import inspect
import os
import re
import textwrap
import typing
from typing import Union
import warnings
from collections import OrderedDict
from rpy2.robjects.robject import RObjectMixin
import rpy2.rinterface as rinterface
import rpy2.rinterface_lib.sexp
from rpy2.robjects import help
from rpy2.robjects import conversion
from rpy2.robjects.vectors import Vector
from rpy2.robjects.packages_utils import (default_symbol_r2python,
default_symbol_resolve,
_map_symbols,
_fix_map_symbols)
baseenv_ri = rinterface.baseenv
# Needed to avoid circular imports.
__formals = baseenv_ri.find('formals')
__args = baseenv_ri.find('args')
__is_null = baseenv_ri.find('is.null')
def _formals_fixed(func):
if func.typeof in (rpy2.rinterface_lib.sexp.RTYPES.SPECIALSXP,
rpy2.rinterface_lib.sexp.RTYPES.BUILTINSXP):
res = rpy2.rinterface_lib.sexp.NULL
else:
res = __formals(func)
if res is rpy2.rinterface_lib.sexp.NULL:
res = __formals(__args(func))
return res
# docstring_property and DocstringProperty
# from Bradley Froehle
# https://gist.github.com/bfroehle/4041015
def docstring_property(class_doc):
def wrapper(fget):
return DocstringProperty(class_doc, fget)
return wrapper
class DocstringProperty(object):
def __init__(self, class_doc, fget):
self.fget = fget
self.class_doc = class_doc
def __get__(self, obj, objtype=None):
if obj is None:
return self.class_doc
else:
return self.fget(obj)
def __set__(self, obj, value):
raise AttributeError("Cannot set the attribute")
def __delete__(self, obj):
raise AttributeError("Cannot delete the attribute")
def _repr_argval(obj):
""" Helper functions to display an R object in the docstring.
This a hack and will be hopefully replaced the extraction of
information from the R help system."""
try:
size = len(obj)
if size == 1:
if obj[0].rid == rinterface.MissingArg.rid:
# no default value
s = None
elif obj[0].rid == rinterface.NULL.rid:
s = 'rinterface.NULL'
else:
s = str(obj[0][0])
elif size > 1:
s = '(%s, ...)' % str(obj[0][0])
else:
s = str(obj)
except Exception:
s = str(obj)
return s
[docs]class Function(RObjectMixin, rinterface.SexpClosure):
""" Python representation of an R function.
"""
__local = baseenv_ri.find('local')
__call = baseenv_ri.find('call')
__assymbol = baseenv_ri.find('as.symbol')
__newenv = baseenv_ri.find('new.env')
_local_env = None
def __init__(self, *args, **kwargs):
super(Function, self).__init__(*args, **kwargs)
self._local_env = self.__newenv(
hash=rinterface.BoolSexpVector((True, ))
)
@docstring_property(__doc__)
def __doc__(self) -> str:
fm = _formals_fixed(self)
doc = list(['Python representation of an R function.',
'R arguments:', ''])
if fm is rinterface.NULL:
doc.append('<No information available>')
else:
for key, val in zip(fm.do_slot('names'), fm):
if key == '...':
val = 'R ellipsis (any number of parameters)'
doc.append('%s: %s' % (key, _repr_argval(val)))
return os.linesep.join(doc)
def __call__(self, *args, **kwargs):
cv = conversion.get_conversion()
new_args = [cv.py2rpy(a) for a in args]
new_kwargs = {}
for k, v in kwargs.items():
# TODO: shouldn't this be handled by the conversion itself ?
if isinstance(v, rinterface.Sexp):
new_kwargs[k] = v
else:
new_kwargs[k] = cv.py2rpy(v)
res = super(Function, self).__call__(*new_args, **new_kwargs)
res = cv.rpy2py(res)
return res
[docs] def rcall(
self,
keyvals,
environment: typing.Optional[rinterface.SexpEnvironment] = None
) -> rinterface.sexp.Sexp:
""" Wrapper around the parent method
rpy2.rinterface.SexpClosure.rcall(). """
res = super(Function, self).rcall(keyvals, environment=environment)
return res
[docs]class SignatureTranslatedFunction(Function):
""" Python representation of an R function, where
the names in named argument are translated to valid
argument names in Python. """
_prm_translate: Union[OrderedDict, dict] = {}
def __init__(self, sexp: rinterface.SexpClosure,
init_prm_translate=None,
on_conflict='warn',
symbol_r2python=default_symbol_r2python,
symbol_resolve=default_symbol_resolve):
super(SignatureTranslatedFunction, self).__init__(sexp)
if init_prm_translate is None:
self._prm_translate = OrderedDict()
else:
assert isinstance(init_prm_translate, dict)
self._prm_translate = init_prm_translate
formals = self.formals()
if formals.__sexp__._cdata != rinterface.NULL.__sexp__._cdata:
(symbol_mapping,
conflicts,
resolutions) = _map_symbols(
formals.names,
translation=self._prm_translate,
symbol_r2python=symbol_r2python,
symbol_resolve=symbol_resolve)
msg_prefix = ('Conflict when converting R symbols'
' in the function\'s signature:\n- ')
exception = ValueError
_fix_map_symbols(symbol_mapping,
conflicts,
on_conflict,
msg_prefix,
exception)
symbol_mapping.update(resolutions)
