From 08be4e231d35a957c11949440b4e695a33f45c64 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Thu, 6 Apr 2017 14:41:43 +0200
Subject: [PATCH] Cython Object API

---
 python/obitools3/dms/object.pxd | 10 ++---
 python/obitools3/dms/object.pyx | 74 +++++++++++++++++----------------
 2 files changed, 43 insertions(+), 41 deletions(-)

diff --git a/python/obitools3/dms/object.pxd b/python/obitools3/dms/object.pxd
index 907866b..93ad286 100644
--- a/python/obitools3/dms/object.pxd
+++ b/python/obitools3/dms/object.pxd
@@ -6,7 +6,7 @@ cdef dict __c_cython_mapping__
 
 cdef class OBIObject:
 
-    cdef dict _dependent_object
+    cdef dict _dependent_objects
    
     cdef register(self, OBIObject object)
     cdef unregister(self, OBIObject object)
@@ -16,12 +16,12 @@ cdef class OBIObject:
 cdef class OBIWrapper(OBIObject):
     
     cdef void*  _pointer
-    cdef size_t cid(self)
-        
-    cpdef bint active(self)
+    
+    cdef inline size_t cid(self)    
+    cdef inline bint active(self)
     
     @staticmethod
-    cdef object new_wrapper(type constructor, void* pointer)
+    cdef object new(type constructor, void* pointer)
 
 
 cdef class OBIObjectClosedInstance(Exception):
diff --git a/python/obitools3/dms/object.pyx b/python/obitools3/dms/object.pyx
index 2fc1fa1..eb70eae 100644
--- a/python/obitools3/dms/object.pyx
+++ b/python/obitools3/dms/object.pyx
@@ -1,83 +1,85 @@
 #cython: language_level=3
 
 
-__c_cython_mapping__={}
+__c_cython_mapping__ = {}
 
 
 cdef class OBIObject:
 
+    def __init__(self, __internalCall__) :
+                
+        if __internalCall__ != 987654 or \
+           type(self) == OBIObject or \
+           type(self) == OBIWrapper or \
+           not isinstance(self, OBIObject) :
+            
+            raise RuntimeError('OBIObject constructor can not be called directly')
+        
+        self._dependent_objects = {}
+
+
     cdef register(self, OBIObject object):
-        self._dependent_object[id(object)]=object
+        self._dependent_objects[id(object)] = object
 
         
     cdef unregister(self, OBIObject object):
-        del self._dependent_object[id(object)]
+        del self._dependent_objects[id(object)]
         
 
     cpdef close(self):
     
         cdef OBIObject object
-        cdef list toclose = list(self._dependent_object.values())
+        cdef list      to_close = list((self._dependent_objects).values())
         
-        for object in toclose:
+        for object in to_close:
             object.close()
-                            
-        assert len(self._dependent_object.values)==0
-
-
-    def __init__(self, __internalCall__):
         
-        if __internalCall__ != 987654 :
-            raise RuntimeError('OBIObject constructor can not be called directly')
-        
-        if type(self) == OBIObject or type(self) == OBIWrapper or not isinstance(self, OBIObject) :
-            raise RuntimeError('OBIObject constructor can not be called directly')
-
-        self._dependent_object={}
+        assert len(self._dependent_objects.values()) == 0
 
 
-cdef class OBIWrapper(OBIObject):
-    """
-    The OBIWrapper class enables to wrap a C object representing a DMS or an element from a DMS
-    """
+cdef class OBIWrapper(OBIObject) :
+    '''
+    The OBIWrapper class enables to wrap a C object representing a DMS or an element from a DMS.
+    '''
     
-    cdef size_t cid(self) :
+    cdef inline size_t cid(self) :
         return <size_t>(self._pointer)
     
 
+    cdef inline bint active(self) :
+        return self._pointer != NULL
+
+
     cpdef close(self):
-    
         if (self._pointer != NULL):
             OBIObject.close(self)
+            del __c_cython_mapping__[<size_t>self._pointer]
             self._pointer = NULL
             
-        assert len(self._dependent_object.values) == 0
-        
-    
-    cpdef bint active(self):
-        return self._pointer != NULL
-            
+        assert len(self._dependent_objects.values()) == 0
+
 
     def __dealloc__(self):
-        """
+        '''
         Destructor of any OBI instance.
         
         The destructor automatically calls the `close` method and
-        therefore frees all the associated memory.
-        """
+        therefore closes and frees all associated objects and memory.
+        '''
         self.close()
 
     
     @staticmethod
-    cdef object new_wrapper(type constructor, void* pointer):
+    cdef object new(type constructor, void* pointer) :
     
-        cdef object o
+        cdef OBIWrapper o
         
         if (<size_t>pointer in __c_cython_mapping__):
+            print("Pointer already in cython dict")
             return __c_cython_mapping__[<size_t>pointer]
         else:
-            o = constructor(<size_t>pointer, 987654)
-            o._pointer = <size_t>pointer
+            o = constructor(987654)
+            o._pointer = pointer
             __c_cython_mapping__[<size_t>pointer] = o
             return o