Revision: 640
http://rpy.svn.sourceforge.net/rpy/?rev=640&view=rev
Author: lgautier
Date: 2008-08-24 13:47:05 +0000 (Sun, 24 Aug 2008)
Log Message:
-----------
rinterface:
- Sexp.named is not a getter (no longer a method)
- fixes for LANGSXP and EXPRSXP
rlike:
- TaggedList.sort() implemented
- new module 'functional'
- new module 'indexing'
Still misc. editing of the documentation
Modified Paths:
--------------
branches/rpy_nextgen/NEWS
branches/rpy_nextgen/doc/source/overview.rst
branches/rpy_nextgen/doc/source/rinterface.rst
branches/rpy_nextgen/doc/source/rlike.rst
branches/rpy_nextgen/rpy/rinterface/rinterface.c
branches/rpy_nextgen/rpy/rinterface/tests/__init__.py
branches/rpy_nextgen/rpy/rinterface/tests/test_EmbeddedR.py
branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
branches/rpy_nextgen/rpy/rlike/container.py
branches/rpy_nextgen/rpy/rlike/tests/__init__.py
branches/rpy_nextgen/rpy/rlike/tests/test_container.py
Added Paths:
-----------
branches/rpy_nextgen/rpy/rlike/functional.py
branches/rpy_nextgen/rpy/rlike/indexing.py
branches/rpy_nextgen/rpy/rlike/tests/test_functional.py
branches/rpy_nextgen/rpy/rlike/tests/test_indexing.py
Modified: branches/rpy_nextgen/NEWS
===================================================================
--- branches/rpy_nextgen/NEWS 2008-08-23 10:15:04 UTC (rev 639)
+++ branches/rpy_nextgen/NEWS 2008-08-24 13:47:05 UTC (rev 640)
@@ -13,12 +13,20 @@
- getter :attr:`__sexp__` to return an opaque C pointer to the underlying R
object
- method :meth:`rsame` to test if the underlying R objects for two
:class:`Sexp` are the same.
-
+
:mod:`rpy2.robjects`:
- R string vectors can now be built from Python unicode objects
+:mod:`rpy2.rlike`:
+- module :mod:`functional` with the functions :func:`tapply`, :func:`listify`,
:func:`iterify`.
+
+- module :mod:`indexing` with the function :func:`order`
+
+- method :meth:`TaggedList.sort` now implemented
+
+
Changes
-------
@@ -26,8 +34,14 @@
- :func:`initEmbeddedR` is only initializing if R is not started (no effect
otherwise, and no exception thrown anymore)
-- the method :meth:`typeof` was replaced by a Python `getter` :attr:`typeof`.
-
+- the method :meth:`Sexp.typeof` was replaced by a Python `getter`
:attr:`typeof`.
+
+- the method :meth:`Sexp.named` was replaced by a Python `getter`
:attr:`named`.
+
+- R objects of type LANGSXP are now one kind of vector (... but this may
change again)
+
+- R objects of type EXPRSXP are now handled as vectors (... but this may
change again)
+
:mod:`rpy2.robjects`:
- :class:`R` remains a singleton, but does not throw an exception when
multiple instances are requested
@@ -36,13 +50,13 @@
Bugs fixed
----------
-- Unable to compile on Python2.4 (definition of aliases to Python2.5-specific
were not where they should be).
+- unable to compile on Python2.4 (definition of aliases to Python2.5-specific
were not where they should be).
-- Overflow issues on Python 2.4/64 bits when indexing R vector with very large
integers.
+- overflow issues on Python 2.4/64 bits when indexing R vector with very large
integers.
-- Handling of negative indexes for :class:`SexpVector`'s :meth:`__getitem__`
and :meth:`__setitem__` was missing
+- handling of negative indexes for :class:`SexpVector`'s :meth:`__getitem__`
and :meth:`__setitem__` was missing
-- Trying to create an instance of :class:`SexpVector` before initializing R
raises a RuntimeException (used to segfault)
+- trying to create an instance of :class:`SexpVector` before initializing R
raises a RuntimeException (used to segfault)
- experimental method :meth:`enclos` was not properly exported
@@ -83,9 +97,9 @@
- R stack checking is disabled (no longer crashes when multithreading)
-- Fixed missing R_PreserveObject for vectors (causing R part of the object to
sometimes vanish during garbage collection)
+- fixed missing R_PreserveObject for vectors (causing R part of the object to
sometimes vanish during garbage collection)
-- Prevents calling an R function when R has been ended (raise
:class:`RuntimeException`).
