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