = self.flush() |
|
207 | text_output = self.flush() | |
199 | ri.set_writeconsole(old_writeconsole) |
|
208 | ri.set_writeconsole(old_writeconsole) | |
200 | return text_output, value |
|
209 | return text_output, value | |
201 |
|
210 | |||
202 | def write_console(self, output): |
|
211 | def write_console(self, output): | |
203 | ''' |
|
212 | ''' | |
204 | A hook to capture R's stdout in a cache. |
|
213 | A hook to capture R's stdout in a cache. | |
205 | ''' |
|
214 | ''' | |
206 | self.Rstdout_cache.append(output) |
|
215 | self.Rstdout_cache.append(output) | |
207 |
|
216 | |||
208 | def flush(self): |
|
217 | def flush(self): | |
209 | ''' |
|
218 | ''' | |
210 | Flush R's stdout cache to a string, returning the string. |
|
219 | Flush R's stdout cache to a string, returning the string. | |
211 | ''' |
|
220 | ''' | |
212 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) |
|
221 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) | |
213 | self.Rstdout_cache = [] |
|
222 | self.Rstdout_cache = [] | |
214 | return value |
|
223 | return value | |
215 |
|
224 | |||
216 | @skip_doctest |
|
225 | @skip_doctest | |
217 | @needs_local_scope |
|
226 | @needs_local_scope | |
218 | @line_magic |
|
227 | @line_magic | |
219 | def Rpush(self, line, local_ns=None): |
|
228 | def Rpush(self, line, local_ns=None): | |
220 | ''' |
|
229 | ''' | |
221 | A line-level magic for R that pushes |
|
230 | A line-level magic for R that pushes | |
222 | variables from python to rpy2. The line should be made up |
|
231 | variables from python to rpy2. The line should be made up | |
223 | of whitespace separated variable names in the IPython |
|
232 | of whitespace separated variable names in the IPython | |
224 | namespace:: |
|
233 | namespace:: | |
225 |
|
234 | |||
226 | In [7]: import numpy as np |
|
235 | In [7]: import numpy as np | |
227 |
|
236 | |||
228 | In [8]: X = np.array([4.5,6.3,7.9]) |
|
237 | In [8]: X = np.array([4.5,6.3,7.9]) | |
229 |
|
238 | |||
230 | In [9]: X.mean() |
|
239 | In [9]: X.mean() | |
231 | Out[9]: 6.2333333333333343 |
|
240 | Out[9]: 6.2333333333333343 | |
232 |
|
241 | |||
233 | In [10]: %Rpush X |
|
242 | In [10]: %Rpush X | |
234 |
|
243 | |||
235 | In [11]: %R mean(X) |
|
244 | In [11]: %R mean(X) | |
236 | Out[11]: array([ 6.23333333]) |
|
245 | Out[11]: array([ 6.23333333]) | |
237 |
|
246 | |||
238 | ''' |
|
247 | ''' | |
239 | if local_ns is None: |
|
248 | if local_ns is None: | |
240 | local_ns = {} |
|
249 | local_ns = {} | |
241 |
|
250 | |||
242 | inputs = line.split(' ') |
|
251 | inputs = line.split(' ') | |
243 | for input in inputs: |
|
252 | for input in inputs: | |
244 | try: |
|
253 | try: | |
245 | val = local_ns[input] |
|
254 | val = local_ns[input] | |
246 | except KeyError: |
|
255 | except KeyError: | |
247 | try: |
|
256 | try: | |
248 | val = self.shell.user_ns[input] |
|
257 | val = self.shell.user_ns[input] | |
249 | except KeyError: |
|
258 | except KeyError: | |
250 | # reraise the KeyError as a NameError so that it looks like |
|
259 | # reraise the KeyError as a NameError so that it looks like | |
251 | # the standard python behavior when you use an unnamed |
|
260 | # the standard python behavior when you use an unnamed | |
252 | # variable |
|
261 | # variable | |
253 | raise NameError("name '%s' is not defined" % input) |
|
262 | raise NameError("name '%s' is not defined" % input) | |
254 |
|
263 | |||
255 | self.r.assign(input, self.pyconverter(val)) |
|
264 | self.r.assign(input, self.pyconverter(val)) | |
256 |
|
265 | |||
257 | @skip_doctest |
|
266 | @skip_doctest | |
258 | @magic_arguments() |
|
267 | @magic_arguments() | |
259 | @argument( |
|
268 | @argument( | |
260 | '-d', '--as_dataframe', action='store_true', |
|
269 | '-d', '--as_dataframe', action='store_true', | |
261 | default=False, |
|
270 | default=False, | |
262 | help='Convert objects to data.frames before returning to ipython.' |
|
271 | help='Convert objects to data.frames before returning to ipython.' | |
