merge

.gitignore

@@ -1,5 +1,5 @@
 .eggs/
 build/
+dist/
 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 +1,46 @@
+
+#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

@@ -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

@@ -1,6 +1,11 @@
 
+#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
 {
@@ -8,32 +13,118 @@ namespace CNORXZ
     class CArrayWrapperBase
     {
     public:
-	DEFAULT_MEMBERS(ArrayWrapperBase);
+	DEFAULT_MEMBERS(CArrayWrapperBase);
 	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>
-    class CArrayWrapper : public CArrayWrapperBase
+    struct Typenum
+    {
+	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<CArrayBase<T>> mArr;
+	Sptr<ArrayBase<T>> mArr;
 	    
     public:
-	DEFAULT_MEMBERS(ArrayWrapper);
-	CArrayWrapper(const RangePtr& r) : mArr( std::make_shared<MArray<T>>(r) ) {}
+	ArrayWrapper() : mArr( std::make_shared<MArray<T>>() ) {}
+	ArrayWrapper(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 PyCArrayB
+struct PyCxArrayB
 {
     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

@@ -0,0 +1,46 @@
+
+#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

@@ -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

@@ -1,46 +1,185 @@
 
-#include "cnorxz/core/include/array_wrapper.h"
+#include "array_wrapper.h"
+#include "range_wrapper.h"
+#include "numpy/arrayobject.h"
 
-using namespace CNORXZ
+using namespace CNORXZ;
+using namespace CNORXZ::cer;
 
-static int PyCArrayB_init(CArrayWrapperBase* self, PyObject* args, PyObject* kwds)
+int PyCxArrayB_init(PyCxArrayB* self, PyObject* args, PyObject* kwds)
 {
     static char* kwlist[] = { "type", "extension" , NULL };
     SizeT ext = 0;
-    const char* type;
+    char* type = NULL;
 
-    if(not PyArg_ParseTupleAndKeywords(args, kwds, "s|k", kwlist, &type, &ext)){
-	return NULL;
+    if(not PyArg_ParseTupleAndKeywords(args, kwds, "|sk", kwlist, &type, &ext)){
+	return -1;
     }
 	    
     if(ext != 0){
 	RangePtr r = CRangeFactory(ext).create();
-	self->ptrObj = new CArrayBase<T>(r);
+	// TODO: different types!!!
+	self->ptrObj = new ArrayWrapper<Double>(r);
     }
     else {
-	self->ptrObj = new CArrayBase<T>();
+	self->ptrObj = new ArrayWrapper<Double>();
     }
     return 0;
 }
 
-static void PyCArrayB_dealloc(CArrayWrapperBase* self)
+void PyCxArrayB_dealloc(PyCxArrayB* self)
 {
-    delete self->ptrObject;
+    delete self->ptrObj;
     Py_TYPE(self)->tp_free(self);
 }
 
-static PyObject* PyCArrayB_size(CArrayWrapperBase* self)
+PyObject* PyCxArrayB_size(PyCxArrayB* 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);
 }
 
-static PyMethodDef PyCArrayB_methods[] = {
-    { "size", (PyCFunction)PyCArrayB_size, METH_VARARGS, "return size of the array" },
-    { NULL }
+PyObject* PyCxArrayB_range(PyCxArrayB* self)
+{
+    if(not self->ptrObj->range()){
+	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

@@ -0,0 +1,106 @@
+
+#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

@@ -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

@@ -1,41 +1,57 @@
 #!/usr/bin/env python
 
-import Cython.Build
+# imports:
+
 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 = "/home/chizeta/repos/cnorxz/install"
-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 = ""
+if 'CNORXZ' in os.environ:
+    path_to_cnorxz = os.environ['CNORXZ']
+version = "0.0.0"
+have_numpy = True
 
-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]
+# flags:
+
+config_bin = path_to_cnorxz+"/bin/cnorxz-config"
+extra_compile_args = sysconfig.get_config_var('CFLAGS').split()
+cnorxz_version = subprocess.run([config_bin,'--version'],stdout=subprocess.PIPE).stdout.decode('ascii')[:-1]
+cnorxz_flags = subprocess.run([config_bin,'--flags'],stdout=subprocess.PIPE).stdout.decode('ascii').split()
+cnorxz_definitions = subprocess.run([config_bin,'--definitions'],stdout=subprocess.PIPE).stdout.decode('ascii').split()
+cnorxz_flags.remove("-Werror")
+cnorxz_flags.append("-Wno-write-strings")
+extra_compile_args += cnorxz_flags
+
+# includes:
 
-assert len(git_tags) != 0, "no version tags found"
-git_tag = git_tags[-1]
-version = git_tag[1:] + 'dev' 
-git_hash_tag = subprocess.run(['git','rev-list','-n','1',git_tag],stdout=subprocess.PIPE).stdout.decode('ascii')[:-1]
-if git_hash_tag == git_hash and expected_cnorxz_version != cnorxz_version:
-    version = git_tag[1:]
-        
 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 != "":
-    inc_dirs.append( path_to_cnorxz + "/lib" )
-lib_dirs.append( "/home/chizeta/repos/cnorxz/install/lib" )
+    lib_dirs.append( path_to_cnorxz + "/lib" )
 
-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()
-extra_compile_args += cnorxz_flags
+# optional dependencies:
+
+if have_numpy:
+    import numpy
+    inc_dirs.append( numpy.get_include() )
+
+# main
 
 default_extension_args = dict(
     language = "c++",
@@ -43,6 +59,7 @@ 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__":
@@ -53,25 +70,15 @@ if __name__ == "__main__":
     for d in lib_dirs:
         print("\t",d)
 
-    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(
+    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','cnorxz/core/lib/range_wrapper.cpp'],
+            **default_extension_args
+        )],
         author = author,
         author_email = author_email,
     )