added xdress integration

.gitignore

@@ -24,3 +24,4 @@ pyne/*/*.cpp
 # Ignore specific files
 examples/BASE_TAPE9.INP
 pyne/tests/test.file
+pyne/tests/test.txt

pyne/CMakeLists.txt

@@ -5,13 +5,17 @@ include_directories(${PYNE_INCLUDE_DIRS})
 get_property(inc_dirs DIRECTORY PROPERTY INCLUDE_DIRECTORIES)
 message("-- C_INCLUDE_PATH for ${CMAKE_CURRENT_SOURCE_DIR}: ${inc_dirs}")
 
+# extra_types
+set_source_files_properties(${PROJECT_SOURCE_DIR}/pyne/extra_types.pyx
+                            PROPERTIES CYTHON_IS_CXX TRUE)
+cython_add_module(extra_types extra_types.pyx)
 
-# STL converters
+# STL containers
 # If the pyx file is a C++ file, we should specify that here.
 # then, add the module
-set_source_files_properties(${PROJECT_SOURCE_DIR}/pyne/stlconverters.pyx 
+set_source_files_properties(${PROJECT_SOURCE_DIR}/pyne/stlcontainers.pyx 
                             PROPERTIES CYTHON_IS_CXX TRUE)
-cython_add_module(stlconverters stlconverters.pyx)
+cython_add_module(stlcontainers stlcontainers.pyx)
 
 # jsoncpp
 set_source_files_properties(${PROJECT_SOURCE_DIR}/pyne/jsoncpp.pyx 

pyne/extra_types.pxd

@@ -7,3 +7,5 @@ cdef extern from "extra_types.h" namespace "extra_types":
     ctypedef struct complex_t:
         double re
         double im
+
+cdef complex_t py2c_complex(object pyv)

pyne/extra_types.pyx

@@ -0,0 +1,9 @@
+cimport extra_types
+
+cdef extra_types.complex_t py2c_complex(object pyv):
+    cdef extra_types.complex_t cv = extra_types.complex_t()
+    pyv = complex(pyv)
+    cv.re = pyv.real
+    cv.im = pyv.imag
+    return cv
+

pyne/stlconverters.pxd → pyne/stlcontainers.pxd

@@ -8,77 +8,37 @@ from libcpp.set cimport set as cpp_set
 from libcpp.vector cimport vector as cpp_vector
 from cython.operator cimport dereference as deref
 from cython.operator cimport preincrement as inc
+from libcpp.string cimport string as std_string
+from libcpp.utility cimport pair
+from libcpp.map cimport map as cpp_map
+from libcpp.vector cimport vector as cpp_vector
 
 # Python Imports
 cimport numpy as np
 
 # Local imports
-include "include/cython_version.pxi"
-IF CYTHON_VERSION_MAJOR == 0 and CYTHON_VERSION_MINOR >= 17:
-    from libcpp.string cimport string as std_string
-    from libcpp.utility cimport pair
-    from libcpp.map cimport map as cpp_map
-    from libcpp.vector cimport vector as cpp_vector
-ELSE:
-    from pyne._includes.libcpp.string cimport string as std_string
-    from pyne._includes.libcpp.utility cimport pair
-    from pyne._includes.libcpp.map cimport map as cpp_map
-    from pyne._includes.libcpp.vector cimport vector as cpp_vector
 cimport extra_types
 