263 | ) |
|
272 | ) | |
264 | @argument( |
|
273 | @argument( | |
265 | 'outputs', |
|
274 | 'outputs', | |
266 | nargs='*', |
|
275 | nargs='*', | |
267 | ) |
|
276 | ) | |
268 | @line_magic |
|
277 | @line_magic | |
269 | def Rpull(self, line): |
|
278 | def Rpull(self, line): | |
270 | ''' |
|
279 | ''' | |
271 | A line-level magic for R that pulls |
|
280 | A line-level magic for R that pulls | |
272 | variables from python to rpy2:: |
|
281 | variables from python to rpy2:: | |
273 |
|
282 | |||
274 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) |
|
283 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) | |
275 |
|
284 | |||
276 | In [19]: %Rpull x y z |
|
285 | In [19]: %Rpull x y z | |
277 |
|
286 | |||
278 | In [20]: x |
|
287 | In [20]: x | |
279 | Out[20]: array([ 3. , 4. , 6.7]) |
|
288 | Out[20]: array([ 3. , 4. , 6.7]) | |
280 |
|
289 | |||
281 | In [21]: y |
|
290 | In [21]: y | |
282 | Out[21]: array([ 4., 6., 7.]) |
|
291 | Out[21]: array([ 4., 6., 7.]) | |
283 |
|
292 | |||
284 | In [22]: z |
|
293 | In [22]: z | |
285 | Out[22]: |
|
294 | Out[22]: | |
286 | array(['a', '3', '4'], |
|
295 | array(['a', '3', '4'], | |
287 | dtype='|S1') |
|
296 | dtype='|S1') | |
288 |
|
297 | |||
289 |
|
298 | |||
290 | If --as_dataframe, then each object is returned as a structured array |
|
299 | If --as_dataframe, then each object is returned as a structured array | |
291 | after first passed through "as.data.frame" in R before |
|
300 | after first passed through "as.data.frame" in R before | |
292 | being calling self.Rconverter. |
|
301 | being calling self.Rconverter. | |
293 | This is useful when a structured array is desired as output, or |
|
302 | This is useful when a structured array is desired as output, or | |
294 | when the object in R has mixed data types. |
|
303 | when the object in R has mixed data types. | |
295 | See the %%R docstring for more examples. |
|
304 | See the %%R docstring for more examples. | |
296 |
|
305 | |||
297 | Notes |
|
306 | Notes | |
298 | ----- |
|
307 | ----- | |
299 |
|
308 | |||
300 | Beware that R names can have '.' so this is not fool proof. |
|
309 | Beware that R names can have '.' so this is not fool proof. | |
301 | To avoid this, don't name your R objects with '.'s... |
|
310 | To avoid this, don't name your R objects with '.'s... | |
302 |
|
311 | |||
303 | ''' |
|
312 | ''' | |
304 | args = parse_argstring(self.Rpull, line) |
|
313 | args = parse_argstring(self.Rpull, line) | |
305 | outputs = args.outputs |
|
314 | outputs = args.outputs | |
306 | for output in outputs: |
|
315 | for output in outputs: | |
307 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) |
|
316 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) | |
308 |
|
317 | |||
309 | @skip_doctest |
|
318 | @skip_doctest | |
310 | @magic_arguments() |
|
319 | @magic_arguments() | |
311 | @argument( |
|
320 | @argument( | |
312 | '-d', '--as_dataframe', action='store_true', |
|
321 | '-d', '--as_dataframe', action='store_true', | |
313 | default=False, |
|
322 | default=False, | |
314 | help='Convert objects to data.frames before returning to ipython.' |
|
323 | help='Convert objects to data.frames before returning to ipython.' | |
315 | ) |
|
324 | ) | |
316 | @argument( |
|
325 | @argument( | |
317 | 'output', |
|
326 | 'output', | |
318 | nargs=1, |
|
327 | nargs=1, | |
319 | type=str, |
|
328 | type=str, | |
320 | ) |
|
329 | ) | |
321 | @line_magic |
|
330 | @line_magic | |
322 | def Rget(self, line): |
|
331 | def Rget(self, line): | |
323 | ''' |
|
332 | ''' | |
324 | Return an object from rpy2, possibly as a structured array (if possible). |
|
333 | Return an object from rpy2, possibly as a structured array (if possible). | |
325 | Similar to Rpull except only one argument is accepted and the value is |
|
334 | Similar to Rpull except only one argument is accepted and the value is | |
326 | returned rather than pushed to self.shell.user_ns:: |
|
