import abc
import atexit
import typing
from rpy2.rinterface_lib import openrlib
import rpy2.rinterface_lib._rinterface_capi as _rinterface
import rpy2.rinterface_lib.embedded as embedded
import rpy2.rinterface_lib.conversion as conversion
import rpy2.rinterface_lib.memorymanagement as memorymanagement
import rpy2.rinterface_lib.na_values as na_values
import rpy2.rinterface_lib.bufferprotocol as bufferprotocol
import rpy2.rinterface_lib.sexp as sexp
Sexp = sexp.Sexp
StrSexpVector = sexp.StrSexpVector
CharSexp = sexp.CharSexp
SexpVector = sexp.SexpVector
RTYPES = sexp.RTYPES
unserialize = sexp.unserialize
_cdata_res_to_rinterface = conversion._cdata_res_to_rinterface
_evaluated_promise = _rinterface._evaluated_promise
R_NilValue = openrlib.rlib.R_NilValue
endr = embedded.endr
@_cdata_res_to_rinterface
def parse(text: str, num: int = -1):
"""Parse a string as R code.
:param:`text` A string with R code to parse.
:param:`num` The maximum number of lines to parse. If -1, no
limit is applied.
"""
if not isinstance(text, str):
raise TypeError('text must be a string.')
robj = StrSexpVector([text])
return _rinterface._parse(robj.__sexp__._cdata, num)
def evalr(source: str, maxlines: int = -1) -> sexp.Sexp:
"""Evaluate a string as R code.
Evaluate a string as R just as it would happen when writing
code in an R terminal.
:param:`text` A string to be evaluated as R code.
:param:`maxlines` The maximum number of lines to parse. If -1, no
limit is applied."""
res = parse(source, num=maxlines)
res = baseenv['eval'](res)
return res
def vector_memoryview(obj: sexp.SexpVector,
sizeof_str: str, cast_str: str) -> memoryview:
"""
- sizeof_str: type in a string to use with ffi.sizeof()
(for example "int")
- cast_str: type in a string to use with memoryview.cast()
(for example "i")
"""
b = openrlib.ffi.buffer(
obj._R_GET_PTR(obj.__sexp__._cdata),
openrlib.ffi.sizeof(sizeof_str) * len(obj))
shape = bufferprotocol.getshape(obj.__sexp__._cdata)
# One could have expected to only need builtin Python
# and do something like
# ```
# mv = memoryview(b).cast(cast_str, shape, order='F')
# ```
# but Python does not handle FORTRAN-ordered arrays without having
# to write C extensions. We have to use numpy.
# TODO: Having numpy a requirement just for this is a problem.
# TODO: numpy needed for memoryview
# (as long as https://bugs.python.org/issue34778 not resolved)
import numpy
a = numpy.frombuffer(b, dtype=cast_str).reshape(shape, order='F')
mv = memoryview(a)
return mv
class NULLType(sexp.Sexp, metaclass=na_values.Singleton):
"""A singleton class for R's NULL."""
def __init__(self):
embedded.assert_isready()
super().__init__(
sexp.Sexp(
_rinterface.UnmanagedSexpCapsule(
openrlib.rlib.R_NilValue
)
)
)
def __bool__(self) -> bool:
"""This is always False."""
return False
@property
def __sexp__(self) -> _rinterface.SexpCapsule:
return self._sexpobject
@property
def rid(self) -> int:
return self._sexpobject.rid
class _MissingArgType(sexp.Sexp, metaclass=na_values.Singleton):
def __init__(self):
embedded.assert_isready()
super().__init__(
sexp.Sexp(
_rinterface.UnmanagedSexpCapsule(
openrlib.rlib.R_MissingArg
)
)
)
def __bool__(self) -> bool:
"""This is always False."""
return False
@property
def __sexp__(self) -> _rinterface.SexpCapsule:
return self._sexpobject
class SexpSymbol(sexp.Sexp):
"""An unevaluated R symbol."""
def __init__(self, obj):
if isinstance(obj, Sexp) or isinstance(obj, _rinterface.SexpCapsule):
super().__init__(obj)
elif isinstance(obj, str):
name_cdata = _rinterface.ffi.new('char []', obj.encode('utf-8'))
sexp = _rinterface.SexpCapsule(
openrlib.rlib.Rf_install(name_cdata))
super().__init__(sexp)
else:
raise TypeError(
'The constructor must be called '
'with that is an instance of rpy2.rinterface.sexp.Sexp '
'or an instance of rpy2.rinterface._rinterface.SexpCapsule')
def __str__(self) -> str:
return conversion._cchar_to_str(
openrlib._STRING_VALUE(
self._sexpobject._cdata
)
)
class SexpEnvironment(sexp.Sexp):
"""Proxy for an R "environment" object.
