switch to cpp wrapper -> first array wrapper works

.gitignore

@@ -2,4 +2,3 @@
 build/
 cnorxz.egg-info/
 *.so
-*.cpp

cnorxz/core/array.pxd

@@ -1,60 +0,0 @@
-
-from libcpp.memory cimport shared_ptr
-from range cimport cpp_RangeBase
-from index cimport cpp_YIndex
-
-
-cdef extern from "array/array.h" namespace "CNORXZ":
-    cdef cppclass cpp_AIndex "CNORXZ::AIndex" [T] (cpp_YIndex):
-        cpp_AIndex() except+
-        cpp_AIndex(const cpp_AIndex&) except+
-        cpp_AIndex(const T*, const shared_ptr[cpp_RangeBase]&, size_t lexpos) except+
-        cpp_AIndex(const T*, const cpp_YIndex&) except+
-
-        cpp_AIndex A_plus "operator+" (int n) except+
-        cpp_AIndex A_minus "operator-" (int n) except+
-
-        const T& A_get "operator*" () except+
-
-
-cdef extern from "array/array.h" namespace "CNORXZ":
-    cdef cppclass cpp_BIndex "CNORXZ::BIndex" [T] (cpp_AIndex[T]):
-        cpp_BIndex() except+
-        cpp_BIndex(const cpp_AIndex[T]&) except+
-        cpp_BIndex(const T*, const shared_ptr[cpp_RangeBase]&, size_t lexpos) except+
-        cpp_BIndex(const T*, const cpp_AIndex[T]&) except+
-
-        cpp_BIndex B_plus "operator+" (int n) except+
-        cpp_BIndex B_minus "operator-" (int n) except+
-
-        T& B_get "operator*" () except+
-
-
-cdef extern from "array/array.h" namespace "CNORXZ":
-    cdef cppclass cpp_CArrayBase "CNORXZ::CArrayBase" [T]:
-        cpp_CArrayBase() except+
-        cpp_CArrayBase(const cpp_CArrayBase[T]&) except+
-        
-        size_t size() except+
-        shared_ptr[cpp_RangeBase] range() except+
-        cpp_AIndex[T] begin() except+
-        cpp_AIndex[T] end() except+
-
-        
-cdef extern from "array/array.h" namespace "CNORXZ":
-    cdef cppclass cpp_ArrayBase "CNORXZ::ArrayBase" [T] (cpp_CArrayBase[T]):
-        cpp_ArrayBase() except+
-        cpp_ArrayBase(const cpp_ArrayBase[T]&) except+
-        
-        cpp_BIndex[T] begin() except+
-        cpp_BIndex[T] end() except+
-
-
-cdef extern from "array/array.h" namespace "CNORXZ":
-    cdef cppclass cpp_MArray "CNORXZ::MArray" [T] (cpp_ArrayBase[T]):
-        cpp_MArray() except+
-        cpp_MArray(const cpp_MArray[T]&) except+        
-
-        cpp_MArray(const shared_ptr[cpp_RangeBase]&) except+
-
-

cnorxz/core/cereal.pxd

@@ -1,24 +0,0 @@
-
-from libcpp.string cimport string
-from array cimport cpp_MArray
-
-cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
-    cdef cppclass cpp_Format "CNORXZ::cer::Format":
-        pass
-
-cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer::Format":
-    cdef cpp_Format BINARY
-    cdef cpp_Format JSON
-    cdef cpp_Format XML
-
-cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
-    cdef void cpp_writeJSONFile "CNORXZ::cer::writeJSONFile" [T] (const string&, const cpp_MArray[T]&)
-
-cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
-    cdef void cpp_writeBINARYFile "CNORXZ::cer::writeBINARYFile" [T] (const string&, const cpp_MArray[T]&)
-
-cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
-    cdef void cpp_readJSONFile "CNORXZ::cer::readJSONFile" [T] (const string&, cpp_MArray[T]&)
-
-cdef extern from "cereal/cnorxz_cereal.h" namespace "CNORXZ::cer":
-    cdef void cpp_readBINARYFile "CNORXZ::cer::readBINARYFile" [T] (const string&, cpp_MArray[T]&)