335 | returned rather than pushed to self.shell.user_ns:: | |
327 |
|
336 | |||
328 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
337 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
329 |
|
338 | |||
330 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
339 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
331 |
|
340 | |||
332 | In [5]: %R -i datapy |
|
341 | In [5]: %R -i datapy | |
333 |
|
342 | |||
334 | In [6]: %Rget datapy |
|
343 | In [6]: %Rget datapy | |
335 | Out[6]: |
|
344 | Out[6]: | |
336 | array([['1', '2', '3', '4'], |
|
345 | array([['1', '2', '3', '4'], | |
337 | ['2', '3', '2', '5'], |
|
346 | ['2', '3', '2', '5'], | |
338 | ['a', 'b', 'c', 'e']], |
|
347 | ['a', 'b', 'c', 'e']], | |
339 | dtype='|S1') |
|
348 | dtype='|S1') | |
340 |
|
349 | |||
341 | In [7]: %Rget -d datapy |
|
350 | In [7]: %Rget -d datapy | |
342 | Out[7]: |
|
351 | Out[7]: | |
343 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
352 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
344 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
353 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
345 |
|
354 | |||
346 | ''' |
|
355 | ''' | |
347 | args = parse_argstring(self.Rget, line) |
|
356 | args = parse_argstring(self.Rget, line) | |
348 | output = args.output |
|
357 | output = args.output | |
349 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) |
|
358 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) | |
350 |
|
359 | |||
351 |
|
360 | |||
352 | @skip_doctest |
|
361 | @skip_doctest | |
353 | @magic_arguments() |
|
362 | @magic_arguments() | |
354 | @argument( |
|
363 | @argument( | |
355 | '-i', '--input', action='append', |
|
364 | '-i', '--input', action='append', | |
356 | help='Names of input variable from shell.user_ns to be assigned to R variables of the same names after calling self.pyconverter. Multiple names can be passed separated only by commas with no whitespace.' |
|
365 | help='Names of input variable from shell.user_ns to be assigned to R variables of the same names after calling self.pyconverter. Multiple names can be passed separated only by commas with no whitespace.' | |
357 | ) |
|
366 | ) | |
358 | @argument( |
|
367 | @argument( | |
359 | '-o', '--output', action='append', |
|
368 | '-o', '--output', action='append', | |
360 | help='Names of variables to be pushed from rpy2 to shell.user_ns after executing cell body and applying self.Rconverter. Multiple names can be passed separated only by commas with no whitespace.' |
|
369 | help='Names of variables to be pushed from rpy2 to shell.user_ns after executing cell body and applying self.Rconverter. Multiple names can be passed separated only by commas with no whitespace.' | |
361 | ) |
|
370 | ) | |
362 | @argument( |
|
371 | @argument( | |
363 | '-w', '--width', type=int, |
|
372 | '-w', '--width', type=int, | |
364 | help='Width of png plotting device sent as an argument to *png* in R.' |
|
373 | help='Width of png plotting device sent as an argument to *png* in R.' | |
365 | ) |
|
374 | ) | |
366 | @argument( |
|
375 | @argument( | |
367 | '-h', '--height', type=int, |
|
376 | '-h', '--height', type=int, | |
368 | help='Height of png plotting device sent as an argument to *png* in R.' |
|
377 | help='Height of png plotting device sent as an argument to *png* in R.' | |
369 | ) |
|
378 | ) | |
370 |
|
379 | |||
371 | @argument( |
|
380 | @argument( | |
372 | '-d', '--dataframe', action='append', |
|
381 | '-d', '--dataframe', action='append', | |
373 | help='Convert these objects to data.frames and return as structured arrays.' |
|
382 | help='Convert these objects to data.frames and return as structured arrays.' | |
374 | ) |
|
383 | ) | |
375 | @argument( |
|
384 | @argument( | |
376 | '-u', '--units', type=unicode, choices=["px", "in", "cm", "mm"], |
|
385 | '-u', '--units', type=unicode, choices=["px", "in", "cm", "mm"], | |
377 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' |
|
386 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' | |
