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1 | # -*- coding: utf-8 -*- |
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1 | # -*- coding: utf-8 -*- | |
2 | """ |
|
2 | """ | |
3 | ====== |
|
3 | ====== | |
4 | Rmagic |
|
4 | Rmagic | |
5 | ====== |
|
5 | ====== | |
6 |
|
6 | |||
7 | Magic command interface for interactive work with R via rpy2 |
|
7 | Magic command interface for interactive work with R via rpy2 | |
8 |
|
8 | |||
9 | Usage |
|
9 | Usage | |
10 | ===== |
|
10 | ===== | |
11 |
|
11 | |||
12 | ``%R`` |
|
12 | ``%R`` | |
13 |
|
13 | |||
14 | {R_DOC} |
|
14 | {R_DOC} | |
15 |
|
15 | |||
16 | ``%Rpush`` |
|
16 | ``%Rpush`` | |
17 |
|
17 | |||
18 | {RPUSH_DOC} |
|
18 | {RPUSH_DOC} | |
19 |
|
19 | |||
20 | ``%Rpull`` |
|
20 | ``%Rpull`` | |
21 |
|
21 | |||
22 | {RPULL_DOC} |
|
22 | {RPULL_DOC} | |
23 |
|
23 | |||
24 | ``%Rget`` |
|
24 | ``%Rget`` | |
25 |
|
25 | |||
26 | {RGET_DOC} |
|
26 | {RGET_DOC} | |
27 |
|
27 | |||
28 | """ |
|
28 | """ | |
29 |
|
29 | |||
30 | #----------------------------------------------------------------------------- |
|
30 | #----------------------------------------------------------------------------- | |
31 | # Copyright (C) 2012 The IPython Development Team |
|
31 | # Copyright (C) 2012 The IPython Development Team | |
32 | # |
|
32 | # | |
33 | # Distributed under the terms of the BSD License. The full license is in |
|
33 | # Distributed under the terms of the BSD License. The full license is in | |
34 | # the file COPYING, distributed as part of this software. |
|
34 | # the file COPYING, distributed as part of this software. | |
35 | #----------------------------------------------------------------------------- |
|
35 | #----------------------------------------------------------------------------- | |
36 |
|
36 | |||
37 | import sys |
|
37 | import sys | |
38 | import tempfile |
|
38 | import tempfile | |
39 | from glob import glob |
|
39 | from glob import glob | |
40 | from shutil import rmtree |
|
40 | from shutil import rmtree | |
41 | from getopt import getopt |
|
41 | from getopt import getopt | |
42 |
|
42 | |||
43 | # numpy and rpy2 imports |
|
43 | # numpy and rpy2 imports | |
44 |
|
44 | |||
45 | import numpy as np |
|
45 | import numpy as np | |
46 |
|
46 | |||
47 | import rpy2.rinterface as ri |
|
47 | import rpy2.rinterface as ri | |
48 | import rpy2.robjects as ro |
|
48 | import rpy2.robjects as ro | |
49 | from rpy2.robjects.numpy2ri import numpy2ri |
|
49 | from rpy2.robjects.numpy2ri import numpy2ri | |
50 | ro.conversion.py2ri = numpy2ri |
|
50 | ro.conversion.py2ri = numpy2ri | |
51 |
|
51 | |||
52 | # IPython imports |
|
52 | # IPython imports | |
53 |
|
53 | |||
54 | from IPython.core.displaypub import publish_display_data |
|
54 | from IPython.core.displaypub import publish_display_data | |
55 | from IPython.core.magic import (Magics, magics_class, cell_magic, line_magic, |
|
55 | from IPython.core.magic import (Magics, magics_class, cell_magic, line_magic, | |
56 | line_cell_magic, needs_local_scope) |
|
56 | line_cell_magic, needs_local_scope) | |
57 | from IPython.testing.skipdoctest import skip_doctest |
|
57 | from IPython.testing.skipdoctest import skip_doctest | |
58 | from IPython.core.magic_arguments import ( |
|
58 | from IPython.core.magic_arguments import ( | |
59 | argument, magic_arguments, parse_argstring |
|
59 | argument, magic_arguments, parse_argstring | |
60 | ) |
|
60 | ) | |
61 | from IPython.utils.py3compat import str_to_unicode, unicode_to_str, PY3 |
|
61 | from IPython.utils.py3compat import str_to_unicode, unicode_to_str, PY3 | |
62 |
|
62 | |||
63 | class RInterpreterError(ri.RRuntimeError): |
|
63 | class RInterpreterError(ri.RRuntimeError): | |
64 | """An error when running R code in a %%R magic cell.""" |
|
64 | """An error when running R code in a %%R magic cell.""" | |
65 | def __init__(self, line, err, stdout): |
|
65 | def __init__(self, line, err, stdout): | |
66 | self.line = line |
|
66 | self.line = line | |
67 | self.err = err.rstrip() |
|
67 | self.err = err.rstrip() | |
68 | self.stdout = stdout.rstrip() |
|
68 | self.stdout = stdout.rstrip() | |
69 |
|
69 | |||
70 | def __unicode__(self): |
|
70 | def __unicode__(self): | |
71 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ |
|
71 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ | |
72 | (self.line, self.err) |
|
72 | (self.line, self.err) | |
73 | if self.stdout and (self.stdout != self.err): |
|
73 | if self.stdout and (self.stdout != self.err): | |
74 | s += '\nR stdout:\n' + self.stdout |
|
74 | s += '\nR stdout:\n' + self.stdout | |
75 | return s |
|
75 | return s | |
76 |
|
76 | |||
77 | if PY3: |
|
77 | if PY3: | |
78 | __str__ = __unicode__ |
|
78 | __str__ = __unicode__ | |
79 | else: |
|
79 | else: | |
80 | def __str__(self): |
|
80 | def __str__(self): | |
81 | return unicode_to_str(unicode(self), 'utf-8') |
|
81 | return unicode_to_str(unicode(self), 'utf-8') | |
82 |
|
82 | |||
83 | def Rconverter(Robj, dataframe=False): |
|
83 | def Rconverter(Robj, dataframe=False): | |
84 | """ |
|
84 | """ | |
85 | Convert an object in R's namespace to one suitable |
|
85 | Convert an object in R's namespace to one suitable | |
86 | for ipython's namespace. |
|
86 | for ipython's namespace. | |
87 |
|
87 | |||
88 | For a data.frame, it tries to return a structured array. |
|
88 | For a data.frame, it tries to return a structured array. | |
89 | It first checks for colnames, then names. |
|
89 | It first checks for colnames, then names. | |
90 | If all are NULL, it returns np.asarray(Robj), else |
|
90 | If all are NULL, it returns np.asarray(Robj), else | |
91 | it tries to construct a recarray |
|
91 | it tries to construct a recarray | |
92 |
|
92 | |||
93 | Parameters |
|
93 | Parameters | |
94 | ---------- |
|
94 | ---------- | |
95 |
|
95 | |||
96 | Robj: an R object returned from rpy2 |
|
96 | Robj: an R object returned from rpy2 | |
97 | """ |
|
97 | """ | |