cnorxz/core/core.cpp

@@ -0,0 +1,34 @@
+
+#include <Python.h>
+#include "array_wrapper.h"
+
+using namespace CNORXZ;
+
+static PyModuleDef cnorxz_core_module = {
+    PyModuleDef_HEAD_INIT,
+    "cnorxz",
+    "cnorxz core module",
+    -1,
+    NULL, NULL, NULL, NULL, NULL
+};
+
+PyMODINIT_FUNC PyInit_cnorxz()
+{
+    PyObject* m;
+
+    PyTypeObject* carray_type = PyCArrayBType_init();
+    if(carray_type == NULL){
+	return NULL;
+    }
+    
+    m = PyModule_Create(&cnorxz_core_module);
+    if(m == NULL){
+	return NULL;
+    }
+
+    Py_INCREF(carray_type);
+
+    PyModule_AddObject(m, "CArray", (PyObject*) carray_type);
+
+    return m;
+}

cnorxz/core/core.pyx

@@ -1,284 +0,0 @@
-#cython: language_level=3
-#cython: c_string_type=str
-#cython: c_string_encoding=ascii
-#cython: boundscheck=False
-#cython: wrapparound=False
-#cython: cdivision=True
-#cython: embedsignature=True
-
-from libcpp.memory cimport shared_ptr, make_shared, dynamic_pointer_cast
-from libcpp.string cimport string
-from libcpp cimport bool
-from cython.operator cimport dereference as deref
-from range cimport cpp_RangeBase
-from range_factory cimport cpp_RangeFactoryBase, cpp_CRangeFactory
-from array cimport cpp_CArrayBase, cpp_MArray, cpp_AIndex
-from index cimport cpp_DIndex
-from cereal cimport cpp_writeJSONFile, cpp_writeBINARYFile, cpp_readJSONFile, cpp_readBINARYFile
-
-
-## ============
-##    Range
-## ============
-
-cdef class Range:
-    cdef shared_ptr[cpp_RangeBase] cpp_range
-
-    def size(self):
-        return self.cpp_range.get().size()
-
-    def dim(self):
-        return self.cpp_range.get().dim()
-
-    def sub(self):
-        return getSubRange(self)
-
-    def index(self):
-        return getRangeIndex(self)
-
-
-cdef class RangeFactory:
-    cdef shared_ptr[cpp_RangeFactoryBase] cpp_rfactory
-
-    def __cinit__(self,rangetype,**kvargs):
-        cdef size_t size = 0
-        if rangetype == 'C':
-            size = kvargs['size']
-            self.cpp_rfactory = dynamic_pointer_cast[cpp_RangeFactoryBase,cpp_CRangeFactory](
-	        make_shared[cpp_CRangeFactory](size))
-        else:
-            raise Exception('unknown range type:'+ rangetype)
-
-    def create(self):
-        r = Range()
-        r.cpp_range = self.cpp_rfactory.get().create()
-        return r
-
-
-## ===========
-##    Index   
-## ===========
-
-cdef class Index:
-
-    def __iter__(self):
-        return self
-        
-    def __next__(self):
-        return self
-
-    def lex(self):
-        return 0
-
-    def dim(self):
-        return 0
-
-    def stringMeta(self):
-        return ''
-
-    
-cdef class DIndex (Index):
-    cdef shared_ptr[cpp_DIndex] cpp_index
-    cdef bool itercall
-    
-    def __cinit__(self,_range,_lexpos=0):
-        cdef Range r = _range
-        cdef size_t l = _lexpos
-        self.cpp_index = make_shared[cpp_DIndex] (r.cpp_range,l)
-        self.itercall = False
-
-    def __iter__(self):
-        self.cpp_index.get().setlpos(0)
-        self.itercall = True # otherwise first (i.e. zeroth) will be excluded
-        return self
-
-    def __next__(self):
-        cdef DIndex ret = self
-        if self.itercall:
-            ret.itercall = False
-            return ret
-        if self.lex() < self.cpp_index.get().range().get().size()-1:
-            ret.cpp_index = make_shared[cpp_DIndex] (self.cpp_index.get().plus(1))
-            return ret
-        else:
-            raise StopIteration
-
-    def lex(self):
-        return self.cpp_index.get().lex()
-
-    def dim(self):
-        return self.cpp_index.get().dim()
-
-    def stringMeta(self):
-        return self.cpp_index.get().stringMeta()
-
-def getRangeIndex(_range):
-    return DIndex(_range)
-
-
-## ===========
-##   Array
-## ===========
-    
-cdef class Array:
-
-    def size(self):
-        return 0
-
-    def range(self):
-        cdef Range r = Range()
-        return r
-    
-
-cdef class Array_Double (Array):
-    cdef shared_ptr[cpp_CArrayBase[double]] cpp_array
-
-    def __cinit__(self,_range=None):
-        cdef Range r
-        if not _range is None:
-            r = _range
-            self.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[double],cpp_MArray[double]] (make_shared[cpp_MArray[double]] (r.cpp_range) )
-
-    def size(self):
-        return self.cpp_array.get().size()
-
-    def range(self):
-        cdef Range r = Range()
-        r.cpp_range = self.cpp_array.get().range()
-        return r
-
-    def index(self):
-        return AIndex_Double(self)
-
-cdef class Array_Range (Array):
-    cdef shared_ptr[cpp_CArrayBase[shared_ptr[cpp_RangeBase]]] cpp_array
-