 cimport numpy as np
 
-cdef extra_types.complex_t py2c_complex(object)
-
-cdef np.ndarray c2py_vector_dbl(cpp_vector[double] *)
-
-cdef cpp_vector[double] py2c_vector_dbl(object)
-
-# integer sets
-cdef cpp_set[int] py_to_cpp_set_int(set)
-cdef set cpp_to_py_set_int(cpp_set[int])
-
-
-# string sets
-cdef cpp_set[std_string] py_to_cpp_set_str(set)
-cdef set cpp_to_py_set_str(cpp_set[std_string])
-
-
-# <integer, integer> conversions
-cdef cpp_map[int, int] dict_to_map_int_int(dict)
-cdef dict map_to_dict_int_int(cpp_map[int, int])
-
-
-
-# <integer, double> conversions
-cdef cpp_map[int, double] dict_to_map_int_dbl(dict)
-cdef dict map_to_dict_int_dbl(cpp_map[int, double])
-
-
-
-# <string, integer> conversions
-cdef cpp_map[std_string, int] dict_to_map_str_int(dict)
-cdef dict map_to_dict_str_int(cpp_map[std_string, int])
-
-
-
-# <integer, string> conversions
-cdef cpp_map[int, std_string] dict_to_map_int_str(dict)
-cdef dict map_to_dict_int_str(cpp_map[int, std_string])
-
+# SetStr
+cdef class _SetIterStr(object):
+    cdef cpp_set[std_string].iterator * iter_now
+    cdef cpp_set[std_string].iterator * iter_end
+    cdef void init(_SetIterStr, cpp_set[std_string] *)
 
+cdef class _SetStr:
+    cdef cpp_set[std_string] * set_ptr
+    cdef public bint _free_set
 
-# <string, double> conversions
-cdef cpp_map[std_string, double] dict_to_map_str_dbl(dict)
-cdef dict map_to_dict_str_dbl(cpp_map[std_string, double])
 
 
 
 # SetInt
-cdef class SetIterInt(object):
+cdef class _SetIterInt(object):
     cdef cpp_set[int].iterator * iter_now
     cdef cpp_set[int].iterator * iter_end
-    cdef void init(SetIterInt, cpp_set[int] *)
+    cdef void init(_SetIterInt, cpp_set[int] *)
 
 cdef class _SetInt:
     cdef cpp_set[int] * set_ptr
@@ -87,24 +47,11 @@ cdef class _SetInt:
 
 
 
-# SetStr
-cdef class SetIterStr(object):
-    cdef cpp_set[std_string].iterator * iter_now
-    cdef cpp_set[std_string].iterator * iter_end
-    cdef void init(SetIterStr, cpp_set[std_string] *)
-
-cdef class _SetStr:
-    cdef cpp_set[std_string] * set_ptr
-    cdef public bint _free_set
-
-
-
-
 # MapStrStr
-cdef class MapIterStrStr(object):
+cdef class _MapIterStrStr(object):
     cdef cpp_map[std_string, std_string].iterator * iter_now
     cdef cpp_map[std_string, std_string].iterator * iter_end
-    cdef void init(MapIterStrStr, cpp_map[std_string, std_string] *)
+    cdef void init(_MapIterStrStr, cpp_map[std_string, std_string] *)
 
 cdef class _MapStrStr:
     cdef cpp_map[std_string, std_string] * map_ptr
@@ -114,10 +61,10 @@ cdef class _MapStrStr:
 
 
 # MapStrInt
-cdef class MapIterStrInt(object):
+cdef class _MapIterStrInt(object):
     cdef cpp_map[std_string, int].iterator * iter_now
     cdef cpp_map[std_string, int].iterator * iter_end
-    cdef void init(MapIterStrInt, cpp_map[std_string, int] *)
+    cdef void init(_MapIterStrInt, cpp_map[std_string, int] *)
 
 cdef class _MapStrInt:
     cdef cpp_map[std_string, int] * map_ptr
@@ -127,10 +74,10 @@ cdef class _MapStrInt:
 
 
 # MapIntStr
-cdef class MapIterIntStr(object):
+cdef class _MapIterIntStr(object):
     cdef cpp_map[int, std_string].iterator * iter_now
     cdef cpp_map[int, std_string].iterator * iter_end
-    cdef void init(MapIterIntStr, cpp_map[int, std_string] *)
+    cdef void init(_MapIterIntStr, cpp_map[int, std_string] *)
 
 cdef class _MapIntStr:
     cdef cpp_map[int, std_string] * map_ptr
@@ -140,10 +87,10 @@ cdef class _MapIntStr:
 