+- prevents calling an R function when R has been ended (raise
:class:`RuntimeException`).
Release 2.0.0a1
@@ -133,7 +147,7 @@
:mod:`rpy2.robjects`:
-- Fixed string representation of R object on Microsoft Windows (using fifo,
not available on win32)
+- fixed string representation of R object on Microsoft Windows (using fifo,
not available on win32)
- :meth:`__getattr__` for :class:`RS4` is now using :meth:`ri2py`
@@ -144,4 +158,4 @@
Release 1.0a0
=============
-- First public release
\ No newline at end of file
+- first public release
\ No newline at end of file
Modified: branches/rpy_nextgen/doc/source/overview.rst
===================================================================
--- branches/rpy_nextgen/doc/source/overview.rst 2008-08-23 10:15:04 UTC
(rev 639)
+++ branches/rpy_nextgen/doc/source/overview.rst 2008-08-24 13:47:05 UTC
(rev 640)
@@ -42,8 +42,11 @@
Python version 2.4 or higher, and R-2.7.0 or higher are required.
This is developped with R-2.7.1 and Python-2.5.2.
-R-2.8.0-dev is sometimes tested, and it does seem to work well.
+R-2.8.0-dev is sometimes tested, and it does seem to play well with `rpy2`.
+Python-2.6.0-dev is sometimes tested as well, and it seems to pass the same
+unit tests Python-2.5 is passing.
+
Download
^^^^^^^^
Modified: branches/rpy_nextgen/doc/source/rinterface.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rinterface.rst 2008-08-23 10:15:04 UTC
(rev 639)
+++ branches/rpy_nextgen/doc/source/rinterface.rst 2008-08-24 13:47:05 UTC
(rev 640)
@@ -200,6 +200,12 @@
Opaque C pointer to the underlying R object
+ .. attribute:: named
+
+ `R` does not count references for its object. This method
+ returns the `NAMED` value (an integer).
+ See the R-extensions manual for further details.
+
.. attribute:: typeof
Internal R type for the underlying R object
@@ -211,9 +217,9 @@
.. method:: do_slot(name)
- R objects can be given attributes. In R the function
- *attr* lets one access attribute, while called :meth:`do_slot`
- in the C interface to R.
+ R objects can be given attributes. In R, the function
+ *attr* lets one access an object's attribute; it is
+ called :meth:`do_slot` in the C interface to R.
:param name: string
:rtype: Sexp (or Sexp-inheriting) object
@@ -226,13 +232,6 @@
[13, 2]
>>>
- .. method:: named()
-
- `R` does not count references for its object. This method
- returns the `NAMED` value (see the R-extensions manual).
-
- :rtype: integer
-
.. method:: rsame(sexp_obj)
Tell whether the underlying R object for sexp_obj is the same or not.
@@ -508,8 +507,9 @@
This is unfortunately not possible in a robust way: the dot character `.`
can be used for symbol names in R (like pretty much any character), and
-this can prevent an exact correspondance between `R` and `Python` names.
-`rpy` uses transformation functions that translates '.' to '_' and back,
+this can make an exact correspondance between `R` and `Python` names
+rather difficult.
+:mod:`rpy` uses transformation functions that translates '.' to '_' and back,
but this can lead to complications since '_' can also be used for R symbols.
There is a way to provide explict access to object in R packages, since
@@ -699,21 +699,46 @@
R types
-------
+Vector types
+^^^^^^^^^^^^
+
+:const:`CPLXSXP`
+ Complex
+
:const:`INTSXP`
- Integer
+ Integer.