378 | ) |
|
387 | ) | |
379 | @argument( |
|
388 | @argument( | |
380 | '-r', '--res', type=int, |
|
389 | '-r', '--res', type=int, | |
381 | help='Resolution of png plotting device sent as an argument to *png* in R. Defaults to 72 if *units* is one of ["in", "cm", "mm"].' |
|
390 | help='Resolution of png plotting device sent as an argument to *png* in R. Defaults to 72 if *units* is one of ["in", "cm", "mm"].' | |
382 | ) |
|
391 | ) | |
383 | @argument( |
|
392 | @argument( | |
384 | '-p', '--pointsize', type=int, |
|
393 | '-p', '--pointsize', type=int, | |
385 | help='Pointsize of png plotting device sent as an argument to *png* in R.' |
|
394 | help='Pointsize of png plotting device sent as an argument to *png* in R.' | |
386 | ) |
|
395 | ) | |
387 | @argument( |
|
396 | @argument( | |
388 | '-b', '--bg', |
|
397 | '-b', '--bg', | |
389 | help='Background of png plotting device sent as an argument to *png* in R.' |
|
398 | help='Background of png plotting device sent as an argument to *png* in R.' | |
390 | ) |
|
399 | ) | |
391 | @argument( |
|
400 | @argument( | |
392 | '-n', '--noreturn', |
|
401 | '-n', '--noreturn', | |
393 | help='Force the magic to not return anything.', |
|
402 | help='Force the magic to not return anything.', | |
394 | action='store_true', |
|
403 | action='store_true', | |
395 | default=False |
|
404 | default=False | |
396 | ) |
|
405 | ) | |
397 | @argument( |
|
406 | @argument( | |
398 | 'code', |
|
407 | 'code', | |
399 | nargs='*', |
|
408 | nargs='*', | |
400 | ) |
|
409 | ) | |
401 | @needs_local_scope |
|
410 | @needs_local_scope | |
402 | @line_cell_magic |
|
411 | @line_cell_magic | |
403 | def R(self, line, cell=None, local_ns=None): |
|
412 | def R(self, line, cell=None, local_ns=None): | |
404 | ''' |
|
413 | ''' | |
405 | Execute code in R, and pull some of the results back into the Python namespace. |
|
414 | Execute code in R, and pull some of the results back into the Python namespace. | |
406 |
|
415 | |||
407 | In line mode, this will evaluate an expression and convert the returned value to a Python object. |
|
416 | In line mode, this will evaluate an expression and convert the returned value to a Python object. | |
408 | The return value is determined by rpy2's behaviour of returning the result of evaluating the |
|
417 | The return value is determined by rpy2's behaviour of returning the result of evaluating the | |
409 | final line. |
|
418 | final line. | |
410 |
|
419 | |||
411 | Multiple R lines can be executed by joining them with semicolons:: |
|
420 | Multiple R lines can be executed by joining them with semicolons:: | |
412 |
|
421 | |||
413 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) |
|
422 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) | |
414 | Out[9]: array([ 4.25]) |
|
423 | Out[9]: array([ 4.25]) | |
415 |
|
424 | |||
416 | As a cell, this will run a block of R code, without bringing anything back by default:: |
|
425 | As a cell, this will run a block of R code, without bringing anything back by default:: | |
417 |
|
426 | |||
418 | In [10]: %%R |
|
427 | In [10]: %%R | |
419 | ....: Y = c(2,4,3,9) |
|
428 | ....: Y = c(2,4,3,9) | |
420 | ....: print(summary(lm(Y~X))) |
|
429 | ....: print(summary(lm(Y~X))) | |
421 | ....: |
|
430 | ....: | |
422 |
|
431 | |||
423 | Call: |
|
432 | Call: | |
424 | lm(formula = Y ~ X) |
|
433 | lm(formula = Y ~ X) | |
425 |
|
434 | |||
426 | Residuals: |
|
435 | Residuals: | |
427 | 1 2 3 4 |
|
436 | 1 2 3 4 | |
428 | 0.88 -0.24 -2.28 1.64 |
|
437 | 0.88 -0.24 -2.28 1.64 | |
429 |
|
438 | |||
430 | Coefficients: |
|
439 | Coefficients: | |
431 | Estimate Std. Error t value Pr(>|t|) |
|
440 | Estimate Std. Error t value Pr(>|t|) | |
432 | (Intercept) 0.0800 2.3000 0.035 0.975 |
|
441 | (Intercept) 0.0800 2.3000 0.035 0.975 | |
433 | X 1.0400 0.4822 2.157 0.164 |
|
442 | X 1.0400 0.4822 2.157 0.164 | |
434 |
|
443 | |||
435 | Residual standard error: 2.088 on 2 degrees of freedom |
