.gitignore

@@ -1,5 +1,5 @@
 .eggs/
 build/
-dist/
 cnorxz.egg-info/
 *.so
+*.cpp

cnorxz/core/array.pxd

@@ -0,0 +1,60 @@
+
+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

@@ -0,0 +1,24 @@
+
+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

@@ -1,46 +0,0 @@
-
-#include <Python.h>
-#include "array_wrapper.h"
-#include "range_wrapper.h"
-
-using namespace CNORXZ;
-
-static PyMethodDef cnorxz_core_methods[] = {
-    { "readFile", (PyCFunction) PyCxReadFile, METH_VARARGS| METH_KEYWORDS, "Read cnorxz-formatted file." },
-    { NULL, NULL, 0, NULL }
-};
-
-static PyModuleDef cnorxz_core_module = {
-    PyModuleDef_HEAD_INIT,
-    "cnorxz",
-    "cnorxz core module",
-    -1,
-    cnorxz_core_methods
-};
-
-PyMODINIT_FUNC PyInit_cnorxz()
-{
-    PyObject* m;
-
-    PyTypeObject* cxarray_type = PyCxArrayBType_init();
-    PyTypeObject* cxrange_type = PyCxRangeType_init();
-    if(cxarray_type == NULL){
-	return NULL;
-    }
-    if(cxrange_type == NULL){
-	return NULL;
-    }
-    
-    m = PyModule_Create(&cnorxz_core_module);
-    if(m == NULL){
-	return NULL;
-    }
-
-    Py_INCREF(cxarray_type);
-    Py_INCREF(cxrange_type);
-
-    PyModule_AddObject(m, "Array", (PyObject*) cxarray_type);
-    PyModule_AddObject(m, "Range", (PyObject*) cxrange_type);
-
-    return m;
-}

cnorxz/core/core.pyx

@@ -0,0 +1,284 @@
+#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

@@ -1,11 +1,6 @@
 
-#ifndef __python_cnorxz_array_wrapper_h__
-#define __python_cnorxz_array_wrapper_h__
-
 #include <Python.h>
 #include "cnorxz.h"
-#include "cereal/cnorxz_cereal.h"
-#include "numpy/ndarraytypes.h"
 
 namespace CNORXZ
 {
@@ -13,118 +8,32 @@ namespace CNORXZ
     class CArrayWrapperBase
     {
     public:
-	DEFAULT_MEMBERS(CArrayWrapperBase);
+	DEFAULT_MEMBERS(ArrayWrapperBase);
 	virtual ~CArrayWrapperBase() = default;
 
 	virtual RangePtr range() const = 0;
 	virtual SizeT size() const = 0;
 	// virtual PyObject* get() const = 0; // operator[]!!
-#ifdef HAVE_CEREAL
-	virtual void writeFile(cer::Format f, const String& fname) const = 0;
-	virtual void readFile(cer::Format f, const String& fname) const = 0;
-#endif
-	virtual int typenum() const = 0;
-	virtual const void* data() const = 0;
-	virtual SizeT datasize() const = 0;
-    };
-
-    class ArrayWrapperBase : public CArrayWrapperBase
-    {
-    public:
-	virtual void* data() = 0;
     };
 
     template <typename T>
-    struct Typenum
+    class CArrayWrapper : public CArrayWrapperBase
-    {
-	static const int value = NPY_NOTYPE;
-    };
-
-    template <>
-    struct Typenum<Double>
-    {
-	static const int value = NPY_DOUBLE;
-    };
-
-    template <>
-    struct Typenum<Int>
-    {
-	static const int value = NPY_INT32;
-    };
-
-    template <>
-    struct Typenum<LInt>
-    {
-	static const int value = NPY_INT64;
-    };
-
-    template <>
-    struct Typenum<SizeT>
-    {
-	static const int value = NPY_UINT64;
-    };
-
-    template <typename T>
-    class ArrayWrapper : public ArrayWrapperBase
     {
     private:
-	Sptr<ArrayBase<T>> mArr;
+	Sptr<CArrayBase<T>> mArr;
 	    