An R "environment" object can be thought of as a mix of a
mapping (like a `dict`) and a scope. To make it more "Pythonic",
both aspects are kept separate and the method `__getitem__` will
get an item as it would for a Python `dict` while the method `find`
will get an item as if it was a scope.
As soon as R is initialized the following main environments become
available to the user:
- `globalenv`: The "workspace" for the current R process. This can
be thought of as when `__name__ == '__main__'` in Python.
- `baseenv`: The namespace of R's "base" package.
"""
@_cdata_res_to_rinterface
@_evaluated_promise
def find(self,
key: str,
wantfun: bool = False) -> sexp.Sexp:
"""Find an item, starting with this R environment.
Raises a `KeyError` if the key cannot be found.
This method is called `find` because it is somewhat different
from the method :meth:`get` in Python mappings such :class:`dict`.
This is looking for a key across enclosing environments, returning
the first key found."""
if not isinstance(key, str):
raise TypeError('The key must be a non-empty string.')
elif not len(key):
raise ValueError('The key must be a non-empty string.')
with memorymanagement.rmemory() as rmemory:
symbol = rmemory.protect(
openrlib.rlib.Rf_install(conversion._str_to_cchar(key))
)
if wantfun:
# One would expect this to be like
# res = _rinterface._findfun(symbol, self.__sexp__._cdata)
# but R's findfun will segfault if the symbol is not in
# the environment. :/
rho = self
while rho.rid != emptyenv.rid:
res = _rinterface._findVarInFrame(symbol,
rho.__sexp__._cdata)
if _rinterface._TYPEOF(res) in (openrlib.rlib.CLOSXP,
openrlib.rlib.BUILTINSXP):
break
# TODO: move check of R_UnboundValue to _rinterface ?
res = openrlib.rlib.R_UnboundValue
rho = rho.enclos
else:
res = _rinterface._findvar(symbol, self.__sexp__._cdata)
# TODO: move check of R_UnboundValue to _rinterface ?
if res == openrlib.rlib.R_UnboundValue:
raise KeyError("'%s' not found" % key)
return res
@_cdata_res_to_rinterface
@_evaluated_promise
def __getitem__(self, key: str) -> typing.Any:
if not (isinstance(key, str) and len(key)):
raise ValueError('The key must be a non-empty string.')
with memorymanagement.rmemory() as rmemory:
symbol = rmemory.protect(
openrlib.rlib.Rf_install(conversion._str_to_cchar(key))
)
res = _rinterface._findVarInFrame(symbol, self.__sexp__._cdata)
# TODO: move check of R_UnboundValue to _rinterface
if res == openrlib.rlib.R_UnboundValue:
raise KeyError("'%s' not found" % key)
return res
def __setitem__(self, key: str, value) -> None:
# TODO: move body to _rinterface-level function
if not (isinstance(key, str) and len(key)):
raise ValueError('The key must be a non-empty string.')
if (self.__sexp__._cdata == openrlib.rlib.R_BaseEnv) or \
(self.__sexp__._cdata == openrlib.rlib.R_EmptyEnv):
raise ValueError('Cannot remove variables from the base or '
'empty environments.')