|
444 | Residual standard error: 2.088 on 2 degrees of freedom | |
436 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 |
|
445 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 | |
437 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 |
|
446 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 | |
438 |
|
447 | |||
439 | In the notebook, plots are published as the output of the cell. |
|
448 | In the notebook, plots are published as the output of the cell. | |
440 |
|
449 | |||
441 | %R plot(X, Y) |
|
450 | %R plot(X, Y) | |
442 |
|
451 | |||
443 | will create a scatter plot of X bs Y. |
|
452 | will create a scatter plot of X bs Y. | |
444 |
|
453 | |||
445 | If cell is not None and line has some R code, it is prepended to |
|
454 | If cell is not None and line has some R code, it is prepended to | |
446 | the R code in cell. |
|
455 | the R code in cell. | |
447 |
|
456 | |||
448 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: |
|
457 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: | |
449 |
|
458 | |||
450 | In [14]: Z = np.array([1,4,5,10]) |
|
459 | In [14]: Z = np.array([1,4,5,10]) | |
451 |
|
460 | |||
452 | In [15]: %R -i Z mean(Z) |
|
461 | In [15]: %R -i Z mean(Z) | |
453 | Out[15]: array([ 5.]) |
|
462 | Out[15]: array([ 5.]) | |
454 |
|
463 | |||
455 |
|
464 | |||
456 | In [16]: %R -o W W=Z*mean(Z) |
|
465 | In [16]: %R -o W W=Z*mean(Z) | |
457 | Out[16]: array([ 5., 20., 25., 50.]) |
|
466 | Out[16]: array([ 5., 20., 25., 50.]) | |
458 |
|
467 | |||
459 | In [17]: W |
|
468 | In [17]: W | |
460 | Out[17]: array([ 5., 20., 25., 50.]) |
|
469 | Out[17]: array([ 5., 20., 25., 50.]) | |
461 |
|
470 | |||
462 | The return value is determined by these rules: |
|
471 | The return value is determined by these rules: | |
463 |
|
472 | |||
464 | * If the cell is not None, the magic returns None. |
|
473 | * If the cell is not None, the magic returns None. | |
465 |
|
474 | |||
466 | * If the cell evaluates as False, the resulting value is returned |
|
475 | * If the cell evaluates as False, the resulting value is returned | |
467 | unless the final line prints something to the console, in |
|
476 | unless the final line prints something to the console, in | |
468 | which case None is returned. |
|
477 | which case None is returned. | |
469 |
|
478 | |||
470 | * If the final line results in a NULL value when evaluated |
|
479 | * If the final line results in a NULL value when evaluated | |
471 | by rpy2, then None is returned. |
|
480 | by rpy2, then None is returned. | |
472 |
|
481 | |||
473 | * No attempt is made to convert the final value to a structured array. |
|
482 | * No attempt is made to convert the final value to a structured array. | |
474 | Use the --dataframe flag or %Rget to push / return a structured array. |
|
483 | Use the --dataframe flag or %Rget to push / return a structured array. | |
475 |
|
484 | |||
476 | * If the -n flag is present, there is no return value. |
|
485 | * If the -n flag is present, there is no return value. | |
477 |
|
486 | |||
478 | * A trailing ';' will also result in no return value as the last |
|
487 | * A trailing ';' will also result in no return value as the last | |
479 | value in the line is an empty string. |
|
488 | value in the line is an empty string. | |
480 |
|
489 | |||
481 | The --dataframe argument will attempt to return structured arrays. |
|
490 | The --dataframe argument will attempt to return structured arrays. | |
482 | This is useful for dataframes with |
|
491 | This is useful for dataframes with | |
483 | mixed data types. Note also that for a data.frame, |
|
492 | mixed data types. Note also that for a data.frame, | |
484 | if it is returned as an ndarray, it is transposed:: |
|
493 | if it is returned as an ndarray, it is transposed:: | |
485 |
|
494 | |||
486 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
495 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
487 |
|
496 | |||
488 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