-    def __cinit__(self,_range=None):
-        cdef Range r
-        if not _range is None:
-            r = _range
-            self.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[shared_ptr[cpp_RangeBase]],cpp_MArray[shared_ptr[cpp_RangeBase]]] (make_shared[cpp_MArray[shared_ptr[cpp_RangeBase]]] (r.cpp_range) )
-
-    def size(self):
-        return self.cpp_array.get().size()
-
-    def range(self):
-        cdef Range r = Range()
-        r.cpp_range = self.cpp_array.get().range()
-        return r
-
-    def index(self):
-        return AIndex_Range(self)
-
-    
-def getSubRange(_range):
-    cdef Range r = _range
-    cdef Array_Range a = Array_Range()
-    a.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[shared_ptr[cpp_RangeBase]],cpp_MArray[shared_ptr[cpp_RangeBase]]] (make_shared[cpp_MArray[shared_ptr[cpp_RangeBase]]] (r.cpp_range.get().sub()) )
-    return a
-
-def writeFile(_fname,_array,_format):
-    cdef Array_Double a = _array
-    cdef shared_ptr[cpp_MArray[double]] ap = dynamic_pointer_cast[cpp_MArray[double],cpp_CArrayBase[double]](a.cpp_array)
-    if _format.upper() == "JSON":
-        cpp_writeJSONFile[double](_fname, deref(ap.get()))
-    elif _format.upper() == "BINARY":
-        cpp_writeBINARYFile[double](_fname, deref(ap.get()))
-    else:
-        raise Exception("unknown array file format '{}'".format(_format))
-
-def readFile(_fname,_format):
-    cdef Array_Double a = Array_Double()
-    cdef shared_ptr[cpp_MArray[double]] ap = make_shared[cpp_MArray[double]]()
-    a.cpp_array = dynamic_pointer_cast[cpp_CArrayBase[double],cpp_MArray[double]](ap)
-    if _format.upper() == "JSON":
-        cpp_readJSONFile[double](_fname, deref(ap.get()))
-    elif _format.upper() == "BINARY":
-        cpp_readBINARYFile[double](_fname, deref(ap.get()))
-    else:
-        raise Exception("unknown array file format '{}'".format(_format))
-    return a
-
-
-cdef class AIndex_Double (Index):
-    cdef shared_ptr[cpp_CArrayBase[double]] cpp_array # keep the instance alive
-    cdef shared_ptr[cpp_AIndex[double]] cpp_index
-    cdef bool itercall
-
-    def __cinit__(self,_array,_lexpos=0):
-        cdef size_t l = _lexpos
-        cdef Array_Double a = _array
-        self.cpp_array = a.cpp_array
-        self.cpp_index = make_shared[cpp_AIndex[double]] (a.cpp_array.get().begin().A_plus(l))
-        self.itercall = False
-
-    def __iter__(self):
-        self.cpp_index.get().setlpos(0)
-        self.itercall = True # otherwise first (i.e. zeroth) will be excluded
-        return self
-
-    def __next__(self):
-        cdef AIndex_Double ret = self
-        if self.itercall:
-            ret.itercall = False
-            return ret
-        if self.lex() < self.cpp_index.get().range().get().size()-1:
-            ret.cpp_index = make_shared[cpp_AIndex[double]] (self.cpp_index.get().A_plus(1))
-            return ret
-        else:
-            raise StopIteration
-
-    def lex(self):
-        return self.cpp_index.get().lex()
-
-    def dim(self):
-        return self.cpp_index.get().dim()
-
-    def stringMeta(self):
-        return self.cpp_index.get().stringMeta()
-    
-    def get(self):
-        return self.cpp_index.get().A_get()
-
-    
-cdef class AIndex_Range (Index):
-    cdef shared_ptr[cpp_CArrayBase[shared_ptr[cpp_RangeBase]]] cpp_array # keep the instance alive
-    cdef shared_ptr[cpp_AIndex[shared_ptr[cpp_RangeBase]]] cpp_index
-    cdef bool itercall
-
-    def __cinit__(self,_array,_lexpos=0):
-        cdef size_t l = _lexpos
-        cdef Array_Range a = _array
-        self.cpp_array = a.cpp_array
-        self.cpp_index = make_shared[cpp_AIndex[shared_ptr[cpp_RangeBase]]] (a.cpp_array.get().begin().A_plus(l))
-        self.itercall = False
-
-    def __iter__(self):
-        self.cpp_index.get().setlpos(0)
-        self.itercall = True # otherwise first (i.e. zeroth) will be excluded
-        return self
-
-    def __next__(self):
-        cdef AIndex_Range ret = self
-        if self.itercall:
-            ret.itercall = False
-            return ret
-        if self.lex() < self.cpp_index.get().range().get().size()-1:
-            ret.cpp_index = make_shared[cpp_AIndex[shared_ptr[cpp_RangeBase]]] (self.cpp_index.get().A_plus(1))
-            return ret
-        else:
-            raise StopIteration
-
-    def lex(self):
-        return self.cpp_index.get().lex()
-
-    def dim(self):
-        return self.cpp_index.get().dim()
-
-    def stringMeta(self):
-        return self.cpp_index.get().stringMeta()
-    
-    def get(self):
-        cdef Range r = Range()
-        r.cpp_range = self.cpp_index.get().A_get()
-        return r

