Revision: 512
http://rpy.svn.sourceforge.net/rpy/?rev=512&view=rev
Author: lgautier
Date: 2008-05-10 06:30:40 -0700 (Sat, 10 May 2008)
Log Message:
-----------
- work on the tests (some of the tests are not passing, but
are here what needs to be done is not forgotten)
rinterface:
- R output to the R console can be customized by a python callback
function (in theory - this is not appearing to completely work for the
moment)
Modified Paths:
--------------
branches/rpy_nextgen/rpy/rinterface/rinterface.c
branches/rpy_nextgen/rpy/rinterface/tests/__init__.py
branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
branches/rpy_nextgen/rpy/robjects/__init__.py
branches/rpy_nextgen/rpy/robjects/tests/testRVector.py
Modified: branches/rpy_nextgen/rpy/rinterface/rinterface.c
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/rinterface.c 2008-05-09 21:17:54 UTC
(rev 511)
+++ branches/rpy_nextgen/rpy/rinterface/rinterface.c 2008-05-10 13:30:40 UTC
(rev 512)
@@ -124,14 +124,87 @@
");
-static PySexpObject* globalEnv;
-static PySexpObject* baseNameSpaceEnv;
+static PySexpObject *globalEnv;
+static PySexpObject *baseNameSpaceEnv;
+static PySexpObject *na_string;
/* early definition of functions */
static PySexpObject* newPySexpObject(const SEXP sexp);
static SEXP newSEXP(PyObject *object, const int rType);
+/* --- set output from the R console ---*/
+
+
+static PyObject* writeConsoleCallback = NULL;
+
+static PyObject* EmbeddedR_setWriteConsole(PyObject *self,
+ PyObject *args)
+{
+
+ PyObject *result = NULL;
+ PyObject *function;
+
+ if ( PyArg_ParseTuple(args, "O:console",
+ &function)) {
+
+ if (!PyCallable_Check(function)) {
+ PyErr_SetString(PyExc_TypeError, "parameter must be callable");
+ return NULL;
+ }
+
+ Py_XDECREF(writeConsoleCallback);
+ Py_XINCREF(function);
+ writeConsoleCallback = function;
+ Py_INCREF(Py_None);
+ result = Py_None;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "The only parameter should be a
callable.");
+ }
+ return result;
+
+}
+
+PyDoc_STRVAR(EmbeddedR_setWriteConsole_doc,
+ "setWriteConsoleEmbeddedR()\n\
+ \n\
+ Set the R console output.");
+
+
+
+static void
+EmbeddedR_WriteConsole(char *buf, int len)
+{
+ PyOS_sighandler_t old_int;
+ PyObject *arglist;
+ PyObject *result;
+
+ /* It is necessary to restore the Python handler when using a Python
+ function for I/O. */
+ old_int = PyOS_getsig(SIGINT);
+ PyOS_setsig(SIGINT, python_sigint);
+ arglist = Py_BuildValue("(s)", buf);
+ if (! arglist) {
+ PyErr_NoMemory();
+ signal(SIGINT, old_int);
+ //return NULL;
+ }
+
+ result = PyEval_CallObject(writeConsoleCallback, arglist);
+
+ Py_DECREF(arglist);
+ signal(SIGINT, old_int);
+
+ if (result == NULL) {
+ return;
+ //return NULL;
+ }
+
+ Py_DECREF(result);
+
+}
+
+
/* --- Initialize and terminate an embedded R --- */
/* Should having multiple threads of R become possible,
* useful routines could appear here...
@@ -154,13 +227,28 @@
options[ii] = PyString_AsString(opt_string);
}
+
int status = Rf_initEmbeddedR(n_args, options);
+ /* FIXME: setup_Rmainloop causes ipython to crash
+ *(bug in ipython ?)
+ */
+/* int status = 1; */
+/* Rf_initialize_R(n_args, options); */
+/* R_Interactive = TRUE; Rf_initialize_R set this based on isatty */
+/* setup_Rmainloop(); */
embeddedR_isInitialized = PyBool_FromLong((long)1);
+ /* Redirect R console output */
+ R_Outputfile = NULL;
+
+ extern void (*ptr_R_WriteConsole)(char *, int);
+ ptr_R_WriteConsole = EmbeddedR_WriteConsole;
+
+
RPY_SEXP(globalEnv) = R_GlobalEnv;
-
RPY_SEXP(baseNameSpaceEnv) = R_BaseNamespace;
+ RPY_SEXP(na_string) = NA_STRING;
PyObject *res = PyInt_FromLong(status);
@@ -209,39 +297,8 @@
Terminate an embedded R.");
-/* --- set output from the R console ---*/
-static void
-EmbeddedR_WriteConsole(char *buf, int len)
-{
- PyOS_sighandler_t old_int;
- /* It is necessary to restore the Python handler when using a Python
- function for I/O. */
- old_int = PyOS_getsig(SIGINT);
- PyOS_setsig(SIGINT, python_sigint);
- PySys_WriteStdout(buf);
- signal(SIGINT, old_int);
-}
-
-
-/* Redirect R console output */
-// R_Outputfile = NULL;
-
-
-/* FIXME: implement possibility to specify arbitrary callback functions */