497 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
489 |
|
498 | |||
490 | In [20]: %%R -o datar |
|
499 | In [20]: %%R -o datar | |
491 | datar = datapy |
|
500 | datar = datapy | |
492 | ....: |
|
501 | ....: | |
493 |
|
502 | |||
494 | In [21]: datar |
|
503 | In [21]: datar | |
495 | Out[21]: |
|
504 | Out[21]: | |
496 | array([['1', '2', '3', '4'], |
|
505 | array([['1', '2', '3', '4'], | |
497 | ['2', '3', '2', '5'], |
|
506 | ['2', '3', '2', '5'], | |
498 | ['a', 'b', 'c', 'e']], |
|
507 | ['a', 'b', 'c', 'e']], | |
499 | dtype='|S1') |
|
508 | dtype='|S1') | |
500 |
|
509 | |||
501 | In [22]: %%R -d datar |
|
510 | In [22]: %%R -d datar | |
502 | datar = datapy |
|
511 | datar = datapy | |
503 | ....: |
|
512 | ....: | |
504 |
|
513 | |||
505 | In [23]: datar |
|
514 | In [23]: datar | |
506 | Out[23]: |
|
515 | Out[23]: | |
507 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
516 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
508 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
517 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
509 |
|
518 | |||
510 | The --dataframe argument first tries colnames, then names. |
|
519 | The --dataframe argument first tries colnames, then names. | |
511 | If both are NULL, it returns an ndarray (i.e. unstructured):: |
|
520 | If both are NULL, it returns an ndarray (i.e. unstructured):: | |
512 |
|
521 | |||
513 | In [1]: %R mydata=c(4,6,8.3); NULL |
|
522 | In [1]: %R mydata=c(4,6,8.3); NULL | |
514 |
|
523 | |||
515 | In [2]: %R -d mydata |
|
524 | In [2]: %R -d mydata | |
516 |
|
525 | |||
517 | In [3]: mydata |
|
526 | In [3]: mydata | |
518 | Out[3]: array([ 4. , 6. , 8.3]) |
|
527 | Out[3]: array([ 4. , 6. , 8.3]) | |
519 |
|
528 | |||
520 | In [4]: %R names(mydata) = c('a','b','c'); NULL |
|
529 | In [4]: %R names(mydata) = c('a','b','c'); NULL | |
521 |
|
530 | |||
522 | In [5]: %R -d mydata |
|
531 | In [5]: %R -d mydata | |
523 |
|
532 | |||
524 | In [6]: mydata |
|
533 | In [6]: mydata | |
525 | Out[6]: |
|
534 | Out[6]: | |
526 | array((4.0, 6.0, 8.3), |
|
535 | array((4.0, 6.0, 8.3), | |
527 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) |
|
536 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) | |
528 |
|
537 | |||
529 | In [7]: %R -o mydata |
|
538 | In [7]: %R -o mydata | |
530 |
|
539 | |||
531 | In [8]: mydata |
|
540 | In [8]: mydata | |
532 | Out[8]: array([ 4. , 6. , 8.3]) |
|
541 | Out[8]: array([ 4. , 6. , 8.3]) | |
533 |
|
542 | |||
534 | ''' |
|
543 | ''' | |
535 |
|
544 | |||
536 | args = parse_argstring(self.R, line) |
|
545 | args = parse_argstring(self.R, line) | |
537 |
|
546 | |||
538 | # arguments 'code' in line are prepended to |
|
547 | # arguments 'code' in line are prepended to | |
539 | # the cell lines |
|
548 | # the cell lines | |
540 |
|
549 | |||
541 | if cell is None: |
|
550 | if cell is None: | |
542 | code = '' |
|
551 | code = '' | |
543 | return_output = True |
|
552 | return_output = True | |
544 | line_mode = True |
|
553 | line_mode = True | |
545 | else: |
|
554 | else: | |
546 | code = cell |
|
555 | code = cell | |
547 | return_output = False |
|
556 | return_output = False | |
548 | line_mode = False |
|
557 | line_mode = False | |
549 |
|
558 | |||
550 | code = ' '.join(args.code) + code |
|
559 | code = ' '.join(args.code) + code | |
551 |
|
560 | |||
552 | # if there is no local namespace then default to an empty dict |
|
561 | # if there is no local namespace then default to an empty dict | |
553 | if local_ns is None: |
|
562 | if local_ns is None: | |
554 | local_ns = {} |
|
563 | local_ns = {} | |
555 |
|
564 | |||
556 | if args.input: |
|
565 | if args.input: | |
557 | for input in ','.join(args.input).split(','): |
|
566 | for input in ','.join(args.input).split(','): | |
558 | try: |
|
567 | try: | |
559 | val = local_ns[input] |
|
568 | val = local_ns[input] | |
560 | except KeyError: |
|
569 | except KeyError: | |
561 | try: |
|
570 | try: | |