+:const:`LGLSXP`
+ Boolean (logical in the R terminology)
+
:const:`REALSXP`
Numerical value (float / double)
-:const:`LGLSXP`
- Boolean (logical in the R terminology)
-
:const:`STRSXP`
String
+:const:`VECSXP`
+ List
+
+:const:`LANGSXP`
+ Language object.
+
+Other types
+^^^^^^^^^^^
+
+:const:`CLOSXP`
+ Function with an enclosure. Represented by
:class:`rpy2.rinterface.SexpClosure`.
+
:const:`ENVSXP`
- Environment
+ Environment. Represented by :class:`rpy2.rinterface.SexpEnvironment`.
-:const:`CPLXSXP`
- Complex
+:const:`S4SXP`
+ Instance of class S4. Represented by :class:`rpy2.rinterface.SexpS4`.
+
+Types you should not meet
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+:const:`PROMSXP`
+ Promise.
+
Modified: branches/rpy_nextgen/doc/source/rlike.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rlike.rst 2008-08-23 10:15:04 UTC (rev
639)
+++ branches/rpy_nextgen/doc/source/rlike.rst 2008-08-24 13:47:05 UTC (rev
640)
@@ -94,4 +94,23 @@
The Python docstring for the class is:
.. autoclass:: rpy2.rlike.container.TaggedList
- :members:
\ No newline at end of file
+ :members:
+
+Tools for working with sequences
+================================
+
+.. autofunction:: rpy2.rlike.functional.tapply
+
+>>> import rpy2.rlike.functional as rlf
+>>> rlf.tapply((1,2,3), ('a', 'b', 'a'), sum)
+[('a', 4), ('b', 2)]
+
+
+Indexing
+========
+
+.. function:: rpy2.rlike.indexing.order
+
+>>> import rpy2.rlike.indexing as rli
+>>> rli.order(('a', 'c', 'b'))
+[0, 2, 1]
Modified: branches/rpy_nextgen/rpy/rinterface/rinterface.c
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/rinterface.c 2008-08-23 10:15:04 UTC
(rev 639)
+++ branches/rpy_nextgen/rpy/rinterface/rinterface.c 2008-08-24 13:47:05 UTC
(rev 640)
@@ -547,7 +547,7 @@
":rtype: instance of type or subtype
:class:`rpy2.rinterface.Sexp`");
static PyObject*
-Sexp_named(PyObject *self)
+Sexp_named_get(PyObject *self)
{
SEXP sexp = RPY_SEXP(((PySexpObject*)self));
if (! sexp) {
@@ -558,7 +558,7 @@
return PyInt_FromLong((long)res);
}
PyDoc_STRVAR(Sexp_named_doc,
-"Return the integer code for the R object reference-pseudo counting.\n\
+"Integer code for the R object reference-pseudo counting.\n\
This method corresponds to the macro NAMED.\n\
See the R-extensions manual for further details.");
@@ -613,13 +613,15 @@
Sexp_do_slot_doc},
{"rsame", (PyCFunction)Sexp_rsame, METH_O,
Sexp_rsame_doc},
- {"named", (PyCFunction)Sexp_named, METH_NOARGS,
- Sexp_named_doc},
{NULL, NULL} /* sentinel */
};
static PyGetSetDef Sexp_getsets[] = {
+ {"named",
+ (getter)Sexp_named_get,
+ (setter)0,
+ Sexp_named_doc},
{"typeof",
(getter)Sexp_typeof_get,
(setter)0,
@@ -1332,6 +1334,7 @@
int vi;
Rcomplex vc;
const char *vs;
+ SEXP tmp, sexp_item; /* needed by LANGSXP */
i_R = (R_len_t)i;
switch (TYPEOF(*sexp)) {
case REALSXP:
@@ -1359,8 +1362,16 @@
/* vs = (CHAR(*sexp)[i_R]); */
/* res = PyString_FromStringAndSize(vs, 1); */
case VECSXP:
- res = (PyObject *)newPySexpObject(VECTOR_ELT(*sexp, i_R));
+ case EXPRSXP:
+ sexp_item = VECTOR_ELT(*sexp, i_R);
+ res = (PyObject *)newPySexpObject(sexp_item);
break;
+ case LANGSXP:
+ tmp = nthcdr(*sexp, i_R);
+ SETCAR(sexp_item, CAR(tmp));
+ SET_TAG(sexp_item, TAG(tmp));
+ res = (PyObject *)newPySexpObject(sexp_item);
+ break;
default:
