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1 | # -*- coding: utf-8 -*- |
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1 | # -*- coding: utf-8 -*- | |
2 | """ |
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2 | """ | |
3 | ====== |
|
3 | ====== | |
4 | Rmagic |
|
4 | Rmagic | |
5 | ====== |
|
5 | ====== | |
6 |
|
6 | |||
7 | Magic command interface for interactive work with R via rpy2 |
|
7 | Magic command interface for interactive work with R via rpy2 | |
8 |
|
8 | |||
9 | .. note:: |
|
9 | .. note:: | |
10 |
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10 | |||
11 | The ``rpy2`` package needs to be installed separately. It |
|
11 | The ``rpy2`` package needs to be installed separately. It | |
12 | can be obtained using ``easy_install`` or ``pip``. |
|
12 | can be obtained using ``easy_install`` or ``pip``. | |
13 |
|
13 | |||
14 | You will also need a working copy of R. |
|
14 | You will also need a working copy of R. | |
15 |
|
15 | |||
16 | Usage |
|
16 | Usage | |
17 | ===== |
|
17 | ===== | |
18 |
|
18 | |||
19 | To enable the magics below, execute ``%load_ext rmagic``. |
|
19 | To enable the magics below, execute ``%load_ext rmagic``. | |
20 |
|
20 | |||
21 | ``%R`` |
|
21 | ``%R`` | |
22 |
|
22 | |||
23 | {R_DOC} |
|
23 | {R_DOC} | |
24 |
|
24 | |||
25 | ``%Rpush`` |
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25 | ``%Rpush`` | |
26 |
|
26 | |||
27 | {RPUSH_DOC} |
|
27 | {RPUSH_DOC} | |
28 |
|
28 | |||
29 | ``%Rpull`` |
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29 | ``%Rpull`` | |
30 |
|
30 | |||
31 | {RPULL_DOC} |
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31 | {RPULL_DOC} | |
32 |
|
32 | |||
33 | ``%Rget`` |
|
33 | ``%Rget`` | |
34 |
|
34 | |||
35 | {RGET_DOC} |
|
35 | {RGET_DOC} | |
36 |
|
36 | |||
37 | """ |
|
37 | """ | |
38 |
|
38 | |||
39 | #----------------------------------------------------------------------------- |
|
39 | #----------------------------------------------------------------------------- | |
40 | # Copyright (C) 2012 The IPython Development Team |
|
40 | # Copyright (C) 2012 The IPython Development Team | |
41 | # |
|
41 | # | |
42 | # Distributed under the terms of the BSD License. The full license is in |
|
42 | # Distributed under the terms of the BSD License. The full license is in | |
43 | # the file COPYING, distributed as part of this software. |
|
43 | # the file COPYING, distributed as part of this software. | |
44 | #----------------------------------------------------------------------------- |
|
44 | #----------------------------------------------------------------------------- | |
45 |
|
45 | |||
46 | import sys |
|
46 | import sys | |
47 | import tempfile |
|
47 | import tempfile | |
48 | from glob import glob |
|
48 | from glob import glob | |
49 | from shutil import rmtree |
|
49 | from shutil import rmtree | |
50 |
|
50 | |||
51 | # numpy and rpy2 imports |
|
51 | # numpy and rpy2 imports | |
52 |
|
52 | |||
53 | import numpy as np |
|
53 | import numpy as np | |
54 |
|
54 | |||
55 | import rpy2.rinterface as ri |
|
55 | import rpy2.rinterface as ri | |
56 | import rpy2.robjects as ro |
|
56 | import rpy2.robjects as ro | |
57 | try: |
|
57 | try: | |
58 | from rpy2.robjects import pandas2ri |
|
58 | from rpy2.robjects import pandas2ri | |
59 | pandas2ri.activate() |
|
59 | pandas2ri.activate() | |
60 | except ImportError: |
|
60 | except ImportError: | |
61 | pandas2ri = None |
|
61 | pandas2ri = None | |
62 | from rpy2.robjects import numpy2ri |
|
62 | from rpy2.robjects import numpy2ri | |
63 | numpy2ri.activate() |
|
63 | numpy2ri.activate() | |
64 |
|
64 | |||
65 | # IPython imports |
|
65 | # IPython imports | |
66 |
|
66 | |||
67 | from IPython.core.displaypub import publish_display_data |
|
67 | from IPython.core.displaypub import publish_display_data | |
68 | from IPython.core.magic import (Magics, magics_class, line_magic, |
|
68 | from IPython.core.magic import (Magics, magics_class, line_magic, | |
69 | line_cell_magic, needs_local_scope) |
|
69 | line_cell_magic, needs_local_scope) | |
70 | from IPython.testing.skipdoctest import skip_doctest |
|
70 | from IPython.testing.skipdoctest import skip_doctest | |
71 | from IPython.core.magic_arguments import ( |
|
71 | from IPython.core.magic_arguments import ( | |
72 | argument, magic_arguments, parse_argstring |
|
72 | argument, magic_arguments, parse_argstring | |
73 | ) |
|
73 | ) | |
74 | from IPython.external.simplegeneric import generic |
|
74 | from IPython.external.simplegeneric import generic | |
75 | from IPython.utils.py3compat import str_to_unicode, unicode_to_str, PY3 |
|
75 | from IPython.utils.py3compat import (str_to_unicode, unicode_to_str, PY3, | |
|
76 | unicode_type) | |||
76 |
|
77 | |||
77 | class RInterpreterError(ri.RRuntimeError): |
|
78 | class RInterpreterError(ri.RRuntimeError): | |
78 | """An error when running R code in a %%R magic cell.""" |
|
79 | """An error when running R code in a %%R magic cell.""" | |
79 | def __init__(self, line, err, stdout): |
|
80 | def __init__(self, line, err, stdout): | |
80 | self.line = line |
|
81 | self.line = line | |
81 | self.err = err.rstrip() |
|
82 | self.err = err.rstrip() | |
82 | self.stdout = stdout.rstrip() |
|
83 | self.stdout = stdout.rstrip() | |
83 |
|
84 | |||
84 | def __unicode__(self): |
|
85 | def __unicode__(self): | |
85 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ |
|
86 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ | |
86 | (self.line, self.err) |
|
87 | (self.line, self.err) | |
87 | if self.stdout and (self.stdout != self.err): |
|
88 | if self.stdout and (self.stdout != self.err): | |
88 | s += '\nR stdout:\n' + self.stdout |
|
89 | s += '\nR stdout:\n' + self.stdout | |
89 | return s |
|
90 | return s | |
90 |
|
91 | |||
91 | if PY3: |
|
92 | if PY3: | |
92 | __str__ = __unicode__ |
|
93 | __str__ = __unicode__ | |
93 | else: |
|
94 | else: | |
94 | def __str__(self): |
|
95 | def __str__(self): | |
95 | return unicode_to_str(unicode(self), 'utf-8') |
|
96 | return unicode_to_str(unicode(self), 'utf-8') | |
96 |
|
97 | |||
97 | def Rconverter(Robj, dataframe=False): |
|
98 | def Rconverter(Robj, dataframe=False): | |
98 | """ |
|
99 | """ | |
99 | Convert an object in R's namespace to one suitable |
|
100 | Convert an object in R's namespace to one suitable | |
100 | for ipython's namespace. |
|
101 | for ipython's namespace. | |
101 |
|
102 | |||
102 | For a data.frame, it tries to return a structured array. |
|
103 | For a data.frame, it tries to return a structured array. | |
103 | It first checks for colnames, then names. |
|
104 | It first checks for colnames, then names. | |
104 | If all are NULL, it returns np.asarray(Robj), else |
|
105 | If all are NULL, it returns np.asarray(Robj), else | |
105 | it tries to construct a recarray |
|
106 | it tries to construct a recarray | |
106 |
|
107 | |||
107 | Parameters |
|
108 | Parameters | |
108 | ---------- |
|
109 | ---------- | |
109 |
|
110 | |||
110 | Robj: an R object returned from rpy2 |
|
111 | Robj: an R object returned from rpy2 | |
111 | """ |
|
112 | """ | |
112 | is_data_frame = ro.r('is.data.frame') |
|
113 | is_data_frame = ro.r('is.data.frame') | |
113 | colnames = ro.r('colnames') |
|
114 | colnames = ro.r('colnames') | |
114 | rownames = ro.r('rownames') # with pandas, these could be used for the index |
|
115 | rownames = ro.r('rownames') # with pandas, these could be used for the index | |
