Now no Neo object can have more than one parent, so we can clean up a bit

Author: apdavison

doc/source/images/generate_diagram.py

@@ -29,7 +29,6 @@ def get_rect_height(name, obj):
     nlines += len(getattr(obj, '_all_attrs', []))
     nlines += len(getattr(obj, '_single_child_objects', []))
     nlines += len(getattr(obj, '_multi_child_objects', []))
-    nlines += len(getattr(obj, '_multi_parent_objects', []))
     return nlines * line_heigth
 
 
@@ -100,8 +99,7 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
     for name, pos in rect_pos.items():
         htotal = all_h[name]
         obj = objs[name]
-        allrelationship = (list(getattr(obj, '_child_containers', []))
-                           + list(getattr(obj, '_multi_parent_containers', [])))
+        allrelationship = list(getattr(obj, '_child_containers', []))
 
         rect = Rectangle(pos, rect_width, htotal,
                          facecolor='w', edgecolor='k', linewidth=2.)
@@ -123,8 +121,7 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
         ax.add_patch(rect)
 
         # multi relationship
-        relationship = (list(getattr(obj, '_multi_child_objects', []))
-                        + list(getattr(obj, '_multi_parent_containers', [])))
+        relationship = list(getattr(obj, '_multi_child_objects', []))
         pos2 = (pos[1] + htotal - line_heigth * (1.5 + len(relationship))
                 - rect_height)
         rect_height = len(relationship) * line_heigth

neo/core/analogsignal.py

@@ -160,8 +160,8 @@ class AnalogSignal(BaseSignal):
 
     '''
 
-    _single_parent_objects = ('Segment', 'ChannelIndex')
-    _single_parent_attrs = ('segment', 'channel_index')
+    _parent_objects = ('Segment', 'ChannelIndex')
+    _parent_attrs = ('segment', 'channel_index')
     _quantity_attr = 'signal'
     _necessary_attrs = (('signal', pq.Quantity, 2),
                         ('sampling_rate', pq.Quantity, 0),

neo/core/baseneo.py

@@ -18,12 +18,6 @@
                             Number, Decimal,
                             np.number, np.bool_)
 
-# handle both Python 2 and Python 3
-try:
-    ALLOWED_ANNOTATION_TYPES += (long, unicode)
-except NameError:
-    pass
-
 logger = logging.getLogger("Neo")
 
 
@@ -179,20 +173,13 @@ class BaseNeo:
     and also sets up the :attr:`annotations` dict for additional arguments.
 
     Each class can define one or more of the following class attributes:
-        :_single_parent_objects: Neo objects that can be parents of this
-                                 object. This attribute is used in cases where
-                                 only one parent of this class is allowed.
-                                 An instance attribute named
-                                 class.__name__.lower() will be automatically
-                                 defined to hold this parent and will be
-                                 initialized to None.
-        :_multi_parent_objects: Neo objects that can be parents of this
-                                object. This attribute is used in cases where
-                                multiple parents of this class is allowed.
-                                An instance attribute named
-                                class.__name__.lower()+'s' will be
-                                automatically defined to hold this parent and
-                                will be initialized to an empty list.
+        :_parent_objects: Neo objects that can be parents of this
+                          object. Note that no Neo object can have
+                          more than one parent.
+                          An instance attribute named
+                          class.__name__.lower() will be automatically
+                          defined to hold this parent and will be
+                          initialized to None.
         :_necessary_attrs: A list of tuples containing the attributes that the
                            class must have. The tuple can have 2-4 elements.
                            The first element is the attribute name.
@@ -210,15 +197,8 @@ class must have. The tuple can have 2-4 elements.
                                    pretty-printing using iPython.
 
     The following helper properties are available:
-        :_parent_objects: All parent objects.
-                         :_single_parent_objects: + :_multi_parent_objects:
-        :_single_parent_containers: The names of the container attributes used
-                                   to store :_single_parent_objects:
-        :_multi_parent_containers: The names of the container attributes used
-                                   to store :_multi_parent_objects:
-        :_parent_containers: All parent container attributes.
-                            :_single_parent_containers: +
-                            :_multi_parent_containers:
+        :_parent_containers: The names of the container attributes used
+                             to store :_parent_objects:
         :parents: All objects that are parents of the current object.
         :_all_attrs: All required and optional attributes.
                      :_necessary_attrs: + :_recommended_attrs:
@@ -264,11 +244,9 @@ class attributes. :_recommended_attrs: should append
     # these attributes control relationships, they need to be
     # specified in each child class
     # Parent objects whose children can have a single parent
-    _single_parent_objects = ()
-    # Attribute names corresponding to _single_parent_objects
-    _single_parent_attrs = ()
-    # Parent objects whose children can have multiple parents
-    _multi_parent_objects = ()
+    _parent_objects = ()
+    # Attribute names corresponding to _parent_objects
+    _parent_attrs = ()
 
     # Attributes that an instance is required to have defined
     _necessary_attrs = ()
@@ -298,10 +276,8 @@ def __init__(self, name=None, description=None, file_origin=None,
         self.file_origin = file_origin
 
         # initialize parent containers
-        for parent in self._single_parent_containers:
+        for parent in self._parent_containers:
             setattr(self, parent, None)
-        for parent in self._multi_parent_containers:
-            setattr(self, parent, [])
 
     def annotate(self, **annotations):
         """
@@ -341,46 +317,21 @@ def _repr_pretty_(self, pp, cycle):
             pp.breakable()
             self._repr_pretty_attrs_(pp, cycle)
 