PyErr_Format(PyExc_ValueError, "Cannot handle type %d",
TYPEOF(*sexp));
@@ -2041,6 +2052,8 @@
case LGLSXP:
case CPLXSXP:
case VECSXP:
+ case LANGSXP:
+ case EXPRSXP:
case STRSXP:
object = (PySexpObject *)Sexp_new(&VectorSexp_Type, Py_None, Py_None);
break;
@@ -2050,9 +2063,6 @@
case S4SXP:
object = (PySexpObject *)Sexp_new(&S4Sexp_Type, Py_None, Py_None);
break;
- case LANGSXP:
- object = (PySexpObject *)Sexp_new(&LangSexp_Type, Py_None, Py_None);
- break;
default:
object = (PySexpObject *)Sexp_new(&Sexp_Type, Py_None, Py_None);
break;
Modified: branches/rpy_nextgen/rpy/rinterface/tests/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/tests/__init__.py 2008-08-23
10:15:04 UTC (rev 639)
+++ branches/rpy_nextgen/rpy/rinterface/tests/__init__.py 2008-08-24
13:47:05 UTC (rev 640)
@@ -5,6 +5,7 @@
import test_Sexp
import test_SexpClosure
import test_SexpVectorNumeric
+
import test_EmbeddedR
#import test_EmbeddedR_multithreaded
Modified: branches/rpy_nextgen/rpy/rinterface/tests/test_EmbeddedR.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/tests/test_EmbeddedR.py 2008-08-23
10:15:04 UTC (rev 639)
+++ branches/rpy_nextgen/rpy/rinterface/tests/test_EmbeddedR.py 2008-08-24
13:47:05 UTC (rev 640)
@@ -24,7 +24,7 @@
self.assertEquals(yes.strip(), res[0])
rinterface.setReadConsole(rinterface.consoleRead)
-#FIXME: end and initializing again causes currently a lot a trouble...
+#FIXME: end and initialize again causes currently a lot a trouble...
def testCallErrorWhenEndedR(self):
self.assertTrue(False) # worked when tested, but calling endEmbeddedR
causes trouble
t = rinterface.baseNameSpaceEnv['date']
@@ -37,7 +37,8 @@
def testObjectDispatchLang(self):
formula = rinterface.globalEnv.get('formula')
obj = formula(rinterface.StrSexpVector(['y ~ x', ]))
- self.assertTrue(isinstance(obj, rinterface.SexpLang))
+ self.assertTrue(isinstance(obj, rinterface.SexpVector))
+ self.assertEquals(rinterface.LANGSXP, obj.typeof)
def testObjectDispatchVector(self):
letters = rinterface.globalEnv.get('letters')
Modified: branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-08-23 10:15:04 UTC (rev 639)
+++ branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-08-24 13:47:05 UTC (rev 640)
@@ -147,6 +147,21 @@
letters_R = ri.globalEnv.get("letters")
self.assertEquals('z', letters_R[-1])
+ def testGetItemLang(self):
+ formula = ri.baseNameSpaceEnv.get('formula')
+ f = formula(ri.StrSexpVector(['y ~ x', ]))
+ y = f[0]
+ self.assertEquals(ri.LANGSXP, y.typeof)
+ self.assertEquals(1, len(y))
+
+ def testGetItemExpression(self):
+ expression = ri.baseNameSpaceEnv.get('expression')
+ e = expression(ri.StrSexpVector(['a', ]),
+ ri.StrSexpVector(['b', ]))
+ y = e[0]
+ self.assertEquals(ri.STRSXP, y.typeof)
+
+
def testGetItemNegativeOutOfBound(self):
letters_R = ri.globalEnv.get("letters")
self.assertRaises(IndexError, letters_R.__getitem__,
Modified: branches/rpy_nextgen/rpy/rlike/container.py
===================================================================
--- branches/rpy_nextgen/rpy/rlike/container.py 2008-08-23 10:15:04 UTC (rev
639)
+++ branches/rpy_nextgen/rpy/rlike/container.py 2008-08-24 13:47:05 UTC (rev
640)
@@ -1,4 +1,5 @@
import itertools
+import rpy2.rlike.indexing as rli
class ArgsDict(dict):
""" Implements the Ordered Dict API defined in PEP 372.