     public:
-	ArrayWrapper() : mArr( std::make_shared<MArray<T>>() ) {}
+	DEFAULT_MEMBERS(ArrayWrapper);
-	ArrayWrapper(const RangePtr& r) : mArr( std::make_shared<MArray<T>>(r) ) {}
+	CArrayWrapper(const RangePtr& r) : mArr( std::make_shared<MArray<T>>(r) ) {}
-	ArrayWrapper(const Sptr<ArrayBase<T>>& arr) : mArr(arr) {}
 
 	virtual RangePtr range() const override final { return mArr->range(); }
 	virtual SizeT size() const override final { return mArr->size(); }
-#ifdef HAVE_CEREAL
-	virtual void writeFile(cer::Format f, const String& fname) const override final
-	{
-	    auto a = std::dynamic_pointer_cast<MArray<T>>( mArr );
-	    if(a){
-		if(f == cer::Format::XML) { cer::writeXMLFile(fname, *a); }
-		else if(f == cer::Format::JSON) { cer::writeJSONFile(fname, *a); }
-		else { cer::writeBINARYFile(fname, *a); }
-	    }
-	}
-	
-	virtual void readFile(cer::Format f, const String& fname) const override final
-	{
-	    auto a = std::dynamic_pointer_cast<MArray<T>>( mArr );
-	    if(a){
-		if(f == cer::Format::XML) { cer::readXMLFile(fname, *a); }
-		else if(f == cer::Format::JSON) { cer::readJSONFile(fname, *a); }
-		else { cer::readBINARYFile(fname, *a); }
-	    }
-	}
-#endif
-	virtual int typenum() const override final { return Typenum<T>::value; }
-	virtual const void* data() const override final
-	{ return reinterpret_cast<const void*>( mArr->data() ); }
-	virtual void* data() override final
-	{ return reinterpret_cast<void*>( mArr->data() ); }
-	virtual SizeT datasize() const override final { return size() * sizeof(T); }
     };
 	
 }
 
-struct PyCxArrayB
+struct PyCArrayB
 {
     PyObject_HEAD
     CNORXZ::CArrayWrapperBase* ptrObj;
 };
-
-int PyCxArrayB_init(PyCxArrayB* self, PyObject* args, PyObject* kwds);
-void PyCxArrayB_dealloc(PyCxArrayB* self);
-PyObject* PyCxArrayB_size(PyCxArrayB* self);
-PyObject* PyCxArrayB_range(PyCxArrayB* self);
-PyObject* PyCxArrayB_writeFile(PyCxArrayB* self, PyObject* args, PyObject* kwds);
-PyObject* PyCxArrayB_readFile(PyCxArrayB* self, PyObject* args, PyObject* kwds);
-PyTypeObject* PyCxArrayBType_init();
-
-PyObject* PyCxReadFile(PyObject* self, PyObject* args, PyObject* kwds);
-
-extern PyMethodDef PyCxArrayB_methods[];
-extern PyTypeObject PyCxArrayBType;
-
-#endif

