Revision: 548
http://rpy.svn.sourceforge.net/rpy/?rev=548&view=rev
Author: lgautier
Date: 2008-06-07 00:05:04 -0700 (Sat, 07 Jun 2008)
Log Message:
-----------
robjects:
- changed class names (now upper-case after the R prefix;
e.g., RVector, RFunction, etc...)
- refactored the classes:
- attribute _sexp, constaining the rinterface.Sexp, is gone
- classes inherit from their rinterface counterpart
- a mixin class RObjectMixin provides common methods
Modified Paths:
--------------
branches/rpy_nextgen/rpy/robjects/__init__.py
branches/rpy_nextgen/rpy/robjects/tests/testRArray.py
branches/rpy_nextgen/rpy/robjects/tests/testREnvironment.py
branches/rpy_nextgen/rpy/robjects/tests/testRFunction.py
branches/rpy_nextgen/rpy/robjects/tests/testRObject.py
branches/rpy_nextgen/rpy/robjects/tests/testRVector.py
branches/rpy_nextgen/rpy/robjects/tests/testRobjects.py
Modified: branches/rpy_nextgen/rpy/robjects/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/__init__.py 2008-06-07 07:01:08 UTC
(rev 547)
+++ branches/rpy_nextgen/rpy/robjects/__init__.py 2008-06-07 07:05:04 UTC
(rev 548)
@@ -13,26 +13,28 @@
#FIXME: close everything when leaving (check RPy for that).
-def defaultRobjects2PyMapper(o):
- if isinstance(o, rinterface.SexpVector):
- res = Rvector(o)
+def default_ri2py(o):
+ if isinstance(o, RObject):
+ res = o
+ elif isinstance(o, rinterface.SexpVector):
+ res = RVector(o)
elif isinstance(o, rinterface.SexpClosure):
- res = Rfunction(o)
+ res = RFunction(o)
elif isinstance(o, rinterface.SexpEnvironment):
- res = Renvironment(o)
+ res = REnvironment(o)
elif isinstance(o, rinterface.SexpS4):
res = RS4(o)
else:
- res = Robject(o)
+ res = RObject(o)
return res
#FIXME: clean and nice mechanism to allow user-specified mapping function
#FIXME: better names for the functions
-mapperR2Py = defaultRobjects2PyMapper
+ri2py = default_ri2py
-def defaultPy2Rinterface(o):
- if isinstance(o, Robject):
- return o._sexp
+def default_py2ri(o):
+ if isinstance(o, RObject):
+ res = rinterface.Sexp(o)
if isinstance(o, rinterface.Sexp):
res = o
elif isinstance(o, array.array):
@@ -51,31 +53,30 @@
elif isinstance(o, str):
res = rinterface.SexpVector([o, ], rinterface.STRSXP)
elif isinstance(o, list):
- res = r.list(*[defaultPy2RobjectsMapper(x) for x in o])
+ res = r.list(*[ri2py(py2ri(x)) for x in o])
else:
raise(ValueError("Nothing can be done for this type at the moment."))
return res
-def defaultPy2RobjectsMapper(o):
- res = defaultPy2Rinterface(o)
- return mapperR2Py(res)
+py2ri = default_py2ri
-mapperPy2R = defaultPy2RobjectsMapper
+def default_py2ro(o):
+ res = default_py2ri(o)
+ return default_ri2py(res)
+py2ro = default_py2ro
+
+
def repr_robject(o):
s = r.deparse(o)
s = str.join(os.linesep, s)
return s
-class Robject(object):
+class RObjectMixin(object):
name = None
- _sexp = None
- def __init__(self, sexp, copy=True):
- self._sexp = rinterface.Sexp(sexp, copy=copy)
-
def __str__(self):
tmp = baseNameSpaceEnv["fifo"]("")
baseNameSpaceEnv["sink"](tmp)
@@ -89,36 +90,36 @@
def __repr__(self):
return repr_robject(self)
+ def typeof(self):
+ return super(rinterface.Sexp, self).typeof()
+
+ def do_slot(self, name):
+ return super(rinterface.Sexp, self).do_slot(name)
+
+ def rclass(self):
+ return baseNameSpaceEnv["class"](self)
+
+
+class RObject(rinterface.Sexp, RObjectMixin):
def __setattr__(self, name, value):
if name == '_sexp':
if not isinstance(value, rinterface.Sexp):
raise ValueError("_attr must contain an object " +\
"that inherits from rinterface.Sexp" +\
"(not from %s)" %type(value))
- super(Robject, self).__setattr__(name, value)
+ super(RObject, self).__setattr__(name, value)
+
- def getSexp(self):
- return self._sexp
- def typeof(self):
- return self._sexp.typeof()
-
- def do_slot(self, name):
- return self._sexp.do_slot(name)
-
- def rclass(self):
- return baseNameSpaceEnv["class"](self.getSexp())
-
-class Rvector(Robject):
+class RVector(rinterface.SexpVector, RObjectMixin):
""" R vector-like object. Items in those instances can
be accessed with the method "__getitem__" ("[" operator),
or with the method "subset"."""