98 | is_data_frame = ro.r('is.data.frame') |
|
98 | is_data_frame = ro.r('is.data.frame') | |
99 | colnames = ro.r('colnames') |
|
99 | colnames = ro.r('colnames') | |
100 | rownames = ro.r('rownames') # with pandas, these could be used for the index |
|
100 | rownames = ro.r('rownames') # with pandas, these could be used for the index | |
101 | names = ro.r('names') |
|
101 | names = ro.r('names') | |
102 |
|
102 | |||
103 | if dataframe: |
|
103 | if dataframe: | |
104 | as_data_frame = ro.r('as.data.frame') |
|
104 | as_data_frame = ro.r('as.data.frame') | |
105 | cols = colnames(Robj) |
|
105 | cols = colnames(Robj) | |
106 | _names = names(Robj) |
|
106 | _names = names(Robj) | |
107 | if cols != ri.NULL: |
|
107 | if cols != ri.NULL: | |
108 | Robj = as_data_frame(Robj) |
|
108 | Robj = as_data_frame(Robj) | |
109 | names = tuple(np.array(cols)) |
|
109 | names = tuple(np.array(cols)) | |
110 | elif _names != ri.NULL: |
|
110 | elif _names != ri.NULL: | |
111 | names = tuple(np.array(_names)) |
|
111 | names = tuple(np.array(_names)) | |
112 | else: # failed to find names |
|
112 | else: # failed to find names | |
113 | return np.asarray(Robj) |
|
113 | return np.asarray(Robj) | |
114 | Robj = np.rec.fromarrays(Robj, names = names) |
|
114 | Robj = np.rec.fromarrays(Robj, names = names) | |
115 | return np.asarray(Robj) |
|
115 | return np.asarray(Robj) | |
116 |
|
116 | |||
117 | @magics_class |
|
117 | @magics_class | |
118 | class RMagics(Magics): |
|
118 | class RMagics(Magics): | |
119 | """A set of magics useful for interactive work with R via rpy2. |
|
119 | """A set of magics useful for interactive work with R via rpy2. | |
120 | """ |
|
120 | """ | |
121 |
|
121 | |||
122 | def __init__(self, shell, Rconverter=Rconverter, |
|
122 | def __init__(self, shell, Rconverter=Rconverter, | |
123 | pyconverter=np.asarray, |
|
123 | pyconverter=np.asarray, | |
124 | cache_display_data=False): |
|
124 | cache_display_data=False): | |
125 | """ |
|
125 | """ | |
126 | Parameters |
|
126 | Parameters | |
127 | ---------- |
|
127 | ---------- | |
128 |
|
128 | |||
129 | shell : IPython shell |
|
129 | shell : IPython shell | |
130 |
|
130 | |||
131 | pyconverter : callable |
|
131 | pyconverter : callable | |
132 | To be called on values in ipython namespace before |
|
132 | To be called on values in ipython namespace before | |
133 | assigning to variables in rpy2. |
|
133 | assigning to variables in rpy2. | |
134 |
|
134 | |||
135 | cache_display_data : bool |
|
135 | cache_display_data : bool | |
136 | If True, the published results of the final call to R are |
|
136 | If True, the published results of the final call to R are | |
137 | cached in the variable 'display_cache'. |
|
137 | cached in the variable 'display_cache'. | |
138 |
|
138 | |||
139 | """ |
|
139 | """ | |
140 | super(RMagics, self).__init__(shell) |
|
140 | super(RMagics, self).__init__(shell) | |
141 | self.cache_display_data = cache_display_data |
|
141 | self.cache_display_data = cache_display_data | |
142 |
|
142 | |||
143 | self.r = ro.R() |
|
143 | self.r = ro.R() | |
144 |
|
144 | |||
145 | self.Rstdout_cache = [] |
|
145 | self.Rstdout_cache = [] | |
146 | self.pyconverter = pyconverter |
|
146 | self.pyconverter = pyconverter | |
147 | self.Rconverter = Rconverter |
|
147 | self.Rconverter = Rconverter | |
148 |
|
148 | |||
149 | def eval(self, line): |
|
149 | def eval(self, line): | |
150 | ''' |
|
150 | ''' | |
151 | Parse and evaluate a line with rpy2. |
|
151 | Parse and evaluate a line with rpy2. | |
152 | Returns the output to R's stdout() connection |
|
152 | Returns the output to R's stdout() connection | |
153 | and the value of eval(parse(line)). |
|
153 | and the value of eval(parse(line)). | |
154 | ''' |
|
154 | ''' | |
155 | old_writeconsole = ri.get_writeconsole() |
|
155 | old_writeconsole = ri.get_writeconsole() | |
156 | ri.set_writeconsole(self.write_console) |
|
156 | ri.set_writeconsole(self.write_console) | |
157 | try: |
|
157 | try: | |
158 | value = ri.baseenv['eval'](ri.parse(line)) |
|
158 | value = ri.baseenv['eval'](ri.parse(line)) | |
159 | except (ri.RRuntimeError, ValueError) as exception: |
|
159 | except (ri.RRuntimeError, ValueError) as exception: | |
160 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error |
|
160 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error | |
161 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) |
|
161 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) | |
162 | text_output = self.flush() |
|
162 | text_output = self.flush() | |
163 | ri.set_writeconsole(old_writeconsole) |
|
163 | ri.set_writeconsole(old_writeconsole) | |
164 | return text_output, value |
|
164 | return text_output, value | |
165 |
|
165 | |||
166 | def write_console(self, output): |
|
166 | def write_console(self, output): | |
167 | ''' |
|
167 | ''' | |
168 | A hook to capture R's stdout in a cache. |
|
168 | A hook to capture R's stdout in a cache. | |
169 | ''' |
|
169 | ''' | |
170 | self.Rstdout_cache.append(output) |
|
170 | self.Rstdout_cache.append(output) | |
171 |
|
171 | |||
172 | def flush(self): |
|
172 | def flush(self): | |
173 | ''' |
|
173 | ''' | |
174 | Flush R's stdout cache to a string, returning the string. |
|
174 | Flush R's stdout cache to a string, returning the string. | |
175 | ''' |
|
175 | ''' | |
176 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) |
|
176 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) | |
177 | self.Rstdout_cache = [] |
|
177 | self.Rstdout_cache = [] | |
178 | return value |
|
178 | return value | |
179 |
|
179 | |||
180 | @skip_doctest |
|
180 | @skip_doctest | |
181 | @needs_local_scope |
|
181 | @needs_local_scope | |
182 | @line_magic |
|
182 | @line_magic | |
183 | def Rpush(self, line, local_ns=None): |
|
183 | def Rpush(self, line, local_ns=None): | |
184 | ''' |
|
184 | ''' | |
185 | A line-level magic for R that pushes |
|
