/usr/lib/python2.7/dist-packages/rpy2/ipython/tests/test_rmagic.py is in python-rpy2 2.8.5-1.
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from itertools import product
# Currently numpy is a testing requirement, but rpy2 should work without numpy
try:
import numpy as np
has_numpy = True
except:
has_numpy = False
try:
import pandas as pd
has_pandas = True
except:
has_pandas = False
from IPython.testing.globalipapp import get_ipython
from IPython.utils.py3compat import PY3
if PY3:
from io import StringIO
np_string_type = 'U'
else:
from StringIO import StringIO
np_string_type = 'S'
from rpy2.ipython import rmagic
# from IPython.core.getipython import get_ipython
from rpy2 import rinterface
from rpy2.robjects import r, vectors, globalenv
import rpy2.robjects.packages as rpacks
class TestRmagic(unittest.TestCase):
@classmethod
def setUpClass(cls):
'''Set up an IPython session just once.
It'd be safer to set it up for each test, but for now, I'm mimicking the
IPython team's logic.
'''
cls.ip = get_ipython()
# This is just to get a minimally modified version of the changes
# working
cls.ip.magic('load_ext rpy2.ipython')
def setUp(self):
if hasattr(rmagic.template_converter, 'activate'):
rmagic.template_converter.activate()
def tearDown(self):
# This seems like the safest thing to return to a safe state
self.ip.run_line_magic('Rdevice', 'png')
if hasattr(rmagic.template_converter, 'deactivate'):
rmagic.template_converter.deactivate()
@unittest.skipIf(not has_numpy, 'numpy not installed')
def test_push(self):
self.ip.push({'X':np.arange(5), 'Y':np.array([3,5,4,6,7])})
self.ip.run_line_magic('Rpush', 'X Y')
np.testing.assert_almost_equal(np.asarray(r('X')), self.ip.user_ns['X'])
np.testing.assert_almost_equal(np.asarray(r('Y')), self.ip.user_ns['Y'])
@unittest.skipIf(not has_numpy, 'numpy not installed')
def test_push_localscope(self):
"""Test that Rpush looks for variables in the local scope first."""
self.ip.run_cell('''
def rmagic_addone(u):
%Rpush u
%R result = u+1
%Rpull result
return result[0]
u = 0
result = rmagic_addone(12344)
''')
result = self.ip.user_ns['result']
np.testing.assert_equal(result, 12345)
@unittest.skipUnless(has_pandas, 'pandas is not available in python')
@unittest.skipIf(not has_numpy, 'numpy not installed')
def test_push_dataframe(self):
df = pd.DataFrame([{'a': 1, 'b': 'bar'}, {'a': 5, 'b': 'foo', 'c': 20}])
self.ip.push({'df':df})
self.ip.run_line_magic('Rpush', 'df')
# This is converted to factors, which are currently converted back to Python
# as integers, so for now we test its representation in R.
sio = StringIO()
rinterface.set_writeconsole_regular(sio.write)
try:
r('print(df$b[1])')
self.assertIn('[1] bar', sio.getvalue())
finally:
rinterface.set_writeconsole_regular(None)
# Values come packaged in arrays, so we unbox them to test.
self.assertEqual(r('df$a[2]')[0], 5)
missing = r('df$c[1]')[0]
assert np.isnan(missing), missing
@unittest.skipIf(not has_numpy, 'numpy not installed')
def test_pull(self):
r('Z=c(11:20)')
self.ip.run_line_magic('Rpull', 'Z')
np.testing.assert_almost_equal(np.asarray(r('Z')), self.ip.user_ns['Z'])
np.testing.assert_almost_equal(self.ip.user_ns['Z'], np.arange(11,21))
@unittest.skipIf(not has_numpy, 'numpy not installed')
def test_Rconverter(self):
# If we get to dropping numpy requirement, we might use something
# like the following:
# self.assertSequenceEqual(buffer(a).buffer_info(),
# buffer(b).buffer_info())
# numpy recarray (numpy's version of a data frame)
dataf_np= np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c')],
dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|%s1' % np_string_type)])
# store it in the notebook's user namespace
self.ip.user_ns['dataf_np'] = dataf_np
# equivalent to:
# %Rpush dataf_np
# that is send Python object 'dataf_np' into R's globalenv
# as 'dataf_np'. The current conversion rules will make it an
# R data frame.
self.ip.run_line_magic('Rpush', 'dataf_np')
# Now retreive 'dataf_np' from R's globalenv. Twice because
# we want to test whether copies are made
fromr_dataf_np = self.ip.run_line_magic('Rget', 'dataf_np')
fromr_dataf_np_again = self.ip.run_line_magic('Rget', 'dataf_np')
# check whether the data frame retrieved has the same content
# as the original recarray
self.assertEqual(len(dataf_np), len(fromr_dataf_np))
for col_i, col_n in enumerate(('x', 'y')):
#np.testing.assert_array_equal(dataf_np[col_i],
# fromr_dataf_np.ix[col_i].values)
if has_pandas:
self.assertSequenceEqual(tuple(dataf_np[col_i]),
tuple(fromr_dataf_np.ix[col_i+1].values))
else:
# has_numpy then
self.assertSequenceEqual(tuple(dataf_np[col_i]),
tuple(fromr_dataf_np[col_i]))
