def setUp(self):
self.console = rinterface.get_writeconsole_regular()
def noconsole(x):
pass
rinterface.set_writeconsole_regular(noconsole)
def eval(self, code):
"""
Parse and evaluate a line of R code with rpy2.
Returns the output to R's stdout() connection,
the value generated by evaluating the code, and a
boolean indicating whether the return value would be
visible if the line of code were evaluated in an R REPL.
R Code evaluation and visibility determination are done via an R call of
the form withVisible(code_string), and this entire expression needs to
be evaluated in R (we can't use rpy2 function proxies here, as
withVisible is a LISPy R function).
"""
old_writeconsole_regular = ri.get_writeconsole_regular()
ri.set_writeconsole_regular(self.write_console_regular)
try:
# Need the newline in case the last line in code is a comment
value, visible = ro.r("withVisible({%s\n})" % code)
except (ri.RRuntimeError, ValueError) as exception:
warning_or_other_msg = self.flush(
) # otherwise next return seems to have copy of error
raise RInterpreterError(code, str(exception), warning_or_other_msg)
text_output = self.flush()
ri.set_writeconsole_regular(old_writeconsole_regular)
return text_output, value, visible[0]
def eval(self, code):
'''
Parse and evaluate a line of R code with rpy2.
Returns the output to R's stdout() connection,
the value generated by evaluating the code, and a
boolean indicating whether the return value would be
visible if the line of code were evaluated in an R REPL.
R Code evaluation and visibility determination are done via an R call of
the form withVisible(code_string), and this entire expression needs to
be evaluated in R (we can't use rpy2 function proxies here, as
withVisible is a LISPy R function).
'''
old_writeconsole_regular = ri.get_writeconsole_regular()
ri.set_writeconsole_regular(self.write_console_regular)
try:
# Need the newline in case the last line in code is a comment
value, visible = ro.r("withVisible({%s\n})" % code)
except (ri.RRuntimeError, ValueError) as exception:
warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error
raise RInterpreterError(code, str_to_unicode(str(exception)), warning_or_other_msg)
text_output = self.flush()
ri.set_writeconsole_regular(old_writeconsole_regular)
return text_output, value, visible[0]
def setUp(self):
self.console = rinterface.get_writeconsole_regular()
def noconsole(x):
pass
rinterface.set_writeconsole_regular(noconsole)
def testSetWriteConsoleRegular(self):
buf = []
def f(x):
buf.append(x)
rinterface.set_writeconsole_regular(f)
self.assertEqual(rinterface.get_writeconsole_regular(), f)
code = rinterface.SexpVector(["3", ], rinterface.STRSXP)
rinterface.baseenv["print"](code)
self.assertEqual('[1] "3"\n', str.join('', buf))
def testSetWriteConsoleRegular(self):
buf = []
def f(x):
buf.append(x)
rinterface.set_writeconsole_regular(f)
self.assertEqual(rinterface.get_writeconsole_regular(), f)
code = rinterface.SexpVector([
"3",
], rinterface.STRSXP)
rinterface.baseenv["print"](code)
self.assertEqual('[1] "3"\n', str.join('', buf))
def R(self, line, cell=None, local_ns=None):
"""
Execute code in R, optionally returning results to the Python runtime.
In line mode, this will evaluate an expression and convert the returned
value to a Python object. The return value is determined by rpy2's
behaviour of returning the result of evaluating the final expression.
Multiple R expressions can be executed by joining them with semicolons::
In [9]: %R X=c(1,4,5,7); sd(X); mean(X)
Out[9]: array([ 4.25])
In cell mode, this will run a block of R code. The resulting value
is printed if it would be printed when evaluating the same code
within a standard R REPL.
Nothing is returned to python by default in cell mode::
In [10]: %%R
....: Y = c(2,4,3,9)
....: summary(lm(Y~X))
Call:
lm(formula = Y ~ X)
Residuals:
1 2 3 4
0.88 -0.24 -2.28 1.64
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.0800 2.3000 0.035 0.975
X 1.0400 0.4822 2.157 0.164
Residual standard error: 2.088 on 2 degrees of freedom
Multiple R-squared: 0.6993,Adjusted R-squared: 0.549
F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638
In the notebook, plots are published as the output of the cell::
%R plot(X, Y)
will create a scatter plot of X bs Y.
If cell is not None and line has some R code, it is prepended to
the R code in cell.