cnorxz/core/include/array_wrapper.h

@@ -1,4 +1,7 @@
 
+#ifndef __python_cnorxz_array_wrapper_h__
+#define __python_cnorxz_array_wrapper_h__
+
 #include <Python.h>
 #include "cnorxz.h"
 
@@ -8,7 +11,7 @@ namespace CNORXZ
     class CArrayWrapperBase
     {
     public:
-	DEFAULT_MEMBERS(ArrayWrapperBase);
+	DEFAULT_MEMBERS(CArrayWrapperBase);
 	virtual ~CArrayWrapperBase() = default;
 
 	virtual RangePtr range() const = 0;
@@ -23,7 +26,8 @@ namespace CNORXZ
 	Sptr<CArrayBase<T>> mArr;
 	    
     public:
-	DEFAULT_MEMBERS(ArrayWrapper);
+	CArrayWrapper() : mArr( std::make_shared<MArray<T>>() ) {}
+	//DEFAULT_MEMBERS(CArrayWrapper);
 	CArrayWrapper(const RangePtr& r) : mArr( std::make_shared<MArray<T>>(r) ) {}
 
 	virtual RangePtr range() const override final { return mArr->range(); }
@@ -37,3 +41,13 @@ struct PyCArrayB
     PyObject_HEAD
     CNORXZ::CArrayWrapperBase* ptrObj;
 };
+
+int PyCArrayB_init(PyCArrayB* self, PyObject* args, PyObject* kwds);
+void PyCArrayB_dealloc(PyCArrayB* self);
+PyObject* PyCArrayB_size(PyCArrayB* self);
+PyTypeObject* PyCArrayBType_init();
+
+extern PyMethodDef PyCArrayB_methods[];
+extern PyTypeObject PyCArrayBType;
+
+#endif

