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@@ -1,5 +1,7 b'' | |||
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1 | 1 | # -*- coding: utf-8 -*- |
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2 | 2 | """ |
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3 | **DEPRECATED** | |
|
4 | ||
|
3 | 5 | The cython magic has been integrated into Cython itself, |
|
4 | 6 | which is now released in version 0.21. |
|
5 | 7 | |
@@ -8,36 +10,12 b' file `Cython/Build/IpythonMagic.py`' | |||
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8 | 10 | """ |
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9 | 11 | #----------------------------------------------------------------------------- |
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10 | 12 | # Copyright (C) 2010-2011, IPython Development Team. |
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11 | # | |
|
12 | # Distributed under the terms of the Modified BSD License. | |
|
13 | # | |
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14 | # The full license is in the file COPYING.txt, distributed with this software. | |
|
15 | 13 | #----------------------------------------------------------------------------- |
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16 | 14 | |
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17 | from __future__ import print_function | |
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18 | ||
|
19 | import IPython.utils.version as version | |
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20 | ||
|
21 | try: | |
|
22 | import Cython | |
|
23 | except: | |
|
24 | Cython = None | |
|
25 | ||
|
26 | try: | |
|
27 | from Cython.Build.IpythonMagic import CythonMagics | |
|
28 | except : | |
|
29 | pass | |
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30 | ||
|
15 | import warnings | |
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31 | 16 | |
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32 | 17 | ## still load the magic in IPython 3.x, remove completely in future versions. |
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33 | 18 | def load_ipython_extension(ip): |
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34 | 19 | """Load the extension in IPython.""" |
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35 | ||
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36 |
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37 | print("""`%load_ext cythonmagic` is deprecated; please use `%load_ext Cython` instead.""") | |
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38 | ||
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39 | if Cython is None or not version.check_version(Cython.__version__, "0.21"): | |
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40 | print("You need Cython version >=0.21 to use the Cython magic") | |
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41 | return | |
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42 | print("""\nThough, because I am nice, I'll still try to load it for you this time.""") | |
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43 | Cython.load_ipython_extension(ip) | |
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20 | ||
|
21 | warnings.warn("""The Cython magic has been moved to the Cython package""") |
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@@ -1,702 +1,12 b'' | |||
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1 | 1 | # -*- coding: utf-8 -*- |
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2 | """ | |
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3 | ====== | |
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4 | Rmagic | |
|
5 | ====== | |
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6 | ||
|
7 | Magic command interface for interactive work with R via rpy2 | |
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8 | ||
|
9 | .. note:: | |
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10 | ||
|
11 | The ``rpy2`` 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 | ||
|
14 | You will also need a working copy of R. | |
|
15 | ||
|
16 | Usage | |
|
17 | ===== | |
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18 | ||
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19 | To enable the magics below, execute ``%load_ext rmagic``. | |
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20 | ||
|
21 | ``%R`` | |
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22 | ||
|
23 | {R_DOC} | |
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24 | ||
|
25 | ``%Rpush`` | |
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26 | ||
|
27 | {RPUSH_DOC} | |
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28 | ||
|
29 | ``%Rpull`` | |
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30 | ||
|
31 | {RPULL_DOC} | |
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32 | ||