115 | names = ro.r('names') |
|
116 | names = ro.r('names') | |
116 |
|
117 | |||
117 | if dataframe: |
|
118 | if dataframe: | |
118 | as_data_frame = ro.r('as.data.frame') |
|
119 | as_data_frame = ro.r('as.data.frame') | |
119 | cols = colnames(Robj) |
|
120 | cols = colnames(Robj) | |
120 | _names = names(Robj) |
|
121 | _names = names(Robj) | |
121 | if cols != ri.NULL: |
|
122 | if cols != ri.NULL: | |
122 | Robj = as_data_frame(Robj) |
|
123 | Robj = as_data_frame(Robj) | |
123 | names = tuple(np.array(cols)) |
|
124 | names = tuple(np.array(cols)) | |
124 | elif _names != ri.NULL: |
|
125 | elif _names != ri.NULL: | |
125 | names = tuple(np.array(_names)) |
|
126 | names = tuple(np.array(_names)) | |
126 | else: # failed to find names |
|
127 | else: # failed to find names | |
127 | return np.asarray(Robj) |
|
128 | return np.asarray(Robj) | |
128 | Robj = np.rec.fromarrays(Robj, names = names) |
|
129 | Robj = np.rec.fromarrays(Robj, names = names) | |
129 | return np.asarray(Robj) |
|
130 | return np.asarray(Robj) | |
130 |
|
131 | |||
131 | @generic |
|
132 | @generic | |
132 | def pyconverter(pyobj): |
|
133 | def pyconverter(pyobj): | |
133 | """Convert Python objects to R objects. Add types using the decorator: |
|
134 | """Convert Python objects to R objects. Add types using the decorator: | |
134 |
|
135 | |||
135 | @pyconverter.when_type |
|
136 | @pyconverter.when_type | |
136 | """ |
|
137 | """ | |
137 | return pyobj |
|
138 | return pyobj | |
138 |
|
139 | |||
139 | # The default conversion for lists seems to make them a nested list. That has |
|
140 | # The default conversion for lists seems to make them a nested list. That has | |
140 | # some advantages, but is rarely convenient, so for interactive use, we convert |
|
141 | # some advantages, but is rarely convenient, so for interactive use, we convert | |
141 | # lists to a numpy array, which becomes an R vector. |
|
142 | # lists to a numpy array, which becomes an R vector. | |
142 | @pyconverter.when_type(list) |
|
143 | @pyconverter.when_type(list) | |
143 | def pyconverter_list(pyobj): |
|
144 | def pyconverter_list(pyobj): | |
144 | return np.asarray(pyobj) |
|
145 | return np.asarray(pyobj) | |
145 |
|
146 | |||
146 | if pandas2ri is None: |
|
147 | if pandas2ri is None: | |
147 | # pandas2ri was new in rpy2 2.3.3, so for now we'll fallback to pandas' |
|
148 | # pandas2ri was new in rpy2 2.3.3, so for now we'll fallback to pandas' | |
148 | # conversion function. |
|
149 | # conversion function. | |
149 | try: |
|
150 | try: | |
150 | from pandas import DataFrame |
|
151 | from pandas import DataFrame | |
151 | from pandas.rpy.common import convert_to_r_dataframe |
|
152 | from pandas.rpy.common import convert_to_r_dataframe | |
152 | @pyconverter.when_type(DataFrame) |
|
153 | @pyconverter.when_type(DataFrame) | |
153 | def pyconverter_dataframe(pyobj): |
|
154 | def pyconverter_dataframe(pyobj): | |
154 | return convert_to_r_dataframe(pyobj, strings_as_factors=True) |
|
155 | return convert_to_r_dataframe(pyobj, strings_as_factors=True) | |
155 | except ImportError: |
|
156 | except ImportError: | |
156 | pass |
|
157 | pass | |
157 |
|
158 | |||
158 | @magics_class |
|
159 | @magics_class | |
159 | class RMagics(Magics): |
|
160 | class RMagics(Magics): | |
160 | """A set of magics useful for interactive work with R via rpy2. |
|
161 | """A set of magics useful for interactive work with R via rpy2. | |
161 | """ |
|
162 | """ | |
162 |
|
163 | |||
163 | def __init__(self, shell, Rconverter=Rconverter, |
|
164 | def __init__(self, shell, Rconverter=Rconverter, | |
164 | pyconverter=pyconverter, |
|
165 | pyconverter=pyconverter, | |
165 | cache_display_data=False): |
|
166 | cache_display_data=False): | |
166 | """ |
|
167 | """ | |
167 | Parameters |
|
168 | Parameters | |
168 | ---------- |
|
169 | ---------- | |
169 |
|
170 | |||
170 | shell : IPython shell |
|
171 | shell : IPython shell | |
171 |
|
172 | |||
172 | Rconverter : callable |
|
173 | Rconverter : callable | |
173 | To be called on values taken from R before putting them in the |
|
174 | To be called on values taken from R before putting them in the | |
174 | IPython namespace. |
|
175 | IPython namespace. | |
175 |
|
176 | |||
176 | pyconverter : callable |
|
177 | pyconverter : callable | |
177 | To be called on values in ipython namespace before |
|
178 | To be called on values in ipython namespace before | |
178 | assigning to variables in rpy2. |
|
179 | assigning to variables in rpy2. | |
179 |
|
180 | |||
180 | cache_display_data : bool |
|
181 | cache_display_data : bool | |
181 | If True, the published results of the final call to R are |
|
182 | If True, the published results of the final call to R are | |
182 | cached in the variable 'display_cache'. |
|
183 | cached in the variable 'display_cache'. | |
183 |
|
184 | |||
184 | """ |
|
185 | """ | |
185 | super(RMagics, self).__init__(shell) |
|
186 | super(RMagics, self).__init__(shell) | |
186 | self.cache_display_data = cache_display_data |
|
187 | self.cache_display_data = cache_display_data | |
187 |
|
188 | |||
188 | self.r = ro.R() |
|
189 | self.r = ro.R() | |
189 |
|
190 | |||
190 | self.Rstdout_cache = [] |
|
191 | self.Rstdout_cache = [] | |
191 | self.pyconverter = pyconverter |
|
192 | self.pyconverter = pyconverter | |
192 | self.Rconverter = Rconverter |
|
193 | self.Rconverter = Rconverter | |
193 |
|
194 | |||
194 | def eval(self, line): |
|
195 | def eval(self, line): | |
195 | ''' |
|
196 | ''' | |
196 | Parse and evaluate a line of R code with rpy2. |
|
197 | Parse and evaluate a line of R code with rpy2. | |
197 | Returns the output to R's stdout() connection, |
|
198 | Returns the output to R's stdout() connection, | |
198 | the value generated by evaluating the code, and a |
|
199 | the value generated by evaluating the code, and a | |
199 | boolean indicating whether the return value would be |
|
200 | boolean indicating whether the return value would be | |
200 | visible if the line of code were evaluated in an R REPL. |
|
201 | visible if the line of code were evaluated in an R REPL. | |
201 |
|
202 | |||
202 | R Code evaluation and visibility determination are |
|
203 | R Code evaluation and visibility determination are | |
203 | done via an R call of the form withVisible({<code>}) |
|
204 | done via an R call of the form withVisible({<code>}) | |
204 |
|
205 | |||
205 | ''' |
|
206 | ''' | |
206 | old_writeconsole = ri.get_writeconsole() |
|
207 | old_writeconsole = ri.get_writeconsole() | |
207 | ri.set_writeconsole(self.write_console) |
|
208 | ri.set_writeconsole(self.write_console) | |
208 | try: |
|
209 | try: | |
209 | res = ro.r("withVisible({%s})" % line) |
|
210 | res = ro.r("withVisible({%s})" % line) | |
210 | value = res[0] #value (R object) |
|
211 | value = res[0] #value (R object) | |
211 | visible = ro.conversion.ri2py(res[1])[0] #visible (boolean) |
|
212 | visible = ro.conversion.ri2py(res[1])[0] #visible (boolean) | |
212 | except (ri.RRuntimeError, ValueError) as exception: |
|
213 | except (ri.RRuntimeError, ValueError) as exception: | |
213 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error |
|
214 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error | |
214 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) |
|
215 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) | |
215 | text_output = self.flush() |
|
216 | text_output = self.flush() | |
216 | ri.set_writeconsole(old_writeconsole) |