185 | A line-level magic for R that pushes | |
186 | variables from python to rpy2. The line should be made up |
|
186 | variables from python to rpy2. The line should be made up | |
187 | of whitespace separated variable names in the IPython |
|
187 | of whitespace separated variable names in the IPython | |
188 | namespace:: |
|
188 | namespace:: | |
189 |
|
189 | |||
190 | In [7]: import numpy as np |
|
190 | In [7]: import numpy as np | |
191 |
|
191 | |||
192 | In [8]: X = np.array([4.5,6.3,7.9]) |
|
192 | In [8]: X = np.array([4.5,6.3,7.9]) | |
193 |
|
193 | |||
194 | In [9]: X.mean() |
|
194 | In [9]: X.mean() | |
195 | Out[9]: 6.2333333333333343 |
|
195 | Out[9]: 6.2333333333333343 | |
196 |
|
196 | |||
197 | In [10]: %Rpush X |
|
197 | In [10]: %Rpush X | |
198 |
|
198 | |||
199 | In [11]: %R mean(X) |
|
199 | In [11]: %R mean(X) | |
200 | Out[11]: array([ 6.23333333]) |
|
200 | Out[11]: array([ 6.23333333]) | |
201 |
|
201 | |||
202 | ''' |
|
202 | ''' | |
203 | if local_ns is None: |
|
203 | if local_ns is None: | |
204 | local_ns = {} |
|
204 | local_ns = {} | |
205 |
|
205 | |||
206 | inputs = line.split(' ') |
|
206 | inputs = line.split(' ') | |
207 | for input in inputs: |
|
207 | for input in inputs: | |
208 | try: |
|
208 | try: | |
209 | val = local_ns[input] |
|
209 | val = local_ns[input] | |
210 | except KeyError: |
|
210 | except KeyError: | |
211 | try: |
|
211 | try: | |
212 | val = self.shell.user_ns[input] |
|
212 | val = self.shell.user_ns[input] | |
213 | except KeyError: |
|
213 | except KeyError: | |
214 | # reraise the KeyError as a NameError so that it looks like |
|
214 | # reraise the KeyError as a NameError so that it looks like | |
215 | # the standard python behavior when you use an unnamed |
|
215 | # the standard python behavior when you use an unnamed | |
216 | # variable |
|
216 | # variable | |
217 | raise NameError("name '%s' is not defined" % input) |
|
217 | raise NameError("name '%s' is not defined" % input) | |
218 |
|
218 | |||
219 | self.r.assign(input, self.pyconverter(val)) |
|
219 | self.r.assign(input, self.pyconverter(val)) | |
220 |
|
220 | |||
221 | @skip_doctest |
|
221 | @skip_doctest | |
222 | @magic_arguments() |
|
222 | @magic_arguments() | |
223 | @argument( |
|
223 | @argument( | |
224 | '-d', '--as_dataframe', action='store_true', |
|
224 | '-d', '--as_dataframe', action='store_true', | |
225 | default=False, |
|
225 | default=False, | |
226 | help='Convert objects to data.frames before returning to ipython.' |
|
226 | help='Convert objects to data.frames before returning to ipython.' | |
227 | ) |
|
227 | ) | |
228 | @argument( |
|
228 | @argument( | |
229 | 'outputs', |
|
229 | 'outputs', | |
230 | nargs='*', |
|
230 | nargs='*', | |
231 | ) |
|
231 | ) | |
232 | @line_magic |
|
232 | @line_magic | |
233 | def Rpull(self, line): |
|
233 | def Rpull(self, line): | |
234 | ''' |
|
234 | ''' | |
235 | A line-level magic for R that pulls |
|
235 | A line-level magic for R that pulls | |
236 | variables from python to rpy2:: |
|
236 | variables from python to rpy2:: | |
237 |
|
237 | |||
238 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) |
|
238 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) | |
239 |
|
239 | |||
240 | In [19]: %Rpull x y z |
|
240 | In [19]: %Rpull x y z | |
241 |
|
241 | |||
242 | In [20]: x |
|
242 | In [20]: x | |
243 | Out[20]: array([ 3. , 4. , 6.7]) |
|
243 | Out[20]: array([ 3. , 4. , 6.7]) | |
244 |
|
244 | |||
245 | In [21]: y |
|
245 | In [21]: y | |
246 | Out[21]: array([ 4., 6., 7.]) |
|
246 | Out[21]: array([ 4., 6., 7.]) | |
247 |
|
247 | |||
248 | In [22]: z |
|
248 | In [22]: z | |
249 | Out[22]: |
|
249 | Out[22]: | |
250 | array(['a', '3', '4'], |
|
250 | array(['a', '3', '4'], | |
251 | dtype='|S1') |
|
251 | dtype='|S1') | |
252 |
|
252 | |||
253 |
|
253 | |||
254 | If --as_dataframe, then each object is returned as a structured array |
|
254 | If --as_dataframe, then each object is returned as a structured array | |
255 | after first passed through "as.data.frame" in R before |
|
255 | after first passed through "as.data.frame" in R before | |
256 | being calling self.Rconverter. |
|
256 | being calling self.Rconverter. | |
257 | This is useful when a structured array is desired as output, or |
|
257 | This is useful when a structured array is desired as output, or | |
258 | when the object in R has mixed data types. |
|
258 | when the object in R has mixed data types. | |
259 | See the %%R docstring for more examples. |
|
259 | See the %%R docstring for more examples. | |
260 |
|
260 | |||
261 | Notes |
|
261 | Notes | |
262 | ----- |
|
262 | ----- | |
263 |
|
263 | |||
264 | Beware that R names can have '.' so this is not fool proof. |
|
264 | Beware that R names can have '.' so this is not fool proof. | |
265 | To avoid this, don't name your R objects with '.'s... |
|
265 | To avoid this, don't name your R objects with '.'s... | |
266 |
|
266 | |||
267 | ''' |
|
267 | ''' | |
268 | args = parse_argstring(self.Rpull, line) |
|
268 | args = parse_argstring(self.Rpull, line) | |
269 | outputs = args.outputs |
|
269 | outputs = args.outputs | |
270 | for output in outputs: |
|
270 | for output in outputs: | |
271 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) |
|
271 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) | |
272 |
|
272 | |||
273 | @skip_doctest |
|
273 | @skip_doctest | |
274 | @magic_arguments() |
|
274 | @magic_arguments() | |
275 | @argument( |
|
275 | @argument( | |
276 | '-d', '--as_dataframe', action='store_true', |
|
276 | '-d', '--as_dataframe', action='store_true', | |
277 | default=False, |
|
277 | default=False, | |
278 | help='Convert objects to data.frames before returning to ipython.' |
|
278 | help='Convert objects to data.frames before returning to ipython.' | |
279 | ) |
|
279 | ) | |
280 | @argument( |
|
280 | @argument( | |
281 | 'output', |
|
281 | 'output', | |
282 | nargs=1, |
|
282 | nargs=1, | |
