test_rmagic.py
122 lines
| 3.7 KiB
| text/x-python
|
PythonLexer
Thomas Kluyver
|
r13354 | from io import StringIO | ||
Thomas Kluyver
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r10018 | |||
Jonathan Taylor
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r7215 | import numpy as np | ||
Thomas Kluyver
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r9495 | from IPython.testing.decorators import skip_without | ||
Jonathan Taylor
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r7215 | from IPython.extensions import rmagic | ||
Thomas Kluyver
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r10018 | from rpy2 import rinterface | ||
Jonathan Taylor
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r7268 | import nose.tools as nt | ||
Jonathan Taylor
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r7215 | |||
Jonathan Taylor
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r7222 | ip = get_ipython() | ||
ip.magic('load_ext rmagic') | ||||
Jonathan Taylor
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r7215 | |||
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']) | ||||
Robert McGibbon
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r8957 | 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) | ||||
Thomas Kluyver
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r9495 | @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') | ||||
Thomas Kluyver
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r10018 | |||
# 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$b[1])') | ||||
nt.assert_in('[1] bar', sio.getvalue()) | ||||
finally: | ||||
rinterface.set_writeconsole(None) | ||||
Thomas Kluyver
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r9495 | # Values come packaged in arrays, so we unbox them to test. | ||
nt.assert_equal(rm.r('df$a[2]')[0], 5) | ||||
missing = rm.r('df$c[1]')[0] | ||||
assert np.isnan(missing), missing | ||||
Jonathan Taylor
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r7215 | 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)) | ||||
Jonathan Taylor
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r7268 | 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 | ||||
Jonathan Taylor
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r7276 | v = ip.run_line_magic('Rget', '-d datapy') | ||
w = ip.run_line_magic('Rget', '-d datapy') | ||||
Jonathan Taylor
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r7268 | 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) | ||||
Thomas Kluyver
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r9496 | ip.run_cell_magic('R', ' -d datar', 'datar=datapy') | ||
Jonathan Taylor
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r7268 | |||
Jonathan Taylor
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r7276 | u = ip.run_line_magic('Rget', ' -d datar') | ||
Jonathan Taylor
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r7268 | 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) | ||||
Jonathan Taylor
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r7215 | |||
def test_cell_magic(): | ||||
ip.push({'x':np.arange(5), 'y':np.array([3,5,4,6,7])}) | ||||
snippet = ''' | ||||
print(summary(a)) | ||||
Jonathan Taylor
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r7268 | plot(x, y, pch=23, bg='orange', cex=2) | ||
plot(x, x) | ||||
print(summary(x)) | ||||
Jonathan Taylor
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r7215 | r = resid(a) | ||
xc = coef(a) | ||||
''' | ||||
Thomas Kluyver
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r9007 | ip.run_cell_magic('R', '-i x,y -o r,xc -w 150 -u mm a=lm(y~x)', snippet) | ||
Jonathan Taylor
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r7215 | 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])) | ||||
Guy Haskin Fernald
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r8262 | |||
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( | ||||
Jens H. Nielsen
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r8963 | NameError, | ||
Guy Haskin Fernald
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r8262 | ip.run_line_magic, | ||
"R", | ||||
"-i var_not_defined 1+1") | ||||