|
217 | ri.set_writeconsole(old_writeconsole) | |
217 | return text_output, value, visible |
|
218 | return text_output, value, visible | |
218 |
|
219 | |||
219 | def write_console(self, output): |
|
220 | def write_console(self, output): | |
220 | ''' |
|
221 | ''' | |
221 | A hook to capture R's stdout in a cache. |
|
222 | A hook to capture R's stdout in a cache. | |
222 | ''' |
|
223 | ''' | |
223 | self.Rstdout_cache.append(output) |
|
224 | self.Rstdout_cache.append(output) | |
224 |
|
225 | |||
225 | def flush(self): |
|
226 | def flush(self): | |
226 | ''' |
|
227 | ''' | |
227 | Flush R's stdout cache to a string, returning the string. |
|
228 | Flush R's stdout cache to a string, returning the string. | |
228 | ''' |
|
229 | ''' | |
229 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) |
|
230 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) | |
230 | self.Rstdout_cache = [] |
|
231 | self.Rstdout_cache = [] | |
231 | return value |
|
232 | return value | |
232 |
|
233 | |||
233 | @skip_doctest |
|
234 | @skip_doctest | |
234 | @needs_local_scope |
|
235 | @needs_local_scope | |
235 | @line_magic |
|
236 | @line_magic | |
236 | def Rpush(self, line, local_ns=None): |
|
237 | def Rpush(self, line, local_ns=None): | |
237 | ''' |
|
238 | ''' | |
238 | A line-level magic for R that pushes |
|
239 | A line-level magic for R that pushes | |
239 | variables from python to rpy2. The line should be made up |
|
240 | variables from python to rpy2. The line should be made up | |
240 | of whitespace separated variable names in the IPython |
|
241 | of whitespace separated variable names in the IPython | |
241 | namespace:: |
|
242 | namespace:: | |
242 |
|
243 | |||
243 | In [7]: import numpy as np |
|
244 | In [7]: import numpy as np | |
244 |
|
245 | |||
245 | In [8]: X = np.array([4.5,6.3,7.9]) |
|
246 | In [8]: X = np.array([4.5,6.3,7.9]) | |
246 |
|
247 | |||
247 | In [9]: X.mean() |
|
248 | In [9]: X.mean() | |
248 | Out[9]: 6.2333333333333343 |
|
249 | Out[9]: 6.2333333333333343 | |
249 |
|
250 | |||
250 | In [10]: %Rpush X |
|
251 | In [10]: %Rpush X | |
251 |
|
252 | |||
252 | In [11]: %R mean(X) |
|
253 | In [11]: %R mean(X) | |
253 | Out[11]: array([ 6.23333333]) |
|
254 | Out[11]: array([ 6.23333333]) | |
254 |
|
255 | |||
255 | ''' |
|
256 | ''' | |
256 | if local_ns is None: |
|
257 | if local_ns is None: | |
257 | local_ns = {} |
|
258 | local_ns = {} | |
258 |
|
259 | |||
259 | inputs = line.split(' ') |
|
260 | inputs = line.split(' ') | |
260 | for input in inputs: |
|
261 | for input in inputs: | |
261 | try: |
|
262 | try: | |
262 | val = local_ns[input] |
|
263 | val = local_ns[input] | |
263 | except KeyError: |
|
264 | except KeyError: | |
264 | try: |
|
265 | try: | |
265 | val = self.shell.user_ns[input] |
|
266 | val = self.shell.user_ns[input] | |
266 | except KeyError: |
|
267 | except KeyError: | |
267 | # reraise the KeyError as a NameError so that it looks like |
|
268 | # reraise the KeyError as a NameError so that it looks like | |
268 | # the standard python behavior when you use an unnamed |
|
269 | # the standard python behavior when you use an unnamed | |
269 | # variable |
|
270 | # variable | |
270 | raise NameError("name '%s' is not defined" % input) |
|
271 | raise NameError("name '%s' is not defined" % input) | |
271 |
|
272 | |||
272 | self.r.assign(input, self.pyconverter(val)) |
|
273 | self.r.assign(input, self.pyconverter(val)) | |
273 |
|
274 | |||
274 | @skip_doctest |
|
275 | @skip_doctest | |
275 | @magic_arguments() |
|
276 | @magic_arguments() | |
276 | @argument( |
|
277 | @argument( | |
277 | '-d', '--as_dataframe', action='store_true', |
|
278 | '-d', '--as_dataframe', action='store_true', | |
278 | default=False, |
|
279 | default=False, | |
279 | help='Convert objects to data.frames before returning to ipython.' |
|
280 | help='Convert objects to data.frames before returning to ipython.' | |
280 | ) |
|
281 | ) | |
281 | @argument( |
|
282 | @argument( | |
282 | 'outputs', |
|
283 | 'outputs', | |
283 | nargs='*', |
|
284 | nargs='*', | |
284 | ) |
|
285 | ) | |
285 | @line_magic |
|
286 | @line_magic | |
286 | def Rpull(self, line): |
|
287 | def Rpull(self, line): | |
287 | ''' |
|
288 | ''' | |
288 | A line-level magic for R that pulls |
|
289 | A line-level magic for R that pulls | |
289 | variables from python to rpy2:: |
|
290 | variables from python to rpy2:: | |
290 |
|
291 | |||
291 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) |
|
292 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) | |
292 |
|
293 | |||
293 | In [19]: %Rpull x y z |
|
294 | In [19]: %Rpull x y z | |
294 |
|
295 | |||
295 | In [20]: x |
|
296 | In [20]: x | |
296 | Out[20]: array([ 3. , 4. , 6.7]) |
|
297 | Out[20]: array([ 3. , 4. , 6.7]) | |
297 |
|
298 | |||
298 | In [21]: y |
|
299 | In [21]: y | |
299 | Out[21]: array([ 4., 6., 7.]) |
|
300 | Out[21]: array([ 4., 6., 7.]) | |
300 |
|
301 | |||
301 | In [22]: z |
|
302 | In [22]: z | |
302 | Out[22]: |
|
303 | Out[22]: | |
303 | array(['a', '3', '4'], |
|
304 | array(['a', '3', '4'], | |
304 | dtype='|S1') |
|
305 | dtype='|S1') | |
305 |
|
306 | |||
306 |
|
307 | |||
307 | If --as_dataframe, then each object is returned as a structured array |
|
308 | If --as_dataframe, then each object is returned as a structured array | |
308 | after first passed through "as.data.frame" in R before |
|
309 | after first passed through "as.data.frame" in R before | |
309 | being calling self.Rconverter. |
|
310 | being calling self.Rconverter. | |
310 | This is useful when a structured array is desired as output, or |
|
311 | This is useful when a structured array is desired as output, or | |
311 | when the object in R has mixed data types. |
|
312 | when the object in R has mixed data types. | |
312 | See the %%R docstring for more examples. |
|
313 | See the %%R docstring for more examples. | |
313 |
|
314 | |||
314 | Notes |
|
315 | Notes | |
315 | ----- |
|
316 | ----- | |
316 |
|
317 | |||
317 | Beware that R names can have '.' so this is not fool proof. |
|
318 | Beware that R names can have '.' so this is not fool proof. | |
318 | To avoid this, don't name your R objects with '.'s... |
|
319 | To avoid this, don't name your R objects with '.'s... | |
319 |
|
320 | |||
320 | ''' |
|
321 | ''' | |
321 | args = parse_argstring(self.Rpull, line) |
|
322 | args = parse_argstring(self.Rpull, line) | |
322 | outputs = args.outputs |
|
323 | outputs = args.outputs | |
323 | for output in outputs: |
|
324 | for output in outputs: | |
324 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) |
|
325 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) | |
325 |
|
326 | |||
326 | @skip_doctest |
|
327 | @skip_doctest | |
327 | @magic_arguments() |
|
328 | @magic_arguments() | |
328 | @argument( |
|
329 | @argument( | |
329 | '-d', '--as_dataframe', action='store_true', |
|
330 | '-d', '--as_dataframe', action='store_true', | |
330 | default=False, |
|
331 | default=False, | |
331 | help='Convert objects to data.frames before returning to ipython.' |
|
332 | help='Convert objects to data.frames before returning to ipython.' | |
332 | ) |
|
333 | ) | |
333 | @argument( |
|
334 | @argument( | |
334 | 'output', |
|
335 | 'output', | |
335 | nargs=1, |
|
336 | nargs=1, | |
336 | type=str, |
|
337 | type=str, | |
337 | ) |
|
338 | ) | |
338 | @line_magic |
|
339 | @line_magic | |
339 | def Rget(self, line): |
|
340 | def Rget(self, line): | |
