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import numpy as np
from IPython.testing.decorators import skip_without
from IPython.extensions import rmagic
from IPython.utils.py3compat import PY3
from rpy2 import rinterface
import nose.tools as nt
if PY3:
from io import StringIO
else:
from StringIO import StringIO
ip = get_ipython()
ip.magic('load_ext rmagic')
def test_push():
rm = rmagic.RMagics(ip)
ip.push({'X':np.arange(5), 'Y':np.array([3,5,4,6,7])})
ip.run_line_magic('Rpush', 'X Y')
np.testing.assert_almost_equal(np.asarray(rm.r('X')), ip.user_ns['X'])
np.testing.assert_almost_equal(np.asarray(rm.r('Y')), ip.user_ns['Y'])
def test_push_localscope():
"""Test that Rpush looks for variables in the local scope first."""
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 = ip.user_ns['result']
np.testing.assert_equal(result, 12345)
@skip_without('pandas')
def test_push_dataframe():
from pandas import DataFrame
rm = rmagic.RMagics(ip)
df = DataFrame([{'a': 1, 'b': 'bar'}, {'a': 5, 'b': 'foo', 'c': 20}])
ip.push({'df':df})
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(sio.write)
try:
rm.r('print(df$b[1])')
nt.assert_in('[1] bar', sio.getvalue())
finally:
rinterface.set_writeconsole(None)
# Values come packaged in arrays, so we unbox them to test.
nt.assert_equal(rm.r('df$a[2]')[0], 5)
missing = rm.r('df$c[1]')[0]
assert np.isnan(missing), missing
def test_pull():
rm = rmagic.RMagics(ip)
rm.r('Z=c(11:20)')
ip.run_line_magic('Rpull', 'Z')
np.testing.assert_almost_equal(np.asarray(rm.r('Z')), ip.user_ns['Z'])
np.testing.assert_almost_equal(ip.user_ns['Z'], np.arange(11,21))
def test_Rconverter():
datapy= np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c')],
dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')])
ip.user_ns['datapy'] = datapy
ip.run_line_magic('Rpush', 'datapy')
# test to see if a copy is being made
v = ip.run_line_magic('Rget', '-d datapy')
w = ip.run_line_magic('Rget', '-d datapy')
np.testing.assert_almost_equal(w['x'], v['x'])
np.testing.assert_almost_equal(w['y'], v['y'])
nt.assert_true(np.all(w['z'] == v['z']))
np.testing.assert_equal(id(w.data), id(v.data))
nt.assert_equal(w.dtype, v.dtype)
ip.run_cell_magic('R', ' -d datar', 'datar=datapy')
u = ip.run_line_magic('Rget', ' -d datar')
np.testing.assert_almost_equal(u['x'], v['x'])
np.testing.assert_almost_equal(u['y'], v['y'])
nt.assert_true(np.all(u['z'] == v['z']))
np.testing.assert_equal(id(u.data), id(v.data))
nt.assert_equal(u.dtype, v.dtype)
def test_cell_magic():
ip.push({'x':np.arange(5), 'y':np.array([3,5,4,6,7])})
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)
'''
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(ip.user_ns['xc'], [3.2, 0.9])
np.testing.assert_almost_equal(ip.user_ns['r'], np.array([-0.2, 0.9, -1. , 0.1, 0.2]))
def test_rmagic_localscope():
ip.push({'x':0})
ip.run_line_magic('R', '-i x -o result result <-x+1')
result = ip.user_ns['result']
nt.assert_equal(result[0], 1)
ip.run_cell('''def rmagic_addone(u):
%R -i u -o result result <- u+1
return result[0]''')
ip.run_cell('result = rmagic_addone(1)')
result = ip.user_ns['result']
nt.assert_equal(result, 2)
nt.assert_raises(
NameError,
ip.run_line_magic,
"R",
"-i var_not_defined 1+1")
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