|
33 | ``%Rget`` | |
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34 | ||
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35 | {RGET_DOC} | |
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36 | ||
|
37 | """ | |
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38 | from __future__ import print_function | |
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39 | 2 | |
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40 | 3 | #----------------------------------------------------------------------------- |
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41 | 4 | # Copyright (C) 2012 The IPython Development Team |
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42 | # | |
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43 | # Distributed under the terms of the BSD License. The full license is in | |
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44 | # the file COPYING, distributed as part of this software. | |
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45 | 5 | #----------------------------------------------------------------------------- |
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46 | 6 | |
|
47 | import sys | |
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48 | import tempfile | |
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49 | from glob import glob | |
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50 | from shutil import rmtree | |
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51 | 7 | import warnings |
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52 | 8 | |
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53 | # numpy and rpy2 imports | |
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54 | ||
|
55 | import numpy as np | |
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56 | ||
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57 | import rpy2.rinterface as ri | |
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58 | import rpy2.robjects as ro | |
|
59 | try: | |
|
60 | from rpy2.robjects import pandas2ri | |
|
61 | pandas2ri.activate() | |
|
62 | except ImportError: | |
|
63 | pandas2ri = None | |
|
64 | from rpy2.robjects import numpy2ri | |
|
65 | numpy2ri.activate() | |
|
66 | ||
|
67 | # IPython imports | |
|
68 | ||
|
69 | from IPython.core.displaypub import publish_display_data | |
|
70 | from IPython.core.magic import (Magics, magics_class, line_magic, | |
|
71 | line_cell_magic, needs_local_scope) | |
|
72 | from IPython.core.magic_arguments import ( | |
|
73 | argument, magic_arguments, parse_argstring | |
|
74 | ) | |
|
75 | from simplegeneric import generic | |
|
76 | from IPython.utils.py3compat import (str_to_unicode, unicode_to_str, PY3, | |
|
77 | unicode_type) | |
|
78 | from IPython.utils.text import dedent | |
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79 | ||
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80 | class RInterpreterError(ri.RRuntimeError): | |
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81 | """An error when running R code in a %%R magic cell.""" | |
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82 | def __init__(self, line, err, stdout): | |
|
83 | self.line = line | |
|
84 | self.err = err.rstrip() | |
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85 | self.stdout = stdout.rstrip() | |
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86 | ||
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87 | def __unicode__(self): | |
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88 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ | |
|
89 | (self.line, self.err) | |
|
90 | if self.stdout and (self.stdout != self.err): | |
|
91 | s += '\nR stdout:\n' + self.stdout | |
|
92 | return s | |
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93 | ||
|
94 | if PY3: | |
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95 | __str__ = __unicode__ | |
|
96 | else: | |
|
97 | def __str__(self): | |
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98 | return unicode_to_str(unicode(self), 'utf-8') | |
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99 | ||
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100 | def Rconverter(Robj, dataframe=False): | |
|
101 | """ | |
|
102 | Convert an object in R's namespace to one suitable | |
|
103 | for ipython's namespace. | |
|
104 | ||
|
105 | For a data.frame, it tries to return a structured array. | |
|
106 | It first checks for colnames, then names. | |
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107 | If all are NULL, it returns np.asarray(Robj), else | |
|
108 | it tries to construct a recarray | |
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109 | ||
|
110 | Parameters | |
|
111 | ---------- | |
|
112 | ||
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113 | Robj: an R object returned from rpy2 | |
|