# TODO: call to Rf_duplicate needed ?
with memorymanagement.rmemory() as rmemory:
symbol = rmemory.protect(
openrlib.rlib.Rf_install(conversion._str_to_cchar(key))
)
cdata = rmemory.protect(conversion._get_cdata(value))
cdata_copy = rmemory.protect(
openrlib.rlib.Rf_duplicate(cdata)
)
openrlib.rlib.Rf_defineVar(symbol,
cdata_copy,
self.__sexp__._cdata)
def __len__(self) -> int:
with memorymanagement.rmemory() as rmemory:
symbols = rmemory.protect(
openrlib.rlib.R_lsInternal(self.__sexp__._cdata,
openrlib.rlib.TRUE)
)
n = openrlib.rlib.Rf_xlength(symbols)
return n
def __delitem__(self, key: str) -> None:
# Testing that key is a non-empty string is implicitly
# performed when checking that the key is in the environment.
if key not in self:
raise KeyError("'%s' not found" % key)
if self.__sexp__ == baseenv.__sexp__:
raise ValueError('Values from the R base environment '
'cannot be removed.')
# TODO: also check it is not R_EmpyEnv or R_BaseNamespace
if self.is_locked():
ValueError('Cannot remove an item from a locked '
'environment.')
with memorymanagement.rmemory() as rmemory:
key_cdata = rmemory.protect(
openrlib.rlib.Rf_mkString(conversion._str_to_cchar(key))
)
_rinterface._remove(key_cdata,
self.__sexp__._cdata,
openrlib.rlib.Rf_ScalarLogical(
openrlib.rlib.FALSE))
@_cdata_res_to_rinterface
def frame(self) -> 'typing.Union[NULLType, SexpEnvironment]':
"""Get the parent frame of the environment."""
return openrlib.rlib.FRAME(self.__sexp__._cdata)
@property
@_cdata_res_to_rinterface
def enclos(self) -> 'typing.Union[NULLType, SexpEnvironment]':
"""Get or set the enclosing environment."""
return openrlib.rlib.ENCLOS(self.__sexp__._cdata)
@enclos.setter
def enclos(self, value: 'SexpEnvironment') -> None:
assert isinstance(value, SexpEnvironment)
openrlib.rlib.SET_ENCLOS(self.__sexp__._cdata,
value.__sexp__.cdata)
def keys(self) -> typing.Generator[str, None, None]:
"""Generator over the keys (symbols) in the environment."""
with memorymanagement.rmemory() as rmemory:
symbols = rmemory.protect(
openrlib.rlib.R_lsInternal(self.__sexp__._cdata,
openrlib.rlib.TRUE)
)
n = openrlib.rlib.Rf_xlength(symbols)
res = []
for i in range(n):
res.append(_rinterface._string_getitem(symbols, i))
for e in res:
yield e
def __iter__(self) -> typing.Generator[str, None, None]:
"""See method `keys()`."""
return self.keys()
def is_locked(self) -> bool:
return openrlib.rlib.R_EnvironmentIsLocked(
self.__sexp__._cdata)
class SexpPromise(Sexp):
@_cdata_res_to_rinterface
def eval(self, env: typing.Optional[SexpEnvironment] = None) -> sexp.Sexp:
""""Evalute the R "promise".
:param:`env` The environment in which to evaluate the
promise.
"""
if not env:
env = embedded.globalenv
return openrlib.rlib.Rf_eval(self.__sexp__._cdata, env)
class NumpyArrayInterface(abc.ABC):
"""Numpy-specific API for accessing the content of a numpy array.
This interface implements version 3 of Numpy's `__array_interface__`
and is only available / possible for some of the R vectors."""
@property
def __array_interface__(self) -> dict:
"""Return an `__array_interface__` version 3.
Note that the pointer returned in the items 'data' corresponds to
a memory area under R's memory management and that it will become
invalid once the area once R frees the object. It is safer to keep
the rpy2 object proxying the R object alive for the duration the
pointer is used in Python / numpy."""
shape = bufferprotocol.getshape(self.__sexp__._cdata)
data = openrlib.ffi.buffer(self._R_GET_PTR(self.__sexp__._cdata))
strides = bufferprotocol.getstrides(self.__sexp__._cdata,
shape,
self._R_SIZEOF_ELT)
return {'shape': shape,
'typestr': self._NP_TYPESTR,
'strides': strides,
'data': data,
'version': 3}
[docs]class ByteSexpVector(SexpVector, NumpyArrayInterface):
"""Array of bytes.
This is the R equivalent to a Python :class:`bytesarray`.