283 | type=str, |
|
283 | type=str, | |
284 | ) |
|
284 | ) | |
285 | @line_magic |
|
285 | @line_magic | |
286 | def Rget(self, line): |
|
286 | def Rget(self, line): | |
287 | ''' |
|
287 | ''' | |
288 | Return an object from rpy2, possibly as a structured array (if possible). |
|
288 | Return an object from rpy2, possibly as a structured array (if possible). | |
289 | Similar to Rpull except only one argument is accepted and the value is |
|
289 | Similar to Rpull except only one argument is accepted and the value is | |
290 | returned rather than pushed to self.shell.user_ns:: |
|
290 | returned rather than pushed to self.shell.user_ns:: | |
291 |
|
291 | |||
292 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
292 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
293 |
|
293 | |||
294 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
294 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
295 |
|
295 | |||
296 | In [5]: %R -i datapy |
|
296 | In [5]: %R -i datapy | |
297 |
|
297 | |||
298 | In [6]: %Rget datapy |
|
298 | In [6]: %Rget datapy | |
299 | Out[6]: |
|
299 | Out[6]: | |
300 | array([['1', '2', '3', '4'], |
|
300 | array([['1', '2', '3', '4'], | |
301 | ['2', '3', '2', '5'], |
|
301 | ['2', '3', '2', '5'], | |
302 | ['a', 'b', 'c', 'e']], |
|
302 | ['a', 'b', 'c', 'e']], | |
303 | dtype='|S1') |
|
303 | dtype='|S1') | |
304 |
|
304 | |||
305 | In [7]: %Rget -d datapy |
|
305 | In [7]: %Rget -d datapy | |
306 | Out[7]: |
|
306 | Out[7]: | |
307 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
307 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
308 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
308 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
309 |
|
309 | |||
310 | ''' |
|
310 | ''' | |
311 | args = parse_argstring(self.Rget, line) |
|
311 | args = parse_argstring(self.Rget, line) | |
312 | output = args.output |
|
312 | output = args.output | |
313 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) |
|
313 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) | |
314 |
|
314 | |||
315 |
|
315 | |||
316 | @skip_doctest |
|
316 | @skip_doctest | |
317 | @magic_arguments() |
|
317 | @magic_arguments() | |
318 | @argument( |
|
318 | @argument( | |
319 | '-i', '--input', action='append', |
|
319 | '-i', '--input', action='append', | |
320 | 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.' |
|
320 | 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.' | |
321 | ) |
|
321 | ) | |
322 | @argument( |
|
322 | @argument( | |
323 | '-o', '--output', action='append', |
|
323 | '-o', '--output', action='append', | |
324 | 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.' |
|
324 | 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.' | |
325 | ) |
|
325 | ) | |
326 | @argument( |
|
326 | @argument( | |
327 | '-w', '--width', type=int, |
|
327 | '-w', '--width', type=int, | |
328 | help='Width of png plotting device sent as an argument to *png* in R.' |
|
328 | help='Width of png plotting device sent as an argument to *png* in R.' | |
329 | ) |
|
329 | ) | |
330 | @argument( |
|
330 | @argument( | |
331 | '-h', '--height', type=int, |
|
331 | '-h', '--height', type=int, | |
332 | help='Height of png plotting device sent as an argument to *png* in R.' |
|
332 | help='Height of png plotting device sent as an argument to *png* in R.' | |
333 | ) |
|
333 | ) | |
334 |
|
334 | |||
335 | @argument( |
|
335 | @argument( | |
336 | '-d', '--dataframe', action='append', |
|
336 | '-d', '--dataframe', action='append', | |
337 | help='Convert these objects to data.frames and return as structured arrays.' |
|
337 | help='Convert these objects to data.frames and return as structured arrays.' | |
338 | ) |
|
338 | ) | |
339 | @argument( |
|
339 | @argument( | |
340 |
'-u', '--units', type= |
|
340 | '-u', '--units', type=unicode, choices=["px", "in", "cm", "mm"], | |
341 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' |
|
341 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' | |
342 | ) |
|
342 | ) | |
343 | @argument( |
|
343 | @argument( | |
|
344 | '-r', '--res', type=int, | |||
|
345 | 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"].' | |||
|
346 | ) | |||
|
347 | @argument( | |||
344 | '-p', '--pointsize', type=int, |
|
348 | '-p', '--pointsize', type=int, | |
345 | help='Pointsize of png plotting device sent as an argument to *png* in R.' |
|
349 | help='Pointsize of png plotting device sent as an argument to *png* in R.' | |
346 | ) |
|
350 | ) | |
347 | @argument( |
|
351 | @argument( | |
348 | '-b', '--bg', |
|
352 | '-b', '--bg', | |
349 | help='Background of png plotting device sent as an argument to *png* in R.' |
|
353 | help='Background of png plotting device sent as an argument to *png* in R.' | |
350 | ) |
|
354 | ) | |
351 | @argument( |
|
355 | @argument( | |
352 | '-n', '--noreturn', |
|
356 | '-n', '--noreturn', | |
353 | help='Force the magic to not return anything.', |
|
357 | help='Force the magic to not return anything.', | |
354 | action='store_true', |
|
358 | action='store_true', | |
355 | default=False |
|
359 | default=False | |
356 | ) |
|
360 | ) | |
357 | @argument( |
|
361 | @argument( | |
358 | 'code', |
|
362 | 'code', | |
359 | nargs='*', |
|
363 | nargs='*', | |
360 | ) |
|
364 | ) | |
361 | @needs_local_scope |
|
365 | @needs_local_scope | |
362 | @line_cell_magic |
|
366 | @line_cell_magic | |
363 | def R(self, line, cell=None, local_ns=None): |
|
367 | def R(self, line, cell=None, local_ns=None): | |
364 | ''' |
|
368 | ''' | |
365 | Execute code in R, and pull some of the results back into the Python namespace. |
|
369 | Execute code in R, and pull some of the results back into the Python namespace. | |
366 |
|
370 | |||
367 | In line mode, this will evaluate an expression and convert the returned value to a Python object. |
|
371 | In line mode, this will evaluate an expression and convert the returned value to a Python object. | |