def __init__(self, o):
if not isinstance(o, rinterface.SexpVector):
- o = mapperPy2R(o)
- o = o.getSexp()
- self._sexp = o
+ o = py2ri(o)
+ super(RVector, self).__init__(o)
def subset(self, *args, **kwargs):
@@ -134,73 +135,68 @@
#for a in args:
# if not isinstance(a, Rvector):
# raise(TypeError("Subset only take R vectors"))
- args = [mapperPy2R(x) for x in args]
+ args = [py2ro(x) for x in args]
for k, v in kwargs.itervalues():
- args[k] = mapperPy2R(v)
+ args[k] = py2ro(v)
res = r["["](*([self, ] + [x for x in args]), **kwargs)
return res
def __getitem__(self, i):
- res = self._sexp[i]
+ res = super(RVector, self).__getitem__(i)
if isinstance(res, rinterface.Sexp):
- res = mapperR2Py(res)
+ res = ri2py(res)
return res
- def __repr__(self):
- return repr_robject(self)
-
def __add__(self, x):
- res = r.get("+")(self.getSexp(), x)
+ res = r.get("+")(self, x)
return res
def __sub__(self, x):
- res = r.get("-")(self.getSexp(), x)
+ res = r.get("-")(self, x)
return res
def __mul__(self, x):
- res = r.get("*")(self.getSexp(), x)
+ res = r.get("*")(self, x)
return res
def __div__(self, x):
- res = r.get("/")(self.getSexp(), x)
+ res = r.get("/")(self, x)
return res
def __divmod__(self, x):
- res = r.get("%%")(self.getSexp(), x)
+ res = r.get("%%")(self, x)
return res
def __or__(self, x):
- res = r.get("|")(self.getSexp(), x)
+ res = r.get("|")(self, x)
return res
def __and__(self, x):
- res = r.get("&")(self.getSexp(), x)
+ res = r.get("&")(self, x)
return res
- def __len__(self):
- return len(self.getSexp())
-
def getNames(self):
- res = r.names(self.getSexp())
+ res = r.names(self)
return res
-class RArray(Rvector):
+class RArray(RVector):
""" An R array """
def __init__(self, o):
super(RArray, self).__init__(o)
- if not r["is.array"](self.getSexp())[0]:
+ #import pdb; pdb.set_trace()
+ if not r["is.array"](self)[0]:
raise(TypeError("The object must be reflecting an R array"))
def __getattr__(self, name):
if name == 'dim':
- res = r.dim(self.getSexp())
- res = mapperR2Py(res)
+ res = r.dim(self)
+ res = ri2py(res)
return res
def __setattr__(self, name, value):
if name == 'dim':
- value = mapperPy2R
+ value = py2ro(value)
res = r["dim<-"](value)
@@ -215,67 +211,53 @@
""" Number of columns """
return self.dim[1]
-class DataFrame(Rvector):
+class DataFrame(RVector):
#FIXME: not implemented
def __init__(self, o):
- if not isinstance(o, rinterface.SexpVector):
- o = mapperPy2R(o)
- o = o.getSexp()
- self._sexp = o
+ raise Exception("not implemented.")
-class Rfunction(Robject):
+class RFunction(rinterface.SexpClosure, RObjectMixin):
""" An R function (aka "closure").