114 | """ | |
|
115 | is_data_frame = ro.r('is.data.frame') | |
|
116 | colnames = ro.r('colnames') | |
|
117 | rownames = ro.r('rownames') # with pandas, these could be used for the index | |
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118 | names = ro.r('names') | |
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119 | ||
|
120 | if dataframe: | |
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121 | as_data_frame = ro.r('as.data.frame') | |
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122 | cols = colnames(Robj) | |
|
123 | _names = names(Robj) | |
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124 | if cols != ri.NULL: | |
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125 | Robj = as_data_frame(Robj) | |
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126 | names = tuple(np.array(cols)) | |
|
127 | elif _names != ri.NULL: | |
|
128 | names = tuple(np.array(_names)) | |
|
129 | else: # failed to find names | |
|
130 | return np.asarray(Robj) | |
|
131 | Robj = np.rec.fromarrays(Robj, names = names) | |
|
132 | return np.asarray(Robj) | |
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133 | ||
|
134 | @generic | |
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135 | def pyconverter(pyobj): | |
|
136 | """Convert Python objects to R objects. Add types using the decorator: | |
|
137 | ||
|
138 | @pyconverter.when_type | |
|
139 | """ | |
|
140 | return pyobj | |
|
141 | ||
|
142 | # The default conversion for lists seems to make them a nested list. That has | |
|
143 | # some advantages, but is rarely convenient, so for interactive use, we convert | |
|
144 | # lists to a numpy array, which becomes an R vector. | |
|
145 | @pyconverter.when_type(list) | |
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146 | def pyconverter_list(pyobj): | |
|
147 | return np.asarray(pyobj) | |
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148 | ||
|
149 | if pandas2ri is None: | |
|
150 | # pandas2ri was new in rpy2 2.3.3, so for now we'll fallback to pandas' | |
|
151 | # conversion function. | |
|
152 | try: | |
|
153 | from pandas import DataFrame | |
|
154 | from pandas.rpy.common import convert_to_r_dataframe | |
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155 | @pyconverter.when_type(DataFrame) | |
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156 | def pyconverter_dataframe(pyobj): | |
|
157 | return convert_to_r_dataframe(pyobj, strings_as_factors=True) | |
|
158 | except ImportError: | |
|
159 | pass | |
|
160 | ||
|
161 | @magics_class | |
|
162 | class RMagics(Magics): | |
|
163 | """A set of magics useful for interactive work with R via rpy2. | |
|
164 | """ | |
|
165 | ||
|
166 | def __init__(self, shell, Rconverter=Rconverter, | |
|
167 | pyconverter=pyconverter, | |
|
168 | cache_display_data=False): | |
|
169 | """ | |
|
170 | Parameters | |
|
171 | ---------- | |
|
172 | ||
|
173 | shell : IPython shell | |
|
174 | ||
|
175 | Rconverter : callable | |
|
176 | To be called on values taken from R before putting them in the | |
|
177 | IPython namespace. | |
|
178 | ||
|
179 | pyconverter : callable | |
|
180 | To be called on values in ipython namespace before | |
|
181 | assigning to variables in rpy2. | |
|
182 | ||
|
183 | cache_display_data : bool | |
|
184 | If True, the published results of the final call to R are | |
|
185 | cached in the variable 'display_cache'. | |
|
186 | ||
|
187 | """ | |
|
188 | super(RMagics, self).__init__(shell) | |
|
189 | self.cache_display_data = cache_display_data | |
|
190 | ||
|
191 | self.r = ro.R() | |
|
192 | ||
|
193 | self.Rstdout_cache = [] | |
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194 | self.pyconverter = pyconverter | |
|
195 | self.Rconverter = Rconverter | |
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196 | ||
|
197 | def eval(self, line): | |
|
198 | ''' | |
|
199 | Parse and evaluate a line of R code with rpy2. | |
|
200 | Returns the output to R's stdout() connection, | |
|
201 | the value generated by evaluating the code, and a | |
|
202 | boolean indicating whether the return value would be | |
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203 | visible if the line of code were evaluated in an R REPL. | |
|
204 | ||
|
205 | R Code evaluation and visibility determination are | |
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206 | done via an R call of the form withVisible({<code>}) | |
|
207 | ||
|
208 | ''' | |
|
209 | old_writeconsole = ri.get_writeconsole() | |
|
210 | ri.set_writeconsole(self.write_console) | |
|
211 | try: | |
|
212 | res = ro.r("withVisible({%s\n})" % line) | |
|
213 | value = res[0] #value (R object) | |
|
214 | visible = ro.conversion.ri2py(res[1])[0] #visible (boolean) | |
|
215 | except (ri.RRuntimeError, ValueError) as exception: | |
|
216 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error | |