368 | The return value is determined by rpy2's behaviour of returning the result of evaluating the |
|
372 | The return value is determined by rpy2's behaviour of returning the result of evaluating the | |
369 | final line. |
|
373 | final line. | |
370 |
|
374 | |||
371 | Multiple R lines can be executed by joining them with semicolons:: |
|
375 | Multiple R lines can be executed by joining them with semicolons:: | |
372 |
|
376 | |||
373 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) |
|
377 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) | |
374 | Out[9]: array([ 4.25]) |
|
378 | Out[9]: array([ 4.25]) | |
375 |
|
379 | |||
376 | As a cell, this will run a block of R code, without bringing anything back by default:: |
|
380 | As a cell, this will run a block of R code, without bringing anything back by default:: | |
377 |
|
381 | |||
378 | In [10]: %%R |
|
382 | In [10]: %%R | |
379 | ....: Y = c(2,4,3,9) |
|
383 | ....: Y = c(2,4,3,9) | |
380 | ....: print(summary(lm(Y~X))) |
|
384 | ....: print(summary(lm(Y~X))) | |
381 | ....: |
|
385 | ....: | |
382 |
|
386 | |||
383 | Call: |
|
387 | Call: | |
384 | lm(formula = Y ~ X) |
|
388 | lm(formula = Y ~ X) | |
385 |
|
389 | |||
386 | Residuals: |
|
390 | Residuals: | |
387 | 1 2 3 4 |
|
391 | 1 2 3 4 | |
388 | 0.88 -0.24 -2.28 1.64 |
|
392 | 0.88 -0.24 -2.28 1.64 | |
389 |
|
393 | |||
390 | Coefficients: |
|
394 | Coefficients: | |
391 | Estimate Std. Error t value Pr(>|t|) |
|
395 | Estimate Std. Error t value Pr(>|t|) | |
392 | (Intercept) 0.0800 2.3000 0.035 0.975 |
|
396 | (Intercept) 0.0800 2.3000 0.035 0.975 | |
393 | X 1.0400 0.4822 2.157 0.164 |
|
397 | X 1.0400 0.4822 2.157 0.164 | |
394 |
|
398 | |||
395 | Residual standard error: 2.088 on 2 degrees of freedom |
|
399 | Residual standard error: 2.088 on 2 degrees of freedom | |
396 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 |
|
400 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 | |
397 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 |
|
401 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 | |
398 |
|
402 | |||
399 | In the notebook, plots are published as the output of the cell. |
|
403 | In the notebook, plots are published as the output of the cell. | |
400 |
|
404 | |||
401 | %R plot(X, Y) |
|
405 | %R plot(X, Y) | |
402 |
|
406 | |||
403 | will create a scatter plot of X bs Y. |
|
407 | will create a scatter plot of X bs Y. | |
404 |
|
408 | |||
405 | If cell is not None and line has some R code, it is prepended to |
|
409 | If cell is not None and line has some R code, it is prepended to | |
406 | the R code in cell. |
|
410 | the R code in cell. | |
407 |
|
411 | |||
408 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: |
|
412 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: | |
409 |
|
413 | |||
410 | In [14]: Z = np.array([1,4,5,10]) |
|
414 | In [14]: Z = np.array([1,4,5,10]) | |
411 |
|
415 | |||
412 | In [15]: %R -i Z mean(Z) |
|
416 | In [15]: %R -i Z mean(Z) | |
413 | Out[15]: array([ 5.]) |
|
417 | Out[15]: array([ 5.]) | |
414 |
|
418 | |||
415 |
|
419 | |||
416 | In [16]: %R -o W W=Z*mean(Z) |
|
420 | In [16]: %R -o W W=Z*mean(Z) | |
417 | Out[16]: array([ 5., 20., 25., 50.]) |
|
421 | Out[16]: array([ 5., 20., 25., 50.]) | |
418 |
|
422 | |||
419 | In [17]: W |
|
423 | In [17]: W | |
420 | Out[17]: array([ 5., 20., 25., 50.]) |
|
424 | Out[17]: array([ 5., 20., 25., 50.]) | |
421 |
|
425 | |||
422 | The return value is determined by these rules: |
|
426 | The return value is determined by these rules: | |
423 |
|
427 | |||
424 | * If the cell is not None, the magic returns None. |
|
428 | * If the cell is not None, the magic returns None. | |
425 |
|
429 | |||
426 | * If the cell evaluates as False, the resulting value is returned |
|
430 | * If the cell evaluates as False, the resulting value is returned | |
427 | unless the final line prints something to the console, in |
|
431 | unless the final line prints something to the console, in | |
428 | which case None is returned. |
|
432 | which case None is returned. | |
429 |
|
433 | |||
430 | * If the final line results in a NULL value when evaluated |
|
434 | * If the final line results in a NULL value when evaluated | |
431 | by rpy2, then None is returned. |
|
435 | by rpy2, then None is returned. | |
432 |
|
436 | |||
433 | * No attempt is made to convert the final value to a structured array. |
|
437 | * No attempt is made to convert the final value to a structured array. | |
434 | Use the --dataframe flag or %Rget to push / return a structured array. |
|
438 | Use the --dataframe flag or %Rget to push / return a structured array. | |
435 |
|
439 | |||
436 | * If the -n flag is present, there is no return value. |
|
440 | * If the -n flag is present, there is no return value. | |
437 |
|
441 | |||
438 | * A trailing ';' will also result in no return value as the last |
|
442 | * A trailing ';' will also result in no return value as the last | |
439 | value in the line is an empty string. |
|
443 | value in the line is an empty string. | |
440 |
|
444 | |||
441 | The --dataframe argument will attempt to return structured arrays. |
|
445 | The --dataframe argument will attempt to return structured arrays. | |
442 | This is useful for dataframes with |
|
446 | This is useful for dataframes with | |
443 | mixed data types. Note also that for a data.frame, |
|
447 | mixed data types. Note also that for a data.frame, | |
444 | if it is returned as an ndarray, it is transposed:: |
|
448 | if it is returned as an ndarray, it is transposed:: | |
445 |
|
449 | |||
446 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
450 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
447 |
|
451 | |||
448 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
452 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
449 |
|
453 | |||
450 | In [20]: %%R -o datar |
|
454 | In [20]: %%R -o datar | |
451 | datar = datapy |
|
455 | datar = datapy | |