"""
- def __init__(self, sexp):
- # arbirtary python functions for v-2.1
- self._sexp = rinterface.SexpClosure(sexp)
def __call__(self, *args, **kwargs):
- new_args = [mapperPy2R(a).getSexp() for a in args]
+ new_args = [py2ri(a) for a in args]
new_kwargs = {}
for k, v in kwargs.iteritems():
- new_kwargs[k] = mapperPy2R(v).getSexp()
- res = self.getSexp()(*new_args, **new_kwargs)
- res = mapperR2Py(res)
+ new_kwargs[k] = py2ri(v)
+ res = super(RFunction, self).__call__(*new_args, **new_kwargs)
+ res = ri2py(res)
return res
#def getSexp(self):
# return super(rinterface.SexpClosure, self).__init__(self)
-class Renvironment(Robject):
+class REnvironment(rinterface.SexpEnvironment, RObjectMixin):
""" An R environement. """
def __init__(self, o=None):
if o is None:
o =
rinterface.baseNameSpaceEnv["new.env"](hash=rinterface.SexpVector([True, ],
rinterface.LGLSXP))
- self._sexp = rinterface.SexpEnvironment(o)
+ super(REnvironment, self).__init__(o)
def __getitem__(self, item):
- res = self._sexp[item]
- res = mapperR2Py(res)
+ res = super(REnvironment, self).__getitem__(item)
+ res = ri2py(res)
return res
def __setitem__(self, item, value):
- robj = mapperPy2R(value)
- self._sexp[item] = robj.getSexp()
+ robj = py2ro(value)
+ super(REnvironment, self).__setitem__(item, robj)
- def __iter__(self):
- return iter(self._sexp)
-
def get(self, item):
- res = self.getSexp().get(item)
- res = mapperR2Py(res)
+ res = super(REnvironment, self).get(item)
+ res = ri2py(res)
return res
-class RS4(Robject):
- def __init__(self, o):
- if (isinstance(o, rinterface.SexpS4)):
- self._sexp = o
- else:
- raise(ValueError("Cannot instantiate"))
+class RS4(rinterface.SexpS4, RObjectMixin):
def __getattr__(self, attr):
res = r.get("@")(self, attr)
@@ -297,7 +279,7 @@
def __getitem__(self, item):
res = rinterface.globalEnv.get(item)
- res = mapperR2Py(res)
+ res = ri2py(res)
return res
#FIXME: check that this is properly working
@@ -317,6 +299,6 @@
r = R()
-globalEnv = mapperR2Py(rinterface.globalEnv)
-baseNameSpaceEnv = mapperR2Py(rinterface.baseNameSpaceEnv)
+globalEnv = ri2py(rinterface.globalEnv)
+baseNameSpaceEnv = ri2py(rinterface.baseNameSpaceEnv)
Modified: branches/rpy_nextgen/rpy/robjects/tests/testRArray.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testRArray.py 2008-06-07
07:01:08 UTC (rev 547)
+++ branches/rpy_nextgen/rpy/robjects/tests/testRArray.py 2008-06-07
07:05:04 UTC (rev 548)
@@ -10,7 +10,8 @@
self.assertRaises(TypeError, robjects.RArray, letters)
m = robjects.r.matrix(1, nrow=5, ncol=3)
a = robjects.RArray(m)
-
+ # only tests that it runs.