562 | val = self.shell.user_ns[input] |
|
571 | val = self.shell.user_ns[input] | |
563 | except KeyError: |
|
572 | except KeyError: | |
564 | raise NameError("name '%s' is not defined" % input) |
|
573 | raise NameError("name '%s' is not defined" % input) | |
565 | self.r.assign(input, self.pyconverter(val)) |
|
574 | self.r.assign(input, self.pyconverter(val)) | |
566 |
|
575 | |||
567 | if getattr(args, 'units') is not None: |
|
576 | if getattr(args, 'units') is not None: | |
568 | if args.units != "px" and getattr(args, 'res') is None: |
|
577 | if args.units != "px" and getattr(args, 'res') is None: | |
569 | args.res = 72 |
|
578 | args.res = 72 | |
570 | args.units = '"%s"' % args.units |
|
579 | args.units = '"%s"' % args.units | |
571 |
|
580 | |||
572 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) |
|
581 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) | |
573 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) |
|
582 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) | |
574 | # execute the R code in a temporary directory |
|
583 | # execute the R code in a temporary directory | |
575 |
|
584 | |||
576 | tmpd = tempfile.mkdtemp() |
|
585 | tmpd = tempfile.mkdtemp() | |
577 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) |
|
586 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) | |
578 |
|
587 | |||
579 | text_output = '' |
|
588 | text_output = '' | |
580 | try: |
|
589 | try: | |
581 | if line_mode: |
|
590 | if line_mode: | |
582 | for line in code.split(';'): |
|
591 | for line in code.split(';'): | |
583 | text_result, result = self.eval(line) |
|
592 | text_result, result = self.eval(line) | |
584 | text_output += text_result |
|
593 | text_output += text_result | |
585 | if text_result: |
|
594 | if text_result: | |
586 | # the last line printed something to the console so we won't return it |
|
595 | # the last line printed something to the console so we won't return it | |
587 | return_output = False |
|
596 | return_output = False | |
588 | else: |
|
597 | else: | |
589 | text_result, result = self.eval(code) |
|
598 | text_result, result = self.eval(code) | |
590 | text_output += text_result |
|
599 | text_output += text_result | |
591 |
|
600 | |||
592 | except RInterpreterError as e: |
|
601 | except RInterpreterError as e: | |
593 | print(e.stdout) |
|
602 | print(e.stdout) | |
594 | if not e.stdout.endswith(e.err): |
|
603 | if not e.stdout.endswith(e.err): | |
595 | print(e.err) |
|
604 | print(e.err) | |
596 | rmtree(tmpd) |
|
605 | rmtree(tmpd) | |
597 | return |
|
606 | return | |
598 |
|
607 | |||
599 | self.r('dev.off()') |
|
608 | self.r('dev.off()') | |
600 |
|
609 | |||
601 | # read out all the saved .png files |
|
610 | # read out all the saved .png files | |
602 |
|
611 | |||
603 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] |
|
612 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] | |
604 |
|
613 | |||
605 | # now publish the images |
|
614 | # now publish the images | |
606 | # mimicking IPython/zmq/pylab/backend_inline.py |
|
615 | # mimicking IPython/zmq/pylab/backend_inline.py | |
607 | fmt = 'png' |
|
616 | fmt = 'png' | |
608 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } |
|
617 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } | |
609 | mime = mimetypes[fmt] |
|
618 | mime = mimetypes[fmt] | |
610 |
|
619 | |||
611 | # publish the printed R objects, if any |
|
620 | # publish the printed R objects, if any | |
612 |
|
621 | |||
613 | display_data = [] |
|
622 | display_data = [] | |
614 | if text_output: |
|
623 | if text_output: | |
615 | display_data.append(('RMagic.R', {'text/plain':text_output})) |
|
624 | display_data.append(('RMagic.R', {'text/plain':text_output})) | |
616 |
|
625 | |||
617 | # flush text streams before sending figures, helps a little with output |
|
626 | # flush text streams before sending figures, helps a little with output | |
618 | for image in images: |
|
627 | for image in images: | |