|
217 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) | |
|
218 | text_output = self.flush() | |
|
219 | ri.set_writeconsole(old_writeconsole) | |
|
220 | return text_output, value, visible | |
|
221 | ||
|
222 | def write_console(self, output): | |
|
223 | ''' | |
|
224 | A hook to capture R's stdout in a cache. | |
|
225 | ''' | |
|
226 | self.Rstdout_cache.append(output) | |
|
227 | ||
|
228 | def flush(self): | |
|
229 | ''' | |
|
230 | Flush R's stdout cache to a string, returning the string. | |
|
231 | ''' | |
|
232 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) | |
|
233 | self.Rstdout_cache = [] | |
|
234 | return value | |
|
235 | ||
|
236 | @needs_local_scope | |
|
237 | @line_magic | |
|
238 | def Rpush(self, line, local_ns=None): | |
|
239 | ''' | |
|
240 | A line-level magic for R that pushes | |
|
241 | variables from python to rpy2. The line should be made up | |
|
242 | of whitespace separated variable names in the IPython | |
|
243 | namespace:: | |
|
244 | ||
|
245 | In [7]: import numpy as np | |
|
246 | ||
|
247 | In [8]: X = np.array([4.5,6.3,7.9]) | |
|
248 | ||
|
249 | In [9]: X.mean() | |
|
250 | Out[9]: 6.2333333333333343 | |
|
251 | ||
|
252 | In [10]: %Rpush X | |
|
253 | ||
|
254 | In [11]: %R mean(X) | |
|
255 | Out[11]: array([ 6.23333333]) | |
|
256 | ||
|
257 | ''' | |
|
258 | if local_ns is None: | |
|
259 | local_ns = {} | |
|
260 | ||
|
261 | inputs = line.split(' ') | |
|
262 | for input in inputs: | |
|
263 | try: | |
|
264 | val = local_ns[input] | |
|
265 | except KeyError: | |
|
266 | try: | |
|
267 | val = self.shell.user_ns[input] | |
|
268 | except KeyError: | |
|
269 | # reraise the KeyError as a NameError so that it looks like | |
|
270 | # the standard python behavior when you use an unnamed | |
|
271 | # variable | |
|
272 | raise NameError("name '%s' is not defined" % input) | |
|
273 | ||
|
274 | self.r.assign(input, self.pyconverter(val)) | |
|
275 | ||
|
276 | @magic_arguments() | |
|
277 | @argument( | |
|
278 | '-d', '--as_dataframe', action='store_true', | |
|
279 | default=False, | |
|
280 | help='Convert objects to data.frames before returning to ipython.' | |
|
281 | ) | |
|
282 | @argument( | |
|
283 | 'outputs', | |
|
284 | nargs='*', | |
|
285 | ) | |
|
286 | @line_magic | |
|
287 | def Rpull(self, line): | |
|
288 | ''' | |
|
289 | A line-level magic for R that pulls | |
|
290 | variables from python to rpy2:: | |
|
291 | ||
|
292 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) | |
|
293 | ||
|
294 | In [19]: %Rpull x y z | |
|
295 | ||
|
296 | In [20]: x | |
|
297 | Out[20]: array([ 3. , 4. , 6.7]) | |
|
298 | ||
|
299 | In [21]: y | |
|
300 | Out[21]: array([ 4., 6., 7.]) | |
|
301 | ||
|
302 | In [22]: z | |
|
303 | Out[22]: | |
|
304 | array(['a', '3', '4'], | |
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305 | dtype='|S1') | |
|
306 | ||
|
307 | ||
|
308 | If --as_dataframe, then each object is returned as a structured array | |
|
309 | after first passed through "as.data.frame" in R before | |
|
310 | being calling self.Rconverter. | |
|
311 | This is useful when a structured array is desired as output, or | |
|
312 | when the object in R has mixed data types. | |
|
313 | See the %%R docstring for more examples. | |
|
314 | ||
|
315 | Notes | |
|
316 | ----- | |
|
317 | ||
|
318 | Beware that R names can have '.' so this is not fool proof. | |
|
319 | To avoid this, don't name your R objects with '.'s... | |
|
320 | ||
|
321 | ''' | |
|
322 | args = parse_argstring(self.Rpull, line) | |
|
323 | outputs = args.outputs | |
|
324 | for output in outputs: | |
|
325 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) | |
|
326 | ||
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327 | @magic_arguments() | |
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328 | @argument( | |
|
329 | '-d', '--as_dataframe', action='store_true', | |
|
330 | default=False, | |
|
331 | help='Convert objects to data.frames before returning to ipython.' | |
|
332 | ) | |
|
333 | @argument( | |
|
334 | 'output', | |
|
335 | nargs=1, | |
|
336 | type=str, | |
|
337 | ) | |
|
338 | @line_magic | |
|
339 | def Rget(self, line): | |
|
340 | ''' | |
|
341 | Return an object from rpy2, possibly as a structured array (if possible). | |
|
342 | Similar to Rpull except only one argument is accepted and the value is | |
|
343 | returned rather than pushed to self.shell.user_ns:: | |
|
344 | ||
|
345 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
|
346 | ||
|
347 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
|
348 | ||
|
349 | In [5]: %R -i datapy | |
|
350 | ||
|
351 | In [6]: %Rget datapy | |
|
352 | Out[6]: | |
|
353 | array([['1', '2', '3', '4'], | |
|
354 | ['2', '3', '2', '5'], | |
|
355 | ['a', 'b', 'c', 'e']], | |
|
356 | dtype='|S1') | |
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357 | ||