"""
_R_TYPE = openrlib.rlib.RAWSXP
_R_SIZEOF_ELT = _rinterface.ffi.sizeof('char')
_NP_TYPESTR = '|u1'
_R_GET_PTR = staticmethod(openrlib.RAW)
@staticmethod
def _CAST_IN(x: typing.Any) -> int:
if isinstance(x, int):
if x > 255:
raise ValueError('byte must be in range(0, 256)')
res = x
elif isinstance(x, (bytes, bytearray)):
if len(x) != 1:
raise ValueError('byte must be a single character')
res = ord(x)
else:
raise ValueError('byte must be an integer [0, 255] or a '
'single byte character')
return res
@staticmethod
def _R_VECTOR_ELT(x, i: int) -> None:
return openrlib.RAW(x)[i]
@staticmethod
def _R_SET_VECTOR_ELT(x, i: int, val) -> None:
openrlib.RAW(x)[i] = val
def __getitem__(self, i: int) -> typing.Union[int, 'ByteSexpVector']:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
res = openrlib.RAW_ELT(cdata, i_c)
elif isinstance(i, slice):
res = type(self).from_iterable(
[openrlib.RAW_ELT(
cdata, i_c
) for i_c in range(*i.indices(len(self)))
]
)
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
return res
def __setitem__(self, i: int, value) -> None:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
openrlib.RAW(cdata)[i_c] = self._CAST_IN(value)
elif isinstance(i, slice):
for i_c, v in zip(range(*i.indices(len(self))), value):
if v > 255:
raise ValueError('byte must be in range(0, 256)')
openrlib.RAW(cdata)[i_c] = self._CAST_IN(v)
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
[docs]class BoolSexpVector(SexpVector, NumpyArrayInterface):
"""Array of booleans.
Note that R is internally storing booleans as integers to
allow an additional "NA" value to represent missingness."""
_R_TYPE = openrlib.rlib.LGLSXP
_R_SIZEOF_ELT = _rinterface.ffi.sizeof('Rboolean')
_NP_TYPESTR = '|i'
_R_VECTOR_ELT = openrlib.LOGICAL_ELT
_R_SET_VECTOR_ELT = openrlib.SET_LOGICAL_ELT
_R_GET_PTR = staticmethod(openrlib.LOGICAL)
@staticmethod
def _CAST_IN(x):
if x is None or x == openrlib.rlib.R_NaInt:
return NA_Logical
else:
return bool(x)
def __getitem__(self, i: int) -> typing.Union[typing.Optional[bool],
'BoolSexpVector']:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
elt = openrlib.LOGICAL_ELT(cdata, i_c)
res = na_values.NA_Logical if elt == NA_Logical else bool(elt)
elif isinstance(i, slice):
res = type(self).from_iterable(
[openrlib.LOGICAL_ELT(cdata, i_c)
for i_c in range(*i.indices(len(self)))]
)
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
return res
def __setitem__(self, i: int, value) -> None:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
openrlib.SET_LOGICAL_ELT(cdata, i_c,
int(value))
elif isinstance(i, slice):
for i_c, v in zip(range(*i.indices(len(self))), value):
openrlib.SET_LOGICAL_ELT(cdata, i_c,
int(v))
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
def memoryview(self) -> memoryview:
return vector_memoryview(self, 'int', 'i')
[docs]class IntSexpVector(SexpVector, NumpyArrayInterface):
_R_TYPE = openrlib.rlib.INTSXP
_R_SET_VECTOR_ELT = openrlib.SET_INTEGER_ELT
_R_VECTOR_ELT = openrlib.INTEGER_ELT
_R_SIZEOF_ELT = _rinterface.ffi.sizeof('int')
_NP_TYPESTR = '|i'
_R_GET_PTR = staticmethod(openrlib.INTEGER)
_CAST_IN = staticmethod(int)
def __getitem__(self, i: int) -> typing.Union[int, 'IntSexpVector']:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
res = openrlib.INTEGER_ELT(cdata, i_c)
if res == NA_Integer:
res = NA_Integer
elif isinstance(i, slice):
res = type(self).from_iterable(
[openrlib.INTEGER_ELT(
cdata, i_c
) for i_c in range(*i.indices(len(self)))]
)
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
return res