619 | # synchronization in the console (though it's a bandaid, not a real sln) |
|
628 | # synchronization in the console (though it's a bandaid, not a real sln) | |
620 | sys.stdout.flush(); sys.stderr.flush() |
|
629 | sys.stdout.flush(); sys.stderr.flush() | |
621 | display_data.append(('RMagic.R', {mime: image})) |
|
630 | display_data.append(('RMagic.R', {mime: image})) | |
622 |
|
631 | |||
623 | # kill the temporary directory |
|
632 | # kill the temporary directory | |
624 | rmtree(tmpd) |
|
633 | rmtree(tmpd) | |
625 |
|
634 | |||
626 | # try to turn every output into a numpy array |
|
635 | # try to turn every output into a numpy array | |
627 | # this means that output are assumed to be castable |
|
636 | # this means that output are assumed to be castable | |
628 | # as numpy arrays |
|
637 | # as numpy arrays | |
629 |
|
638 | |||
630 | if args.output: |
|
639 | if args.output: | |
631 | for output in ','.join(args.output).split(','): |
|
640 | for output in ','.join(args.output).split(','): | |
632 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) |
|
641 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) | |
633 |
|
642 | |||
634 | if args.dataframe: |
|
643 | if args.dataframe: | |
635 | for output in ','.join(args.dataframe).split(','): |
|
644 | for output in ','.join(args.dataframe).split(','): | |
636 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) |
|
645 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) | |
637 |
|
646 | |||
638 | for tag, disp_d in display_data: |
|
647 | for tag, disp_d in display_data: | |
639 | publish_display_data(tag, disp_d) |
|
648 | publish_display_data(tag, disp_d) | |
640 |
|
649 | |||
641 | # this will keep a reference to the display_data |
|
650 | # this will keep a reference to the display_data | |
642 | # which might be useful to other objects who happen to use |
|
651 | # which might be useful to other objects who happen to use | |
643 | # this method |
|
652 | # this method | |
644 |
|
653 | |||
645 | if self.cache_display_data: |
|
654 | if self.cache_display_data: | |
646 | self.display_cache = display_data |
|
655 | self.display_cache = display_data | |
647 |
|
656 | |||
648 | # if in line mode and return_output, return the result as an ndarray |
|
657 | # if in line mode and return_output, return the result as an ndarray | |
649 | if return_output and not args.noreturn: |
|
658 | if return_output and not args.noreturn: | |
650 | if result != ri.NULL: |
|
659 | if result != ri.NULL: | |
651 | return self.Rconverter(result, dataframe=False) |
|
660 | return self.Rconverter(result, dataframe=False) | |
652 |
|
661 | |||
653 | __doc__ = __doc__.format( |
|
662 | __doc__ = __doc__.format( | |
654 | R_DOC = ' '*8 + RMagics.R.__doc__, |
|
663 | R_DOC = ' '*8 + RMagics.R.__doc__, | |
655 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, |
|
664 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, | |
656 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__, |
|
665 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__, | |
657 | RGET_DOC = ' '*8 + RMagics.Rget.__doc__ |
|
666 | RGET_DOC = ' '*8 + RMagics.Rget.__doc__ | |
658 | ) |
|
667 | ) | |
659 |
|
668 | |||
660 |
|
669 | |||
661 | def load_ipython_extension(ip): |
|
670 | def load_ipython_extension(ip): | |
662 | """Load the extension in IPython.""" |
|
671 | """Load the extension in IPython.""" | |
663 | ip.register_magics(RMagics) |
|
672 | ip.register_magics(RMagics) | |
664 | # Initialising rpy2 interferes with readline. Since, at this point, we've |
|
673 | # Initialising rpy2 interferes with readline. Since, at this point, we've | |
665 | # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. |
|
674 | # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. | |
666 | if ip.has_readline: |
|
675 | if ip.has_readline: | |
667 | ip.readline.set_completer_delims(ip.readline_delims) |
|
676 | ip.readline.set_completer_delims(ip.readline_delims) |
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