|
358 | In [7]: %Rget -d datapy | |
|
359 | Out[7]: | |
|
360 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
|
361 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
|
362 | ||
|
363 | ''' | |
|
364 | args = parse_argstring(self.Rget, line) | |
|
365 | output = args.output | |
|
366 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) | |
|
367 | ||
|
368 | ||
|
369 | @magic_arguments() | |
|
370 | @argument( | |
|
371 | '-i', '--input', action='append', | |
|
372 | 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.' | |
|
373 | ) | |
|
374 | @argument( | |
|
375 | '-o', '--output', action='append', | |
|
376 | 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.' | |
|
377 | ) | |
|
378 | @argument( | |
|
379 | '-w', '--width', type=int, | |
|
380 | help='Width of png plotting device sent as an argument to *png* in R.' | |
|
381 | ) | |
|
382 | @argument( | |
|
383 | '-h', '--height', type=int, | |
|
384 | help='Height of png plotting device sent as an argument to *png* in R.' | |
|
385 | ) | |
|
386 | ||
|
387 | @argument( | |
|
388 | '-d', '--dataframe', action='append', | |
|
389 | help='Convert these objects to data.frames and return as structured arrays.' | |
|
390 | ) | |
|
391 | @argument( | |
|
392 | '-u', '--units', type=unicode_type, choices=["px", "in", "cm", "mm"], | |
|
393 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' | |
|
394 | ) | |
|
395 | @argument( | |
|
396 | '-r', '--res', type=int, | |
|
397 | 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"].' | |
|
398 | ) | |
|
399 | @argument( | |
|
400 | '-p', '--pointsize', type=int, | |
|
401 | help='Pointsize of png plotting device sent as an argument to *png* in R.' | |
|
402 | ) | |
|
403 | @argument( | |
|
404 | '-b', '--bg', | |
|
405 | help='Background of png plotting device sent as an argument to *png* in R.' | |
|
406 | ) | |
|
407 | @argument( | |
|
408 | '-n', '--noreturn', | |
|
409 | help='Force the magic to not return anything.', | |
|
410 | action='store_true', | |
|
411 | default=False | |
|
412 | ) | |
|
413 | @argument( | |
|
414 | 'code', | |
|
415 | nargs='*', | |
|
416 | ) | |
|
417 | @needs_local_scope | |
|
418 | @line_cell_magic | |
|
419 | def R(self, line, cell=None, local_ns=None): | |
|
420 | ''' | |
|
421 | Execute code in R, and pull some of the results back into the Python namespace. | |
|
422 | ||
|
423 | In line mode, this will evaluate an expression and convert the returned value to a Python object. | |
|
424 | The return value is determined by rpy2's behaviour of returning the result of evaluating the | |
|
425 | final line. | |
|
426 | ||
|
427 | Multiple R lines can be executed by joining them with semicolons:: | |
|
428 | ||
|
429 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) | |
|
430 | Out[9]: array([ 4.25]) | |
|
431 | ||
|
432 | In cell mode, this will run a block of R code. The resulting value | |
|
433 | is printed if it would printed be when evaluating the same code | |
|
434 | within a standard R REPL. | |
|
435 | ||
|
436 | Nothing is returned to python by default in cell mode:: | |
|
437 | ||
|
438 | In [10]: %%R | |
|
439 | ....: Y = c(2,4,3,9) | |
|
440 | ....: summary(lm(Y~X)) | |
|
441 | ||
|
442 | Call: | |
|
443 | lm(formula = Y ~ X) | |
|
444 | ||
|
445 | Residuals: | |
|
446 | 1 2 3 4 | |
|
447 | 0.88 -0.24 -2.28 1.64 | |
|
448 | ||
|
449 | Coefficients: | |
|
450 | Estimate Std. Error t value Pr(>|t|) | |
|
451 | (Intercept) 0.0800 2.3000 0.035 0.975 | |
|
452 | X 1.0400 0.4822 2.157 0.164 | |
|
453 | ||
|
454 | Residual standard error: 2.088 on 2 degrees of freedom | |
|
455 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 | |
|
456 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 | |
|
457 | ||
|
458 | In the notebook, plots are published as the output of the cell:: | |
|
459 | ||
|
460 | %R plot(X, Y) | |
|
461 | ||
|
462 | will create a scatter plot of X bs Y. | |
|
463 | ||
|
464 | If cell is not None and line has some R code, it is prepended to | |
|
465 | the R code in cell. | |
|
466 | ||
|
467 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: | |
|
468 | ||
|
469 | In [14]: Z = np.array([1,4,5,10]) | |
|
470 | ||
|
471 | In [15]: %R -i Z mean(Z) | |
|
472 | Out[15]: array([ 5.]) | |
|
473 | ||
|
474 | ||
|
475 | In [16]: %R -o W W=Z*mean(Z) | |
|
476 | Out[16]: array([ 5., 20., 25., 50.]) | |
|
477 | ||
|
478 | In [17]: W | |
|
479 | Out[17]: array([ 5., 20., 25., 50.]) | |
|
480 | ||
|
481 | The return value is determined by these rules: | |
|
482 | ||
|
483 | * If the cell is not None, the magic returns None. | |
|
484 | ||
|
485 | * If the cell evaluates as False, the resulting value is returned | |
|
486 | unless the final line prints something to the console, in | |
|
487 | which case None is returned. | |
|
488 | ||
|
489 | * If the final line results in a NULL value when evaluated | |