def __setitem__(self, i: int, value) -> None:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
openrlib.SET_INTEGER_ELT(cdata, i_c,
int(value))
elif isinstance(i, slice):
for i_c, v in zip(range(*i.indices(len(self))), value):
openrlib.SET_INTEGER_ELT(cdata, i_c,
int(v))
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
def memoryview(self) -> memoryview:
return vector_memoryview(self, 'int', 'i')
[docs]class FloatSexpVector(SexpVector, NumpyArrayInterface):
_R_TYPE = openrlib.rlib.REALSXP
_R_VECTOR_ELT = openrlib.REAL_ELT
_R_SET_VECTOR_ELT = openrlib.SET_REAL_ELT
_R_SIZEOF_ELT = _rinterface.ffi.sizeof('double')
_NP_TYPESTR = '|d'
_CAST_IN = staticmethod(float)
_R_GET_PTR = staticmethod(openrlib.REAL)
def __getitem__(self, i: int) -> typing.Union[float, 'FloatSexpVector']:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
res = openrlib.REAL_ELT(cdata, i_c)
elif isinstance(i, slice):
res = type(self).from_iterable(
[openrlib.REAL_ELT(
cdata, i_c) for i_c in range(*i.indices(len(self)))]
)
else:
raise TypeError('Indices must be integers or slices, not %s' %
type(i))
return res
def __setitem__(self, i: int, value) -> None:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
openrlib.SET_REAL_ELT(cdata, i_c,
float(value))
elif isinstance(i, slice):
for i_c, v in zip(range(*i.indices(len(self))), value):
openrlib.SET_REAL_ELT(cdata, i_c,
float(v))
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
def memoryview(self) -> memoryview:
return vector_memoryview(self, 'double', 'd')
[docs]class ComplexSexpVector(SexpVector):
_R_TYPE = openrlib.rlib.CPLXSXP
_R_GET_PTR = staticmethod(openrlib.COMPLEX)
_R_SIZEOF_ELT = _rinterface.ffi.sizeof('Rcomplex')
@staticmethod
def _R_VECTOR_ELT(x, i):
return openrlib.COMPLEX(x)[i]
@staticmethod
def _R_SET_VECTOR_ELT(x, i, v):
openrlib.COMPLEX(x).__setitem__(i, v)
@staticmethod
def _CAST_IN(x):
if isinstance(x, complex):
res = (x.real, x.imag)
else:
try:
res = (x.r, x.i)
except AttributeError:
raise TypeError(
'Unable to turn value into an R complex number.'
)
return res
def __getitem__(self,
i: int) -> typing.Union[complex, 'ComplexSexpVector']:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
_ = openrlib.COMPLEX_ELT(cdata, i_c)
res = complex(_.r, _.i)
elif isinstance(i, slice):
res = type(self).from_iterable(
[openrlib.COMPLEX_ELT(
cdata, i_c) for i_c in range(*i.indices(len(self)))]
)
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
return res
def __setitem__(self, i: int, value) -> None:
cdata = self.__sexp__._cdata
if isinstance(i, int):
i_c = _rinterface._python_index_to_c(cdata, i)
openrlib.COMPLEX(cdata)[i_c] = self._CAST_IN(value)
elif isinstance(i, slice):
for i_c, v in zip(range(*i.indices(len(self))), value):
openrlib.COMPLEX(cdata)[i_c] = self._CAST_IN(v)
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
[docs]class ListSexpVector(SexpVector):
"""R list.
An R list an R vector (array) that is similar to a Python list in
the sense that items in the list can be of any type, whereas most
other R vectors are homogeneous (all items are of the same type).
"""
_R_TYPE = openrlib.rlib.VECSXP
_R_GET_PTR = staticmethod(openrlib._VECTOR_PTR)
_R_SIZEOF_ELT = None
_R_VECTOR_ELT = openrlib.rlib.VECTOR_ELT
_R_SET_VECTOR_ELT = openrlib.rlib.SET_VECTOR_ELT
_CAST_IN = staticmethod(conversion._get_cdata)
[docs]class PairlistSexpVector(SexpVector):
"""R pairlist.
A R pairlist is rarely used outside of R's internal libraries and
a relatively small number of use cases. It is essentially a LISP-like
list of (name, value) pairs.
