Revision: 531
http://rpy.svn.sourceforge.net/rpy/?rev=531&view=rev
Author: lgautier
Date: 2008-05-23 12:22:03 -0700 (Fri, 23 May 2008)
Log Message:
-----------
rpy "classic" (v-1.x):
- fixes. Now roughly working
rinterface:
- Fixes around Py_True and Py_False (ref counting)
- Functions are now evaluated in their enclosing environments
(previously was in globalEnv)... and there is a new test for that.
Modified Paths:
--------------
branches/rpy_nextgen/rpy/rinterface/rinterface.c
branches/rpy_nextgen/rpy/rinterface/tests/test_SexpClosure.py
branches/rpy_nextgen/rpy/rpy_classic.py
Modified: branches/rpy_nextgen/rpy/rinterface/rinterface.c
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/rinterface.c 2008-05-22 20:29:40 UTC
(rev 530)
+++ branches/rpy_nextgen/rpy/rinterface/rinterface.c 2008-05-23 19:22:03 UTC
(rev 531)
@@ -197,7 +197,6 @@
if (result == NULL) {
return;
- //return NULL;
}
Py_DECREF(result);
@@ -237,7 +236,9 @@
/* R_Interactive = TRUE; Rf_initialize_R set this based on isatty */
/* setup_Rmainloop(); */
- embeddedR_isInitialized = PyBool_FromLong((long)1);
+ Py_XDECREF(embeddedR_isInitialized);
+ embeddedR_isInitialized = Py_True;
+ Py_INCREF(Py_True);
#ifdef R_INTERFACE_PTRS
/* Redirect R console output */
@@ -288,6 +289,11 @@
RPY_SEXP(globalEnv) = R_EmptyEnv;
RPY_SEXP(baseNameSpaceEnv) = R_EmptyEnv;
+ //FIXME: Is it possible to reinitialize R later ?
+ //Py_XDECREF(embeddedR_isInitialized);
+ //embeddedR_isInitialized = Py_False;
+ //Py_INCREF(Py_False);
+
Py_RETURN_NONE;
}
PyDoc_STRVAR(EmbeddedR_end_doc,
@@ -728,8 +734,8 @@
}
//FIXME: R_GlobalContext ?
- PROTECT(res_R = do_eval_expr(call_R, R_GlobalEnv));
- //PROTECT(res_R = do_eval_expr(call_R, CLOENV(fun_R)));
+ //PROTECT(res_R = do_eval_expr(call_R, R_GlobalEnv));
+ PROTECT(res_R = do_eval_expr(call_R, CLOENV(fun_R)));
/* if (!res) { */
/* UNPROTECT(2); */
@@ -781,7 +787,6 @@
{NULL, NULL} /* sentinel */
};
-//FIXME: write more doc
PyDoc_STRVAR(ClosureSexp_Type_doc,
"A R object that is a closure, that is a function. \
In R a function is defined within an enclosing \
@@ -1053,7 +1058,6 @@
};
-//FIXME: write more doc
PyDoc_STRVAR(VectorSexp_Type_doc,
"R object that is a vector."
" R vectors start their indexing at one,"
@@ -1062,10 +1066,6 @@
"In the hope to avoid confusion, the indexing"
" from the Python subset operator (__getitem__)"
" is done at zero.");
-/* ", while an other method to perform\ */
-/* it at one is provided (_not yet implemented_).\ */
-/* That other method is also performing indexing."); */
-//FIXME: implement offset-one indexing.
static int
VectorSexp_init(PySexpObject *self, PyObject *args, PyObject *kwds);
@@ -1902,7 +1902,9 @@
Py_INCREF(ErrorObject);
PyModule_AddObject(m, "RobjectNotFound", ErrorObject);
- embeddedR_isInitialized = PyBool_FromLong((long)0);
+ embeddedR_isInitialized = Py_False;
+ Py_INCREF(Py_False);
+
if (PyModule_AddObject(m, "isInitialized", embeddedR_isInitialized) < 0)
return;
//FIXME: DECREF ?