|
490 | by rpy2, then None is returned. | |
|
491 | ||
|
492 | * No attempt is made to convert the final value to a structured array. | |
|
493 | Use the --dataframe flag or %Rget to push / return a structured array. | |
|
494 | ||
|
495 | * If the -n flag is present, there is no return value. | |
|
496 | ||
|
497 | * A trailing ';' will also result in no return value as the last | |
|
498 | value in the line is an empty string. | |
|
499 | ||
|
500 | The --dataframe argument will attempt to return structured arrays. | |
|
501 | This is useful for dataframes with | |
|
502 | mixed data types. Note also that for a data.frame, | |
|
503 | if it is returned as an ndarray, it is transposed:: | |
|
504 | ||
|
505 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
|
506 | ||
|
507 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
|
508 | ||
|
509 | In [20]: %%R -o datar | |
|
510 | datar = datapy | |
|
511 | ....: | |
|
512 | ||
|
513 | In [21]: datar | |
|
514 | Out[21]: | |
|
515 | array([['1', '2', '3', '4'], | |
|
516 | ['2', '3', '2', '5'], | |
|
517 | ['a', 'b', 'c', 'e']], | |
|
518 | dtype='|S1') | |
|
519 | ||
|
520 | In [22]: %%R -d datar | |
|
521 | datar = datapy | |
|
522 | ....: | |
|
523 | ||
|
524 | In [23]: datar | |
|
525 | Out[23]: | |
|
526 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
|
527 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
|
528 | ||
|
529 | The --dataframe argument first tries colnames, then names. | |
|
530 | If both are NULL, it returns an ndarray (i.e. unstructured):: | |
|
531 | ||
|
532 | In [1]: %R mydata=c(4,6,8.3); NULL | |
|
533 | ||
|
534 | In [2]: %R -d mydata | |
|
535 | ||
|
536 | In [3]: mydata | |
|
537 | Out[3]: array([ 4. , 6. , 8.3]) | |
|
538 | ||
|
539 | In [4]: %R names(mydata) = c('a','b','c'); NULL | |
|
540 | ||
|
541 | In [5]: %R -d mydata | |
|
542 | ||
|
543 | In [6]: mydata | |
|
544 | Out[6]: | |
|
545 | array((4.0, 6.0, 8.3), | |
|
546 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) | |
|
547 | ||
|
548 | In [7]: %R -o mydata | |
|
549 | ||
|
550 | In [8]: mydata | |
|
551 | Out[8]: array([ 4. , 6. , 8.3]) | |
|
552 | ||
|
553 | ''' | |
|
554 | ||
|
555 | args = parse_argstring(self.R, line) | |
|
556 | ||
|
557 | # arguments 'code' in line are prepended to | |
|
558 | # the cell lines | |
|
559 | ||
|
560 | if cell is None: | |
|
561 | code = '' | |
|
562 | return_output = True | |
|
563 | line_mode = True | |
|
564 | else: | |
|
565 | code = cell | |
|
566 | return_output = False | |
|
567 | line_mode = False | |
|
568 | ||
|
569 | code = ' '.join(args.code) + code | |
|
570 | ||
|
571 | # if there is no local namespace then default to an empty dict | |
|
572 | if local_ns is None: | |
|
573 | local_ns = {} | |
|
574 | ||
|
575 | if args.input: | |
|
576 | for input in ','.join(args.input).split(','): | |
|
577 | try: | |
|
578 | val = local_ns[input] | |
|
579 | except KeyError: | |
|
580 | try: | |
|
581 | val = self.shell.user_ns[input] | |
|
582 | except KeyError: | |
|
583 | raise NameError("name '%s' is not defined" % input) | |
|
584 | self.r.assign(input, self.pyconverter(val)) | |
|
585 | ||
|
586 | if getattr(args, 'units') is not None: | |
|
587 | if args.units != "px" and getattr(args, 'res') is None: | |
|
588 | args.res = 72 | |
|
589 | args.units = '"%s"' % args.units | |
|
590 | ||
|
591 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) | |
|
592 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) | |
|
593 | # execute the R code in a temporary directory | |
|
594 | ||
|
595 | tmpd = tempfile.mkdtemp() | |
|
596 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) | |
|
597 | ||
|
598 | text_output = '' | |
|
599 | try: | |
|
600 | if line_mode: | |
|
601 | for line in code.split(';'): | |
|
602 | text_result, result, visible = self.eval(line) | |
|
603 | text_output += text_result | |
|
604 | if text_result: | |
|
605 | # the last line printed something to the console so we won't return it | |
|
606 | return_output = False | |
|
607 | else: | |
|
608 | text_result, result, visible = self.eval(code) | |
|
609 | text_output += text_result | |
|
610 | if visible: | |
|
611 | old_writeconsole = ri.get_writeconsole() | |
|
612 | ri.set_writeconsole(self.write_console) | |
|
613 | ro.r.show(result) | |
|
614 | text_output += self.flush() | |
|
615 | ri.set_writeconsole(old_writeconsole) | |
|
616 | ||
|
617 | except RInterpreterError as e: | |
|
618 | print(e.stdout) | |
|
619 | if not e.stdout.endswith(e.err): | |
|
620 | print(e.err) | |
|
621 | rmtree(tmpd) | |
|
622 | return | |
|
623 | finally: | |
|
624 | self.r('dev.off()') | |
|
625 | ||
|
626 | # read out all the saved .png files | |
|
627 | ||
|
628 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] | |
|
629 | ||
|
630 | # now publish the images | |
|
631 | # mimicking IPython/zmq/pylab/backend_inline.py | |
|