@@ -264,11 +265,15 @@
super(TaggedList, self).reverse()
self.__tags.reverse()
- def sort(self):
- #FIXME: implement
- raise Exception("Not yet implemented.")
+ def sort(self, reverse = False):
+ """
+ Sort in place
+ """
+ o = rli.order(self, reverse = reverse)
+ super(TaggedList, self).sort(reverse = reverse)
+ self.__tags = [self.__tags[i] for i in o]
-
+
def tags(self):
"""
Return a tuple of all tags
@@ -289,3 +294,4 @@
"""
self.__tags[i] = t
+
Added: branches/rpy_nextgen/rpy/rlike/functional.py
===================================================================
--- branches/rpy_nextgen/rpy/rlike/functional.py
(rev 0)
+++ branches/rpy_nextgen/rpy/rlike/functional.py 2008-08-24 13:47:05 UTC
(rev 640)
@@ -0,0 +1,44 @@
+import itertools
+
+
+def tapply(seq, tag, fun):
+ """ Apply the function `fun` to the items in `seq`,
+ grouped by the tags defined in `tag`.
+
+ :param seq: sequence
+ :param tag: any sequence of tags
+ :param fun: function
+ :rtype: list
+ """
+
+ if len(seq) != len(tag):
+ raise ValueError("seq and tag should have the same length.")
+
+ tag_grp = {}
+ for i, t in enumerate(tag):
+ try:
+ tag_grp[t].append(i)
+ except LookupError, le:
+ tag_grp[t] = [i, ]
+
+ res = [(tag, fun([seq[i] for i in ti])) for tag, ti in tag_grp.items()]
+ return res
+
+
+def listify(fun):
+ """ Decorator to make a function apply
+ to each item in a sequence, and return a list. """
+ def f(seq):
+ res = [fun(x) for x in seq]
+ return res
+ return f
+
+def iterify(fun):
+ """ Decorator to make a function apply
+ to each item in a sequence, and return an iterator. """
+ def f(seq):
+ for x in seq:
+ yield fun(x)
+ return f
+
+
Property changes on: branches/rpy_nextgen/rpy/rlike/functional.py
___________________________________________________________________
Added: svn:eol-style
+ native
Added: branches/rpy_nextgen/rpy/rlike/indexing.py
===================================================================
--- branches/rpy_nextgen/rpy/rlike/indexing.py (rev 0)
+++ branches/rpy_nextgen/rpy/rlike/indexing.py 2008-08-24 13:47:05 UTC (rev
640)
@@ -0,0 +1,18 @@
+
+def order(sortable, reverse = False):
+ o = range(len(sortable))
+ def cmp(x, y):
+ x = sortable[x]
+ y = sortable[y]
+ if x < y:
+ return -1
+ elif x > y:
+ return +1
+ else:
+ return 0
+
+ o.sort(cmp = cmp, reverse = reverse)
+
+ return o
+
+
Property changes on: branches/rpy_nextgen/rpy/rlike/indexing.py
___________________________________________________________________
Added: svn:eol-style
+ native
Modified: branches/rpy_nextgen/rpy/rlike/tests/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/rlike/tests/__init__.py 2008-08-23 10:15:04 UTC
(rev 639)
+++ branches/rpy_nextgen/rpy/rlike/tests/__init__.py 2008-08-24 13:47:05 UTC
(rev 640)
@@ -1,11 +1,16 @@
import unittest
import test_container
+import test_functional
+import test_indexing
def suite():
suite_container = test_container.suite()
+ suite_functional = test_functional.suite()
+ suite_indexing = test_indexing.suite()
alltests = unittest.TestSuite([suite_container,
- ])
+ suite_functional,
+ suite_indexing])
return alltests
def main():
Modified: branches/rpy_nextgen/rpy/rlike/tests/test_container.py
