def __doc__(self):
doc = ['Python representation of an R function.']
description = help.docstring(self.__rpackagename__,
self.__rname__,
sections=['description'])
doc.append(description)
fm = _formals_fixed(self)
names = fm.do_slot('names')
doc.append(self.__rname__+'(')
for key, val in self._prm_translate.items():
if key == '___':
description = ('(was "..."). R ellipsis '
'(any number of parameters)')
else:
description = _repr_argval(fm[names.index(val)])
if description is None:
doc.append(' %s,' % key)
else:
doc.append(' %s = %s,' % (key, description))
doc.extend((')', ''))
package = help.Package(self.__rpackagename__)
page = package.fetch(self.__rname__)
for item in page.arguments():
description = item.value
description = description.replace('\n', '')
description, count = pattern_link.subn(r'\1', description)
description, count = pattern_code.subn(r'`\1`', description)
description, count = pattern_samp.subn(r'`\1`', description)
doc.append(' '.join((item.name, ': ', description, ',')))
doc.append('')
return os.linesep.join(doc)
def __doc__(self):
doc = [
'Wrapper around an R function.', '',
'The docstring below is built from the R documentation.', ''
]
description = help.docstring(self.__rpackagename__,
self.__rname__,
sections=['\\description'])
doc.append(description)
fm = _formals_fixed(self)
names = fm.do_slot('names')
doc.append(self.__rname__ + '(')
for key, val in self._prm_translate.items():
if key == '___':
description = ('(was "..."). R ellipsis '
'(any number of parameters)')
else:
description = _repr_argval(fm[names.index(val)])
if description is None:
doc.append(' %s,' % key)
else:
doc.append(' %s = %s,' % (key, description))
doc.extend((')', ''))
package = help.Package(self.__rpackagename__)
page = package.fetch(self.__rname__)
doc.append('Args:')
for item in page.arguments():
description = ('%s ' % os.linesep).join(item.value)
doc.append(' '.join((' ', item.name, ': ', description)))
doc.append('')
doc.append(
help.docstring(self.__rpackagename__,
self.__rname__,
sections=['\\details']))
return os.linesep.join(doc)
def test_init(self):
base_help = rh.Package('base')
assert base_help.name == 'base'
def test_description(self):
base_help = rh.Package('base')
p = base_help.fetch('print')
d = p.description()
assert isinstance(d, str)
assert len(d) > 0
def test_usage(self):
base_help = rh.Package('base')
p = base_help.fetch('print')
d = p.usage()
assert isinstance(d, str)
assert len(d) > 0
def test_fetch(self):
base_help = rh.Package('base')
f = base_help.fetch('print')
assert 'title' in f.sections.keys()
def test_to_docstring(self):
base_help = rh.Package('base')
p = base_help.fetch('print')
ds = p.to_docstring()
assert ds[:5] == 'title'
def __initialize_wrapper():
global version, Fort
import numpy
import pandas
import rpy2
import rpy2.robjects as robjects
import rpy2.robjects.help as rh
import rpy2.robjects.numpy2ri as numpy2ri
from rpy2.robjects.packages import importr
import fnmatch
import os
import re
from rpy2.robjects import pandas2ri
#rpy2.robjects.activate()
pandas2ri.activate()
numpy2ri.activate()
root_dir = os.path.dirname(os.path.realpath(__file__))
__extRemes__ = importr("extRemes")
__climextRemes__ = importr("climextRemes")
__climextRemesHelp__ = rh.Package("climextRemes")
__version__ = robjects.r('''
packageVersion("climextRemes")
''')[0]
__version__ = ".".join([str(f) for f in __version__])
version = __version__
Fort = pandas.DataFrame(robjects.r('''
data(Fort)
ord <- order(Fort$year, Fort$month, Fort$day)
Fort <- Fort[ord, ]
'''))
examples = {}