 
 # MapStrUInt
-cdef class MapIterStrUInt(object):
+cdef class _MapIterStrUInt(object):
     cdef cpp_map[std_string, extra_types.uint].iterator * iter_now
     cdef cpp_map[std_string, extra_types.uint].iterator * iter_end
-    cdef void init(MapIterStrUInt, cpp_map[std_string, extra_types.uint] *)
+    cdef void init(_MapIterStrUInt, cpp_map[std_string, extra_types.uint] *)
 
 cdef class _MapStrUInt:
     cdef cpp_map[std_string, extra_types.uint] * map_ptr
@@ -153,10 +100,10 @@ cdef class _MapStrUInt:
 
 
 # MapUIntStr
-cdef class MapIterUIntStr(object):
+cdef class _MapIterUIntStr(object):
     cdef cpp_map[extra_types.uint, std_string].iterator * iter_now
     cdef cpp_map[extra_types.uint, std_string].iterator * iter_end
-    cdef void init(MapIterUIntStr, cpp_map[extra_types.uint, std_string] *)
+    cdef void init(_MapIterUIntStr, cpp_map[extra_types.uint, std_string] *)
 
 cdef class _MapUIntStr:
     cdef cpp_map[extra_types.uint, std_string] * map_ptr
@@ -165,37 +112,37 @@ cdef class _MapUIntStr:
 
 
 
-# MapUIntUInt
-cdef class MapIterUIntUInt(object):
-    cdef cpp_map[extra_types.uint, extra_types.uint].iterator * iter_now
-    cdef cpp_map[extra_types.uint, extra_types.uint].iterator * iter_end
-    cdef void init(MapIterUIntUInt, cpp_map[extra_types.uint, extra_types.uint] *)
+# MapStrDouble
+cdef class _MapIterStrDouble(object):
+    cdef cpp_map[std_string, double].iterator * iter_now
+    cdef cpp_map[std_string, double].iterator * iter_end
+    cdef void init(_MapIterStrDouble, cpp_map[std_string, double] *)
 
-cdef class _MapUIntUInt:
-    cdef cpp_map[extra_types.uint, extra_types.uint] * map_ptr
+cdef class _MapStrDouble:
+    cdef cpp_map[std_string, double] * map_ptr
     cdef public bint _free_map
 
 
 
 
-# MapStrDouble
-cdef class MapIterStrDouble(object):
-    cdef cpp_map[std_string, double].iterator * iter_now
-    cdef cpp_map[std_string, double].iterator * iter_end
-    cdef void init(MapIterStrDouble, cpp_map[std_string, double] *)
+# MapUIntUInt
+cdef class _MapIterUIntUInt(object):
+    cdef cpp_map[extra_types.uint, extra_types.uint].iterator * iter_now
+    cdef cpp_map[extra_types.uint, extra_types.uint].iterator * iter_end
+    cdef void init(_MapIterUIntUInt, cpp_map[extra_types.uint, extra_types.uint] *)
 
-cdef class _MapStrDouble:
-    cdef cpp_map[std_string, double] * map_ptr
+cdef class _MapUIntUInt:
+    cdef cpp_map[extra_types.uint, extra_types.uint] * map_ptr
     cdef public bint _free_map
 
 
 
 
 # MapIntInt
-cdef class MapIterIntInt(object):
+cdef class _MapIterIntInt(object):
     cdef cpp_map[int, int].iterator * iter_now
     cdef cpp_map[int, int].iterator * iter_end
-    cdef void init(MapIterIntInt, cpp_map[int, int] *)
+    cdef void init(_MapIterIntInt, cpp_map[int, int] *)
 
 cdef class _MapIntInt:
     cdef cpp_map[int, int] * map_ptr
@@ -205,10 +152,10 @@ cdef class _MapIntInt:
 
