def test_install():
r('''
packages <- c('rprojroot', 'lifecycle')
new.packages <- packages[!(packages %in% installed.packages()[,"Package"])]
if (length(new.packages)) install.packages(new.packages)
''')
eq_(
r(path='scriptpath.R')[0],
os.path.join(folder, 'flags.csv').replace(os.sep, '/'))
def test_init():
# This part of the test leads to a segfault on Linux. Run only on Windows
if sys.platform == 'win32':
# R_HOME is set to a non-existent directory
os.environ['R_HOME'] = os.path.join(folder, 'R')
with assert_raises(RuntimeError):
import rpy2.robjects # NOQA: F401
# But Gramex uses Conda PATH
r('1 + 2')
import rpy2.rinterface
# Note: in your machine, ensure "conda" is part of your Anaconda PATH
ok_('conda' in rpy2.rinterface.R_HOME)
def test_plots():
if os.environ.get('BRANCH', '') not in {'dev', 'master'}:
raise SkipTest('Install slow ggplot2 only on dev/master')
r('''
packages <- c('ggplot2')
new.packages <- packages[!(packages %in% installed.packages()[,"Package"])]
if (length(new.packages)) install.packages(new.packages)
''')
path = r(path='scriptplot.R')
img = Image.open(path[0])
eq_(img.size, (512, 512)) # noqa: E912 Size matches
freq = {color: count for count, color in img.convert('RGB').getcolors()}
ok_(freq[255, 255, 255] < 50000) # noqa: E912 Not filled with white
ok_(freq[235, 235, 235] > 100000) # noqa: E912 Mostly light grey
ok_(freq[89, 89, 89] > 20000) # noqa: E912 and some dark grey
def test_args():
r(path='script1.R')
eq_(r('incr(n)', n=5)[0], 6)
eq_(
r(
'mean(x, na.rm=narm, trim=trim)',
x=pd.Series([0, 1, 2, 3, 4, 5, 6, None]),
narm=True,
trim=0.2,
)[0], 3)
cars = r('''
data(cars)
cars
''')
ok_(isinstance(cars, pd.DataFrame))
def test_rmarkdown(self):
# install rmarkdown if missing
r('''
packages <- c('rmarkdown')
new.packages <- packages[!(packages %in% installed.packages()[,"Package"])]
if (length(new.packages)) install.packages(new.packages)
''')
def _callback(f):
f = f.result()
return f
path = server.info.folder / 'dir/rmarkdown.Rmd'
handler = AttrDict(file=path)
result = rmarkdown('', handler).add_done_callback(_callback)
self.check('/dir/transform/rmarkdown.Rmd', text=result)
htmlpath = str(server.info.folder / 'dir/rmarkdown.html')
tempfiles[htmlpath] = htmlpath
def test_plots():
path = r(path='scriptplot.R')
img = Image.open(path[0])
eq_(img.size, (512, 512)) # noqa: E912 Size matches
freq = {color: count for count, color in img.convert('RGB').getcolors()}
ok_(freq[255, 255, 255] < 50000) # noqa: E912 Not filled with white
ok_(freq[235, 235, 235] > 100000) # noqa: E912 Mostly light grey
ok_(freq[89, 89, 89] > 20000) # noqa: E912 and some dark grey
def test_rmarkdown(self):
if os.environ.get('BRANCH', '') not in {'dev', 'master'}:
raise SkipTest('Install slow rmarkdown installation only on dev/master')
# install rmarkdown if missing
r('''
packages <- c('rmarkdown')
new.packages <- packages[!(packages %in% installed.packages()[,"Package"])]
if (length(new.packages)) install.packages(new.packages)
''')
def _callback(f):
f = f.result()
return f
path = server.info.folder / 'dir/rmarkdown.Rmd'
handler = AttrDict(file=path)
result = rmarkdown('', handler).add_done_callback(_callback)
self.check('/dir/transform/rmarkdown.Rmd', text=result)
htmlpath = str(server.info.folder / 'dir/rmarkdown.html')
tempfiles[htmlpath] = htmlpath
def test_rmarkdown(self):
# rmarkdown must be installed
ok_(r('"rmarkdown" %in% installed.packages()')[0],
'rmarkdown must be installed. Run conda install -c r r-rmarkdown')
def _callback(f):
f = f.result()
return f
path = server.info.folder / 'dir/rmarkdown.Rmd'
handler = AttrDict(file=path)
result = rmarkdown('', handler).add_done_callback(_callback)
try:
self.check('/dir/transform/rmarkdown.Rmd', text=result)
except AssertionError:
raise SkipTest('TODO: Once NumPy & rpy2 work together, remove this SkipTest. #259')
htmlpath = str(server.info.folder / 'dir/rmarkdown.html')
tempfiles[htmlpath] = htmlpath
def test_command():
eq_(r('1 + 2')[0], 3)
eq_(r('sum(c(1,2,3))')[0], 6)
# Multi-ine command
total = r('''
x <- c(1,2,3,4)
sum(x)
''')
eq_(total[0], 10)
# Variables preserved across calls
r('x <- c(5,4,3)')
eq_(r('sum(x)')[0], 12)
def test_script():
r(path='script1.R')
eq_(r('first()')[0], 60)
eq_(r('second()')[0], 100)