# TODO: Why was this done?
# reserved_pynames = set(dir(self))
self._prm_translate.update((k, v[0])
for k, v in symbol_mapping.items())
if hasattr(sexp, '__rname__'):
# TODO: mypy does not use the line above and trips on
# __rname__ being not always present.
self.__rname__ = sexp.__rname__ # type: ignore
def __call__(self, *args, **kwargs):
prm_translate = self._prm_translate
for k in tuple(kwargs.keys()):
r_k = prm_translate.get(k, None)
if r_k is not None:
v = kwargs.pop(k)
kwargs[r_k] = v
return (super(SignatureTranslatedFunction, self)
.__call__(*args, **kwargs))
pattern_link = re.compile(r'\\link\{(.+?)\}')
pattern_code = re.compile(r'\\code\{(.+?)\}')
pattern_samp = re.compile(r'\\samp\{(.+?)\}')
class DocumentedSTFunction(SignatureTranslatedFunction):
def __init__(self, sexp: rinterface.SexpClosure,
init_prm_translate=None,
packagename: typing.Optional[str] = None):
super(DocumentedSTFunction,
self).__init__(sexp,
init_prm_translate=init_prm_translate)
self.__rpackagename__ = packagename
@docstring_property(__doc__)
def __doc__(self):
package = help.Package(self.__rpackagename__)
page = package.fetch(self.__rname__)
doc = ['Wrapper around an R function.',
'',
'The docstring below is built from the R documentation.',
'']
if r'\description' in page.sections:
doc.append(
page.to_docstring(
section_names=[r'\description']
)
)
fm = _formals_fixed(self)
if fm is rpy2.rinterface_lib.sexp.NULL:
# If still NULL there is no argument.
names = tuple()
else:
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((')', ''))
####
doc.append('Args:')
for item in page.arguments():
description = ('%s ' % os.linesep).join(item.value)
doc.append(' '.join((' ', item.name, ': ', description)))
doc.append('')
if r'\details' in page.sections:
doc.append(
page.to_docstring(
section_names=[r'\details']
)
)
return os.linesep.join(doc)
# TODO: shouldn't this be in a more central place / or more general interest ?
_SCALAR_COMPAT_RTYPES = set(
getattr(rinterface.RTYPES, name).value
for name in ('STRSXP', 'INTSXP', 'REALSXP', 'LGLSXP', 'CPLXSXP')
)
def _map_default_value(value: rinterface.Sexp):
"""
Map default in the R signature.
Because of R's lazy evaluation some default might be unevaluated
expressions.
Args:
value:
"""
if value.__sexp__.typeof in _SCALAR_COMPAT_RTYPES:
# TODO: The dynamic check of typeof (to ensure that that
# the underlying R object is of a compatible type makes
# mypy trip. There is no way to check type outside of runtime.
# Code refactoring would be needed.
if len(value) == 1: # type: ignore
res = value[0] # type: ignore
else:
res = value
else:
res = value
return res
def map_signature(
r_func: SignatureTranslatedFunction,
is_method: bool = False,
map_default: typing.Optional[
typing.Callable[[rinterface.Sexp], typing.Any]
] = _map_default_value
) -> typing.Tuple[inspect.Signature, typing.Optional[int]]:
"""
Map the signature of an function to the signature of a Python function.
While mapping the signature, it will report the eventual presence of
an R ellipsis.
Args:
r_func (SignatureTranslatedFunction): an R function
is_method (bool): Whether the function should be treated as a method
(adds a `self` param to the signature if so).
map_default (function): Function to map default values in the Python
signature. No mapping to default values is done if None.
Returns:
A tuple (inspect.Signature, int or None).
