def importr(packname, newname = None, verbose = False):
""" Wrapper around rpy2.robjects.packages.importr,
adding the following feature(s):
- package instance added to the pseudo-module 'packages'
"""
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
return packinstance
def importr(packname, newname = None, verbose = False):
""" Wrapper around rpy2.robjects.packages.importr,
adding the following feature(s):
- package instance added to the pseudo-module 'packages'
"""
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
return packinstance
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, hnfe:
# No R documentation could be found for the object
if verbose:
print('Pydoc generator: no help for "%s"' %(obj_name, ))
continue
except AttributeError, ae:
# No __rname__ for the object
print('Pydoc generator: oddity with "%s"' %(obj_name, ))
continue
def importr(packname, newname=None):
assert isinstance(packname, str)
packinstance = _importr(packname)
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
return packinstance
def importr(packname, newname=None):
assert isinstance(packname, str)
packinstance = _importr(packname)
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
return packinstance
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 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
