Python 3 compatibility.

Simplified version of scipy strategy: copy files into build/py3k, and
patch them using lib2to3.

Author: Fabian Pedregosa

scikits/learn/qda.py

@@ -6,7 +6,6 @@
 #
 # License: BSD Style.
 
-import exceptions
 import warnings
 
 import numpy as np
@@ -83,7 +82,7 @@ def fit(self, X, y, store_covariances=False, tol=1.0e-4, **params):
         X = np.asanyarray(X)
         y = np.asanyarray(y)
         if X.ndim!=2:
-            raise exceptions.ValueError('X must be a 2D array')
+            raise ValueError('X must be a 2D array')
         if X.shape[0] != y.shape[0]:
             raise ValueError(
                 'Incompatible shapes: X has %s samples, while y '
@@ -100,7 +99,7 @@ def fit(self, X, y, store_covariances=False, tol=1.0e-4, **params):
         classes = np.unique(y)
         n_classes = classes.size
         if n_classes < 2:
-            raise exceptions.ValueError('y has less than 2 classes')
+            raise ValueError('y has less than 2 classes')
         classes_indices = [(y == c).ravel() for c in classes]
         if self.priors is None:
             counts = np.array(ndimage.measurements.sum(

scikits/learn/utils/sparsetools/csgraph.py

@@ -1,5 +1,5 @@
 # This file was automatically generated by SWIG (http://www.swig.org).
-# Version 1.3.40
+# Version 2.0.1+capsulehack
 #
 # Do not make changes to this file unless you know what you are doing--modify
 # the SWIG interface file instead.

scikits/learn/utils/sparsetools/csgraph_wrap.cxx

@@ -1,6 +1,6 @@
 /* ----------------------------------------------------------------------------
  * This file was automatically generated by SWIG (http://www.swig.org).
- * Version 1.3.40
+ * Version 2.0.1+capsulehack
  * 
  * This file is not intended to be easily readable and contains a number of 
  * coding conventions designed to improve portability and efficiency. Do not make
@@ -201,7 +201,7 @@ template <typename T> T SwigValueInit() {
 /* 
    Flags/methods for returning states.
    
-   The SWIG conversion methods, as ConvertPtr, return and integer 
+   The SWIG conversion methods, as ConvertPtr, return an integer 
    that tells if the conversion was successful or not. And if not,
    an error code can be returned (see swigerrors.swg for the codes).
    
@@ -1088,9 +1088,6 @@ SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *self, PyObject *func)
 
 
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * pyrun.swg
  *
  * This file contains the runtime support for Python modules
@@ -1137,8 +1134,18 @@ SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *self, PyObject *func)
 #define SWIG_SetErrorMsg                        	SWIG_Python_SetErrorMsg				   
 #define SWIG_ErrorType(code)                    	SWIG_Python_ErrorType(code)                        
 #define SWIG_Error(code, msg)            		SWIG_Python_SetErrorMsg(SWIG_ErrorType(code), msg) 
-#define SWIG_fail                        		goto fail					   
+#define SWIG_fail                        		goto fail				
 
+/*
+ * Python 2.7 and newer and Python 3.1 and newer should use Capsules API instead of
+ * CObjects API.
+ */
+#if ((PY_MAJOR_VERSION == 2 && PY_MINOR_VERSION > 6) || \
+     (PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION > 0))
+#define USE_CAPSULES
+#define TYPE_POINTER_NAME \
+    ((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION ".type_pointer_capsule" SWIG_TYPE_TABLE_NAME)
+#endif
 
 /* Runtime API implementation */
 
@@ -2071,10 +2078,13 @@ _SWIG_This(void)
     return SWIG_Python_str_FromChar("this");
 }
 
+static PyObject *swig_this = NULL;
+
 SWIGRUNTIME PyObject *
 SWIG_This(void)
 {
-  static PyObject *SWIG_STATIC_POINTER(swig_this) = _SWIG_This();
+  if (swig_this == NULL)
+    swig_this = _SWIG_This();
   return swig_this;
 }
 