Objects can be passed back and forth between rpy2 and python via the -i -o flags in line::
In [14]: Z = np.array([1,4,5,10])
In [15]: %R -i Z mean(Z)
Out[15]: array([ 5.])
In [16]: %R -o W W=Z*mean(Z)
Out[16]: array([ 5., 20., 25., 50.])
In [17]: W
Out[17]: array([ 5., 20., 25., 50.])
The return value is determined by these rules:
* If the cell is not None (i.e., has contents), the magic returns None.
* If the final line results in a NULL value when evaluated
by rpy2, then None is returned.
* No attempt is made to convert the final value to a structured array.
Use %Rget to push a structured array.
* If the -n flag is present, there is no return value.
* A trailing ';' will also result in no return value as the last
value in the line is an empty string.
"""
args = parse_argstring(self.R, line)
# arguments 'code' in line are prepended to
# the cell lines
if cell is None:
code = ''
return_output = True
line_mode = True
else:
code = cell
return_output = False
line_mode = False
code = ' '.join(args.code) + code
# if there is no local namespace then default to an empty dict
if local_ns is None:
local_ns = {}
if args.converter is None:
converter = self.converter
else:
try:
converter = local_ns[args.converter]
except KeyError:
try:
converter = self.shell.user_ns[args.converter]
except KeyError:
raise NameError("name '%s' is not defined" %
args.converter)
if not isinstance(converter, Converter):
raise ValueError(
"'%s' must be a %s object (but it is a %s)." %
(args.converter, Converter, type(localconverter)))
if args.input:
for input in ','.join(args.input).split(','):
try:
val = local_ns[input]
except KeyError:
try:
val = self.shell.user_ns[input]
except KeyError:
raise NameError("name '%s' is not defined" % input)
with localconverter(converter) as cv:
ro.r.assign(input, val)
tmpd = self.setup_graphics(args)
text_output = ''
try:
if line_mode:
for line in code.split(';'):
text_result, result, visible = self.eval(line)
text_output += text_result
if text_result:
# the last line printed something to the console so we won't return it
return_output = False
else:
text_result, result, visible = self.eval(code)
text_output += text_result
if visible:
old_writeconsole_regular = ri.get_writeconsole_regular()
ri.set_writeconsole_regular(self.write_console_regular)
ro.r.show(result)
text_output += self.flush()
ri.set_writeconsole_regular(old_writeconsole_regular)
except RInterpreterError as e:
# TODO: Maybe we should make this red or something?
print(e.stdout)
if not e.stdout.endswith(e.err):
print(e.err)
if tmpd:
rmtree(tmpd)
return
finally:
if self.device in ['png', 'svg']:
ro.r('dev.off()')
if text_output:
# display_data.append(('RMagic.R', {'text/plain':text_output}))
publish_display_data(data={'text/plain': text_output},
source='RMagic.R')
# publish the R images
if self.device in ['png', 'svg']:
display_data, md = self.publish_graphics(tmpd, args.isolate_svgs)
for tag, disp_d in display_data:
publish_display_data(data=disp_d, source=tag, metadata=md)
# kill the temporary directory - currently created only for "svg"
# and "png" (else it's None)
rmtree(tmpd)
if args.output:
with localconverter(converter) as cv:
for output in ','.join(args.output).split(','):
output_ipy = ro.globalenv.get(output)
self.shell.push({output: output_ipy})
# this will keep a reference to the display_data
# which might be useful to other objects who happen to use
# this method
if self.cache_display_data:
self.display_cache = display_data
# We're in line mode and return_output is still True,
# so return the converted result
if return_output and not args.noreturn:
if result is not ri.NULL:
with localconverter(converter) as cv:
res = cv.ri2py(result)
return res
def R(self, line, cell=None, local_ns=None):
'''
Execute code in R, optionally returning results to the Python runtime.
In line mode, this will evaluate an expression and convert the returned
value to a Python object. The return value is determined by rpy2's
behaviour of returning the result of evaluating the final expression.
Multiple R expressions can be executed by joining them with semicolons::
In [9]: %R X=c(1,4,5,7); sd(X); mean(X)
Out[9]: array([ 4.25])
In cell mode, this will run a block of R code. The resulting value
is printed if it would be printed when evaluating the same code
within a standard R REPL.