340 | ''' |
|
341 | ''' | |
341 | Return an object from rpy2, possibly as a structured array (if possible). |
|
342 | 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 | Similar to Rpull except only one argument is accepted and the value is | |
343 | returned rather than pushed to self.shell.user_ns:: |
|
344 | returned rather than pushed to self.shell.user_ns:: | |
344 |
|
345 | |||
345 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
346 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
346 |
|
347 | |||
347 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
348 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
348 |
|
349 | |||
349 | In [5]: %R -i datapy |
|
350 | In [5]: %R -i datapy | |
350 |
|
351 | |||
351 | In [6]: %Rget datapy |
|
352 | In [6]: %Rget datapy | |
352 | Out[6]: |
|
353 | Out[6]: | |
353 | array([['1', '2', '3', '4'], |
|
354 | array([['1', '2', '3', '4'], | |
354 | ['2', '3', '2', '5'], |
|
355 | ['2', '3', '2', '5'], | |
355 | ['a', 'b', 'c', 'e']], |
|
356 | ['a', 'b', 'c', 'e']], | |
356 | dtype='|S1') |
|
357 | dtype='|S1') | |
357 |
|
358 | |||
358 | In [7]: %Rget -d datapy |
|
359 | In [7]: %Rget -d datapy | |
359 | Out[7]: |
|
360 | Out[7]: | |
360 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
361 | 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 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
362 |
|
363 | |||
363 | ''' |
|
364 | ''' | |
364 | args = parse_argstring(self.Rget, line) |
|
365 | args = parse_argstring(self.Rget, line) | |
365 | output = args.output |
|
366 | output = args.output | |
366 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) |
|
367 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) | |
367 |
|
368 | |||
368 |
|
369 | |||
369 | @skip_doctest |
|
370 | @skip_doctest | |
370 | @magic_arguments() |
|
371 | @magic_arguments() | |
371 | @argument( |
|
372 | @argument( | |
372 | '-i', '--input', action='append', |
|
373 | '-i', '--input', action='append', | |
373 | 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.' |
|
374 | 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.' | |
374 | ) |
|
375 | ) | |
375 | @argument( |
|
376 | @argument( | |
376 | '-o', '--output', action='append', |
|
377 | '-o', '--output', action='append', | |
377 | 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.' |
|
378 | 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.' | |
378 | ) |
|
379 | ) | |
379 | @argument( |
|
380 | @argument( | |
380 | '-w', '--width', type=int, |
|
381 | '-w', '--width', type=int, | |
381 | help='Width of png plotting device sent as an argument to *png* in R.' |
|
382 | help='Width of png plotting device sent as an argument to *png* in R.' | |
382 | ) |
|
383 | ) | |
383 | @argument( |
|
384 | @argument( | |
384 | '-h', '--height', type=int, |
|
385 | '-h', '--height', type=int, | |
385 | help='Height of png plotting device sent as an argument to *png* in R.' |
|
386 | help='Height of png plotting device sent as an argument to *png* in R.' | |
386 | ) |
|
387 | ) | |
387 |
|
388 | |||
388 | @argument( |
|
389 | @argument( | |
389 | '-d', '--dataframe', action='append', |
|
390 | '-d', '--dataframe', action='append', | |
390 | help='Convert these objects to data.frames and return as structured arrays.' |
|
391 | help='Convert these objects to data.frames and return as structured arrays.' | |
391 | ) |
|
392 | ) | |
392 | @argument( |
|
393 | @argument( | |
393 | '-u', '--units', type=unicode, choices=["px", "in", "cm", "mm"], |
|
394 | '-u', '--units', type=unicode_type, choices=["px", "in", "cm", "mm"], | |
394 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' |
|
395 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' | |
395 | ) |
|
396 | ) | |
396 | @argument( |
|
397 | @argument( | |
397 | '-r', '--res', type=int, |
|
398 | '-r', '--res', type=int, | |
398 | 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"].' |
|
399 | 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"].' | |
399 | ) |
|
400 | ) | |
400 | @argument( |
|
401 | @argument( | |
401 | '-p', '--pointsize', type=int, |
|
402 | '-p', '--pointsize', type=int, | |
402 | help='Pointsize of png plotting device sent as an argument to *png* in R.' |
|
403 | help='Pointsize of png plotting device sent as an argument to *png* in R.' | |
403 | ) |
|
404 | ) | |
404 | @argument( |
|
405 | @argument( | |
405 | '-b', '--bg', |
|
406 | '-b', '--bg', | |
406 | help='Background of png plotting device sent as an argument to *png* in R.' |
|
407 | help='Background of png plotting device sent as an argument to *png* in R.' | |
407 | ) |
|
408 | ) | |
408 | @argument( |
|
409 | @argument( | |
409 | '-n', '--noreturn', |
|
410 | '-n', '--noreturn', | |
410 | help='Force the magic to not return anything.', |
|
411 | help='Force the magic to not return anything.', | |
411 | action='store_true', |
|
412 | action='store_true', | |
412 | default=False |
|
413 | default=False | |
413 | ) |
|
414 | ) | |
414 | @argument( |
|
415 | @argument( | |
415 | 'code', |
|
416 | 'code', | |
416 | nargs='*', |
|
417 | nargs='*', | |
417 | ) |
|
418 | ) | |
418 | @needs_local_scope |
|
419 | @needs_local_scope | |
419 | @line_cell_magic |
|
420 | @line_cell_magic | |
420 | def R(self, line, cell=None, local_ns=None): |
|
421 | def R(self, line, cell=None, local_ns=None): | |
421 | ''' |
|
422 | ''' | |
422 | Execute code in R, and pull some of the results back into the Python namespace. |
|
423 | Execute code in R, and pull some of the results back into the Python namespace. | |
423 |
|
424 | |||
424 | In line mode, this will evaluate an expression and convert the returned value to a Python object. |
|
425 | In line mode, this will evaluate an expression and convert the returned value to a Python object. | |
425 | The return value is determined by rpy2's behaviour of returning the result of evaluating the |
|
426 | The return value is determined by rpy2's behaviour of returning the result of evaluating the | |
426 | final line. |
|
427 | final line. | |
427 |
|
428 | |||
428 | Multiple R lines can be executed by joining them with semicolons:: |
|
429 | Multiple R lines can be executed by joining them with semicolons:: | |
429 |
|
430 | |||
430 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) |
|
431 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) | |
431 | Out[9]: array([ 4.25]) |
|
432 | Out[9]: array([ 4.25]) | |
432 |
|
433 | |||
433 | In cell mode, this will run a block of R code. The resulting value |
|
434 | In cell mode, this will run a block of R code. The resulting value | |
434 | is printed if it would printed be when evaluating the same code |
|
435 | is printed if it would printed be when evaluating the same code | |
435 | within a standard R REPL. |
|
436 | within a standard R REPL. | |
436 |
|
437 | |||
437 | Nothing is returned to python by default in cell mode:: |
|
438 | Nothing is returned to python by default in cell mode:: | |
438 |
|
439 | |||
439 | In [10]: %%R |
|
440 | In [10]: %%R | |
440 | ....: Y = c(2,4,3,9) |
|
441 | ....: Y = c(2,4,3,9) | |
441 | ....: summary(lm(Y~X)) |
|
442 | ....: summary(lm(Y~X)) | |
442 |
|
443 | |||
443 | Call: |
|
444 | Call: | |
444 | lm(formula = Y ~ X) |
|
445 | lm(formula = Y ~ X) | |
445 |
|
446 | |||
446 | Residuals: |
|
447 | Residuals: | |
447 | 1 2 3 4 |
|
448 | 1 2 3 4 | |
448 | 0.88 -0.24 -2.28 1.64 |
|
449 | 0.88 -0.24 -2.28 1.64 | |
449 |
|
450 | |||
450 | Coefficients: |
|
451 | Coefficients: | |