452 | ....: |
|
456 | ....: | |
453 |
|
457 | |||
454 | In [21]: datar |
|
458 | In [21]: datar | |
455 | Out[21]: |
|
459 | Out[21]: | |
456 | array([['1', '2', '3', '4'], |
|
460 | array([['1', '2', '3', '4'], | |
457 | ['2', '3', '2', '5'], |
|
461 | ['2', '3', '2', '5'], | |
458 | ['a', 'b', 'c', 'e']], |
|
462 | ['a', 'b', 'c', 'e']], | |
459 | dtype='|S1') |
|
463 | dtype='|S1') | |
460 |
|
464 | |||
461 | In [22]: %%R -d datar |
|
465 | In [22]: %%R -d datar | |
462 | datar = datapy |
|
466 | datar = datapy | |
463 | ....: |
|
467 | ....: | |
464 |
|
468 | |||
465 | In [23]: datar |
|
469 | In [23]: datar | |
466 | Out[23]: |
|
470 | Out[23]: | |
467 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
471 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
468 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
472 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
469 |
|
473 | |||
470 | The --dataframe argument first tries colnames, then names. |
|
474 | The --dataframe argument first tries colnames, then names. | |
471 | If both are NULL, it returns an ndarray (i.e. unstructured):: |
|
475 | If both are NULL, it returns an ndarray (i.e. unstructured):: | |
472 |
|
476 | |||
473 | In [1]: %R mydata=c(4,6,8.3); NULL |
|
477 | In [1]: %R mydata=c(4,6,8.3); NULL | |
474 |
|
478 | |||
475 | In [2]: %R -d mydata |
|
479 | In [2]: %R -d mydata | |
476 |
|
480 | |||
477 | In [3]: mydata |
|
481 | In [3]: mydata | |
478 | Out[3]: array([ 4. , 6. , 8.3]) |
|
482 | Out[3]: array([ 4. , 6. , 8.3]) | |
479 |
|
483 | |||
480 | In [4]: %R names(mydata) = c('a','b','c'); NULL |
|
484 | In [4]: %R names(mydata) = c('a','b','c'); NULL | |
481 |
|
485 | |||
482 | In [5]: %R -d mydata |
|
486 | In [5]: %R -d mydata | |
483 |
|
487 | |||
484 | In [6]: mydata |
|
488 | In [6]: mydata | |
485 | Out[6]: |
|
489 | Out[6]: | |
486 | array((4.0, 6.0, 8.3), |
|
490 | array((4.0, 6.0, 8.3), | |
487 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) |
|
491 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) | |
488 |
|
492 | |||
489 | In [7]: %R -o mydata |
|
493 | In [7]: %R -o mydata | |
490 |
|
494 | |||
491 | In [8]: mydata |
|
495 | In [8]: mydata | |
492 | Out[8]: array([ 4. , 6. , 8.3]) |
|
496 | Out[8]: array([ 4. , 6. , 8.3]) | |
493 |
|
497 | |||
494 | ''' |
|
498 | ''' | |
495 |
|
499 | |||
496 | args = parse_argstring(self.R, line) |
|
500 | args = parse_argstring(self.R, line) | |
497 |
|
501 | |||
498 | # arguments 'code' in line are prepended to |
|
502 | # arguments 'code' in line are prepended to | |
499 | # the cell lines |
|
503 | # the cell lines | |
500 |
|
504 | |||
501 | if cell is None: |
|
505 | if cell is None: | |
502 | code = '' |
|
506 | code = '' | |
503 | return_output = True |
|
507 | return_output = True | |
504 | line_mode = True |
|
508 | line_mode = True | |
505 | else: |
|
509 | else: | |
506 | code = cell |
|
510 | code = cell | |
507 | return_output = False |
|
511 | return_output = False | |
508 | line_mode = False |
|
512 | line_mode = False | |
509 |
|
513 | |||
510 | code = ' '.join(args.code) + code |
|
514 | code = ' '.join(args.code) + code | |
511 |
|
515 | |||
512 | # if there is no local namespace then default to an empty dict |
|
516 | # if there is no local namespace then default to an empty dict | |
513 | if local_ns is None: |
|
517 | if local_ns is None: | |
514 | local_ns = {} |
|
518 | local_ns = {} | |
515 |
|
519 | |||
516 | if args.input: |
|
520 | if args.input: | |
517 | for input in ','.join(args.input).split(','): |
|
521 | for input in ','.join(args.input).split(','): | |
518 | try: |
|
522 | try: | |
519 | val = local_ns[input] |
|
523 | val = local_ns[input] | |
520 | except KeyError: |
|
524 | except KeyError: | |
521 | try: |
|
525 | try: | |
522 | val = self.shell.user_ns[input] |
|
526 | val = self.shell.user_ns[input] | |
523 | except KeyError: |
|
527 | except KeyError: | |
524 | raise NameError("name '%s' is not defined" % input) |
|
528 | raise NameError("name '%s' is not defined" % input) | |
525 | self.r.assign(input, self.pyconverter(val)) |
|
529 | self.r.assign(input, self.pyconverter(val)) | |
526 |
|
530 | |||
527 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'height', 'width', 'bg', 'pointsize']]) |
|
531 | if getattr(args, 'units') is not None: | |
|
532 | if args.units != "px" and getattr(args, 'res') is None: | |||
|
533 | args.res = 72 | |||
|
534 | args.units = '"%s"' % args.units | |||
|
535 | ||||
|
536 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) | |||
528 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) |
|
537 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) | |
529 | # execute the R code in a temporary directory |
|
538 | # execute the R code in a temporary directory | |
530 |
|
539 | |||
531 | tmpd = tempfile.mkdtemp() |
|
540 | tmpd = tempfile.mkdtemp() | |
532 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) |
|
541 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) | |
533 |
|
542 | |||
534 | text_output = '' |
|
543 | text_output = '' | |
535 | if line_mode: |
|
544 | if line_mode: | |
536 | for line in code.split(';'): |
|
545 | for line in code.split(';'): | |
537 | text_result, result = self.eval(line) |
|
546 | text_result, result = self.eval(line) | |
538 | text_output += text_result |
|
547 | text_output += text_result | |
539 | if text_result: |
|
548 | if text_result: | |
540 | # the last line printed something to the console so we won't return it |
|
549 | # the last line printed something to the console so we won't return it | |
541 | return_output = False |
|
550 | return_output = False | |
542 | else: |
|
551 | else: | |
543 | text_result, result = self.eval(code) |
|
552 | text_result, result = self.eval(code) | |
544 | text_output += text_result |
|
553 | text_output += text_result | |
545 |
|
554 | |||
546 | self.r('dev.off()') |
|
555 | self.r('dev.off()') | |
547 |
|
556 | |||