"""
_R_TYPE = openrlib.rlib.LISTSXP
_R_GET_PTR = None
_R_SIZEOF_ELT = None
_R_VECTOR_ELT = None
_R_SET_VECTOR_ELT = None
_CAST_IN = staticmethod(conversion._get_cdata)
def __getitem__(self, i: int) -> Sexp:
cdata = self.__sexp__._cdata
rlib = openrlib.rlib
if isinstance(i, int):
# R-exts says that it is converted to a VECSXP when subsetted.
i_c = _rinterface._python_index_to_c(cdata, i)
item_cdata = rlib.Rf_nthcdr(cdata, i_c)
with memorymanagement.rmemory() as rmemory:
res_cdata = rmemory.protect(
rlib.Rf_allocVector(RTYPES.VECSXP, 1))
rlib.SET_VECTOR_ELT(
res_cdata,
0,
rlib.CAR(
item_cdata
))
res_name = rmemory.protect(
rlib.Rf_allocVector(RTYPES.STRSXP, 1))
rlib.SET_STRING_ELT(
res_name,
0,
rlib.PRINTNAME(rlib.TAG(item_cdata)))
rlib.Rf_namesgets(res_cdata, res_name)
res = conversion._cdata_to_rinterface(res_cdata)
elif isinstance(i, slice):
iter_indices = range(*i.indices(len(self)))
n = len(iter_indices)
with memorymanagement.rmemory() as rmemory:
res_cdata = rmemory.protect(
rlib.Rf_allocVector(
self._R_TYPE, n)
)
iter_res_cdata = res_cdata
prev_i = 0
lst_cdata = self.__sexp__._cdata
for i in iter_indices:
if i >= len(self):
raise IndexError('index out of range')
lst_cdata = rlib.Rf_nthcdr(lst_cdata, i - prev_i)
prev_i = i
rlib.SETCAR(iter_res_cdata,
rlib.CAR(lst_cdata))
rlib.SET_TAG(iter_res_cdata,
rlib.TAG(lst_cdata))
iter_res_cdata = rlib.CDR(iter_res_cdata)
res = conversion._cdata_to_rinterface(res_cdata)
else:
raise TypeError(
'Indices must be integers or slices, not %s' % type(i))
return res
@classmethod
@_cdata_res_to_rinterface
def from_iterable(cls, iterable, cast_in=None):
raise NotImplementedError()
class ExprSexpVector(SexpVector):
_R_TYPE = openrlib.rlib.EXPRSXP
_R_GET_PTR = None
_CAST_IN = None
_R_SIZEOF_ELT = None
_R_VECTOR_ELT = openrlib.rlib.VECTOR_ELT
_R_SET_VECTOR_ELT = None
[docs]class LangSexpVector(SexpVector):
_R_TYPE = openrlib.rlib.LANGSXP
_R_GET_PTR = None
_CAST_IN = None
_R_SIZEOF_ELT = None
_R_VECTOR_ELT = None
_R_SET_VECTOR_ELT = None
@_cdata_res_to_rinterface
def __getitem__(self, i: int):
cdata = self.__sexp__._cdata
i_c = _rinterface._python_index_to_c(cdata, i)
return openrlib.rlib.CAR(
openrlib.rlib.Rf_nthcdr(cdata, i_c)
)
def __setitem__(self, i: int, value) -> None:
cdata = self.__sexp__._cdata
i_c = _rinterface._python_index_to_c(cdata, i)
openrlib.rlib.SETCAR(
openrlib.rlib.Rf_nthcdr(cdata, i_c),
value.__sexp__._cdata
)
class SexpClosure(Sexp):
@_cdata_res_to_rinterface
def __call__(self, *args, **kwargs) -> Sexp:
error_occured = _rinterface.ffi.new('int *', 0)
with memorymanagement.rmemory() as rmemory:
call_r = rmemory.protect(
_rinterface.build_rcall(self.__sexp__._cdata, args,
kwargs.items()))
res = rmemory.protect(
openrlib.rlib.R_tryEval(
call_r,
embedded.globalenv.__sexp__._cdata,
error_occured))
if error_occured[0]:
raise embedded.RRuntimeError(_rinterface._geterrmessage())
return res
@_cdata_res_to_rinterface
def rcall(self, keyvals, environment: SexpEnvironment):
"""Call/evaluate an R function.