cnorxz/core/include/range_wrapper.h

@@ -1,46 +0,0 @@
-
-#ifndef __python_cnorxz_range_wrapper_h__
-#define __python_cnorxz_range_wrapper_h__
-
-#include <Python.h>
-#include "cnorxz.h"
-
-namespace CNORXZ
-{
-    class RangeWrapper
-    {
-    public:
-	DEFAULT_MEMBERS(RangeWrapper);
-	RangeWrapper(const RangePtr r) : mR(r) {}
-	inline bool _init() const { return mR != nullptr; }
-	inline SizeT size() const { return mR->size(); }
-	inline SizeT dim() const { return mR->dim(); }
-	inline RangePtr sub(SizeT pos) { return mR->sub(pos); }
-	inline String stringMeta(SizeT pos) const { return mR->stringMeta(pos); }
-	inline MArray<RangePtr> sub() const { return mR->sub(); }
-	inline RangePtr sub(SizeT pos) const { return mR->sub(pos); }
-	
-    private:
-	RangePtr mR;
-    };
-}
-
-struct PyCxRange
-{
-    PyObject_HEAD
-    CNORXZ::RangeWrapper* ptrObj;
-};
-
-int PyCxRange_init(PyCxRange* self, PyObject* args, PyObject* kwds);
-void PyCxRange_dealloc(PyCxRange* self);
-PyObject* PyCxRange_size(PyCxRange* self);
-PyObject* PyCxRange_dim(PyCxRange* self);
-PyObject* PyCxRange_sub(PyCxRange* self, PyObject* args, PyObject* kwds);
-PyObject* PyCxRange_stringMeta(PyCxRange* self, PyObject* args, PyObject* kwds);
-PyObject* PyCxRange_sub(PyCxRange* self, PyObject* args, PyObject* kwds);
-PyTypeObject* PyCxRangeType_init();
-
-extern PyMethodDef PyCxRange_methods[];
-extern PyTypeObject PyCxRangeType;
-
-#endif

cnorxz/core/index.pxd

@@ -0,0 +1,44 @@
+
+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

@@ -1,185 +1,46 @@
 
-#include "array_wrapper.h"
+#include "cnorxz/core/include/array_wrapper.h"
-#include "range_wrapper.h"
-#include "numpy/arrayobject.h"
 
-using namespace CNORXZ;
+using namespace CNORXZ
-using namespace CNORXZ::cer;
 
-int PyCxArrayB_init(PyCxArrayB* self, PyObject* args, PyObject* kwds)
+static int PyCArrayB_init(CArrayWrapperBase* self, PyObject* args, PyObject* kwds)
 {
     static char* kwlist[] = { "type", "extension" , NULL };
     SizeT ext = 0;
-    char* type = NULL;
+    const char* type;
 
-    if(not PyArg_ParseTupleAndKeywords(args, kwds, "|sk", kwlist, &type, &ext)){
+    if(not PyArg_ParseTupleAndKeywords(args, kwds, "s|k", kwlist, &type, &ext)){
-	return -1;
+	return NULL;
     }
 	    
     if(ext != 0){
 	RangePtr r = CRangeFactory(ext).create();
-	// TODO: different types!!!
+	self->ptrObj = new CArrayBase<T>(r);
-	self->ptrObj = new ArrayWrapper<Double>(r);
     }
     else {
-	self->ptrObj = new ArrayWrapper<Double>();
+	self->ptrObj = new CArrayBase<T>();
     }
     return 0;
 }
 
-void PyCxArrayB_dealloc(PyCxArrayB* self)
+static void PyCArrayB_dealloc(CArrayWrapperBase* self)
 {
-    delete self->ptrObj;
+    delete self->ptrObject;
     Py_TYPE(self)->tp_free(self);
 }
 
-PyObject* PyCxArrayB_size(PyCxArrayB* self)
+static PyObject* PyCArrayB_size(CArrayWrapperBase* self)
 {
     if(not self->ptrObj->range()){
 	PyErr_SetString(PyExc_RuntimeError, "array not initialized");
 	return NULL;
     }
     const SizeT retval = self->ptrObj->size();
-    return Py_BuildValue("k", retval);
+    return Py_BuildValue("k",retval);
 }
 