451 | Estimate Std. Error t value Pr(>|t|) |
|
452 | Estimate Std. Error t value Pr(>|t|) | |
452 | (Intercept) 0.0800 2.3000 0.035 0.975 |
|
453 | (Intercept) 0.0800 2.3000 0.035 0.975 | |
453 | X 1.0400 0.4822 2.157 0.164 |
|
454 | X 1.0400 0.4822 2.157 0.164 | |
454 |
|
455 | |||
455 | Residual standard error: 2.088 on 2 degrees of freedom |
|
456 | Residual standard error: 2.088 on 2 degrees of freedom | |
456 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 |
|
457 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 | |
457 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 |
|
458 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 | |
458 |
|
459 | |||
459 | In the notebook, plots are published as the output of the cell:: |
|
460 | In the notebook, plots are published as the output of the cell:: | |
460 |
|
461 | |||
461 | %R plot(X, Y) |
|
462 | %R plot(X, Y) | |
462 |
|
463 | |||
463 | will create a scatter plot of X bs Y. |
|
464 | will create a scatter plot of X bs Y. | |
464 |
|
465 | |||
465 | If cell is not None and line has some R code, it is prepended to |
|
466 | If cell is not None and line has some R code, it is prepended to | |
466 | the R code in cell. |
|
467 | the R code in cell. | |
467 |
|
468 | |||
468 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: |
|
469 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: | |
469 |
|
470 | |||
470 | In [14]: Z = np.array([1,4,5,10]) |
|
471 | In [14]: Z = np.array([1,4,5,10]) | |
471 |
|
472 | |||
472 | In [15]: %R -i Z mean(Z) |
|
473 | In [15]: %R -i Z mean(Z) | |
473 | Out[15]: array([ 5.]) |
|
474 | Out[15]: array([ 5.]) | |
474 |
|
475 | |||
475 |
|
476 | |||
476 | In [16]: %R -o W W=Z*mean(Z) |
|
477 | In [16]: %R -o W W=Z*mean(Z) | |
477 | Out[16]: array([ 5., 20., 25., 50.]) |
|
478 | Out[16]: array([ 5., 20., 25., 50.]) | |
478 |
|
479 | |||
479 | In [17]: W |
|
480 | In [17]: W | |
480 | Out[17]: array([ 5., 20., 25., 50.]) |
|
481 | Out[17]: array([ 5., 20., 25., 50.]) | |
481 |
|
482 | |||
482 | The return value is determined by these rules: |
|
483 | The return value is determined by these rules: | |
483 |
|
484 | |||
484 | * If the cell is not None, the magic returns None. |
|
485 | * If the cell is not None, the magic returns None. | |
485 |
|
486 | |||
486 | * If the cell evaluates as False, the resulting value is returned |
|
487 | * If the cell evaluates as False, the resulting value is returned | |
487 | unless the final line prints something to the console, in |
|
488 | unless the final line prints something to the console, in | |
488 | which case None is returned. |
|
489 | which case None is returned. | |
489 |
|
490 | |||
490 | * If the final line results in a NULL value when evaluated |
|
491 | * If the final line results in a NULL value when evaluated | |
491 | by rpy2, then None is returned. |
|
492 | by rpy2, then None is returned. | |
492 |
|
493 | |||
493 | * No attempt is made to convert the final value to a structured array. |
|
494 | * No attempt is made to convert the final value to a structured array. | |
494 | Use the --dataframe flag or %Rget to push / return a structured array. |
|
495 | Use the --dataframe flag or %Rget to push / return a structured array. | |
495 |
|
496 | |||
496 | * If the -n flag is present, there is no return value. |
|
497 | * If the -n flag is present, there is no return value. | |
497 |
|
498 | |||
498 | * A trailing ';' will also result in no return value as the last |
|
499 | * A trailing ';' will also result in no return value as the last | |
499 | value in the line is an empty string. |
|
500 | value in the line is an empty string. | |
500 |
|
501 | |||
501 | The --dataframe argument will attempt to return structured arrays. |
|
502 | The --dataframe argument will attempt to return structured arrays. | |
502 | This is useful for dataframes with |
|
503 | This is useful for dataframes with | |
503 | mixed data types. Note also that for a data.frame, |
|
504 | mixed data types. Note also that for a data.frame, | |
504 | if it is returned as an ndarray, it is transposed:: |
|
505 | if it is returned as an ndarray, it is transposed:: | |
505 |
|
506 | |||
506 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
507 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
507 |
|
508 | |||
508 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
509 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
509 |
|
510 | |||
510 | In [20]: %%R -o datar |
|
511 | In [20]: %%R -o datar | |
511 | datar = datapy |
|
512 | datar = datapy | |
512 | ....: |
|
513 | ....: | |
513 |
|
514 | |||
514 | In [21]: datar |
|
515 | In [21]: datar | |
515 | Out[21]: |
|
516 | Out[21]: | |
516 | array([['1', '2', '3', '4'], |
|
517 | array([['1', '2', '3', '4'], | |
517 | ['2', '3', '2', '5'], |
|
518 | ['2', '3', '2', '5'], | |
518 | ['a', 'b', 'c', 'e']], |
|
519 | ['a', 'b', 'c', 'e']], | |
519 | dtype='|S1') |
|
520 | dtype='|S1') | |
520 |
|
521 | |||
521 | In [22]: %%R -d datar |
|
522 | In [22]: %%R -d datar | |
522 | datar = datapy |
|
523 | datar = datapy | |
523 | ....: |
|
524 | ....: | |
524 |
|
525 | |||
525 | In [23]: datar |
|
526 | In [23]: datar | |
526 | Out[23]: |
|
527 | Out[23]: | |
527 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
528 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
528 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
529 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
529 |
|
530 | |||
530 | The --dataframe argument first tries colnames, then names. |
|
531 | The --dataframe argument first tries colnames, then names. | |
531 | If both are NULL, it returns an ndarray (i.e. unstructured):: |
|
532 | If both are NULL, it returns an ndarray (i.e. unstructured):: | |
532 |
|
533 | |||
533 | In [1]: %R mydata=c(4,6,8.3); NULL |
|
534 | In [1]: %R mydata=c(4,6,8.3); NULL | |
534 |
|
535 | |||
535 | In [2]: %R -d mydata |
|
536 | In [2]: %R -d mydata | |
536 |
|
537 | |||
537 | In [3]: mydata |
|
538 | In [3]: mydata | |
538 | Out[3]: array([ 4. , 6. , 8.3]) |
|
539 | Out[3]: array([ 4. , 6. , 8.3]) | |
539 |
|
540 | |||
540 | In [4]: %R names(mydata) = c('a','b','c'); NULL |
|
541 | In [4]: %R names(mydata) = c('a','b','c'); NULL | |
541 |
|
542 | |||
542 | In [5]: %R -d mydata |
|
543 | In [5]: %R -d mydata | |
543 |
|
544 | |||
544 | In [6]: mydata |
|
545 | In [6]: mydata | |
545 | Out[6]: |
|
546 | Out[6]: | |
546 | array((4.0, 6.0, 8.3), |
|
547 | array((4.0, 6.0, 8.3), | |
547 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) |
|
548 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) | |
548 |
|
549 | |||
549 | In [7]: %R -o mydata |
|
550 | In [7]: %R -o mydata | |
550 |
|
551 | |||
551 | In [8]: mydata |
|
552 | In [8]: mydata | |
552 | Out[8]: array([ 4. , 6. , 8.3]) |
|
553 | Out[8]: array([ 4. , 6. , 8.3]) | |
553 |
|
554 | |||
554 | ''' |
|
555 | ''' | |
555 |
|
556 | |||
556 | args = parse_argstring(self.R, line) |
|
557 | args = parse_argstring(self.R, line) | |
557 |
|
558 | |||
558 | # arguments 'code' in line are prepended to |
|
559 | # arguments 'code' in line are prepended to | |
559 | # the cell lines |
|
560 | # the cell lines | |
560 |
|
561 | |||
561 | if cell is None: |
|
562 | if cell is None: | |
562 | code = '' |
|
563 | code = '' | |
563 | return_output = True |
|
564 | return_output = True | |
564 | line_mode = True |
|
565 | line_mode = True | |
565 | else: |
|
566 | else: | |
566 | code = cell |
|
567 | code = cell | |