cnorxz/core/index.pxd

@@ -1,44 +0,0 @@
-
-from libcpp.memory cimport shared_ptr
-from libcpp.string cimport string
-from range cimport cpp_RangeBase
-
-
-cdef extern from "ranges/ranges.h" namespace "CNORXZ":
-    cdef cppclass cpp_DIndex "CNORXZ::DIndex":
-        cpp_DIndex() except+
-        cpp_DIndex(const cpp_DIndex&) except+
-        cpp_DIndex(const shared_ptr[cpp_RangeBase]&, size_t lexpos) except+
-        cpp_DIndex setlpos "operator=" (size_t n) except+
-        cpp_DIndex setincr "operator++"() except+
-        cpp_DIndex setdecr "operator--"() except+
-        cpp_DIndex plus "operator+"(int n) except+
-        cpp_DIndex minus "operator-"(int n) except+
-
-        size_t lex() except+
-        size_t dim() except+
-
-        shared_ptr[cpp_RangeBase] range() except+
-
-        string stringMeta() except+
-
-
-cdef extern from "ranges/ranges.h" namespace "CNORXZ":
-    cdef cppclass cpp_YIndex "CNORXZ::YIndex":
-        cpp_YIndex() except+
-        cpp_YIndex(const cpp_YIndex&) except+
-        cpp_YIndex(const shared_ptr[cpp_RangeBase]&, size_t lexpos) except+
-        
-        cpp_YIndex setlpos "operator=" (size_t n) except+
-        cpp_YIndex setincr "operator++"() except+
-        cpp_YIndex setdecr "operator--"() except+
-        cpp_YIndex plus "operator+"(int n) except+
-        cpp_YIndex minus "operator-"(int n) except+
-
-        size_t lex() except+
-        size_t dim() except+
-
-        shared_ptr[cpp_RangeBase] range() except+
-
-        string stringMeta() except+
-        

cnorxz/core/lib/array_wrapper.cpp

@@ -1,35 +1,36 @@
 
-#include "cnorxz/core/include/array_wrapper.h"
+#include "array_wrapper.h"
 
-using namespace CNORXZ
+using namespace CNORXZ;
 
-static int PyCArrayB_init(CArrayWrapperBase* self, PyObject* args, PyObject* kwds)
+int PyCArrayB_init(PyCArrayB* self, PyObject* args, PyObject* kwds)
 {
     static char* kwlist[] = { "type", "extension" , NULL };
     SizeT ext = 0;
     const char* type;
 
     if(not PyArg_ParseTupleAndKeywords(args, kwds, "s|k", kwlist, &type, &ext)){
-	return NULL;
+	return -1;
     }
 	    
     if(ext != 0){
 	RangePtr r = CRangeFactory(ext).create();
-	self->ptrObj = new CArrayBase<T>(r);
+	// TODO: different types!!!
+	self->ptrObj = new CArrayWrapper<Double>(r);
     }
     else {
-	self->ptrObj = new CArrayBase<T>();
+	self->ptrObj = new CArrayWrapper<Double>();
     }
     return 0;
 }
 
-static void PyCArrayB_dealloc(CArrayWrapperBase* self)
+void PyCArrayB_dealloc(PyCArrayB* self)
 {
-    delete self->ptrObject;
+    delete self->ptrObj;
     Py_TYPE(self)->tp_free(self);
 }
 
-static PyObject* PyCArrayB_size(CArrayWrapperBase* self)
+PyObject* PyCArrayB_size(PyCArrayB* self)
 {
     if(not self->ptrObj->range()){
 	PyErr_SetString(PyExc_RuntimeError, "array not initialized");
@@ -39,8 +40,27 @@ static PyObject* PyCArrayB_size(CArrayWrapperBase* self)
     return Py_BuildValue("k",retval);
 }
 
-static PyMethodDef PyCArrayB_methods[] = {
+PyMethodDef PyCArrayB_methods[] = {
     { "size", (PyCFunction) PyCArrayB_size, METH_VARARGS, "return size of the array" },
     { NULL }
 };
 