examples_dir = "{0}/../examples".format(root_dir)
for file in os.listdir(examples_dir):
if fnmatch.fnmatch(file, '*_examples.py'):
filename = examples_dir + "/" + file
with open(filename, "r") as infile:
key = file.replace("_examples.py", "")
value = infile.read()
examples[key] = value
arguments_dir = "{0}/../python_help".format(root_dir)
for file in os.listdir(arguments_dir):
if fnmatch.fnmatch(file, '*_args.txt'):
filename = arguments_dir + "/" + file
with open(filename, "r") as infile:
key = file.replace("_args.txt", "")
value = infile.read()
examples[key + "_arguments"] = value
#print("examples", examples.keys())
class climextRemesReturnObject(object):
def __init__(self):
pass
def __repr__(self):
return str(self.__dict__.keys())
def __parseResult(obj):
result = None
if hasattr(obj, 'names') == False:
return obj
#print obj.names, rpy2.rinterface.NULL, type(obj), rpy2.rinterface.RNULLType
if obj.names is rpy2.rinterface.NULL or \
type(obj.names) is rpy2.rinterface.RNULLType or \
(len(obj.names) == 1 and obj.names[0].replace(".","").isdigit()):
if isinstance(obj, robjects.Vector) and len(obj) == 1:
result = obj[0]
else:
result = robjects.conversion.ri2py(obj)
elif isinstance(obj, robjects.Vector):
result = climextRemesReturnObject()
result.names = numpy.array(obj.names)
for i in range(len(obj.names)):
#print obj.names[i]
result.__dict__[obj.names[i] + "_r"] = numpy.array(obj[i])
result.__dict__[obj.names[i]] = __parseResult(obj[i])
return result
def __climextRemesWrapFunction(method_name, override_examples):
names = []
defaults = []
signature = robjects.r('''
library(climextRemes)
as.list(args({0}))
'''.format(method_name))
def quote_args(text, arg_names):
text = re.sub("( " + " | ".join(arg_names) + " )", "‘\\1’", text)
text = text.replace("‘ ", "‘")
text = text.replace(" ’", "’")
return(text)
for (i,name) in enumerate(signature.names):
if len(name) > 0:
name = name.replace(".","_")
names.append(name)
try:
d = signature[i][0]
if isinstance(d, rpy2.robjects.robject.RObject):
defaults.append(None)
else:
defaults.append(d)
except:
defaults.append(None)
gdoc = __climextRemesHelp__.fetch(method_name)
gdoc_help = gdoc.to_docstring(['title', 'description'])
if method_name + "_arguments" in override_examples:
new_arguments = override_examples[method_name + "_arguments"]
arguments = new_arguments.split("@param ")
new_arguments = "arguments\n"
new_arguments += "---------\n"
argument_names = []
for arg in arguments[1:]:
n_arg = arg.split(" ")
argument_names.append(n_arg[0])
n_arg[0] = n_arg[0] + ":"
arg = " ".join(n_arg)
new_arguments += arg + "\n"
#new_arguments = new_arguments.replace("@param ", "")
#gdoc_help += "arguments\n"
#gdoc_help += "----------\n"
#gdoc_help += new_arguments #.replace("\n", "\n\n")
#gdoc_help.replace("\n\ndetails\n", "\n" + new_arguments + "\n\ndetails\n")
gdoc_help += new_arguments
else:
gdoc_arguments = gdoc.to_docstring(["arguments"])
res = gdoc_arguments.split("\n")
output = ""
argument_names = []
for r in res:
r2 = r.split()
if len(r2) >= 2:
argument_names.append(r2[0])
r2[0] = r2[0] + ":"
r2 = " ".join(r2)
output += " " + r2 + "\n"
else:
output += r + "\n"
gdoc_help += output + "\n\n"
#method = getattr(__climextRemes__, method_name)
#arglist = method.formals().names
help_keys = list(gdoc.sections.keys())
if "details" in help_keys:
details = gdoc.to_docstring(["details"])
details = quote_args(details, argument_names)
gdoc_help += details
help_keys.remove('details')
if "value" in help_keys:
value = gdoc.value()
value = value.replace("\code{", "‘")
value = value.replace("}", "’")