632 | fmt = 'png' | |
|
633 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } | |
|
634 | mime = mimetypes[fmt] | |
|
635 | ||
|
636 | # publish the printed R objects, if any | |
|
637 | ||
|
638 | display_data = [] | |
|
639 | if text_output: | |
|
640 | display_data.append(('RMagic.R', {'text/plain':text_output})) | |
|
641 | ||
|
642 | # flush text streams before sending figures, helps a little with output | |
|
643 | for image in images: | |
|
644 | # synchronization in the console (though it's a bandaid, not a real sln) | |
|
645 | sys.stdout.flush(); sys.stderr.flush() | |
|
646 | display_data.append(('RMagic.R', {mime: image})) | |
|
647 | ||
|
648 | # kill the temporary directory | |
|
649 | rmtree(tmpd) | |
|
650 | ||
|
651 | # try to turn every output into a numpy array | |
|
652 | # this means that output are assumed to be castable | |
|
653 | # as numpy arrays | |
|
654 | ||
|
655 | if args.output: | |
|
656 | for output in ','.join(args.output).split(','): | |
|
657 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) | |
|
658 | ||
|
659 | if args.dataframe: | |
|
660 | for output in ','.join(args.dataframe).split(','): | |
|
661 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) | |
|
662 | ||
|
663 | for tag, disp_d in display_data: | |
|
664 | publish_display_data(data=disp_d, source=tag) | |
|
665 | ||
|
666 | # this will keep a reference to the display_data | |
|
667 | # which might be useful to other objects who happen to use | |
|
668 | # this method | |
|
669 | ||
|
670 | if self.cache_display_data: | |
|
671 | self.display_cache = display_data | |
|
672 | ||
|
673 | # if in line mode and return_output, return the result as an ndarray | |
|
674 | if return_output and not args.noreturn: | |
|
675 | if result != ri.NULL: | |
|
676 | return self.Rconverter(result, dataframe=False) | |
|
677 | ||
|
678 | __doc__ = __doc__.format( | |
|
679 | R_DOC = dedent(RMagics.R.__doc__), | |
|
680 | RPUSH_DOC = dedent(RMagics.Rpush.__doc__), | |
|
681 | RPULL_DOC = dedent(RMagics.Rpull.__doc__), | |
|
682 | RGET_DOC = dedent(RMagics.Rget.__doc__) | |
|
683 | ) | |
|
684 | ||
|
685 | ||
|
686 | 9 | def load_ipython_extension(ip): |
|
687 | 10 | """Load the extension in IPython.""" |
|
688 |
warnings.warn("The rmagic extension in IPython |
|
|
689 | "rpy2.ipython. If available, that will be loaded instead.\n" | |
|
690 | "http://rpy.sourceforge.net/") | |
|
691 | try: | |
|
692 | import rpy2.ipython | |
|
693 | except ImportError: | |
|
694 | pass # Fall back to our own implementation for now | |
|
695 | else: | |
|
696 | return rpy2.ipython.load_ipython_extension(ip) | |
|
697 | ||
|
698 | ip.register_magics(RMagics) | |
|
699 | # Initialising rpy2 interferes with readline. Since, at this point, we've | |
|
700 | # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. | |
|
701 | if ip.has_readline: | |
|
702 | ip.readline.set_completer_delims(ip.readline_delims) | |
|
11 | warnings.warn("The rmagic extension in IPython has moved to " | |
|
12 | "`rpy2.ipython`, please see `rpy2` documentation.") |
@@ -1,4 +1,6 b'' | |||
|
1 | 1 | """ |
|
2 | **DEPRECATED** | |
|
3 | ||
|
2 | 4 | A print function that pretty prints sympy Basic objects. |
|
3 | 5 | |
|
4 | 6 | :moduleauthor: Brian Granger |
@@ -17,154 +19,14 b' maintained here for backwards compatablitiy with old SymPy versions.' | |||
|
17 | 19 | """ |
|
18 | 20 | #----------------------------------------------------------------------------- |
|
19 | 21 | # Copyright (C) 2008 The IPython Development Team |
|
20 | # | |
|
21 | # Distributed under the terms of the BSD License. The full license is in | |
|
22 | # the file COPYING, distributed as part of this software. | |
|
23 | 22 | #----------------------------------------------------------------------------- |
|
24 | 23 | |
|
25 | 24 | #----------------------------------------------------------------------------- |
|
26 | 25 | # Imports |
|
27 | 26 | #----------------------------------------------------------------------------- |
|
28 | 27 | |
|
29 | from IPython.lib.latextools import latex_to_png | |
|
30 | from IPython.utils.py3compat import string_types | |
|
31 | ||
|
32 | try: | |
|
33 | from sympy import pretty, latex | |
|
34 | except ImportError: | |
|
35 | pass | |
|
36 | ||
|
37 | 28 | import warnings |
|
38 | 29 | |
|
39 | #----------------------------------------------------------------------------- | |
|
40 | # Definitions of special display functions for use with IPython | |
|
41 | #----------------------------------------------------------------------------- | |
|
42 | ||
|
43 | def print_basic_unicode(o, p, cycle): | |
|
44 | """A function to pretty print sympy Basic objects.""" | |
|
45 | if cycle: | |
|
46 | return p.text('Basic(...)') | |
|
47 | out = pretty(o, use_unicode=True) | |
|
48 | if '\n' in out: | |
|
49 | p.text(u'\n') | |
|
50 | p.text(out) | |