Modified: branches/rpy_nextgen/rpy/rinterface/tests/test_SexpClosure.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/tests/test_SexpClosure.py
2008-05-22 20:29:40 UTC (rev 530)
+++ branches/rpy_nextgen/rpy/rinterface/tests/test_SexpClosure.py
2008-05-23 19:22:03 UTC (rev 531)
@@ -28,7 +28,23 @@
letters = rinterface.baseNameSpaceEnv["letters"]
self.assertRaises(RuntimeError, sum, letters)
+ def testClosureEnv(self):
+ parse = rinterface.baseNameSpaceEnv["parse"]
+ exp = parse(text = rinterface.SexpVector(["function(x) { x[y] }", ],
+ rinterface.STRSXP))
+ fun = rinterface.baseNameSpaceEnv["eval"](exp)
+ vec = rinterface.baseNameSpaceEnv["letters"]
+ self.assertRaises(RuntimeError, fun, vec)
+ fun.closureEnv()["y"] = rinterface.SexpVector([1, ],
+ rinterface.INTSXP)
+ self.assertEquals('a', fun(vec)[0])
+
+ fun.closureEnv()["y"] = rinterface.SexpVector([2, ],
+ rinterface.INTSXP)
+ self.assertEquals('b', fun(vec)[0])
+
+
def suite():
suite = unittest.TestLoader().loadTestsFromTestCase(SexpClosureTestCase)
return suite
Modified: branches/rpy_nextgen/rpy/rpy_classic.py
===================================================================
--- branches/rpy_nextgen/rpy/rpy_classic.py 2008-05-22 20:29:40 UTC (rev
530)
+++ branches/rpy_nextgen/rpy/rpy_classic.py 2008-05-23 19:22:03 UTC (rev
531)
@@ -5,8 +5,9 @@
import rpy2.rinterface as ri
import array
+#
+RPY_VERSION = '1.x'
-
# --- options in 'rpy_options.py'
rpy_options = {
@@ -67,25 +68,9 @@
# --- "CONVERSION" system
-class ModuleMode(object):
- # same default as in "rpymodule.c"
- __mode = -1
+# same default as in "rpymodule.c"
+default_mode = -1
- def __init__(self):
- pass
-
- @classmethod
- def __eq__(self, val):
- return ModuleMode.__mode == val
- @classmethod
- def set_mode(val):
- ModuleMode.__mode == val
- @classmethod
- def get_mode():
- return ModuleMode.__mode
-
-default_mode = ModuleMode()
-
# Wrap a function in safe modes to avoid infinite recursion when
# called from within the conversion system
def with_mode(i, fun):
@@ -104,10 +89,12 @@
raise ValueError("mode should be an int.")
if (mode < -1) or (mode > TOP_MODE):
raise ValueError("wrong mode.")
- default_mode.set_mode(mode)
+ global default_mode
+ default_mode = mode
def get_default_mode():
- return default_mode.get_mode()
+ global default_mode
+ return default_mode
@@ -161,19 +148,24 @@
def rpy2py_basic(obj):
if hasattr(obj, '__len__'):
- if obj.typeof() in [ri.INTSXP, ri.REALSXP, ri.CPLSXP,
+ if obj.typeof() in [ri.INTSXP, ri.REALSXP, ri.CPLXSXP,
ri.STRSXP]:
res = [x for x in obj]
elif obj.typeof() in [ri.VECSXP]:
- res = [rpy2py for x in obj]
+ res = [rpy2py(x) for x in obj]
else:
raise ValueError("Invalid type for 'obj'.")
- return res
- raise ValueError("Invalid type for 'obj'.")
+ else:
+ res = Robj(obj)
+ return res
+ #raise ValueError("Invalid type for 'obj'.")
-def rpy2py(obj, mode=default_mode):
+def rpy2py(obj, mode=None):
+ """ Transform RPy objects into pure python objects. """
+ if mode is None:
+ mode = default_mode
if mode == NO_CONVERSION:
- res = obj
+ res = Robj(obj)
return res
if mode == BASIC_CONVERSION:
res = rpy2py_basic(obj)
@@ -217,6 +209,7 @@
kwargs_r[a_n] = a
#import pdb; pdb.set_trace()
res = self.__sexp(*args_r, **kwargs_r)
+ res = rpy2py(res)
return res
def __getitem__(self, item):
@@ -228,9 +221,9 @@
def getSexp(self):
return self.__sexp
- def __repr__(self):
- res = rpy2r(self)
- return res
+ #def __repr__(self):
+ # res = rpy2py(self)
+ # return res
def as_py(mode = default_mode):
res = rpy2py(self, mode)
@@ -258,6 +251,7 @@
def __getitem__(self, name):
#FIXME: "get function only" vs "get anything"
+ # wantFun = True ?
res = ri.globalEnv.get(name)
res = rpy2py(res)
return res
@@ -269,8 +263,9 @@
helpobj.helpfun(*arg, **kw)
def __repr__(self):
- rversion = self.__getitem__('R.version.sting')
- res = 'RPy version %s [%s]' %(rpy_version, r_version)
+ r_version = ri.baseNameSpaceEnv['R.version.string'][0]
+ res = 'RPy version %s with %s' %(RPY_VERSION, r_version)
+ return res
def __str__(self):
return repr(self)
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