-extern void (*ptr_R_WriteConsole)(char *, int);
-static PyObject* EmbeddedR_setWriteConsole(PyObject *self)
-{
- ptr_R_WriteConsole = EmbeddedR_WriteConsole;
- Py_RETURN_NONE;
-}
-PyDoc_STRVAR(EmbeddedR_setWriteConsole_doc,
- "setWriteConsoleEmbeddedR()\n\
- \n\
- Set the R console output to the Python console.");
-
-
static PyObject*
EmbeddedR_exception_from_errmessage(void)
{
@@ -879,11 +936,15 @@
vs = translateChar(STRING_ELT(*sexp, i_R));
res = PyString_FromString(vs);
break;
+/* case CHARSXP: */
+/* //FIXME: implement handling of single char (if possible ?) */
+/* vs = (CHAR(*sexp)[i_R]); */
+/* res = PyString_FromStringAndSize(vs, 1); */
case VECSXP:
res = (PyObject *)newPySexpObject(VECTOR_ELT(*sexp, i_R));
break;
default:
- PyErr_Format(PyExc_ValueError, "cannot handle type %d",
+ PyErr_Format(PyExc_ValueError, "Cannot handle type %d",
TYPEOF(*sexp));
res = NULL;
break;
@@ -1649,7 +1710,7 @@
EmbeddedR_init_doc},
{"endEmbeddedR", (PyCFunction)EmbeddedR_end, METH_O,
EmbeddedR_end_doc},
- {"setWriteConsole", (PyCFunction)EmbeddedR_setWriteConsole, METH_NOARGS,
+ {"setWriteConsole", (PyCFunction)EmbeddedR_setWriteConsole, METH_VARARGS,
EmbeddedR_setWriteConsole_doc},
{"findVarEmbeddedR", (PyCFunction)EmbeddedR_findVar, METH_VARARGS,
EmbeddedR_findVar_doc},
@@ -1926,8 +1987,8 @@
/* /\* Rinternals.h *\/ */
- PySexpObject *na_string = (PySexpObject *)Sexp_new(&VectorSexp_Type,
- Py_None, Py_None);
+ na_string = (PySexpObject *)Sexp_new(&VectorSexp_Type,
+ Py_None, Py_None);
RPY_SEXP(na_string) = NA_STRING;
if (PyDict_SetItemString(d, "NA_STRING", (PyObject *)na_string) < 0)
Modified: branches/rpy_nextgen/rpy/rinterface/tests/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/tests/__init__.py 2008-05-09
21:17:54 UTC (rev 511)
+++ branches/rpy_nextgen/rpy/rinterface/tests/__init__.py 2008-05-10
13:30:40 UTC (rev 512)
@@ -5,6 +5,7 @@
import test_Sexp
import test_SexpClosure
import test_SexpVectorNumeric
+import test_EmbeddedR
def suite():
@@ -13,11 +14,13 @@
suite_Sexp = test_Sexp.suite()
suite_SexpClosure = test_SexpClosure.suite()
suite_SexpVectorNumeric = test_SexpVectorNumeric.suite()
+ suite_EmbeddedR = test_EmbeddedR.suite()
alltests = unittest.TestSuite([suite_SexpVector,
suite_SexpEnvironment,
suite_Sexp,
suite_SexpClosure,
- suite_SexpVectorNumeric])
+ suite_SexpVectorNumeric,
+ suite_EmbeddedR])
return alltests
def main():
Modified: branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-05-09 21:17:54 UTC (rev 511)
+++ branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-05-10 13:30:40 UTC (rev 512)
@@ -73,6 +73,8 @@
ok = isCharacter(sexp)[0]
self.assertTrue(ok)
+ ri.NA_STRING[0]
+
def testNewVector(self):
sexp_char = ri.SexpVector(["abc", ],
ri.STRSXP)
Modified: branches/rpy_nextgen/rpy/robjects/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/__init__.py 2008-05-09 21:17:54 UTC
(rev 511)
+++ branches/rpy_nextgen/rpy/robjects/__init__.py 2008-05-10 13:30:40 UTC
(rev 512)
@@ -183,7 +183,6 @@
def getNames(self):
res = r.names(self.getSexp())
- import pdb; pdb.set_trace()
return res
class RArray(Rvector):
Modified: branches/rpy_nextgen/rpy/robjects/tests/testRVector.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testRVector.py 2008-05-09
21:17:54 UTC (rev 511)
+++ branches/rpy_nextgen/rpy/robjects/tests/testRVector.py 2008-05-10
13:30:40 UTC (rev 512)
@@ -6,6 +6,7 @@
rlist = robjects.baseNameSpaceEnv["list"]
class RvectorTestCase(unittest.TestCase):
+
def testNew(self):
identical = ri.baseNameSpaceEnv["identical"]
py_a = array.array('i', [1,2,3])
@@ -17,8 +18,7 @@
self.assertTrue(identical(ro_v._sexp, ri_v)[0])
- #FIXME: why isn't this working ?
- #del(ri_v)
+ del(ri_v)
self.assertEquals(ri.INTSXP, ro_v.typeof())
def testOperators(self):
@@ -72,8 +72,7 @@
v_names = [robjects.baseNameSpaceEnv["letters"][x] for x in (0,1,2)]
#FIXME: simplify this
r_names = robjects.baseNameSpaceEnv["c"](*v_names)
- robjects.r["names<-"](vec, r_names)
-
+ vec = robjects.r["names<-"](vec, r_names)
for i in xrange(len(vec)):
self.assertEquals(v_names[i], vec.getNames()[i])
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