548 | # read out all the saved .png files |
|
557 | # read out all the saved .png files | |
549 |
|
558 | |||
550 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] |
|
559 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] | |
551 |
|
560 | |||
552 | # now publish the images |
|
561 | # now publish the images | |
553 | # mimicking IPython/zmq/pylab/backend_inline.py |
|
562 | # mimicking IPython/zmq/pylab/backend_inline.py | |
554 | fmt = 'png' |
|
563 | fmt = 'png' | |
555 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } |
|
564 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } | |
556 | mime = mimetypes[fmt] |
|
565 | mime = mimetypes[fmt] | |
557 |
|
566 | |||
558 | # publish the printed R objects, if any |
|
567 | # publish the printed R objects, if any | |
559 |
|
568 | |||
560 | display_data = [] |
|
569 | display_data = [] | |
561 | if text_output: |
|
570 | if text_output: | |
562 | display_data.append(('RMagic.R', {'text/plain':text_output})) |
|
571 | display_data.append(('RMagic.R', {'text/plain':text_output})) | |
563 |
|
572 | |||
564 | # flush text streams before sending figures, helps a little with output |
|
573 | # flush text streams before sending figures, helps a little with output | |
565 | for image in images: |
|
574 | for image in images: | |
566 | # synchronization in the console (though it's a bandaid, not a real sln) |
|
575 | # synchronization in the console (though it's a bandaid, not a real sln) | |
567 | sys.stdout.flush(); sys.stderr.flush() |
|
576 | sys.stdout.flush(); sys.stderr.flush() | |
568 | display_data.append(('RMagic.R', {mime: image})) |
|
577 | display_data.append(('RMagic.R', {mime: image})) | |
569 |
|
578 | |||
570 | # kill the temporary directory |
|
579 | # kill the temporary directory | |
571 | rmtree(tmpd) |
|
580 | rmtree(tmpd) | |
572 |
|
581 | |||
573 | # try to turn every output into a numpy array |
|
582 | # try to turn every output into a numpy array | |
574 | # this means that output are assumed to be castable |
|
583 | # this means that output are assumed to be castable | |
575 | # as numpy arrays |
|
584 | # as numpy arrays | |
576 |
|
585 | |||
577 | if args.output: |
|
586 | if args.output: | |
578 | for output in ','.join(args.output).split(','): |
|
587 | for output in ','.join(args.output).split(','): | |
579 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) |
|
588 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) | |
580 |
|
589 | |||
581 | if args.dataframe: |
|
590 | if args.dataframe: | |
582 | for output in ','.join(args.dataframe).split(','): |
|
591 | for output in ','.join(args.dataframe).split(','): | |
583 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) |
|
592 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) | |
584 |
|
593 | |||
585 | for tag, disp_d in display_data: |
|
594 | for tag, disp_d in display_data: | |
586 | publish_display_data(tag, disp_d) |
|
595 | publish_display_data(tag, disp_d) | |
587 |
|
596 | |||
588 | # this will keep a reference to the display_data |
|
597 | # this will keep a reference to the display_data | |
589 | # which might be useful to other objects who happen to use |
|
598 | # which might be useful to other objects who happen to use | |
590 | # this method |
|
599 | # this method | |
591 |
|
600 | |||
592 | if self.cache_display_data: |
|
601 | if self.cache_display_data: | |
593 | self.display_cache = display_data |
|
602 | self.display_cache = display_data | |
594 |
|
603 | |||
595 | # if in line mode and return_output, return the result as an ndarray |
|
604 | # if in line mode and return_output, return the result as an ndarray | |
596 | if return_output and not args.noreturn: |
|
605 | if return_output and not args.noreturn: | |
597 | if result != ri.NULL: |
|
606 | if result != ri.NULL: | |
598 | return self.Rconverter(result, dataframe=False) |
|
607 | return self.Rconverter(result, dataframe=False) | |
599 |
|
608 | |||
600 | __doc__ = __doc__.format( |
|
609 | __doc__ = __doc__.format( | |
601 | R_DOC = ' '*8 + RMagics.R.__doc__, |
|
610 | R_DOC = ' '*8 + RMagics.R.__doc__, | |
602 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, |
|
611 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, | |
603 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__, |
|
612 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__, | |
604 | RGET_DOC = ' '*8 + RMagics.Rget.__doc__ |
|
613 | RGET_DOC = ' '*8 + RMagics.Rget.__doc__ | |
605 | ) |
|
614 | ) | |
606 |
|
615 | |||
607 |
|
616 | |||
608 | def load_ipython_extension(ip): |
|
617 | def load_ipython_extension(ip): | |
609 | """Load the extension in IPython.""" |
|
618 | """Load the extension in IPython.""" | |
610 | ip.register_magics(RMagics) |
|
619 | ip.register_magics(RMagics) |
@@ -1,96 +1,96 b'' | |||||
1 | import numpy as np |
|
1 | import numpy as np | |
2 | from IPython.core.interactiveshell import InteractiveShell |
|
2 | from IPython.core.interactiveshell import InteractiveShell | |
3 | from IPython.extensions import rmagic |
|
3 | from IPython.extensions import rmagic | |
4 | import nose.tools as nt |
|
4 | import nose.tools as nt | |
5 |
|
5 | |||
6 | ip = get_ipython() |
|
6 | ip = get_ipython() | |
7 | ip.magic('load_ext rmagic') |
|
7 | ip.magic('load_ext rmagic') | |
8 |
|
8 | |||
9 |
|
9 | |||
10 | def test_push(): |
|
10 | def test_push(): | |
11 | rm = rmagic.RMagics(ip) |
|
11 | rm = rmagic.RMagics(ip) | |
12 | ip.push({'X':np.arange(5), 'Y':np.array([3,5,4,6,7])}) |
|
12 | ip.push({'X':np.arange(5), 'Y':np.array([3,5,4,6,7])}) | |
13 | ip.run_line_magic('Rpush', 'X Y') |
|
13 | ip.run_line_magic('Rpush', 'X Y') | |
14 | np.testing.assert_almost_equal(np.asarray(rm.r('X')), ip.user_ns['X']) |
|
14 | np.testing.assert_almost_equal(np.asarray(rm.r('X')), ip.user_ns['X']) | |
15 | np.testing.assert_almost_equal(np.asarray(rm.r('Y')), ip.user_ns['Y']) |
|
15 | np.testing.assert_almost_equal(np.asarray(rm.r('Y')), ip.user_ns['Y']) | |
16 |