Args:
- keyvals: a sequence of key/value (name/parameter) pairs. A
name/parameter that is None will indicated an unnamed parameter.
Like in R, keys/names do not have to be unique, partial matching
can be used, and named/unnamed parameters can occur at any position
in the sequence.
- environment: a R environment in which to evaluate the function.
"""
# TODO: check keyvals are pairs ?
assert isinstance(environment, SexpEnvironment)
error_occured = _rinterface.ffi.new('int *', 0)
with memorymanagement.rmemory() as rmemory:
call_r = rmemory.protect(
_rinterface.build_rcall(self.__sexp__._cdata, [],
keyvals))
res = rmemory.protect(
openrlib.rlib.R_tryEval(call_r,
environment.__sexp__._cdata,
error_occured))
if error_occured[0]:
raise embedded.RRuntimeError(_rinterface._geterrmessage())
return res
@property
@_cdata_res_to_rinterface
def closureenv(self) -> SexpEnvironment:
"""Closure of the R function."""
return openrlib.rlib.CLOENV(self.__sexp__._cdata)
[docs]class SexpS4(Sexp):
"""R "S4" object."""
pass
# TODO: clean up
def make_extptr(obj, tag, protected):
if protected is None:
cdata_protected = openrlib.rlib.R_NilValue
else:
try:
cdata_protected = protected.__sexp__._cdata
except AttributeError:
raise TypeError('Argument protected must inherit from %s' %
type(Sexp))
ptr = _rinterface.ffi.new_handle(obj)
with memorymanagement.rmemory() as rmemory:
cdata = rmemory.protect(
openrlib.rlib.R_MakeExternalPtr(
ptr,
tag,
cdata_protected))
openrlib.rlib.R_RegisterCFinalizer(
cdata,
_rinterface._capsule_finalizer)
res = _rinterface.SexpCapsuleWithPassenger(cdata, obj, ptr)
return res
[docs]class SexpExtPtr(Sexp):
TYPE_TAG = 'Python'
@classmethod
def from_pyobject(cls, func, tag: str = TYPE_TAG,
protected=None):
if not isinstance(tag, str):
raise TypeError('The tag must be a string.')
scaps = make_extptr(func,
conversion._str_to_charsxp(cls.TYPE_TAG),
protected)
res = cls(scaps)
if tag != cls.TYPE_TAG:
res.TYPE_TAG = tag
return res
# TODO: Only use rinterface-level ?
conversion._R_RPY2_MAP.update({
openrlib.rlib.NILSXP: NULLType,
openrlib.rlib.EXPRSXP: ExprSexpVector,
openrlib.rlib.LANGSXP: LangSexpVector,
openrlib.rlib.ENVSXP: SexpEnvironment,
openrlib.rlib.RAWSXP: ByteSexpVector,
openrlib.rlib.LGLSXP: BoolSexpVector,
openrlib.rlib.INTSXP: IntSexpVector,
openrlib.rlib.REALSXP: FloatSexpVector,
openrlib.rlib.CPLXSXP: ComplexSexpVector,
openrlib.rlib.STRSXP: StrSexpVector,
openrlib.rlib.VECSXP: ListSexpVector,
openrlib.rlib.LISTSXP: PairlistSexpVector,
openrlib.rlib.CLOSXP: SexpClosure,
openrlib.rlib.BUILTINSXP: SexpClosure,
openrlib.rlib.SPECIALSXP: SexpClosure,
openrlib.rlib.EXTPTRSXP: SexpExtPtr,
openrlib.rlib.SYMSXP: SexpSymbol,
openrlib.rlib.S4SXP: SexpS4
})
conversion._R_RPY2_DEFAULT_MAP = Sexp
conversion._PY_RPY2_MAP.update({
int: conversion._int_to_sexp,
float: conversion._float_to_sexp,
complex: conversion._complex_to_sexp
})
conversion._PY_R_MAP.update({
_rinterface.ffi.CData: False,
# integer
int: conversion._int_to_sexp,
na_values.NAIntegerType: conversion._int_to_sexp,
# float
float: conversion._float_to_sexp,
na_values.NARealType: conversion._float_to_sexp,
# boolean
bool: conversion._bool_to_sexp,
na_values.NALogicalType: conversion._bool_to_sexp,
# string
str: conversion._str_to_sexp,
sexp.CharSexp: None,
na_values.NACharacterType: None,
# complex
complex: conversion._complex_to_sexp,
na_values.NAComplexType: conversion._complex_to_sexp,
# None
type(None): lambda x: openrlib.rlib.R_NilValue})
def vector(iterable, rtype: RTYPES) -> SexpVector:
"""Create an R vector.