-PyObject* PyCxArrayB_range(PyCxArrayB* self)
+static PyMethodDef PyCArrayB_methods[] = {
-{
+    { "size", (PyCFunction)PyCArrayB_size, METH_VARARGS, "return size of the array" },
-    if(not self->ptrObj->range()){
+    { NULL }
-	PyErr_SetString(PyExc_RuntimeError, "array not initialized");
-	return NULL;
-    }
-    const RangePtr r = self->ptrObj->range();
-    PyCxRange* o;
-    o = PyObject_New(PyCxRange, &PyCxRangeType);
-    o->ptrObj = new RangeWrapper(r);
-    return Py_BuildValue("O", o);
-}
-
-Format formatFromString(const char* fstr)
-{
-    Format f = Format::BINARY;
-    if(fstr != NULL){
-	if(strcmp(fstr,"binary") == 0){
-	    f = Format::BINARY;
-	}
-	else if(strcmp(fstr,"json") == 0){
-	    f = Format::JSON;
-	}
-	else if(strcmp(fstr,"xml") == 0){
-	    f = Format::XML;
-	}
-	else {
-	    PyErr_SetString(PyExc_RuntimeError, "unknown format");
-	}
-    }
-    return f;
-}
-
-#ifdef HAVE_CEREAL
-
-PyObject* PyCxArrayB_writeFile(PyCxArrayB* self, PyObject* args, PyObject* kwds)
-{
-    if(not self->ptrObj->range()){
-	PyErr_SetString(PyExc_RuntimeError, "array not initialized");
-    }
-    static char* kwlist[] = { "format", "filename" , NULL };
-    char* fname = NULL;
-    char* format = NULL;
-
-    if(not PyArg_ParseTupleAndKeywords(args, kwds, "ss|", kwlist, &fname, &format)){
-	return NULL;
-    }
-    const String fn(fname);
-    const Format f = formatFromString(format);
-    self->ptrObj->writeFile(f, fn);
-    Py_RETURN_NONE;
-}
-
-PyObject* PyCxArrayB_readFile(PyCxArrayB* self, PyObject* args, PyObject* kwds)
-{
-    static char* kwlist[] = { "format", "filename" , NULL };
-    char* fname = NULL;
-    char* format = NULL;
-
-    if(not PyArg_ParseTupleAndKeywords(args, kwds, "ss|", kwlist, &fname, &format)){
-	return NULL;
-    }
-    const String fn(fname);
-    const Format f = formatFromString(format);
-    self->ptrObj->readFile(f, fn);
-    Py_RETURN_NONE;
-}
-#endif
-
-PyObject* PyCxArrayB_npa(PyCxArrayB* self)
-{
-    // return viewing (!) numpy array
-    if(not self->ptrObj->range()){
-	PyErr_SetString(PyExc_RuntimeError, "array not initialized");
-	return NULL;
-    }
-    const SizeT d = self->ptrObj->range()->dim();
-    std::vector<npy_intp> dims(d);
-    for(SizeT i = 0; i != dims.size(); ++i){
-	dims[i] = self->ptrObj->range()->sub(i)->size();
-    }
-    // TODO: Do the following for mutable arrays!!!
-    /*
-    Py_INCREF(self); // keep data alive
-    PyObject* o = PyArray_SimpleNewFromData
-	( static_cast<int>( d ) , dims.data(), self->ptrObj->typenum(), self->ptrObj->data() );
-    PyArray_BASE(o) = (PyObject*) self;
-    */
-    PyObject* o = PyArray_SimpleNew
-	( static_cast<int>( d ) , dims.data(), self->ptrObj->typenum() );
-    void* data = PyArray_DATA(o);
-    //const npy_intp s = PyArray_NBYTES(o);
-    const SizeT s = static_cast<SizeT>( PyArray_NBYTES(o) );
-    if(s != self->ptrObj->datasize()) {
-	PyErr_Format(PyExc_RuntimeError, "lib error %d vs %d", s, self->ptrObj->datasize());
-	//PyErr_SetString(PyExc_RuntimeError, "lib error");
-	return NULL;
-    }
-    memcpy( data, self->ptrObj->data(), self->ptrObj->datasize() );
-    return o;
-}
-
-PyMethodDef PyCxArrayB_methods[] = {
-    { "size", (PyCFunction) PyCxArrayB_size, METH_VARARGS| METH_KEYWORDS, "return size of the array" },
-    { "range", (PyCFunction) PyCxArrayB_range, METH_VARARGS| METH_KEYWORDS, "return array range" },
-    { "writeFile", (PyCFunction) PyCxArrayB_writeFile, METH_VARARGS| METH_KEYWORDS, "write array to file" },
-    { "readFile", (PyCFunction) PyCxArrayB_readFile, METH_VARARGS| METH_KEYWORDS, "read array from file" },
-    { "npa", (PyCFunction) PyCxArrayB_npa, METH_VARARGS| METH_KEYWORDS, "return numpy array (view)" },
-    { NULL, NULL, 0, NULL }
 };
 