|
16 | |||
17 | def test_push_localscope(): |
|
17 | def test_push_localscope(): | |
18 | """Test that Rpush looks for variables in the local scope first.""" |
|
18 | """Test that Rpush looks for variables in the local scope first.""" | |
19 | ip.run_cell(''' |
|
19 | ip.run_cell(''' | |
20 | def rmagic_addone(u): |
|
20 | def rmagic_addone(u): | |
21 | %Rpush u |
|
21 | %Rpush u | |
22 | %R result = u+1 |
|
22 | %R result = u+1 | |
23 | %Rpull result |
|
23 | %Rpull result | |
24 | return result[0] |
|
24 | return result[0] | |
25 | u = 0 |
|
25 | u = 0 | |
26 | result = rmagic_addone(12344) |
|
26 | result = rmagic_addone(12344) | |
27 | ''') |
|
27 | ''') | |
28 | result = ip.user_ns['result'] |
|
28 | result = ip.user_ns['result'] | |
29 | np.testing.assert_equal(result, 12345) |
|
29 | np.testing.assert_equal(result, 12345) | |
30 |
|
30 | |||
31 | def test_pull(): |
|
31 | def test_pull(): | |
32 | rm = rmagic.RMagics(ip) |
|
32 | rm = rmagic.RMagics(ip) | |
33 | rm.r('Z=c(11:20)') |
|
33 | rm.r('Z=c(11:20)') | |
34 | ip.run_line_magic('Rpull', 'Z') |
|
34 | ip.run_line_magic('Rpull', 'Z') | |
35 | np.testing.assert_almost_equal(np.asarray(rm.r('Z')), ip.user_ns['Z']) |
|
35 | np.testing.assert_almost_equal(np.asarray(rm.r('Z')), ip.user_ns['Z']) | |
36 | np.testing.assert_almost_equal(ip.user_ns['Z'], np.arange(11,21)) |
|
36 | np.testing.assert_almost_equal(ip.user_ns['Z'], np.arange(11,21)) | |
37 |
|
37 | |||
38 | def test_Rconverter(): |
|
38 | def test_Rconverter(): | |
39 | datapy= np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c')], |
|
39 | datapy= np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c')], | |
40 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
40 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
41 | ip.user_ns['datapy'] = datapy |
|
41 | ip.user_ns['datapy'] = datapy | |
42 | ip.run_line_magic('Rpush', 'datapy') |
|
42 | ip.run_line_magic('Rpush', 'datapy') | |
43 |
|
43 | |||
44 | # test to see if a copy is being made |
|
44 | # test to see if a copy is being made | |
45 | v = ip.run_line_magic('Rget', '-d datapy') |
|
45 | v = ip.run_line_magic('Rget', '-d datapy') | |
46 | w = ip.run_line_magic('Rget', '-d datapy') |
|
46 | w = ip.run_line_magic('Rget', '-d datapy') | |
47 | np.testing.assert_almost_equal(w['x'], v['x']) |
|
47 | np.testing.assert_almost_equal(w['x'], v['x']) | |
48 | np.testing.assert_almost_equal(w['y'], v['y']) |
|
48 | np.testing.assert_almost_equal(w['y'], v['y']) | |
49 | nt.assert_true(np.all(w['z'] == v['z'])) |
|
49 | nt.assert_true(np.all(w['z'] == v['z'])) | |
50 | np.testing.assert_equal(id(w.data), id(v.data)) |
|
50 | np.testing.assert_equal(id(w.data), id(v.data)) | |
51 | nt.assert_equal(w.dtype, v.dtype) |
|
51 | nt.assert_equal(w.dtype, v.dtype) | |
52 |
|
52 | |||
53 | ip.run_cell_magic('R', ' -d datar datar=datapy', '') |
|
53 | ip.run_cell_magic('R', ' -d datar datar=datapy', '') | |
54 |
|
54 | |||
55 | u = ip.run_line_magic('Rget', ' -d datar') |
|
55 | u = ip.run_line_magic('Rget', ' -d datar') | |
56 | np.testing.assert_almost_equal(u['x'], v['x']) |
|
56 | np.testing.assert_almost_equal(u['x'], v['x']) | |
57 | np.testing.assert_almost_equal(u['y'], v['y']) |
|
57 | np.testing.assert_almost_equal(u['y'], v['y']) | |
58 | nt.assert_true(np.all(u['z'] == v['z'])) |
|
58 | nt.assert_true(np.all(u['z'] == v['z'])) | |
59 | np.testing.assert_equal(id(u.data), id(v.data)) |
|
59 | np.testing.assert_equal(id(u.data), id(v.data)) | |
60 | nt.assert_equal(u.dtype, v.dtype) |
|
60 | nt.assert_equal(u.dtype, v.dtype) | |
61 |
|
61 | |||
62 |
|
62 | |||
63 | def test_cell_magic(): |
|
63 | def test_cell_magic(): | |
64 |
|
64 | |||
65 | ip.push({'x':np.arange(5), 'y':np.array([3,5,4,6,7])}) |
|
65 | ip.push({'x':np.arange(5), 'y':np.array([3,5,4,6,7])}) | |
66 | snippet = ''' |
|
66 | snippet = ''' | |
67 | print(summary(a)) |
|
67 | print(summary(a)) | |
68 | plot(x, y, pch=23, bg='orange', cex=2) |
|
68 | plot(x, y, pch=23, bg='orange', cex=2) | |
69 | plot(x, x) |
|
69 | plot(x, x) | |
70 | print(summary(x)) |
|
70 | print(summary(x)) | |
71 | r = resid(a) |
|
71 | r = resid(a) | |
72 | xc = coef(a) |
|
72 | xc = coef(a) | |
73 | ''' |
|
73 | ''' | |
74 | ip.run_cell_magic('R', '-i x,y -o r,xc a=lm(y~x)', snippet) |
|
74 | ip.run_cell_magic('R', '-i x,y -o r,xc -w 150 -u mm a=lm(y~x)', snippet) | |
75 | np.testing.assert_almost_equal(ip.user_ns['xc'], [3.2, 0.9]) |
|
75 | np.testing.assert_almost_equal(ip.user_ns['xc'], [3.2, 0.9]) | |
76 | np.testing.assert_almost_equal(ip.user_ns['r'], np.array([-0.2, 0.9, -1. , 0.1, 0.2])) |
|
76 | np.testing.assert_almost_equal(ip.user_ns['r'], np.array([-0.2, 0.9, -1. , 0.1, 0.2])) | |
77 |
|
77 | |||
78 |
|
78 | |||
79 | def test_rmagic_localscope(): |
|
79 | def test_rmagic_localscope(): | |
80 | ip.push({'x':0}) |
|
80 | ip.push({'x':0}) | |
81 | ip.run_line_magic('R', '-i x -o result result <-x+1') |
|
81 | ip.run_line_magic('R', '-i x -o result result <-x+1') | |
82 | result = ip.user_ns['result'] |
|
82 | result = ip.user_ns['result'] | |
83 | nt.assert_equal(result[0], 1) |
|
83 | nt.assert_equal(result[0], 1) | |
84 |
|
84 | |||
85 | ip.run_cell('''def rmagic_addone(u): |
|
85 | ip.run_cell('''def rmagic_addone(u): | |
86 | %R -i u -o result result <- u+1 |
|
86 | %R -i u -o result result <- u+1 | |
87 | return result[0]''') |
|
87 | return result[0]''') | |
88 | ip.run_cell('result = rmagic_addone(1)') |
|
88 | ip.run_cell('result = rmagic_addone(1)') | |
89 | result = ip.user_ns['result'] |
|
89 | result = ip.user_ns['result'] | |
90 | nt.assert_equal(result, 2) |
|
90 | nt.assert_equal(result, 2) | |
91 |
|
91 | |||
92 | nt.assert_raises( |
|
92 | nt.assert_raises( | |
93 | NameError, |
|
93 | NameError, | |
94 | ip.run_line_magic, |
|
94 | ip.run_line_magic, | |
95 | "R", |
|
95 | "R", | |
96 | "-i var_not_defined 1+1") |
|
96 | "-i var_not_defined 1+1") |
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