|
51 | ||
|
52 | ||
|
53 | def print_png(o): | |
|
54 | """ | |
|
55 | A function to display sympy expression using inline style LaTeX in PNG. | |
|
56 | """ | |
|
57 | s = latex(o, mode='inline') | |
|
58 | # mathtext does not understand certain latex flags, so we try to replace | |
|
59 | # them with suitable subs. | |
|
60 | s = s.replace('\\operatorname','') | |
|
61 | s = s.replace('\\overline', '\\bar') | |
|
62 | png = latex_to_png(s) | |
|
63 | return png | |
|
64 | ||
|
65 | ||
|
66 | def print_display_png(o): | |
|
67 | """ | |
|
68 | A function to display sympy expression using display style LaTeX in PNG. | |
|
69 | """ | |
|
70 | s = latex(o, mode='plain') | |
|
71 | s = s.strip('$') | |
|
72 | # As matplotlib does not support display style, dvipng backend is | |
|
73 | # used here. | |
|
74 | png = latex_to_png(s, backend='dvipng', wrap=True) | |
|
75 | return png | |
|
76 | ||
|
77 | ||
|
78 | def can_print_latex(o): | |
|
79 | """ | |
|
80 | Return True if type o can be printed with LaTeX. | |
|
81 | ||
|
82 | If o is a container type, this is True if and only if every element of o | |
|
83 | can be printed with LaTeX. | |
|
84 | """ | |
|
85 | import sympy | |
|
86 | if isinstance(o, (list, tuple, set, frozenset)): | |
|
87 | return all(can_print_latex(i) for i in o) | |
|
88 | elif isinstance(o, dict): | |
|
89 | return all((isinstance(i, string_types) or can_print_latex(i)) and can_print_latex(o[i]) for i in o) | |
|
90 | elif isinstance(o,(sympy.Basic, sympy.matrices.Matrix, int, long, float)): | |
|
91 | return True | |
|
92 | return False | |
|
93 | ||
|
94 | def print_latex(o): | |
|
95 | """A function to generate the latex representation of sympy | |
|
96 | expressions.""" | |
|
97 | if can_print_latex(o): | |
|
98 | s = latex(o, mode='plain') | |
|
99 | s = s.replace('\\dag','\\dagger') | |
|
100 | s = s.strip('$') | |
|
101 | return '$$%s$$' % s | |
|
102 | # Fallback to the string printer | |
|
103 | return None | |
|
104 | ||
|
105 | _loaded = False | |
|
106 | ||
|
107 | 30 | def load_ipython_extension(ip): |
|
108 | """Load the extension in IPython.""" | |
|
109 | import sympy | |
|
110 | ||
|
111 | # sympyprinting extension has been moved to SymPy as of 0.7.2, if it | |
|
112 | # exists there, warn the user and import it | |
|
113 | try: | |
|
114 | import sympy.interactive.ipythonprinting | |
|
115 | except ImportError: | |
|
116 | pass | |
|
117 | else: | |
|
118 | warnings.warn("The sympyprinting extension in IPython is deprecated, " | |
|
119 | "use 'from sympy import init_printing; init_printing()'") | |
|
120 | ip.extension_manager.load_extension('sympy.interactive.ipythonprinting') | |
|
121 | return | |
|
122 | ||
|
123 | global _loaded | |
|
124 | if not _loaded: | |
|
125 | plaintext_formatter = ip.display_formatter.formatters['text/plain'] | |
|
126 | ||
|
127 | for cls in (object, str): | |
|
128 | plaintext_formatter.for_type(cls, print_basic_unicode) | |
|
129 | ||
|
130 | printable_containers = [list, tuple] | |
|
131 | ||
|
132 | # set and frozen set were broken with SymPy's latex() function, but | |
|
133 | # was fixed in the 0.7.1-git development version. See | |
|
134 | # http://code.google.com/p/sympy/issues/detail?id=3062. | |
|
135 | if sympy.__version__ > '0.7.1': | |
|
136 | printable_containers += [set, frozenset] | |
|
137 | else: | |
|
138 | plaintext_formatter.for_type(cls, print_basic_unicode) | |
|
139 | ||
|
140 | plaintext_formatter.for_type_by_name( | |
|
141 | 'sympy.core.basic', 'Basic', print_basic_unicode | |
|
142 | ) | |
|
143 | plaintext_formatter.for_type_by_name( | |
|
144 | 'sympy.matrices.matrices', 'Matrix', print_basic_unicode | |
|
145 | ) | |
|
146 | ||
|
147 | png_formatter = ip.display_formatter.formatters['image/png'] | |
|
148 | ||
|
149 | png_formatter.for_type_by_name( | |
|
150 | 'sympy.core.basic', 'Basic', print_png | |
|
151 | ) | |
|
152 | png_formatter.for_type_by_name( | |
|
153 | 'sympy.matrices.matrices', 'Matrix', print_display_png | |
|
154 | ) | |
|
155 | for cls in [dict, int, long, float] + printable_containers: | |
|
156 | png_formatter.for_type(cls, print_png) | |
|
157 | ||
|
158 | latex_formatter = ip.display_formatter.formatters['text/latex'] | |
|
159 | latex_formatter.for_type_by_name( | |
|
160 | 'sympy.core.basic', 'Basic', print_latex | |
|
161 | ) | |
|
162 | latex_formatter.for_type_by_name( | |
|
163 | 'sympy.matrices.matrices', 'Matrix', print_latex | |
|
164 | ) | |
|
165 | ||
|
166 | for cls in printable_containers: | |
|
167 | # Use LaTeX only if every element is printable by latex | |
|
168 | latex_formatter.for_type(cls, print_latex) | |
|
169 | ||
|
170 | _loaded = True | |
|
31 | warnings.warn("The sympyprinting extension in IPython is deprecated, " | |
|
32 | "use 'from sympy import init_printing; init_printing()'") |
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