"""
params = []
r_ellipsis = None
if is_method:
params.append(inspect.Parameter('self',
inspect.Parameter.POSITIONAL_ONLY))
r_params = r_func.formals()
rev_prm_transl = {v: k for k, v in r_func._prm_translate.items()}
if r_params.names is not rinterface.NULL:
for i, (name, default_orig) in enumerate(
zip(r_params.names, r_params)
):
if default_orig == '...':
r_ellipsis = i
warnings.warn('The R ellispsis is not yet well supported.')
transl_name = rev_prm_transl.get(name)
if isinstance(default_orig, Vector):
default_orig = default_orig[0]
if map_default and not rinterface.MissingArg.rsame(default_orig):
default_mapped = map_default(default_orig)
else:
default_mapped = inspect.Parameter.empty
else:
default_mapped = default_orig
prm = inspect.Parameter(
transl_name if transl_name else name,
inspect.Parameter.POSITIONAL_OR_KEYWORD,
default=default_mapped
)
params.append(prm)
return (inspect.Signature(params), r_ellipsis)
def wrap_docstring_default(
r_func: SignatureTranslatedFunction,
is_method: bool,
signature: inspect.Signature,
r_ellipsis: typing.Optional[int], *,
full_repr: bool = False
) -> str:
"""
Create a docstring that for a wrapped function.
Args:
r_func (SignatureTranslatedFunction): an R function
is_method (bool): Whether the function should be treated as a method
(a `self` parameter is added to the signature if so).
signature (inspect.Signature): A mapped signature for `r_func`
r_ellipsis (bool): Index of the parameter containing the R ellipsis
(`...`). None if the R ellipsis is not in the function signature.
full_repr (bool): Whether to have the full body of the R function in
the docstring dynamically generated.
Returns:
A string.
"""
docstring = []
docstring.append('This {} wraps the following R function.'
.format('method' if is_method else 'function'))
if r_ellipsis:
docstring.extend(
('',
textwrap.dedent(
"""The R ellipsis "..." present in the function's parameters
is mapped to a python iterable of (name, value) pairs (such as
it is returned by the `dict` method `items()` for example."""
),
'')
)
if full_repr:
docstring.append('\n{}'.format(r_func.r_repr()))
else:
r_repr = r_func.r_repr()
i = r_repr.find('\n{')
if i == -1:
docstring.append('\n{}'.format(r_func.r_repr()))
else:
docstring.append('\n{}\n{{\n ...\n}}'.format(r_repr[:i]))
return '\n'.join(docstring)
def wrap_r_function(
r_func: SignatureTranslatedFunction, name: str, *,
is_method: bool = False, full_repr: bool = False,
map_default: typing.Optional[
typing.Callable[[rinterface.Sexp],
typing.Any]
] = _map_default_value,
wrap_docstring: typing.Optional[
typing.Callable[[SignatureTranslatedFunction,
bool,
inspect.Signature,
typing.Optional[int]],
str]
] = wrap_docstring_default
) -> typing.Callable:
"""
Wrap an rpy2 function handle with a Python function of matching signature.
Args:
r_func (rpy2.robjects.functions.SignatureTranslatedFunction): The
function to be wrapped.
name (str): The name of the function.
is_method (bool): Whether the function should be treated as a method
(adds a `self` param to the signature if so).
map_default (function): Function to map default values in the Python
signature. No mapping to default values is done if None.
Returns:
A function wrapping an underlying R function.
"""
name = name.replace('.', '_')
signature, r_ellipsis = map_signature(r_func, is_method=is_method,
map_default=map_default)
if r_ellipsis:
def wrapped_func(*args, **kwargs):
new_args = (
list((None, x) for x in rinterface.args[:r_ellipsis]) +
list(args[r_ellipsis]) +
list((None, x)
for x in args[min(r_ellipsis+1, len(args)-1):]) +
list(kwargs.items()))
value = r_func.rcall(new_args)
return value
else:
def wrapped_func(*args, **kwargs):
value = r_func(*args, **kwargs)
return value
if wrap_docstring:
docstring = wrap_docstring(r_func, is_method, signature, r_ellipsis)
else:
docstring = 'This is a dynamically created wrapper for an R function.'
wrapped_func.__name__ = name
wrapped_func.__qualname__ = name
# TODO: Open issue in mypy about __signature.
# https://github.com/python/mypy/issues/5958
# Ignore the type check for now.
wrapped_func.__signature__ = signature # type: ignore
wrapped_func.__doc__ = docstring
return wrapped_func