+
def testDim(self):
m = robjects.r.matrix(1, nrow=5, ncol=3)
a = robjects.RArray(m)
Modified: branches/rpy_nextgen/rpy/robjects/tests/testREnvironment.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testREnvironment.py 2008-06-07
07:01:08 UTC (rev 547)
+++ branches/rpy_nextgen/rpy/robjects/tests/testREnvironment.py 2008-06-07
07:05:04 UTC (rev 548)
@@ -5,12 +5,12 @@
class REnvironmentTestCase(unittest.TestCase):
def testNew(self):
- env = robjects.Renvironment()
- self.assertEquals(rinterface.ENVSXP, env.getSexp().typeof())
- self.assertRaises(ValueError, robjects.Renvironment, 'a')
+ env = robjects.REnvironment()
+ self.assertEquals(rinterface.ENVSXP, env.typeof())
+ self.assertRaises(ValueError, robjects.REnvironment, 'a')
def testSetItem(self):
- env = robjects.Renvironment()
+ env = robjects.REnvironment()
env['a'] = 123
self.assertTrue('a' in env)
Modified: branches/rpy_nextgen/rpy/robjects/tests/testRFunction.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testRFunction.py 2008-06-07
07:01:08 UTC (rev 547)
+++ branches/rpy_nextgen/rpy/robjects/tests/testRFunction.py 2008-06-07
07:05:04 UTC (rev 548)
@@ -6,19 +6,19 @@
class RFunctionTestCase(unittest.TestCase):
def testNew(self):
identical = rinterface.baseNameSpaceEnv["identical"]
- self.assertRaises(ValueError, robjects.Rfunction, 'a')
+ self.assertRaises(ValueError, robjects.RFunction, 'a')
ri_f = rinterface.baseNameSpaceEnv.get('help')
- ro_f = robjects.Rfunction(ri_f)
+ ro_f = robjects.RFunction(ri_f)
- self.assertTrue(identical(ri_f, ro_f.getSexp()))
+ self.assertTrue(identical(ri_f, ro_f))
def testCall(self):
ri_f = rinterface.baseNameSpaceEnv.get('sum')
- ro_f = robjects.Rfunction(ri_f)
+ ro_f = robjects.RFunction(ri_f)
- ro_v = robjects.Rvector(array.array('i', [1,2,3]))
+ ro_v = robjects.RVector(array.array('i', [1,2,3]))
s = ro_f(ro_v)
Modified: branches/rpy_nextgen/rpy/robjects/tests/testRObject.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testRObject.py 2008-06-07
07:01:08 UTC (rev 547)
+++ branches/rpy_nextgen/rpy/robjects/tests/testRObject.py 2008-06-07
07:05:04 UTC (rev 548)
@@ -8,12 +8,12 @@
identical = rinterface.baseNameSpaceEnv["identical"]
py_a = array.array('i', [1,2,3])
- self.assertRaises(ValueError, robjects.Robject, py_a)
+ self.assertRaises(ValueError, robjects.RObject, py_a)
ri_v = rinterface.SexpVector(py_a, rinterface.INTSXP)
- ro_v = robjects.Robject(ri_v)
+ ro_v = robjects.RObject(ri_v)
- self.assertTrue(identical(ro_v._sexp, ri_v)[0])
+ self.assertTrue(identical(ro_v, ri_v)[0])
#FIXME: why isn't this working ?
#del(ri_v)
Modified: branches/rpy_nextgen/rpy/robjects/tests/testRVector.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testRVector.py 2008-06-07
07:01:08 UTC (rev 547)
+++ branches/rpy_nextgen/rpy/robjects/tests/testRVector.py 2008-06-07
07:05:04 UTC (rev 548)
@@ -5,18 +5,18 @@
rlist = robjects.baseNameSpaceEnv["list"]
-class RvectorTestCase(unittest.TestCase):
+class RVectorTestCase(unittest.TestCase):
def testNew(self):
identical = ri.baseNameSpaceEnv["identical"]
py_a = array.array('i', [1,2,3])
- ro_v = robjects.Rvector(py_a)
+ ro_v = robjects.RVector(py_a)
self.assertEquals(ro_v.typeof(), ri.INTSXP)
ri_v = ri.SexpVector(py_a, ri.INTSXP)
- ro_v = robjects.Rvector(ri_v)
+ ro_v = robjects.RVector(ri_v)
- self.assertTrue(identical(ro_v._sexp, ri_v)[0])
+ self.assertTrue(identical(ro_v, ri_v)[0])
del(ri_v)
self.assertEquals(ri.INTSXP, ro_v.typeof())
@@ -37,14 +37,14 @@
seq_R = robjects.baseNameSpaceEnv["seq"]
mySeq = seq_R(0, 10)
# R indexing starts at one
- myIndex = robjects.Rvector(array.array('i', range(1, 11, 2)))
+ myIndex = robjects.RVector(array.array('i', range(1, 11, 2)))
mySubset = mySeq.subset(myIndex)
for i, si in enumerate(myIndex):