While the different types of R vectors all have their own class,
the creation of array in Python is often available through factory
function that accept the type of the array as a parameters. This
function is providing a similar functionality for R vectors."""
error = False
try:
cls = conversion._R_RPY2_MAP[rtype]
except KeyError:
error = True
if not error and not issubclass(cls, SexpVector):
error = True
if error:
raise ValueError(
'Unable to build a vector from type "%s"' % RTYPES(rtype))
return cls.from_iterable(iterable)
class RRuntimeWarning(RuntimeWarning):
pass
emptyenv = None
baseenv = None
globalenv = None
NULL = None
MissingArg = None
NA_Character = None
NA_Integer = None
NA_Logical = None
NA = None
NA_Real = None
NA_Complex = None
def initr_simple() -> int:
"""Initialize R's embedded C library."""
status = embedded._initr()
atexit.register(endr, 0)
_rinterface._register_external_symbols()
_post_initr_setup()
return status
def initr_checkenv():
# Force the internal initialization flag if there is an environment
# variable that indicates that R was alreay initialized in the current
# process.
status = None
if embedded.is_r_externally_initialized():
embedded.setinitialized()
else:
status = embedded._initr()
embedded.set_python_process_info()
_rinterface._register_external_symbols()
_post_initr_setup()
return status
initr = initr_checkenv
def _post_initr_setup():
embedded.emptyenv = SexpEnvironment(
_rinterface.SexpCapsule(openrlib.rlib.R_EmptyEnv)
)
global emptyenv
emptyenv = embedded.emptyenv
embedded.baseenv = SexpEnvironment(
_rinterface.SexpCapsule(openrlib.rlib.R_BaseEnv)
)
global baseenv
baseenv = embedded.baseenv
embedded.globalenv = SexpEnvironment(
_rinterface.SexpCapsule(openrlib.rlib.R_GlobalEnv)
)
global globalenv
globalenv = embedded.globalenv
global NULL
NULL = NULLType()
global MissingArg
MissingArg = _MissingArgType()
global NA_Character
na_values.NA_Character = na_values.NACharacterType()
NA_Character = na_values.NA_Character
global NA_Integer
na_values.NA_Integer = na_values.NAIntegerType(openrlib.rlib.R_NaInt)
NA_Integer = na_values.NA_Integer
global NA_Logical, NA
na_values.NA_Logical = na_values.NALogicalType(openrlib.rlib.R_NaInt)
NA_Logical = na_values.NA_Logical
NA = NA_Logical
global NA_Real
na_values.NA_Real = na_values.NARealType(openrlib.rlib.R_NaReal)
NA_Real = na_values.NA_Real
global NA_Complex
na_values.NA_Complex = na_values.NAComplexType(
_rinterface.ffi.new(
'Rcomplex *',
[openrlib.rlib.R_NaReal, openrlib.rlib.R_NaReal])
)
NA_Complex = na_values.NA_Complex
[docs]def rternalize(function: typing.Callable) -> SexpClosure:
""" Takes an arbitrary Python function and wrap it
in such a way that it can be called from the R side. """
assert callable(function)
rpy_fun = SexpExtPtr.from_pyobject(function)
# TODO: this is a hack. Find a better way.
template = parse("""
function(...) { .External(".Python", foo, ...);
}
""")
template[0][2][1][2] = rpy_fun
# TODO: use lower-level eval ?
res = baseenv['eval'](template)
# TODO: hack to prevent the nested function from having its
# refcount down to zero when returning
res.__nested_sexp__ = rpy_fun.__sexp__
return res