567 | return_output = False |
|
568 | return_output = False | |
568 | line_mode = False |
|
569 | line_mode = False | |
569 |
|
570 | |||
570 | code = ' '.join(args.code) + code |
|
571 | code = ' '.join(args.code) + code | |
571 |
|
572 | |||
572 | # if there is no local namespace then default to an empty dict |
|
573 | # if there is no local namespace then default to an empty dict | |
573 | if local_ns is None: |
|
574 | if local_ns is None: | |
574 | local_ns = {} |
|
575 | local_ns = {} | |
575 |
|
576 | |||
576 | if args.input: |
|
577 | if args.input: | |
577 | for input in ','.join(args.input).split(','): |
|
578 | for input in ','.join(args.input).split(','): | |
578 | try: |
|
579 | try: | |
579 | val = local_ns[input] |
|
580 | val = local_ns[input] | |
580 | except KeyError: |
|
581 | except KeyError: | |
581 | try: |
|
582 | try: | |
582 | val = self.shell.user_ns[input] |
|
583 | val = self.shell.user_ns[input] | |
583 | except KeyError: |
|
584 | except KeyError: | |
584 | raise NameError("name '%s' is not defined" % input) |
|
585 | raise NameError("name '%s' is not defined" % input) | |
585 | self.r.assign(input, self.pyconverter(val)) |
|
586 | self.r.assign(input, self.pyconverter(val)) | |
586 |
|
587 | |||
587 | if getattr(args, 'units') is not None: |
|
588 | if getattr(args, 'units') is not None: | |
588 | if args.units != "px" and getattr(args, 'res') is None: |
|
589 | if args.units != "px" and getattr(args, 'res') is None: | |
589 | args.res = 72 |
|
590 | args.res = 72 | |
590 | args.units = '"%s"' % args.units |
|
591 | args.units = '"%s"' % args.units | |
591 |
|
592 | |||
592 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) |
|
593 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) | |
593 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) |
|
594 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) | |
594 | # execute the R code in a temporary directory |
|
595 | # execute the R code in a temporary directory | |
595 |
|
596 | |||
596 | tmpd = tempfile.mkdtemp() |
|
597 | tmpd = tempfile.mkdtemp() | |
597 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) |
|
598 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) | |
598 |
|
599 | |||
599 | text_output = '' |
|
600 | text_output = '' | |
600 | try: |
|
601 | try: | |
601 | if line_mode: |
|
602 | if line_mode: | |
602 | for line in code.split(';'): |
|
603 | for line in code.split(';'): | |
603 | text_result, result, visible = self.eval(line) |
|
604 | text_result, result, visible = self.eval(line) | |
604 | text_output += text_result |
|
605 | text_output += text_result | |
605 | if text_result: |
|
606 | if text_result: | |
606 | # the last line printed something to the console so we won't return it |
|
607 | # the last line printed something to the console so we won't return it | |
607 | return_output = False |
|
608 | return_output = False | |
608 | else: |
|
609 | else: | |
609 | text_result, result, visible = self.eval(code) |
|
610 | text_result, result, visible = self.eval(code) | |
610 | text_output += text_result |
|
611 | text_output += text_result | |
611 | if visible: |
|
612 | if visible: | |
612 | old_writeconsole = ri.get_writeconsole() |
|
613 | old_writeconsole = ri.get_writeconsole() | |
613 | ri.set_writeconsole(self.write_console) |
|
614 | ri.set_writeconsole(self.write_console) | |
614 | ro.r.show(result) |
|
615 | ro.r.show(result) | |
615 | text_output += self.flush() |
|
616 | text_output += self.flush() | |
616 | ri.set_writeconsole(old_writeconsole) |
|
617 | ri.set_writeconsole(old_writeconsole) | |
617 |
|
618 | |||
618 | except RInterpreterError as e: |
|
619 | except RInterpreterError as e: | |
619 | print(e.stdout) |
|
620 | print(e.stdout) | |
620 | if not e.stdout.endswith(e.err): |
|
621 | if not e.stdout.endswith(e.err): | |
621 | print(e.err) |
|
622 | print(e.err) | |
622 | rmtree(tmpd) |
|
623 | rmtree(tmpd) | |
623 | return |
|
624 | return | |
624 |
|
625 | |||
625 | self.r('dev.off()') |
|
626 | self.r('dev.off()') | |
626 |
|
627 | |||
627 | # read out all the saved .png files |
|
628 | # read out all the saved .png files | |
628 |
|
629 | |||
629 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] |
|
630 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] | |
630 |
|
631 | |||
631 | # now publish the images |
|
632 | # now publish the images | |
632 | # mimicking IPython/zmq/pylab/backend_inline.py |
|
633 | # mimicking IPython/zmq/pylab/backend_inline.py | |
633 | fmt = 'png' |
|
634 | fmt = 'png' | |
634 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } |
|
635 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } | |
635 | mime = mimetypes[fmt] |
|
636 | mime = mimetypes[fmt] | |
636 |
|
637 | |||
637 | # publish the printed R objects, if any |
|
638 | # publish the printed R objects, if any | |
638 |
|
639 | |||
639 | display_data = [] |
|
640 | display_data = [] | |
640 | if text_output: |
|
641 | if text_output: | |
641 | display_data.append(('RMagic.R', {'text/plain':text_output})) |
|
642 | display_data.append(('RMagic.R', {'text/plain':text_output})) | |
642 |
|
643 | |||
643 | # flush text streams before sending figures, helps a little with output |
|
644 | # flush text streams before sending figures, helps a little with output | |
644 | for image in images: |
|
645 | for image in images: | |
645 | # synchronization in the console (though it's a bandaid, not a real sln) |
|
646 | # synchronization in the console (though it's a bandaid, not a real sln) | |
646 | sys.stdout.flush(); sys.stderr.flush() |
|
647 | sys.stdout.flush(); sys.stderr.flush() | |
647 | display_data.append(('RMagic.R', {mime: image})) |
|
648 | display_data.append(('RMagic.R', {mime: image})) | |
648 |
|
649 | |||
649 | # kill the temporary directory |
|
650 | # kill the temporary directory | |
650 | rmtree(tmpd) |
|
651 | rmtree(tmpd) | |
651 |
|
652 | |||
652 | # try to turn every output into a numpy array |
|
653 | # try to turn every output into a numpy array | |
653 | # this means that output are assumed to be castable |
|
654 | # this means that output are assumed to be castable | |
654 | # as numpy arrays |
|
655 | # as numpy arrays | |
655 |
|
656 | |||
656 | if args.output: |
|
657 | if args.output: | |
657 | for output in ','.join(args.output).split(','): |
|
658 | for output in ','.join(args.output).split(','): | |
658 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) |
|
659 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) | |
659 |
|
660 | |||
660 | if args.dataframe: |
|
661 | if args.dataframe: | |
661 | for output in ','.join(args.dataframe).split(','): |
|
662 | for output in ','.join(args.dataframe).split(','): | |
662 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) |
|
663 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) | |
663 |
|
664 | |||
664 | for tag, disp_d in display_data: |
|
665 | for tag, disp_d in display_data: | |
665 | publish_display_data(tag, disp_d) |
|
666 | publish_display_data(tag, disp_d) | |
666 |
|
667 | |||
667 | # this will keep a reference to the display_data |
|
668 | # this will keep a reference to the display_data | |
668 | # which might be useful to other objects who happen to use |
|
669 | # which might be useful to other objects who happen to use | |
669 | # this method |
|
670 | # this method | |
670 |
|
671 | |||
671 | if self.cache_display_data: |
|
672 | if self.cache_display_data: | |
672 | self.display_cache = display_data |
|