===================================================================
--- branches/rpy_nextgen/rpy/rlike/tests/test_container.py 2008-08-23
10:15:04 UTC (rev 639)
+++ branches/rpy_nextgen/rpy/rlike/tests/test_container.py 2008-08-24
13:47:05 UTC (rev 640)
@@ -215,8 +215,14 @@
self.assertEquals(tuple(tl), (3, 2, 1))
def testsort(self):
- self.assertTrue(False) # not implemented (yet)
-
+ tn = ['a', 'c', 'b']
+ tv = [1,3,2]
+ tl = rlc.TaggedList(tv, tags = tn)
+ tl.sort()
+
+ self.assertEquals(tl.tags(), ('a', 'b', 'c'))
+ self.assertEquals(tuple(tl), (1, 2, 3))
+
def testtags(self):
tn = ['a', 'b', 'c']
tv = [1,2,3]
Added: branches/rpy_nextgen/rpy/rlike/tests/test_functional.py
===================================================================
--- branches/rpy_nextgen/rpy/rlike/tests/test_functional.py
(rev 0)
+++ branches/rpy_nextgen/rpy/rlike/tests/test_functional.py 2008-08-24
13:47:05 UTC (rev 640)
@@ -0,0 +1,44 @@
+import unittest
+import itertools
+import rpy2.rlike.functional as rlf
+
+class TapplyTestCase(unittest.TestCase):
+
+ def testSumByString(self):
+ seq = ( 1, 2, 3, 4, 5, 6)
+ tags = ('a', 'b', 'a', 'c', 'b', 'a')
+ expected = {'a': 1+3+6,
+ 'b': 2+5,
+ 'c': 4}
+ res = rlf.tapply(seq, tags, sum)
+ for k, v in res:
+ self.assertEquals(expected[k], v)
+
+class VectorizeTestCase(unittest.TestCase):
+
+ def simpleFunction(self, subject_fun):
+ def f(x):
+ return x ** 2
+ f_iter = subject_fun(f)
+
+ seq = (1, 2, 3)
+ res = f_iter(seq)
+
+ for va, vb in itertools.izip(seq, res):
+ self.assertEquals(va ** 2, vb)
+
+ def testIterify(self):
+ self.simpleFunction(rlf.iterify)
+
+ def testListify(self):
+ self.simpleFunction(rlf.listify)
+
+
+
+def suite():
+ suite = unittest.TestLoader().loadTestsFromTestCase(TapplyTestCase)
+
suite.addTest(unittest.TestLoader().loadTestsFromTestCase(VectorizeTestCase))
+ return suite
+
+if __name__ == '__main__':
+ unittest.main()
Property changes on: branches/rpy_nextgen/rpy/rlike/tests/test_functional.py
___________________________________________________________________
Added: svn:eol-style
+ native
Added: branches/rpy_nextgen/rpy/rlike/tests/test_indexing.py
===================================================================
--- branches/rpy_nextgen/rpy/rlike/tests/test_indexing.py
(rev 0)
+++ branches/rpy_nextgen/rpy/rlike/tests/test_indexing.py 2008-08-24
13:47:05 UTC (rev 640)
@@ -0,0 +1,21 @@
+import unittest
+import itertools
+import rpy2.rlike.indexing as rfi
+
+class OrderTestCase(unittest.TestCase):
+
+ def testOrder(self):
+ seq = ( 2, 1, 5, 3, 4)
+ expected = (1, 2, 3, 4, 5)
+ res = rfi.order(seq)
+ for va, vb in itertools.izip(expected, res):
+ self.assertEquals(va, seq[vb])
+
+
+def suite():
+ suite = unittest.TestLoader().loadTestsFromTestCase(OrderTestCase)
+
#suite.addTest(unittest.TestLoader().loadTestsFromTestCase(VectorizeTestCase))
+ return suite
+
+if __name__ == '__main__':
+ unittest.main()
Property changes on: branches/rpy_nextgen/rpy/rlike/tests/test_indexing.py
___________________________________________________________________
Added: svn:eol-style
+ native
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