-PyTypeObject PyCxArrayBType = { PyVarObject_HEAD_INIT(NULL,0) "cnorxz.Array" };
-
-PyTypeObject* PyCxArrayBType_init()
-{
-    PyCxArrayBType.tp_new = PyType_GenericNew;
-    PyCxArrayBType.tp_basicsize = sizeof(PyCxArrayB);
-    PyCxArrayBType.tp_dealloc = (destructor) PyCxArrayB_dealloc;
-    PyCxArrayBType.tp_flags = Py_TPFLAGS_DEFAULT;
-    PyCxArrayBType.tp_doc = "cnorxz Array wrapper";
-    PyCxArrayBType.tp_methods = PyCxArrayB_methods;
-    PyCxArrayBType.tp_init = (initproc) PyCxArrayB_init;
-    
-    import_array();
-    
-    if(PyType_Ready(&PyCxArrayBType) < 0) {
-	return NULL;
-    }
-    else {
-	return &PyCxArrayBType;
-    }
-}
-
-PyObject* PyCxReadFile(PyObject* self, PyObject* args, PyObject* kwds)
-{
-    PyCxArrayB* out = (PyCxArrayB*) PyObject_NEW(PyCxArrayB, &PyCxArrayBType);
-    out->ptrObj = new ArrayWrapper<Double>();
-    PyCxArrayB_readFile(out,args,kwds);
-    return Py_BuildValue("O", out);;
-}