@@ -2178,7 +2188,7 @@ SWIG_Python_ConvertPtrAndOwn(PyObject *obj, void **ptr, swig_type_info *ty, int
               int newmemory = 0;
               *ptr = SWIG_TypeCast(tc,vptr,&newmemory);
               if (newmemory == SWIG_CAST_NEW_MEMORY) {
-                assert(own);
+                assert(own); /* badly formed typemap which will lead to a memory leak - it must set and use own to delete *ptr */
                 if (own)
                   *own = *own | SWIG_CAST_NEW_MEMORY;
               }
@@ -2447,9 +2457,13 @@ SWIG_Python_GetModule(void) {
   if (!type_pointer) {
 #ifdef SWIG_LINK_RUNTIME
     type_pointer = SWIG_ReturnGlobalTypeList((void *)0);
+#else
+#ifdef USE_CAPSULES
+    type_pointer = PyCapsule_Import(TYPE_POINTER_NAME, 0);
 #else
     type_pointer = PyCObject_Import((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION,
 				    (char*)"type_pointer" SWIG_TYPE_TABLE_NAME);
+#endif
     if (PyErr_Occurred()) {
       PyErr_Clear();
       type_pointer = (void *)0;
@@ -2494,9 +2508,14 @@ PyModule_AddObject(PyObject *m, char *name, PyObject *o)
 SWIGRUNTIME void
 SWIG_Python_DestroyModule(void *vptr)
 {
+  size_t i;
+#ifdef USE_CAPSULES
+  swig_module_info *swig_module =
+    (swig_module_info *) PyCapsule_GetPointer((PyObject *)vptr, TYPE_POINTER_NAME);
+#else
   swig_module_info *swig_module = (swig_module_info *) vptr;
+#endif
   swig_type_info **types = swig_module->types;
-  size_t i;
   for (i =0; i < swig_module->size; ++i) {
     swig_type_info *ty = types[i];
     if (ty->owndata) {
@@ -2505,6 +2524,7 @@ SWIG_Python_DestroyModule(void *vptr)
     }
   }
   Py_DECREF(SWIG_This());
+  swig_this = NULL;
 }
 
 SWIGRUNTIME void
@@ -2518,9 +2538,18 @@ SWIG_Python_SetModule(swig_module_info *swig_module) {
   PyObject *module = Py_InitModule((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION,
 				   swig_empty_runtime_method_table);
 #endif
+#ifdef USE_CAPSULES
+  PyObject *pointer = PyCapsule_New((void *)swig_module, TYPE_POINTER_NAME,
+				    (PyCapsule_Destructor)SWIG_Python_DestroyModule);
+#else
   PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule);
+#endif
   if (pointer && module) {
+#ifdef USE_CAPSULES
+    PyModule_AddObject(module, (char*)"type_pointer_capsule" SWIG_TYPE_TABLE_NAME, pointer);
+#else
     PyModule_AddObject(module, (char*)"type_pointer" SWIG_TYPE_TABLE_NAME, pointer);
+#endif
   } else {
     Py_XDECREF(pointer);
   }
@@ -2541,12 +2570,20 @@ SWIG_Python_TypeQuery(const char *type)
   PyObject *obj = PyDict_GetItem(cache, key);
   swig_type_info *descriptor;
   if (obj) {
+#ifdef USE_CAPSULES
+    descriptor = (swig_type_info *) PyCapsule_GetPointer(obj, type);
+#else
     descriptor = (swig_type_info *) PyCObject_AsVoidPtr(obj);
+#endif
   } else {
     swig_module_info *swig_module = SWIG_Python_GetModule();
     descriptor = SWIG_TypeQueryModule(swig_module, swig_module, type);
     if (descriptor) {
+#ifdef USE_CAPSULES
+      obj = PyCapsule_New(descriptor, type, NULL);
+#else
       obj = PyCObject_FromVoidPtr(descriptor, NULL);
+#endif
       PyDict_SetItem(cache, key, obj);
       Py_DECREF(obj);
     }
@@ -2708,7 +2745,7 @@ static swig_module_info swig_module = {swig_types, 1, 0, 0, 0, 0};
 #endif
 #define SWIG_name    "_csgraph"
 