673 | self.display_cache = display_data | |
673 |
|
674 | |||
674 | # if in line mode and return_output, return the result as an ndarray |
|
675 | # if in line mode and return_output, return the result as an ndarray | |
675 | if return_output and not args.noreturn: |
|
676 | if return_output and not args.noreturn: | |
676 | if result != ri.NULL: |
|
677 | if result != ri.NULL: | |
677 | return self.Rconverter(result, dataframe=False) |
|
678 | return self.Rconverter(result, dataframe=False) | |
678 |
|
679 | |||
679 | __doc__ = __doc__.format( |
|
680 | __doc__ = __doc__.format( | |
680 | R_DOC = ' '*8 + RMagics.R.__doc__, |
|
681 | R_DOC = ' '*8 + RMagics.R.__doc__, | |
681 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, |
|
682 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, | |
682 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__, |
|
683 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__, | |
683 | RGET_DOC = ' '*8 + RMagics.Rget.__doc__ |
|
684 | RGET_DOC = ' '*8 + RMagics.Rget.__doc__ | |
684 | ) |
|
685 | ) | |
685 |
|
686 | |||
686 |
|
687 | |||
687 | def load_ipython_extension(ip): |
|
688 | def load_ipython_extension(ip): | |
688 | """Load the extension in IPython.""" |
|
689 | """Load the extension in IPython.""" | |
689 | ip.register_magics(RMagics) |
|
690 | ip.register_magics(RMagics) | |
690 | # Initialising rpy2 interferes with readline. Since, at this point, we've |
|
691 | # Initialising rpy2 interferes with readline. Since, at this point, we've | |
691 | # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. |
|
692 | # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. | |
692 | if ip.has_readline: |
|
693 | if ip.has_readline: | |
693 | ip.readline.set_completer_delims(ip.readline_delims) |
|
694 | ip.readline.set_completer_delims(ip.readline_delims) |
@@ -1,204 +1,206 b'' | |||||
1 | # coding: utf-8 |
|
1 | # coding: utf-8 | |
2 | """Compatibility tricks for Python 3. Mainly to do with unicode.""" |
|
2 | """Compatibility tricks for Python 3. Mainly to do with unicode.""" | |
3 | import __builtin__ |
|
3 | import __builtin__ | |
4 | import functools |
|
4 | import functools | |
5 | import sys |
|
5 | import sys | |
6 | import re |
|
6 | import re | |
7 | import types |
|
7 | import types | |
8 |
|
8 | |||
9 | from .encoding import DEFAULT_ENCODING |
|
9 | from .encoding import DEFAULT_ENCODING | |
10 |
|
10 | |||
11 | orig_open = open |
|
11 | orig_open = open | |
12 |
|
12 | |||
13 | def no_code(x, encoding=None): |
|
13 | def no_code(x, encoding=None): | |
14 | return x |
|
14 | return x | |
15 |
|
15 | |||
16 | def decode(s, encoding=None): |
|
16 | def decode(s, encoding=None): | |
17 | encoding = encoding or DEFAULT_ENCODING |
|
17 | encoding = encoding or DEFAULT_ENCODING | |
18 | return s.decode(encoding, "replace") |
|
18 | return s.decode(encoding, "replace") | |
19 |
|
19 | |||
20 | def encode(u, encoding=None): |
|
20 | def encode(u, encoding=None): | |
21 | encoding = encoding or DEFAULT_ENCODING |
|
21 | encoding = encoding or DEFAULT_ENCODING | |
22 | return u.encode(encoding, "replace") |
|
22 | return u.encode(encoding, "replace") | |
23 |
|
23 | |||
24 |
|
24 | |||
25 | def cast_unicode(s, encoding=None): |
|
25 | def cast_unicode(s, encoding=None): | |
26 | if isinstance(s, bytes): |
|
26 | if isinstance(s, bytes): | |
27 | return decode(s, encoding) |
|
27 | return decode(s, encoding) | |
28 | return s |
|
28 | return s | |
29 |
|
29 | |||
30 | def cast_bytes(s, encoding=None): |
|
30 | def cast_bytes(s, encoding=None): | |
31 | if not isinstance(s, bytes): |
|
31 | if not isinstance(s, bytes): | |
32 | return encode(s, encoding) |
|
32 | return encode(s, encoding) | |
33 | return s |
|
33 | return s | |
34 |
|
34 | |||
35 | def _modify_str_or_docstring(str_change_func): |
|
35 | def _modify_str_or_docstring(str_change_func): | |
36 | @functools.wraps(str_change_func) |
|
36 | @functools.wraps(str_change_func) | |
37 | def wrapper(func_or_str): |
|
37 | def wrapper(func_or_str): | |
38 | if isinstance(func_or_str, basestring): |
|
38 | if isinstance(func_or_str, basestring): | |
39 | func = None |
|
39 | func = None | |
40 | doc = func_or_str |
|
40 | doc = func_or_str | |
41 | else: |
|
41 | else: | |
42 | func = func_or_str |
|
42 | func = func_or_str | |
43 | doc = func.__doc__ |
|
43 | doc = func.__doc__ | |
44 |
|
44 | |||
45 | doc = str_change_func(doc) |
|
45 | doc = str_change_func(doc) | |
46 |
|
46 | |||
47 | if func: |
|
47 | if func: | |
48 | func.__doc__ = doc |
|
48 | func.__doc__ = doc | |
49 | return func |
|
49 | return func | |
50 | return doc |
|
50 | return doc | |
51 | return wrapper |
|
51 | return wrapper | |
52 |
|
52 | |||
53 | def safe_unicode(e): |
|
53 | def safe_unicode(e): | |
54 | """unicode(e) with various fallbacks. Used for exceptions, which may not be |
|
54 | """unicode(e) with various fallbacks. Used for exceptions, which may not be | |
55 | safe to call unicode() on. |
|
55 | safe to call unicode() on. | |
56 | """ |
|
56 | """ | |
57 | try: |
|
57 | try: | |
58 | return unicode(e) |
|
58 | return unicode(e) | |
59 | except UnicodeError: |
|
59 | except UnicodeError: | |
60 | pass |
|
60 | pass | |
61 |
|
61 | |||
62 | try: |
|
62 | try: | |
63 | return str_to_unicode(str(e)) |
|
63 | return str_to_unicode(str(e)) | |
64 | except UnicodeError: |
|
64 | except UnicodeError: | |
65 | pass |
|
65 | pass | |
66 |
|
66 | |||
67 | try: |
|
67 | try: | |
68 | return str_to_unicode(repr(e)) |
|
68 | return str_to_unicode(repr(e)) | |
69 | except UnicodeError: |
|
69 | except UnicodeError: | |
70 | pass |
|
70 | pass | |
71 |
|
71 | |||
72 | return u'Unrecoverably corrupt evalue' |
|
72 | return u'Unrecoverably corrupt evalue' | |
73 |
|
73 | |||
74 | if sys.version_info[0] >= 3: |
|
74 | if sys.version_info[0] >= 3: | |
75 | PY3 = True |
|
75 | PY3 = True | |
76 |
|
76 | |||
77 | input = input |
|
77 | input = input | |
78 | builtin_mod_name = "builtins" |
|
78 | builtin_mod_name = "builtins" | |
79 |
|
79 | |||
80 | str_to_unicode = no_code |
|
80 | str_to_unicode = no_code | |
81 | unicode_to_str = no_code |
|
81 | unicode_to_str = no_code | |
82 | str_to_bytes = encode |
|
82 | str_to_bytes = encode | |
83 | bytes_to_str = decode |
|
83 | bytes_to_str = decode | |
84 | cast_bytes_py2 = no_code |
|
84 | cast_bytes_py2 = no_code | |
85 |
|
85 | |||
86 | string_types = (str,) |
|
86 | string_types = (str,) | |
|
87 | unicode_type = str | |||
87 |
|
88 | |||
88 | def isidentifier(s, dotted=False): |
|
89 | def isidentifier(s, dotted=False): | |
89 | if dotted: |
|
90 | if dotted: | |
90 | return all(isidentifier(a) for a in s.split(".")) |
|
91 | return all(isidentifier(a) for a in s.split(".")) | |
91 | return s.isidentifier() |
|
92 | return s.isidentifier() | |
92 |
|
93 | |||
93 | open = orig_open |
|
94 | open = orig_open | |
94 |
|
95 | |||
95 | MethodType = types.MethodType |
|
96 | MethodType = types.MethodType | |
96 |
|
97 | |||
97 | def execfile(fname, glob, loc=None): |
|
98 | def execfile(fname, glob, loc=None): | |
98 | loc = loc if (loc is not None) else glob |
|
99 | loc = loc if (loc is not None) else glob | |
99 | with open(fname, 'rb') as f: |
|
100 | with open(fname, 'rb') as f: | |
100 | exec compile(f.read(), fname, 'exec') in glob, loc |
|
101 | exec compile(f.read(), fname, 'exec') in glob, loc | |
101 |
|
102 | |||
102 | # Refactor print statements in doctests. |
|
103 | # Refactor print statements in doctests. | |