cnorxz/core/lib/range_wrapper.cpp

@@ -1,106 +0,0 @@
-
-#include "array_wrapper.h"
-#include "range_wrapper.h"
-
-using namespace CNORXZ;
-
-int PyCxRange_init(PyCxRange* self, PyObject* args, PyObject* kwds)
-{
-
-    //!!!
-    return 0;
-}
-
-void PyCxRange_dealloc(PyCxRange* self)
-{
-    delete self->ptrObj;
-    Py_TYPE(self)->tp_free(self);
-}
-
-PyObject* PyCxRange_size(PyCxRange* self)
-{
-    if(not self->ptrObj->_init()){
-	const SizeT retval = 0;
-	return Py_BuildValue("k", retval);
-    }
-    const SizeT retval = self->ptrObj->size();
-    return Py_BuildValue("k", retval);
-}
-
-PyObject* PyCxRange_dim(PyCxRange* self)
-{
-    if(not self->ptrObj->_init()){
-	const SizeT retval = 0;
-	return Py_BuildValue("k", retval);
-    }
-    const SizeT retval = self->ptrObj->dim();
-    return Py_BuildValue("k", retval);
-}
-
-PyObject* PyCxRange_sub(PyCxRange* self, PyObject* args, PyObject* kwds)
-{
-    static char* kwlist[] = { "pos", NULL };
-    SizeT pos = 0;
-    
-    if(not PyArg_ParseTupleAndKeywords(args, kwds, "k|", kwlist, &pos)){
-	return NULL;
-    }
-
-    SizeT dim = self->ptrObj->dim();
-    if(pos >= dim){
-	return PyErr_Format(PyExc_RuntimeError, "requested sub-range position (%d) exceeds range dimension (%d)", pos, dim);
-    }
-
-    // entire set of sub-ranges:
-    /*
-    PyCxArrayB* o;
-    o = PyObject_New(PyCxArrayB, &PyCxArrayBType);
-    o->ptrObj = new ArrayWrapper<RangePtr>( std::make_shared<MArray<RangePtr>>(self->ptrObj->sub()) );
-    return Py_BuildValue("O", o);
-    */
-    
-    const RangePtr r = self->ptrObj->sub(pos);
-    PyCxRange* o = PyObject_New(PyCxRange, &PyCxRangeType);
-    o->ptrObj = new RangeWrapper(r);
-    return Py_BuildValue("O", o);
-}
-
-PyObject* PyCxRange_stringMeta(PyCxRange* self, PyObject* args, PyObject* kwds)
-{
-    const SizeT size = self->ptrObj->size();
-    PyObject* out = PyList_New(size);
-    for(SizeT i = 0; i != size; ++i){
-	PyObject* s = Py_BuildValue("s", self->ptrObj->stringMeta(i).c_str() );
-	PyList_SetItem(out, i, s);
-    }
-    return out;
-}
-
-PyMethodDef PyCxRange_methods[] = {
-    { "size", (PyCFunction) PyCxRange_size, METH_VARARGS, "return range size" },
-    { "dim", (PyCFunction) PyCxRange_dim, METH_VARARGS, "return range dimension" },
-    { "sub", (PyCFunction) PyCxRange_sub, METH_VARARGS|METH_KEYWORDS, "return sub-range for given dimension" },
-    { "stringMeta", (PyCFunction) PyCxRange_stringMeta, METH_VARARGS,
-      "return string meta data for given range position" },
-    { NULL }
-};
-
-PyTypeObject PyCxRangeType = { PyVarObject_HEAD_INIT(NULL,0) "cnorxz.Range" };
-
-PyTypeObject* PyCxRangeType_init()
-{
-    PyCxRangeType.tp_new = PyType_GenericNew;
-    PyCxRangeType.tp_basicsize = sizeof(PyCxRange);
-    PyCxRangeType.tp_dealloc = (destructor) PyCxRange_dealloc;
-    PyCxRangeType.tp_flags = Py_TPFLAGS_DEFAULT;
-    PyCxRangeType.tp_doc = "cnorxz Range wrapper";
-    PyCxRangeType.tp_methods = PyCxRange_methods;
-    PyCxRangeType.tp_init = (initproc) PyCxRange_init;
-
-    if(PyType_Ready(&PyCxRangeType) < 0){
-	return NULL;
-    }
-    else {
-	return &PyCxRangeType;
-    }
-}

cnorxz/core/range.pxd

@@ -0,0 +1,11 @@
+
+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

@@ -0,0 +1,12 @@
+
+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

@@ -1,57 +1,41 @@
 #!/usr/bin/env python
 
-# imports:
+import Cython.Build
-
 import setuptools
-from distutils.core import setup, Extension
-import os
 import sysconfig
 import subprocess
 
-# basic variables:
-
 libname = "cnorxz"
 author = "Christian Zimmermann"
 author_email = "chizeta@f3l.de"
-path_to_cnorxz = ""
+path_to_cnorxz = "/home/chizeta/repos/cnorxz/install"
-if 'CNORXZ' in os.environ:
+expected_cnorxz_version = "1.0.0" # dummy for now; in the future this is supposed to be the c++ version which is guaranteed to be compatible with py cnorxz
-    path_to_cnorxz = os.environ['CNORXZ']
-version = "0.0.0"
-have_numpy = True
 
-# flags:
+git_hash = subprocess.run(['git','rev-parse','HEAD'],stdout=subprocess.PIPE).stdout.decode('ascii')[:-1]
+git_tags = subprocess.run(['git', 'tag', '-l', '--sort=refname', 'v*'],stdout=subprocess.PIPE).stdout.decode('ascii').split()
+cnorxz_version = subprocess.run([path_to_cnorxz+"/bin/cnorxz-config",'--version'],stdout=subprocess.PIPE).stdout.decode('ascii')[:-1]
 
