Revision: 495
http://rpy.svn.sourceforge.net/rpy/?rev=495&view=rev
Author: lgautier
Date: 2008-04-18 13:56:30 -0700 (Fri, 18 Apr 2008)
Log Message:
-----------
- Improved handling of multiple versions of R
- Automagic setting of R_HOME at install time
- SexpObject defined in a header
- Added back A. Belopolsky's functions and structures for integration with numpy
(not yet used)
Modified Paths:
--------------
branches/rpy_nextgen/rpy/rinterface/__init__.py
branches/rpy_nextgen/setup.py
Added Paths:
-----------
branches/rpy_nextgen/rpy/rinterface/__init__.py.in
branches/rpy_nextgen/rpy/rinterface/array.c
branches/rpy_nextgen/rpy/rinterface/rinterface.h
Modified: branches/rpy_nextgen/rpy/rinterface/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/__init__.py 2008-04-17 20:44:44 UTC
(rev 494)
+++ branches/rpy_nextgen/rpy/rinterface/__init__.py 2008-04-18 20:56:30 UTC
(rev 495)
@@ -1,2 +1,6 @@
-from rpy2.rinterface.rinterface import *
+# This file is automatically generated when installing rpy2
+# For permanent changes, edit __init__py.in in the source directory.
+import os
+
+from rinterface import *
Added: branches/rpy_nextgen/rpy/rinterface/__init__.py.in
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/__init__.py.in
(rev 0)
+++ branches/rpy_nextgen/rpy/rinterface/__init__.py.in 2008-04-18 20:56:30 UTC
(rev 495)
@@ -0,0 +1,4 @@
+import os
+os.environ["R_HOME"]="%R_HOME%"
+
+from rinterface import *
Added: branches/rpy_nextgen/rpy/rinterface/array.c
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/array.c (rev 0)
+++ branches/rpy_nextgen/rpy/rinterface/array.c 2008-04-18 20:56:30 UTC (rev
495)
@@ -0,0 +1,125 @@
+/* A. Belopolsky's Array interface */
+
+
+#include <Python.h>
+#include <Rdefines.h>
+#include <Rinternals.h>
+#include "rinterface.h"
+
+#define ARRAY_INTERFACE_VERSION 2
+
+/* Array Interface flags */
+#define FORTRAN 0x002
+#define ALIGNED 0x100
+#define NOTSWAPPED 0x200
+#define WRITEABLE 0x400
+
+typedef struct {
+ int version;
+ int nd;
+ char typekind;
+ int itemsize;
+ int flags;
+ Py_intptr_t *shape;
+ Py_intptr_t *strides;
+ void *data;
+} PyArrayInterface;
+
+static int
+sexp_typekind(SEXP sexp)
+{
+ switch (TYPEOF(sexp)) {
+ case REALSXP: return 'f';
+ case INTSXP: return 'i';
+ case STRSXP: return 'S';
+ case CPLXSXP: return 'c';
+ //FIXME: correct type ?
+ case LGLSXP: return 'b';
+ }
+ return 0;
+}
+
+
+static int
+sexp_itemsize(SEXP sexp)
+{
+ switch (TYPEOF(sexp)) {
+ case REALSXP: return sizeof(*REAL(sexp));
+ case INTSXP: return sizeof(*INTEGER(sexp));
+ case STRSXP: return sizeof(*CHAR(sexp));
+ case CPLXSXP: return sizeof(*COMPLEX(sexp));
+ case LGLSXP: return sizeof(*LOGICAL(sexp));
+ }
+ return 0;
+}
+
+static int
+sexp_rank(SEXP sexp)
+{
+ SEXP dim = getAttrib(sexp, R_DimSymbol);
+ if (dim == R_NilValue)
+ return 1;
+ return LENGTH(dim);
+}
+
+static void
+sexp_shape(SEXP sexp, Py_intptr_t* shape, int nd)
+{
+ int i;
+ SEXP dim = getAttrib(sexp, R_DimSymbol);
+ if (dim == R_NilValue)
+ shape[0] = LENGTH(sexp);
+ else for (i = 0; i < nd; ++i) {
+ shape[i] = INTEGER(dim)[i];
+ }
+}
+
+static void
+array_struct_free(void *ptr, void *arr)
+{
+ PyArrayInterface *inter = (PyArrayInterface *)ptr;
+ free(inter->shape);
+ free(inter);
+ Py_DECREF((PyObject *)arr);
+}
+
+
+static PyObject*
+array_struct_get(SexpObject *self)