# pandas2ri is currently making copies
# # modify the data frame retrieved to check whether
# # a copy was made
# fromr_dataf_np['x'].values[0] = 11
# self.assertEqual(11, fromr_dataf_np_again['x'][0])
# fromr_dataf_np['x'].values[0] = 1
# retrieve `dataf_np` from R into `fromr_dataf_np` in the notebook.
self.ip.run_cell_magic('R',
'-o dataf_np',
'dataf_np')
dataf_np_roundtrip = self.ip.user_ns['dataf_np']
self.assertSequenceEqual(tuple(fromr_dataf_np['x']),
tuple(dataf_np_roundtrip['x']))
self.assertSequenceEqual(tuple(fromr_dataf_np['y']),
tuple(dataf_np_roundtrip['y']))
@unittest.skipIf(not has_numpy, 'numpy not installed')
def test_cell_magic(self):
self.ip.push({'x':np.arange(5), 'y':np.array([3,5,4,6,7])})
# For now, print statements are commented out because they print
# erroneous ERRORs when running via rpy2.tests
snippet = '''
print(summary(a))
plot(x, y, pch=23, bg='orange', cex=2)
plot(x, x)
print(summary(x))
r = resid(a)
xc = coef(a)
'''
self.ip.run_cell_magic('R', '-i x,y -o r,xc -w 150 -u mm a=lm(y~x)',
snippet)
np.testing.assert_almost_equal(self.ip.user_ns['xc'], [3.2, 0.9])
np.testing.assert_almost_equal(self.ip.user_ns['r'], np.array([-0.2, 0.9, -1. , 0.1, 0.2]))
def test_cell_magic_localconverter(self):
x = (1,2,3)
from rpy2.rinterface import StrSexpVector
def tuple_str(tpl):
res = StrSexpVector(tpl)
return res
from rpy2.robjects.conversion import Converter
my_converter = Converter('my converter')
my_converter.py2ri.register(tuple, tuple_str)
from rpy2.robjects import default_converter
foo = default_converter + my_converter
self.ip.push({'x':x,
'foo': foo})
snippet = '''
x
'''
self.assertRaises(NotImplementedError,
self.ip.run_cell_magic,
'R', '-i x', snippet)
self.ip.run_cell_magic('R', '-i x -c foo',
snippet)
self.assertTrue(isinstance(globalenv['x'],
vectors.StrVector))
def test_rmagic_localscope(self):
self.ip.push({'x':0})
self.ip.run_line_magic('R', '-i x -o result result <-x+1')
result = self.ip.user_ns['result']
self.assertEqual(result[0], 1)
self.ip.run_cell('''def rmagic_addone(u):
%R -i u -o result result <- u+1
return result[0]''')
self.ip.run_cell('result = rmagic_addone(1)')
result = self.ip.user_ns['result']
self.assertEqual(result, 2)
self.assertRaises(
NameError,
self.ip.run_line_magic,
"R",
"-i var_not_defined 1+1")
@unittest.skipIf(not has_numpy, 'numpy not installed')
def test_png_plotting_args(self):
'''Exercise the PNG plotting machinery'''
self.ip.push({'x':np.arange(5), 'y':np.array([3,5,4,6,7])})
cell = '''
plot(x, y, pch=23, bg='orange', cex=2)
'''
png_px_args = [' '.join(('--units=px',w,h,p)) for
w, h, p in product(['--width=400 ',''],
['--height=400',''],
['-p=10', ''])]
for line in png_px_args:
self.ip.run_line_magic('Rdevice', 'png')
self.ip.run_cell_magic('R', line, cell)
@unittest.skipUnless(rpacks.isinstalled('Cairo'), 'Cairo not installed')
def test_svg_plotting_args(self):
'''Exercise the plotting machinery
To pass SVG tests, we need Cairo installed in R.'''
self.ip.push({'x':np.arange(5), 'y':np.array([3,5,4,6,7])})
cell = '''
plot(x, y, pch=23, bg='orange', cex=2)
'''
basic_args = [' '.join((w,h,p)) for w, h, p in product(['--width=6 ',''],
['--height=6',''],
['-p=10', ''])]
for line in basic_args:
self.ip.run_line_magic('Rdevice', 'svg')
self.ip.run_cell_magic('R', line, cell)
png_args = ['--units=in --res=1 ' + s for s in basic_args]
for line in png_args:
self.ip.run_line_magic('Rdevice', 'png')
self.ip.run_cell_magic('R', line, cell)
@unittest.skip('Test for X11 skipped.')
def test_plotting_X11(self):
self.ip.push({'x':np.arange(5), 'y':np.array([3,5,4,6,7])})
cell = '''
plot(x, y, pch=23, bg='orange', cex=2)
'''
self.ip.run_line_magic('Rdevice', 'X11')
self.ip.run_cell_magic('R', '', cell)
if __name__ == '__main__':
unittest.main()
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