self.assertEquals(mySeq[si-1], mySubset[i])
# recycling rule
- v = robjects.Rvector(array.array('i', range(1, 23)))
+ v = robjects.RVector(array.array('i', range(1, 23)))
m = robjects.r.matrix(v, ncol = 2)
col = m.subset(True, 1)
self.assertEquals(11, len(col))
@@ -68,7 +68,7 @@
self.assertTrue(idem("foo", mylist[1]))
def testGetNames(self):
- vec = robjects.Rvector(array.array('i', [1,2,3]))
+ vec = robjects.RVector(array.array('i', [1,2,3]))
v_names = [robjects.baseNameSpaceEnv["letters"][x] for x in (0,1,2)]
#FIXME: simplify this
r_names = robjects.baseNameSpaceEnv["c"](*v_names)
@@ -77,7 +77,7 @@
self.assertEquals(v_names[i], vec.getNames()[i])
def suite():
- suite = unittest.TestLoader().loadTestsFromTestCase(RvectorTestCase)
+ suite = unittest.TestLoader().loadTestsFromTestCase(RVectorTestCase)
return suite
if __name__ == '__main__':
Modified: branches/rpy_nextgen/rpy/robjects/tests/testRobjects.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testRobjects.py 2008-06-07
07:01:08 UTC (rev 547)
+++ branches/rpy_nextgen/rpy/robjects/tests/testRobjects.py 2008-06-07
07:05:04 UTC (rev 548)
@@ -7,7 +7,7 @@
def testGetItem(self):
letters_R = robjects.r["letters"]
- self.assertTrue(isinstance(letters_R, robjects.Rvector))
+ self.assertTrue(isinstance(letters_R, robjects.RVector))
letters = (('a', 0), ('b', 1), ('c', 2), ('x', 23), ('y', 24), ('z',
25))
for l, i in letters:
self.assertTrue(letters_R[i] == l)
@@ -22,42 +22,65 @@
for i, li in enumerate(myList):
self.assertEquals(i, myList[i][0])
-
- def testMapperR2Python(self):
+ def testMapperR2Python_string(self):
sexp = rinterface.globalEnv.get("letters")
- ob = robjects.defaultRobjects2PyMapper(sexp)
+ ob = robjects.default_ri2py(sexp)
self.assertTrue(isinstance(ob,
- robjects.Rvector))
+ robjects.RVector))
+ def testMapperR2Python_boolean(self):
sexp = rinterface.globalEnv.get("T")
- ob = robjects.defaultRobjects2PyMapper(sexp)
+ ob = robjects.default_ri2py(sexp)
self.assertTrue(isinstance(ob,
- robjects.Rvector))
+ robjects.RVector))
+ def testMapperR2Python_function(self):
sexp = rinterface.globalEnv.get("plot")
- ob = robjects.defaultRobjects2PyMapper(sexp)
+ ob = robjects.default_ri2py(sexp)
self.assertTrue(isinstance(ob,
- robjects.Rfunction))
+ robjects.RFunction))
+ def testMapperR2Python_environment(self):
sexp = rinterface.globalEnv.get(".GlobalEnv")
- self.assertTrue(isinstance(robjects.defaultRobjects2PyMapper(sexp),
robjects.Renvironment))
+ self.assertTrue(isinstance(robjects.default_ri2py(sexp),
+ robjects.Renvironment))
#FIXME: test S4
- def testMapperPy2R(self):
+ def testMapperPy2R_integer(self):
py = 1
- rob = robjects.defaultPy2RobjectsMapper(py)
- self.assertTrue(isinstance(rob, robjects.Rvector))
-
+ rob = robjects.default_py2ro(py)
+ self.assertTrue(isinstance(rob, robjects.RVector))
+
+ def testMapperPy2R_boolean(self):
py = True
- rob = robjects.defaultPy2RobjectsMapper(py)
- self.assertTrue(isinstance(rob, robjects.Rvector))
+ rob = robjects.default_py2ro(py)
+ self.assertTrue(isinstance(rob, robjects.RVector))
self.assertEquals(rinterface.LGLSXP, rob.typeof())
#FIXME: more tests
+ def testOverride_ri2py(self):
+ class Density(object):
+ def __init__(self, x):
+ self._x = x
+
+ def f(obj):
+ pyobj = robjects.default_ri2py(obj)
+ inherits = rinterface.baseNameSpaceEnv["inherits"]
+ classname = rinterface.SexpVector(["density", ],
+ rinterface.STRSXP)
+ if inherits(pyobj, classname)[0]:
+ pyobj = Density(pyobj)
+ return pyobj
+ robjects.ri2py = f
+ x = robjects.r.rnorm(100)
+ d = robjects.r.density(x)
+
+ self.assertTrue(isinstance(d, Density))
+
def suite():
suite = unittest.TestLoader().loadTestsFromTestCase(RObjectTestCase)
return suite
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