-config_bin = path_to_cnorxz+"/bin/cnorxz-config"
+assert len(git_tags) != 0, "no version tags found"
-extra_compile_args = sysconfig.get_config_var('CFLAGS').split()
+git_tag = git_tags[-1]
-cnorxz_version = subprocess.run([config_bin,'--version'],stdout=subprocess.PIPE).stdout.decode('ascii')[:-1]
+version = git_tag[1:] + 'dev' 
-cnorxz_flags = subprocess.run([config_bin,'--flags'],stdout=subprocess.PIPE).stdout.decode('ascii').split()
+git_hash_tag = subprocess.run(['git','rev-list','-n','1',git_tag],stdout=subprocess.PIPE).stdout.decode('ascii')[:-1]
-cnorxz_definitions = subprocess.run([config_bin,'--definitions'],stdout=subprocess.PIPE).stdout.decode('ascii').split()
+if git_hash_tag == git_hash and expected_cnorxz_version != cnorxz_version:
-cnorxz_flags.remove("-Werror")
+    version = git_tag[1:]
-cnorxz_flags.append("-Wno-write-strings")
-extra_compile_args += cnorxz_flags
-
-# includes:
         
 inc_dirs = list()
 if path_to_cnorxz != "":
     inc_dirs.append( path_to_cnorxz + "/include/cnorxz" )
-inc_dirs.append( "cnorxz/core/include" )
-
-# library dirs:
 
 lib_dirs = list()
 lib_dirs.append( "/usr/lib" )
 lib_dirs.append( "/usr/local/lib" )
 if path_to_cnorxz != "":
-    lib_dirs.append( path_to_cnorxz + "/lib" )
+    inc_dirs.append( path_to_cnorxz + "/lib" )
+lib_dirs.append( "/home/chizeta/repos/cnorxz/install/lib" )
 
-# optional dependencies:
+extra_compile_args = sysconfig.get_config_var('CFLAGS').split()
-
+cnorxz_flags = subprocess.run([path_to_cnorxz+"/bin/cnorxz-config",'--flags'],stdout=subprocess.PIPE).stdout.decode('ascii').split()
-if have_numpy:
+extra_compile_args += cnorxz_flags
-    import numpy
-    inc_dirs.append( numpy.get_include() )
-
-# main
 
 default_extension_args = dict(
     language = "c++",
@@ -59,7 +43,6 @@ default_extension_args = dict(
     libraries = [libname],
     library_dirs = lib_dirs,
     extra_compile_args = extra_compile_args,
-    define_macros = [(mac,None) for mac in cnorxz_definitions]
 )
 
 if __name__ == "__main__":
@@ -70,15 +53,25 @@ if __name__ == "__main__":
     for d in lib_dirs:
         print("\t",d)
 
-    setup(
+    extensions = list()
+    extensions.append(
+        setuptools.Extension(
+            name = libname + ".core",
+            sources = [
+                "cnorxz/core/core.pyx",
+            ],
+            define_macros=[('HAVE_CEREAL',None)],
+            **default_extension_args
+        )
+    )
+    # append further extensions (cereal, hdf5, mpi ...) here
+    
+    setuptools.setup(
         name = libname,
         packages = setuptools.find_packages(),
         version = version,
         include_dirs = inc_dirs,
-        ext_modules = [Extension(
+        ext_modules = Cython.Build.cythonize(extensions),
-            'cnorxz', ['cnorxz/core/core.cpp','cnorxz/core/lib/array_wrapper.cpp','cnorxz/core/lib/range_wrapper.cpp'],
-            **default_extension_args
-        )],
         author = author,
         author_email = author_email,
     )