+{
+ SEXP sexp = self->sexp;
+ if (!sexp) {
+ PyErr_SetString(PyExc_AttributeError, "Null sexp");
+ return NULL;
+ }
+ PyArrayInterface *inter;
+ int typekind = sexp_typekind(sexp);
+ if (!typekind) {
+ PyErr_SetString(PyExc_AttributeError, "Unsupported SEXP type");
+ return NULL;
+ }
+ inter = (PyArrayInterface *)malloc(sizeof(PyArrayInterface));
+ if (!inter) {
+ return PyErr_NoMemory();
+ }
+ int nd = sexp_rank(sexp);
+ int i;
+ inter->version = ARRAY_INTERFACE_VERSION;
+ inter->nd = nd;
+ inter->typekind = typekind;
+ inter->itemsize = sexp_itemsize(sexp);
+ inter->flags = FORTRAN|ALIGNED|NOTSWAPPED|WRITEABLE;
+ inter->shape = (Py_intptr_t*)malloc(sizeof(Py_intptr_t)*nd*2);
+ sexp_shape(sexp, inter->shape, nd);
+ inter->strides = inter->shape + nd;
+ Py_intptr_t stride = inter->itemsize;
+ inter->strides[0] = stride;
+ for (i = 1; i < nd; ++i) {
+ stride *= inter->shape[i-1];
+ inter->strides[i] = stride;
+ }
+ inter->data = RAW(sexp);
+ Py_INCREF(self);
+ return PyCObject_FromVoidPtrAndDesc(inter, self, array_struct_free);
+}
+
Property changes on: branches/rpy_nextgen/rpy/rinterface/array.c
___________________________________________________________________
Name: svn:eol-style
+ native
Added: branches/rpy_nextgen/rpy/rinterface/rinterface.h
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/rinterface.h
(rev 0)
+++ branches/rpy_nextgen/rpy/rinterface/rinterface.h 2008-04-18 20:56:30 UTC
(rev 495)
@@ -0,0 +1,16 @@
+
+#ifndef RPY_RI_H
+#define RPY_RI_H
+
+#include <R.h>
+#include <Python.h>
+
+/* Representation of R objects (instances) as instances in Python.
+ */
+typedef struct {
+ PyObject_HEAD
+ SEXP sexp;
+} SexpObject;
+
+
+#endif /* !RPY_RI_H */
Property changes on: branches/rpy_nextgen/rpy/rinterface/rinterface.h
___________________________________________________________________
Name: svn:eol-style
+ native
Modified: branches/rpy_nextgen/setup.py
===================================================================
--- branches/rpy_nextgen/setup.py 2008-04-17 20:44:44 UTC (rev 494)
+++ branches/rpy_nextgen/setup.py 2008-04-18 20:56:30 UTC (rev 495)
@@ -60,15 +60,30 @@
r_libs = [os.path.join(RHOME, 'lib'), os.path.join(RHOME, 'modules')]
pack_name = 'rpy2'
- pack_version = '0.0.1'
+ pack_version = '0.0.1-dev'
if r_packversion is not None:
pack_name = pack_name + '_' + r_packversion
pack_version = pack_version + '_' + r_packversion
+ f_in = open(os.path.join('rpy', 'rinterface', '__init__.py.in'), 'r')
+ f_out = open(os.path.join('rpy', 'rinterface', '__init__.py'), 'w')
+ f_out.write('# This file is automatically generated when installing
rpy2\n')
+ f_out.write('# For permanent changes, ' +\
+ 'edit __init__py.in in the source directory.\n\n')
+
+ for row in f_in:
+ row = row.replace('%R_HOME%', RHOME)
+ f_out.write(row)
+
+ f_in.close()
+ f_out.close()
+
rinterface = Extension(
pack_name + ".rinterface.rinterface",
- ["rpy/rinterface/rinterface.c", ],
- include_dirs=[ os.path.join(RHOME, 'include'),],
+ [os.path.join('rpy', 'rinterface', 'rinterface.c'),
+ os.path.join('rpy', 'rinterface', 'array.c')],
+ include_dirs=[ os.path.join(RHOME, 'include'),
+ os.path.join('rpy', 'rinterface')],
libraries=['R', 'Rlapack', 'Rblas'],
library_dirs=r_libs,
runtime_library_dirs=r_libs,
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