 
 # MapIntDouble
-cdef class MapIterIntDouble(object):
+cdef class _MapIterIntDouble(object):
     cdef cpp_map[int, double].iterator * iter_now
     cdef cpp_map[int, double].iterator * iter_end
-    cdef void init(MapIterIntDouble, cpp_map[int, double] *)
+    cdef void init(_MapIterIntDouble, cpp_map[int, double] *)
 
 cdef class _MapIntDouble:
     cdef cpp_map[int, double] * map_ptr
@@ -217,24 +164,11 @@ cdef class _MapIntDouble:
 
 
 
-# MapUIntDouble
-cdef class MapIterUIntDouble(object):
-    cdef cpp_map[extra_types.uint, double].iterator * iter_now
-    cdef cpp_map[extra_types.uint, double].iterator * iter_end
-    cdef void init(MapIterUIntDouble, cpp_map[extra_types.uint, double] *)
-
-cdef class _MapUIntDouble:
-    cdef cpp_map[extra_types.uint, double] * map_ptr
-    cdef public bint _free_map
-
-
-
-
 # MapIntComplex
-cdef class MapIterIntComplex(object):
+cdef class _MapIterIntComplex(object):
     cdef cpp_map[int, extra_types.complex_t].iterator * iter_now
     cdef cpp_map[int, extra_types.complex_t].iterator * iter_end
-    cdef void init(MapIterIntComplex, cpp_map[int, extra_types.complex_t] *)
+    cdef void init(_MapIterIntComplex, cpp_map[int, extra_types.complex_t] *)
 
 cdef class _MapIntComplex:
     cdef cpp_map[int, extra_types.complex_t] * map_ptr
@@ -243,24 +177,24 @@ cdef class _MapIntComplex:
 
 
 
-# MapIntVectorDouble
-cdef class MapIterIntVectorDouble(object):
-    cdef cpp_map[int, cpp_vector[double]].iterator * iter_now
-    cdef cpp_map[int, cpp_vector[double]].iterator * iter_end
-    cdef void init(MapIterIntVectorDouble, cpp_map[int, cpp_vector[double]] *)
+# MapUIntDouble
+cdef class _MapIterUIntDouble(object):
+    cdef cpp_map[extra_types.uint, double].iterator * iter_now
+    cdef cpp_map[extra_types.uint, double].iterator * iter_end
+    cdef void init(_MapIterUIntDouble, cpp_map[extra_types.uint, double] *)
 
-cdef class _MapIntVectorDouble:
-    cdef cpp_map[int, cpp_vector[double]] * map_ptr
+cdef class _MapUIntDouble:
+    cdef cpp_map[extra_types.uint, double] * map_ptr
     cdef public bint _free_map
 
 
 
 
 # MapStrVectorDouble
-cdef class MapIterStrVectorDouble(object):
+cdef class _MapIterStrVectorDouble(object):
     cdef cpp_map[std_string, cpp_vector[double]].iterator * iter_now
     cdef cpp_map[std_string, cpp_vector[double]].iterator * iter_end
-    cdef void init(MapIterStrVectorDouble, cpp_map[std_string, cpp_vector[double]] *)
+    cdef void init(_MapIterStrVectorDouble, cpp_map[std_string, cpp_vector[double]] *)
 
 cdef class _MapStrVectorDouble:
     cdef cpp_map[std_string, cpp_vector[double]] * map_ptr
@@ -269,3 +203,16 @@ cdef class _MapStrVectorDouble:
 
 
 
+# MapIntVectorDouble
+cdef class _MapIterIntVectorDouble(object):
+    cdef cpp_map[int, cpp_vector[double]].iterator * iter_now
+    cdef cpp_map[int, cpp_vector[double]].iterator * iter_end
+    cdef void init(_MapIterIntVectorDouble, cpp_map[int, cpp_vector[double]] *)
+
+cdef class _MapIntVectorDouble:
+    cdef cpp_map[int, cpp_vector[double]] * map_ptr
+    cdef public bint _free_map
+
+
+
+