-#define SWIGVERSION 0x010340 
+#define SWIGVERSION 0x020001 
 #define SWIG_VERSION SWIGVERSION
 
 
@@ -2781,6 +2818,7 @@ namespace swig {
 }
 
 
+#include "py3k.h"
 #define SWIG_FILE_WITH_INIT
 #include "Python.h"
 #include "numpy/arrayobject.h"
@@ -3919,15 +3957,15 @@ extern "C" {
           }
         }
         if (ci) {
-          size_t shift = (ci->ptype) - types;
-          swig_type_info *ty = types_initial[shift];
-          size_t ldoc = (c - methods[i].ml_doc);
-          size_t lptr = strlen(ty->name)+2*sizeof(void*)+2;
-          char *ndoc = (char*)malloc(ldoc + lptr + 10);
-          if (ndoc) {
-            char *buff = ndoc;
-            void *ptr = (ci->type == SWIG_PY_POINTER) ? ci->pvalue : 0;
-            if (ptr) {
+          void *ptr = (ci->type == SWIG_PY_POINTER) ? ci->pvalue : 0;
+          if (ptr) {
+            size_t shift = (ci->ptype) - types;
+            swig_type_info *ty = types_initial[shift];
+            size_t ldoc = (c - methods[i].ml_doc);
+            size_t lptr = strlen(ty->name)+2*sizeof(void*)+2;
+            char *ndoc = (char*)malloc(ldoc + lptr + 10);
+            if (ndoc) {
+              char *buff = ndoc;
               strncpy(buff, methods[i].ml_doc, ldoc);
               buff += ldoc;
               strncpy(buff, "swig_ptr: ", 10);

scikits/learn/utils/sparsetools/py3k.h

@@ -0,0 +1,23 @@
+/*
+ * Undefine macros defined by SWIG
+ */
+#if PY_VERSION_HEX >= 0x03000000
+
+#ifdef PyInt_Check
+#undef PyInt_Check
+#endif
+
+static int __pyfile_check_guard(PyObject *x)
+{
+    return 0;
+}
+#define PyFile_Check(x) __pyfile_check_guard((x))
+static int __pyinstance_check_guard(PyObject *x)
+{
+    return 0;
+}
+#define PyInstance_Check(x) __pyinstance_check_guard((x))
+
+#endif
+
+#include "numpy/npy_3kcompat.h"

setup.py

@@ -5,7 +5,7 @@
 
 descr   = """A set of python modules for machine learning and data mining"""
 
-import os
+import sys, os, shutil
 
 DISTNAME            = 'scikits.learn'
 DESCRIPTION         = 'A set of python modules for machine learning and data mining'
@@ -33,6 +33,39 @@ def configuration(parent_package='',top_path=None):
     return config
 
 if __name__ == "__main__":
+
+    old_path = os.getcwd()
+    local_path = os.path.dirname(os.path.abspath(sys.argv[0]))
+    # python 3 compatibility stuff.
+    # Simplified version of scipy strategy: copy files into
+    # build/py3k, and patch them using lib2to3.
+    if sys.version_info[0] == 3:
+        try:
+            import lib2to3cache
+        except ImportError:
+            pass
+        local_path = os.path.join(local_path, 'build', 'py3k')
+        if os.path.exists(local_path):
+            shutil.rmtree(local_path)
+        print("Copying source tree into build/py3k for 2to3 transformation ...")
+        shutil.copytree(os.path.join(old_path, 'scikits'),
+                        os.path.join(local_path, 'scikits'))
+        import lib2to3.main
+        from io import StringIO
+        print("Converting to Python3 via 2to3...")
+        _old_stdout = sys.stdout
+        try:
+            sys.stdout = StringIO() # supress noisy output
+            res = lib2to3.main.main("lib2to3.fixes", ['-w'] + [local_path])
+        finally:
+            sys.stdout = _old_stdout
+
+        if res != 0:
+            raise Exception('2to3 failed, exiting ...')
+
+    os.chdir(local_path)
+    sys.path.insert(0,local_path)
+        
     setup(configuration = configuration,
         name = DISTNAME,
         maintainer  = MAINTAINER,