103 | _print_statement_re = re.compile(r"\bprint (?P<expr>.*)$", re.MULTILINE) |
|
104 | _print_statement_re = re.compile(r"\bprint (?P<expr>.*)$", re.MULTILINE) | |
104 | def _print_statement_sub(match): |
|
105 | def _print_statement_sub(match): | |
105 | expr = match.groups('expr') |
|
106 | expr = match.groups('expr') | |
106 | return "print(%s)" % expr |
|
107 | return "print(%s)" % expr | |
107 |
|
108 | |||
108 | @_modify_str_or_docstring |
|
109 | @_modify_str_or_docstring | |
109 | def doctest_refactor_print(doc): |
|
110 | def doctest_refactor_print(doc): | |
110 | """Refactor 'print x' statements in a doctest to print(x) style. 2to3 |
|
111 | """Refactor 'print x' statements in a doctest to print(x) style. 2to3 | |
111 | unfortunately doesn't pick up on our doctests. |
|
112 | unfortunately doesn't pick up on our doctests. | |
112 |
|
113 | |||
113 | Can accept a string or a function, so it can be used as a decorator.""" |
|
114 | Can accept a string or a function, so it can be used as a decorator.""" | |
114 | return _print_statement_re.sub(_print_statement_sub, doc) |
|
115 | return _print_statement_re.sub(_print_statement_sub, doc) | |
115 |
|
116 | |||
116 | # Abstract u'abc' syntax: |
|
117 | # Abstract u'abc' syntax: | |
117 | @_modify_str_or_docstring |
|
118 | @_modify_str_or_docstring | |
118 | def u_format(s): |
|
119 | def u_format(s): | |
119 | """"{u}'abc'" --> "'abc'" (Python 3) |
|
120 | """"{u}'abc'" --> "'abc'" (Python 3) | |
120 |
|
121 | |||
121 | Accepts a string or a function, so it can be used as a decorator.""" |
|
122 | Accepts a string or a function, so it can be used as a decorator.""" | |
122 | return s.format(u='') |
|
123 | return s.format(u='') | |
123 |
|
124 | |||
124 | else: |
|
125 | else: | |
125 | PY3 = False |
|
126 | PY3 = False | |
126 |
|
127 | |||
127 | input = raw_input |
|
128 | input = raw_input | |
128 | builtin_mod_name = "__builtin__" |
|
129 | builtin_mod_name = "__builtin__" | |
129 |
|
130 | |||
130 | str_to_unicode = decode |
|
131 | str_to_unicode = decode | |
131 | unicode_to_str = encode |
|
132 | unicode_to_str = encode | |
132 | str_to_bytes = no_code |
|
133 | str_to_bytes = no_code | |
133 | bytes_to_str = no_code |
|
134 | bytes_to_str = no_code | |
134 | cast_bytes_py2 = cast_bytes |
|
135 | cast_bytes_py2 = cast_bytes | |
135 |
|
136 | |||
136 | string_types = (str, unicode) |
|
137 | string_types = (str, unicode) | |
|
138 | unicode_type = unicode | |||
137 |
|
139 | |||
138 | import re |
|
140 | import re | |
139 | _name_re = re.compile(r"[a-zA-Z_][a-zA-Z0-9_]*$") |
|
141 | _name_re = re.compile(r"[a-zA-Z_][a-zA-Z0-9_]*$") | |
140 | def isidentifier(s, dotted=False): |
|
142 | def isidentifier(s, dotted=False): | |
141 | if dotted: |
|
143 | if dotted: | |
142 | return all(isidentifier(a) for a in s.split(".")) |
|
144 | return all(isidentifier(a) for a in s.split(".")) | |
143 | return bool(_name_re.match(s)) |
|
145 | return bool(_name_re.match(s)) | |
144 |
|
146 | |||
145 | class open(object): |
|
147 | class open(object): | |
146 | """Wrapper providing key part of Python 3 open() interface.""" |
|
148 | """Wrapper providing key part of Python 3 open() interface.""" | |
147 | def __init__(self, fname, mode="r", encoding="utf-8"): |
|
149 | def __init__(self, fname, mode="r", encoding="utf-8"): | |
148 | self.f = orig_open(fname, mode) |
|
150 | self.f = orig_open(fname, mode) | |
149 | self.enc = encoding |
|
151 | self.enc = encoding | |
150 |
|
152 | |||
151 | def write(self, s): |
|
153 | def write(self, s): | |
152 | return self.f.write(s.encode(self.enc)) |
|
154 | return self.f.write(s.encode(self.enc)) | |
153 |
|
155 | |||
154 | def read(self, size=-1): |
|
156 | def read(self, size=-1): | |
155 | return self.f.read(size).decode(self.enc) |
|
157 | return self.f.read(size).decode(self.enc) | |
156 |
|
158 | |||
157 | def close(self): |
|
159 | def close(self): | |
158 | return self.f.close() |
|
160 | return self.f.close() | |
159 |
|
161 | |||
160 | def __enter__(self): |
|
162 | def __enter__(self): | |
161 | return self |
|
163 | return self | |
162 |
|
164 | |||
163 | def __exit__(self, etype, value, traceback): |
|
165 | def __exit__(self, etype, value, traceback): | |
164 | self.f.close() |
|
166 | self.f.close() | |
165 |
|
167 | |||
166 | def MethodType(func, instance): |
|
168 | def MethodType(func, instance): | |
167 | return types.MethodType(func, instance, type(instance)) |
|
169 | return types.MethodType(func, instance, type(instance)) | |
168 |
|
170 | |||
169 | # don't override system execfile on 2.x: |
|
171 | # don't override system execfile on 2.x: | |
170 | execfile = execfile |
|
172 | execfile = execfile | |
171 |
|
173 | |||
172 | def doctest_refactor_print(func_or_str): |
|
174 | def doctest_refactor_print(func_or_str): | |
173 | return func_or_str |
|
175 | return func_or_str | |
174 |
|
176 | |||
175 |
|
177 | |||
176 | # Abstract u'abc' syntax: |
|
178 | # Abstract u'abc' syntax: | |
177 | @_modify_str_or_docstring |
|
179 | @_modify_str_or_docstring | |
178 | def u_format(s): |
|
180 | def u_format(s): | |
179 | """"{u}'abc'" --> "u'abc'" (Python 2) |
|
181 | """"{u}'abc'" --> "u'abc'" (Python 2) | |
180 |
|
182 | |||
181 | Accepts a string or a function, so it can be used as a decorator.""" |
|
183 | Accepts a string or a function, so it can be used as a decorator.""" | |
182 | return s.format(u='u') |
|
184 | return s.format(u='u') | |
183 |
|
185 | |||
184 | if sys.platform == 'win32': |
|
186 | if sys.platform == 'win32': | |
185 | def execfile(fname, glob=None, loc=None): |
|
187 | def execfile(fname, glob=None, loc=None): | |
186 | loc = loc if (loc is not None) else glob |
|
188 | loc = loc if (loc is not None) else glob | |
187 | # The rstrip() is necessary b/c trailing whitespace in files will |
|
189 | # The rstrip() is necessary b/c trailing whitespace in files will | |
188 | # cause an IndentationError in Python 2.6 (this was fixed in 2.7, |
|
190 | # cause an IndentationError in Python 2.6 (this was fixed in 2.7, | |
189 | # but we still support 2.6). See issue 1027. |
|
191 | # but we still support 2.6). See issue 1027. | |
190 | scripttext = __builtin__.open(fname).read().rstrip() + '\n' |
|
192 | scripttext = __builtin__.open(fname).read().rstrip() + '\n' | |
191 | # compile converts unicode filename to str assuming |
|
193 | # compile converts unicode filename to str assuming | |
192 | # ascii. Let's do the conversion before calling compile |
|
194 | # ascii. Let's do the conversion before calling compile | |
193 | if isinstance(fname, unicode): |
|
195 | if isinstance(fname, unicode): | |
194 | filename = unicode_to_str(fname) |
|
196 | filename = unicode_to_str(fname) | |
195 | else: |
|
197 | else: | |
196 | filename = fname |
|
198 | filename = fname | |
197 | exec compile(scripttext, filename, 'exec') in glob, loc |
|
199 | exec compile(scripttext, filename, 'exec') in glob, loc | |
198 | else: |
|
200 | else: | |
199 | def execfile(fname, *where): |
|
201 | def execfile(fname, *where): | |
200 | if isinstance(fname, unicode): |
|
202 | if isinstance(fname, unicode): | |
201 | filename = fname.encode(sys.getfilesystemencoding()) |
|
203 | filename = fname.encode(sys.getfilesystemencoding()) | |
202 | else: |
|
204 | else: | |
203 | filename = fname |
|
205 | filename = fname | |
204 | __builtin__.execfile(filename, *where) |
|
206 | __builtin__.execfile(filename, *where) |
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