-    @property
-    def _single_parent_containers(self):
-        """
-        Containers for parent objects whose children can have a single parent.
-        """
-        return tuple([_reference_name(parent) for parent in
-                      self._single_parent_objects])
-
-    @property
-    def _multi_parent_containers(self):
-        """
-        Containers for parent objects whose children can have multiple parents.
-        """
-        return tuple([_container_name(parent) for parent in
-                      self._multi_parent_objects])
-
-    @property
-    def _parent_objects(self):
-        """
-        All types for parent objects.
-        """
-        return self._single_parent_objects + self._multi_parent_objects
-
     @property
     def _parent_containers(self):
         """
-        All containers for parent objects.
+        Containers for parent objects.
         """
-        return self._single_parent_containers + self._multi_parent_containers
+        return tuple([_reference_name(parent) for parent in
+                      self._parent_objects])
 
     @property
     def parents(self):
         """
         All parent objects storing the current object.
         """
-        single = [getattr(self, attr) for attr in
-                  self._single_parent_containers]
-        multi = [list(getattr(self, attr)) for attr in
-                 self._multi_parent_containers]
-        return tuple(single + sum(multi, []))
+        return tuple([getattr(self, attr) for attr in
+                      self._parent_containers])
 
     @property
     def _all_attrs(self):
@@ -420,9 +371,9 @@ def set_parent(self, obj):
         Set the appropriate "parent" attribute of this object
         according to the type of "obj"
         """
-        if obj.__class__.__name__ not in self._single_parent_objects:
+        if obj.__class__.__name__ not in self._parent_objects:
             raise TypeError("{} can only have parents of type {}, not {}".format(
-                self.__class__.__name__, self._single_parent_objects, obj.__class__.__name__))
-        loc = self._single_parent_objects.index(obj.__class__.__name__)
-        parent_attr = self._single_parent_attrs[loc]
+                self.__class__.__name__, self._parent_objects, obj.__class__.__name__))
+        loc = self._parent_objects.index(obj.__class__.__name__)
+        parent_attr = self._parent_attrs[loc]
         setattr(self, parent_attr, obj)

neo/core/channelindex.py

@@ -154,7 +154,7 @@ class ChannelIndex(Container):
 
     _container_child_objects = ('Unit',)
     _data_child_objects = ('AnalogSignal', 'IrregularlySampledSignal')
-    _single_parent_objects = ('Block',)
+    _parent_objects = ('Block',)
     _necessary_attrs = (('index', np.ndarray, 1, np.dtype('i')),)
     _recommended_attrs = ((('channel_names', np.ndarray, 1, np.dtype('U')),
                            ('channel_ids', np.ndarray, 1, np.dtype('i')),

neo/core/dataobject.py

@@ -357,7 +357,7 @@ def __deepcopy__(self, memo):
             # thus creating a lot of overhead
             # But keeping the reference to the same parent is not desired either, because this would be unidirectional
             # When deepcopying top-down, e.g. a whole block, the links will be handled by the parent
-            if k in self._single_parent_attrs:
+            if k in self._parent_attrs:
                 setattr(new_obj, k, None)
                 continue
             try:

neo/core/epoch.py

@@ -72,8 +72,8 @@ class Epoch(DataObject):
 
     '''
 
-    _single_parent_objects = ('Segment',)
-    _single_parent_attrs = ('segment',)
+    _parent_objects = ('Segment',)
+    _parent_attrs = ('segment',)
     _quantity_attr = 'times'
     _necessary_attrs = (('times', pq.Quantity, 1), ('durations', pq.Quantity, 1),
                         ('labels', np.ndarray, 1, np.dtype('U')))

neo/core/event.py

@@ -65,8 +65,8 @@ class Event(DataObject):
 
     '''
 
-    _single_parent_objects = ('Segment',)
-    _single_parent_attrs = ('segment',)
+    _parent_objects = ('Segment',)
+    _parent_attrs = ('segment',)
     _quantity_attr = 'times'
     _necessary_attrs = (('times', pq.Quantity, 1), ('labels', np.ndarray, 1, np.dtype('U')))
 

neo/core/group.py

@@ -42,7 +42,7 @@ class Group(Container):
         'Event', 'Epoch', 'ChannelView', 'ImageSequence'
     )
     _container_child_objects = ('Segment', 'Group')
-    _single_parent_objects = ('Block',)
+    _parent_objects = ('Block',)
 
     def __init__(self, objects=None, name=None, description=None, file_origin=None,
                  allowed_types=None, **annotations):

neo/core/imagesequence.py

@@ -86,8 +86,8 @@ class ImageSequence(BaseSignal):
             (:attr:`t_start` + :attr:`duration`)
      """
 
-    _single_parent_objects = ("Segment",)
-    _single_parent_attrs = ("segment",)
+    _parent_objects = ("Segment",)
+    _parent_attrs = ("segment",)
     _quantity_attr = "image_data"
     _necessary_attrs = (
         ("image_data", pq.Quantity, 3),

neo/core/irregularlysampledsignal.py

@@ -123,8 +123,8 @@ class IrregularlySampledSignal(BaseSignal):
 
     '''
 
-    _single_parent_objects = ('Segment', 'ChannelIndex')
-    _single_parent_attrs = ('segment', 'channel_index')
+    _parent_objects = ('Segment', 'ChannelIndex')
+    _parent_attrs = ('segment', 'channel_index')
     _quantity_attr = 'signal'
     _necessary_attrs = (('times', pq.Quantity, 1), ('signal', pq.Quantity, 2))