gdoc_help += "value\n-----\n\n" + value + "\n"
help_keys.remove('value')
if "usage" in help_keys: help_keys.remove('usage') # this is the R usage so exclude
if "alias" in help_keys: help_keys.remove('alias') # this is the R alias so exclude
if "arguments" in help_keys: help_keys.remove('arguments') # handled separately
if "examples" in help_keys: help_keys.remove('examples') # handled separately
if "name" in help_keys: help_keys.remove('name') # this is redundant so exclude
if "title" in help_keys: help_keys.remove('title') # handled separately
if "description" in help_keys: help_keys.remove('description') # handled separately
others = gdoc.to_docstring(help_keys)
others = quote_args(others, argument_names)
gdoc_help += others
if method_name in override_examples:
gdoc_help += "examples\n"
gdoc_help += "--------\n"
gdoc_help += ">>> " + override_examples[method_name].replace("\n", "\n... ")
#index = gdoc_help.find("examples")
#if index >= 0:
# gdoc_help = gdoc_help[0:index]
# if method_name in override_examples:
# gdoc_help += "examples\n"
# gdoc_help += "---------\n"
# gdoc_help += override_examples[method_name].replace("\n", "\n\n")
# some cleanup
gdoc_help = gdoc_help.replace("title\n-----", "\n", 1) # 'title' is extraneous
gdoc_help = gdoc_help.replace("\n \n", "\n\n")
gdoc_help = gdoc_help.replace("---\n\n\n", "---\n")
gdoc_help = gdoc_help.replace("\n\n\n", "\n\n")
help_keys.extend(["arguments", "examples", "description", "details", "value"])
for help in help_keys: # Sphinx thinks repeated characters are section titles
gdoc_help = gdoc_help.replace(help + "\n" + "-"*len(help), "**" + help + "**\n")
gdoc_help = gdoc_help.replace('TRUE', 'True')
gdoc_help = gdoc_help.replace('FALSE', 'False')
gdoc_help = gdoc_help.replace('NULL', 'None')
def decorator(*args, **kwargs):
#print kwargs, args
new_args = []
new_kwargs = {}
for a in args:
if isinstance(a, dict):
new_args.append(rpy2.robjects.vectors.ListVector(a))
else:
if a is None:
a = rpy2.rinterface.NULL
new_args.append(a)
for b in kwargs.keys():
if isinstance(kwargs[b], dict):
new_kwargs[b] = rpy2.robjects.vectors.ListVector(kwargs[b])
else:
if b is None:
b = rpy2.rinterface.NULL
new_kwargs[b] = kwargs[b]
method = getattr(__climextRemes__, method_name)
retobj = method(*new_args, **new_kwargs)
#return __parseResult(retobj)
return compute_input_map(retobj)
decorator.__doc__ = gdoc_help
decorator.__name__ = method_name + "_"
decorator.__names__ = names
decorator.__defaults__ = tuple(defaults)
argstr = ", ".join(names)
fakefunc = "def %s(%s):\n return %s(%s)\n" % (method_name, argstr, method_name + "_", argstr)
fakefunc_code = compile(fakefunc, "fakesource", "exec")
fakeglobals = {}
eval(fakefunc_code, {method_name + "_": decorator}, fakeglobals)
f_with_good_sig = fakeglobals[method_name]
f_with_good_sig.__doc__ = gdoc_help
f_with_good_sig.__name__ = method_name
f_with_good_sig.__defaults__ = tuple(defaults)
return f_with_good_sig
for __i__ in __climextRemes__._exported_names:
result = __climextRemesWrapFunction(__i__, examples)
globals()[__i__] = result
def test_init(self):
base_help = rh.Package('base')
p = base_help.fetch('print')
assert tuple(p.sections.keys())[0] == 'title'
def test_usage(self):
base_help = rh.Package('base')
p = base_help.fetch('print')
d = p.usage()
assert all(isinstance(x, str) for x in d)
assert len(d) > 0
def testToDocstring(self):
base_help = rh.Package('base')
p = base_help.fetch('print')
ds = p.to_docstring()
self.assertEqual('title', ds[:5])
def testInit(self):
base_help = rh.Package('base')