Nothing is returned to python by default in cell mode::
In [10]: %%R
....: Y = c(2,4,3,9)
....: summary(lm(Y~X))
Call:
lm(formula = Y ~ X)
Residuals:
1 2 3 4
0.88 -0.24 -2.28 1.64
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.0800 2.3000 0.035 0.975
X 1.0400 0.4822 2.157 0.164
Residual standard error: 2.088 on 2 degrees of freedom
Multiple R-squared: 0.6993,Adjusted R-squared: 0.549
F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638
In the notebook, plots are published as the output of the cell::
%R plot(X, Y)
will create a scatter plot of X bs Y.
If cell is not None and line has some R code, it is prepended to
the R code in cell.
Objects can be passed back and forth between rpy2 and python via the -i -o flags in line::
In [14]: Z = np.array([1,4,5,10])
In [15]: %R -i Z mean(Z)
Out[15]: array([ 5.])
In [16]: %R -o W W=Z*mean(Z)
Out[16]: array([ 5., 20., 25., 50.])
In [17]: W
Out[17]: array([ 5., 20., 25., 50.])
The return value is determined by these rules:
* If the cell is not None (i.e., has contents), the magic returns None.
* If the final line results in a NULL value when evaluated
by rpy2, then None is returned.
* No attempt is made to convert the final value to a structured array.
Use %Rget to push a structured array.
* If the -n flag is present, there is no return value.
* A trailing ';' will also result in no return value as the last
value in the line is an empty string.
'''
args = parse_argstring(self.R, line)
# arguments 'code' in line are prepended to
# the cell lines
if cell is None:
code = ''
return_output = True
line_mode = True
else:
code = cell
return_output = False
line_mode = False
code = ' '.join(args.code) + code
# if there is no local namespace then default to an empty dict
if local_ns is None:
local_ns = {}
if args.converter is None:
pass
else:
try:
localconverter = local_ns[args.converter]
except KeyError:
try:
localconverter = self.shell.user_ns[args.converter]
except KeyError:
raise NameError("name '%s' is not defined" % args.converter)
if not isinstance(localconverter, Converter):
raise ValueError("'%s' must be a Converter object.")
if args.input:
for input in ','.join(args.input).split(','):
try:
val = local_ns[input]
except KeyError:
try:
val = self.shell.user_ns[input]
except KeyError:
raise NameError("name '%s' is not defined" % input)
if args.converter is None:
ro.r.assign(input, self.pyconverter(val))
else:
ro.r.assign(input, localconverter.py2ri(val))
tmpd = self.setup_graphics(args)
text_output = ''
try:
if line_mode:
for line in code.split(';'):
text_result, result, visible = self.eval(line)
text_output += text_result
if text_result:
# the last line printed something to the console so we won't return it
return_output = False
else:
text_result, result, visible = self.eval(code)
text_output += text_result
if visible:
old_writeconsole_regular = ri.get_writeconsole_regular()
ri.set_writeconsole_regular(self.write_console_regular)
ro.r.show(result)
text_output += self.flush()
ri.set_writeconsole_regular(old_writeconsole_regular)
except RInterpreterError as e:
# XXX - Maybe we should make this red or something?
print(e.stdout)
if not e.stdout.endswith(e.err):
print(e.err)
if tmpd: rmtree(tmpd)
return
finally:
if self.device in ['png', 'svg']:
ro.r('dev.off()')
if text_output:
# display_data.append(('RMagic.R', {'text/plain':text_output}))
publish_display_data(data={'text/plain':text_output}, source='RMagic.R')
# publish the R images
if self.device in ['png', 'svg']:
display_data, md = self.publish_graphics(tmpd, args.isolate_svgs)
for tag, disp_d in display_data:
publish_display_data(data=disp_d, source=tag, metadata=md)
# kill the temporary directory - currently created only for "svg"
# and "png" (else it's None)
rmtree(tmpd)
if args.output:
for output in ','.join(args.output).split(','):
if args.converter is None:
output_ipy = converter.ri2py(ri.globalenv.get(output))
else:
output_ipy = localconverter.ri2py(ri.globalenv.get(output))
self.shell.push({output: output_ipy })
# this will keep a reference to the display_data
# which might be useful to other objects who happen to use
# this method
if self.cache_display_data:
self.display_cache = display_data
# We're in line mode and return_output is still True,
# so return the converted result
if return_output and not args.noreturn:
if result is not ri.NULL:
if args.converter is None:
return converter.ri2py(result)
else:
return localconverter.ri2py(result)