+PyTypeObject PyCArrayBType = { PyVarObject_HEAD_INIT(NULL,0) "cnorxz.CArray" };
+
+PyTypeObject* PyCArrayBType_init()
+{
+    PyCArrayBType.tp_new = PyType_GenericNew;
+    PyCArrayBType.tp_basicsize = sizeof(PyCArrayB);
+    PyCArrayBType.tp_dealloc = (destructor) PyCArrayB_dealloc;
+    PyCArrayBType.tp_flags = Py_TPFLAGS_DEFAULT;
+    PyCArrayBType.tp_doc = "cnorxz CArray wrapper";
+    PyCArrayBType.tp_methods = PyCArrayB_methods;
+    PyCArrayBType.tp_init = (initproc) PyCArrayB_init;
+    
+    if(PyType_Ready(&PyCArrayBType) < 0) {
+	return NULL;
+    }
+    else {
+	return &PyCArrayBType;
+    }
+}

cnorxz/core/range.pxd

@@ -1,11 +0,0 @@
-
-from libcpp.memory cimport shared_ptr
-from array cimport cpp_MArray
-from range cimport cpp_RangeBase
-
-cdef extern from "ranges/ranges.h" namespace "CNORXZ":
-    cdef cppclass cpp_RangeBase "CNORXZ::RangeBase":
-        size_t size() except +
-        size_t dim() except +
-        cpp_MArray[shared_ptr[cpp_RangeBase]] sub() except+
-        

cnorxz/core/range_factory.pxd

@@ -1,12 +0,0 @@
-
-from libcpp.memory cimport shared_ptr
-from range cimport cpp_RangeBase
-
-cdef extern from "ranges/ranges.h" namespace "CNORXZ":
-    cdef cppclass cpp_RangeFactoryBase "CNORXZ::RangeFactoryBase":
-        shared_ptr[cpp_RangeBase] create() except +
-
-cdef extern from "ranges/ranges.h" namespace "CNORXZ":
-    cdef cppclass cpp_CRangeFactory "CNORXZ::CRangeFactory" (cpp_RangeFactoryBase):
-        cpp_CRangeFactory(size_t size) except +
-        shared_ptr[cpp_RangeBase] create() except +

setup.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python
 
 import Cython.Build
-import setuptools
+#import setuptools
+from distutils.core import setup, Extension
 import sysconfig
 import subprocess
 
@@ -25,6 +26,7 @@ if git_hash_tag == git_hash and expected_cnorxz_version != cnorxz_version:
 inc_dirs = list()
 if path_to_cnorxz != "":
     inc_dirs.append( path_to_cnorxz + "/include/cnorxz" )
+inc_dirs.append( "cnorxz/core/include" )
     
 lib_dirs = list()
 lib_dirs.append( "/usr/lib" )
@@ -53,25 +55,32 @@ if __name__ == "__main__":
     for d in lib_dirs:
         print("\t",d)
 
-    extensions = list()
+    #extensions = list()
-    extensions.append(
+    #extensions.append(
-        setuptools.Extension(
+    #    setuptools.Extension(
-            name = libname + ".core",
+    #        #name = libname + ".core",
-            sources = [
+    #        name = libname,
-                "cnorxz/core/core.pyx",
+    #        sources = [
-            ],
+    #            "cnorxz/core/core.cpp",
-            define_macros=[('HAVE_CEREAL',None)],
+    #            "cnorxz/core/lib/array_wrapper.cpp"
-            **default_extension_args
+    #        ],
-        )
+    #        define_macros=[('HAVE_CEREAL',None)],
-    )
+    #        **default_extension_args
+    #    )
+    #)
     # append further extensions (cereal, hdf5, mpi ...) here
     
-    setuptools.setup(
+    setup(
         name = libname,
         packages = setuptools.find_packages(),
         version = version,
         include_dirs = inc_dirs,
-        ext_modules = Cython.Build.cythonize(extensions),
+        ext_modules = [Extension(
+            'cnorxz', ['cnorxz/core/core.cpp','cnorxz/core/lib/array_wrapper.cpp'],
+            define_macros=[('HAVE_CEREAL',None)],
+            **default_extension_args
+        )],
+        #ext_modules = Cython.Build.cythonize(extensions),
         author = author,
         author_email = author_email,
     )