self.assertEqual('NULL', base_help.object2alias['NULL'])
def importr(packname, newname=None, verbose=False):
""" Wrapper around rpy2.robjects.packages.importr,
adding the following features:
- package instance added to the pseudo-module 'packages'
- automatic pydoc generation from the R help pages
"""
assert isinstance(packname, str)
packinstance = _importr(packname, on_conflict='warn')
# fix the package name (dots possible in R package names)
if newname is None:
newname = packname.replace('.', '_')
Packages().__dict__[newname] = packinstance
## Currently too slow for a serious usage: R's introspection
## of S4 classes is not fast enough
# d = {}
# for cn in methods.get_classnames(packname):
# class AutoS4(RS4):
# __metaclass__ = methods.RS4Auto_Type
# __rpackagename__ = packname
# __rname__ = cn
# newcn = cn.replace('.', '_')
# d[newcn] = AutoS4
# S4Classes().__dict__[newname] = d
p_latex_code = re.compile('\\\\code{([^}]+)}')
p_latex_link = re.compile('\\\\link{([^}]+)}')
p_latex_any_curly = re.compile('\\\\[^ ]+{([^}]+)}')
p_latex_any = re.compile('\\\\([^ ]+)')
p_latex_usage = re.compile(
'\\\\method{(?P<method>[^}]+)}{(?P<class>[^}]+)}(?P<signature>.+)')
doc = rhelp.Package(packname)
for obj_name in packinstance.__dict__:
obj = packinstance.__dict__[obj_name]
# ignore class-defined attributes to only consider
# the ones defined dynamically
if hasattr(type(packinstance), obj_name):
continue
try:
p = doc.fetch(obj.__rname__)
except rhelp.HelpNotFoundError as hnfe:
# No R documentation could be found for the object
if verbose:
print('Pydoc generator: no help for "%s"' % (obj_name, ))
continue
except AttributeError as ae:
# No __rname__ for the object
print('Pydoc generator: oddity with "%s"' % (obj_name, ))
continue
except:
print('Pydoc generator: oddity with "%s" ("%s")' %
(obj_name, obj.__rname__))
continue
if obj_name in packinstance._exported_names:
exported = True
else:
exported = False
#if verbose:
# print('Pydoc generator: "%s" not exported' %(obj_name, ))
#continue
docstring = [
p.title(),
'[ %s - %s exported ]' % (p._type, 'not' if not exported else ''),
'** Experimental dynamic conversion of the associated R documentation **'
]
tmp = p.description()
tmp = re.sub(p_latex_any_curly, "'\\1'", tmp)
docstring.append(tmp)
docstring.append('')
tmp_usage = p.usage().split(linesep)
for i, row in enumerate(tmp_usage):
tmp_m = p_latex_usage.match(row)
if tmp_m is not None:
tmp_usage[i] = '%s_%s%s' % (tmp_m.group('method'),
tmp_m.group('class'),
tmp_m.group('signature'))
tmp_usage = linesep.join(tmp_usage)
docstring.extend([tmp_usage, ''])
if obj_name not in packinstance._exported_names:
tmp = p.seealso()
tmp = re.sub(p_latex_code, "'\\1'", tmp)
tmp = re.sub(p_latex_any_curly, '\\1', tmp)
tmp = re.sub(p_latex_any, "'\\1'", tmp)
docstring.extend(['', 'See Also:', tmp])
docstring = linesep.join(docstring)
obj.__doc__ = docstring
continue
try:
arguments = p.arguments()
except KeyError as ke:
#FIXME: no arguments - should the handling differ a bit ?
arguments = tuple()
# Assume uniqueness of values in the dict. This is making sense since
# parameters to the function should have unique names ans... this appears to be enforced
# by R when declaring a function
arguments = OrderedDict(arguments)
if hasattr(obj, '_prm_translate'):
docstring.extend(['', 'Parameters:', ''])
for k, v in obj._prm_translate.items():
try:
tmp = arguments[v]
tmp = re.sub(p_latex_code, "'\\1'", tmp)
tmp = re.sub(p_latex_any_curly, '\\1', tmp)
tmp = re.sub(p_latex_any, "'\\1'", tmp)
docstring.append('%s -- %s' % (k, tmp))
except KeyError:
# This is an inconsistency in the R documentation
# (the parameter in the function's signature does
# not have an entry in the R documentation).
# Do nothing.
#
if verbose:
print(
'Pydoc generator: no help for parameter "%s" in %s'
% (k, obj_name))
docstring.append(
'%s -- [error fetching the documentation]' % (k))
#print('Pydoc generator: oddity with R\'s "%s" over the parameter "%s"' %(obj_name, v))
tmp = p.value()
tmp = re.sub(p_latex_code, "'\\1'", tmp)
tmp = re.sub(p_latex_any, '\\1', tmp)
docstring.extend(['', 'Returns:', tmp])
tmp = p.seealso()
tmp = re.sub(p_latex_code, "'\\1'", tmp)
tmp = re.sub(p_latex_any_curly, '\\1', tmp)
tmp = re.sub(p_latex_any, "'\\1'", tmp)
docstring.extend(['', 'See Also:', tmp])
docstring = linesep.join(docstring)
obj.__doc__ = docstring
return packinstance
def testToDocstring(self):
base_help = rh.Package('base')
p = base_help.fetch('RdUtils')
ds = p.to_docstring()
self.assertEqual('title', ds[0])
self.assertEqual('-----', ds[2])
def testInit(self):
base_help = rh.Package('base')
p = base_help.fetch('RdUtils')
self.assertEqual('title', p.sections.keys()[0])
def testFetch(self):
base_help = rh.Package('base')
f = base_help.fetch('RdUtils')
self.assertTrue('title' in f.sections.keys())
def __new__(mcs, name, bases, cls_dict):
try:
cls_rname = cls_dict['__rname__']
except KeyError as ke:
cls_rname = name
try:
cls_rpackagename = cls_dict['__rpackagename__']
except KeyError as ke:
cls_rpackagename = None
try:
cls_attr_translation = cls_dict['__attr_translation__']
except KeyError as ke:
cls_attr_translation = {}
try:
cls_meth_translation = cls_dict['__meth_translation__']
except KeyError as ke:
cls_meth_translation = {}
cls_def = getclassdef(cls_rname, cls_rpackagename)
# documentation / help
if cls_rpackagename is None:
cls_dict['__doc__'] = "Undocumented class from the R workspace."
else:
pack_help = rhelp.Package(cls_rpackagename)
page_help = None
try:
#R's classes are sometimes documented with a prefix 'class.'
page_help = pack_help.fetch(cls_def.__rname__ + "-class")
except rhelp.HelpNotFoundError as hnf:
pass
if page_help is None:
try:
page_help = pack_help.fetch(cls_def.__rname__)
except rhelp.HelpNotFoundError as hnf:
pass
if page_help is None:
cls_dict['__doc__'] = 'Unable to fetch R documentation for the class'
else:
cls_dict['__doc__'] = ''.join(page_help.to_docstring())
for slt_name in cls_def.slots:
#FIXME: sanity check on the slot name
try:
slt_name = cls_attr_translation[slt_name]
except KeyError as ke:
# no translation: abort
pass
#FIXME: isolate the slot documentation and have it here
cls_dict[slt_name] = property(lambda self: self.do_slot(slt_name),
None, None,
None)
# Now tackle the methods
all_generics = methods_env['getGenerics']()
findmethods = methods_env['findMethods']
# does not seem elegant, but there is probably nothing else to do
# than loop across all generics
r_cls_rname = StrSexpVector((cls_rname, ))
for funcname in all_generics:
all_methods = findmethods(StrSexpVector((funcname, )),
classes = r_cls_rname)
# skip if no methods (issue #301). R's findMethods() result
# does not have an attribute "names" if of length zero.
if len(all_methods) == 0:
continue
# all_methods contains all method/signature pairs
# having the class we are considering somewhere in the signature
# (the R/S4 systems allows multiple dispatch)
for name, meth in zip(all_methods.do_slot("names"), all_methods):
# R/S4 is storing each method/signature as a string,
# with the argument type separated by the character '#'
# We will re-use that name for the Python name
# (no multiple dispatch in python, the method name
# will not be enough), replacing the '#'s with '__'s.
signature = name.split("#")
meth_name = '__'.join(signature)
# function names ending with '<-' indicate that the function
# is a setter of some sort. We reflect that by adding a 'set_'
# prefix to the Python name (and of course remove the suffix '<-').
if funcname.endswith('<-'):
meth_name = 'set_' + funcname[:-2] + '__' + meth_name
else:
meth_name = funcname + '__' + meth_name
# finally replace remaining '.'s in the Python name with '_'s
meth_name = meth_name.replace('.', '_')
#FIXME: sanity check on the function name
try:
meth_name = cls_meth_translation[meth_name]
except KeyError as ke:
# no translation: abort
pass
#FIXME: isolate the slot documentation and have it here
if meth_name in cls_dict:
raise Error("Duplicated attribute/method name.")
cls_dict[meth_name] = meth
return type.__new__(mcs, name, bases, cls_dict)
def test_repr(self):
base_help = rh.Package('base')
assert isinstance(repr(base_help), str)
def testInit(self):
base_help = rh.Package('base')
p = base_help.fetch('print')
self.assertEqual('title', tuple(p.sections.keys())[0])
def testInit(self):
base_help = rh.Package('base')
self.assertEqual('base', base_help.name)
