Merge pull request #179 from NeuralEnsemble/experimental

Use natsort to properly sort segments/groups when optimising

doc/userdocs/coreclasses_list.txt

@@ -605,6 +605,17 @@ DecayingPoolConcentrationModel
 
 
 
+DerivedParameter
+################
+
+.. autoclass:: neuroml.nml.nml.DerivedParameter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
 DerivedVariable
 ###############
 
@@ -715,6 +726,17 @@ ElectricalProjection
 
 
 
+EventOut
+########
+
+.. autoclass:: neuroml.nml.nml.EventOut
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
 ExpCondSynapse
 ##############
 
@@ -1482,6 +1504,50 @@ NeuroMLDocument
 
 
 
+OnCondition
+###########
+
+.. autoclass:: neuroml.nml.nml.OnCondition
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
+OnEntry
+#######
+
+.. autoclass:: neuroml.nml.nml.OnEntry
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
+OnEvent
+#######
+
+.. autoclass:: neuroml.nml.nml.OnEvent
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
+OnStart
+#######
+
+.. autoclass:: neuroml.nml.nml.OnStart
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
 OpenState
 #########
 
@@ -1691,6 +1757,17 @@ ReactionScheme
 
 
 
+Regime
+######
+
+.. autoclass:: neuroml.nml.nml.Regime
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
 Region
 ######
 
@@ -1955,6 +2032,17 @@ Standalone
 
 
 
+StateAssignment
+###############
+
+.. autoclass:: neuroml.nml.nml.StateAssignment
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
 StateVariable
 #############
 
@@ -2032,6 +2120,28 @@ TransientPoissonFiringSynapse
 
 
 
+Transition
+##########
+
+.. autoclass:: neuroml.nml.nml.Transition
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
+TrueOrFalse
+###########
+
+.. autoclass:: neuroml.nml.nml.TrueOrFalse
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :inherited-members:
+
+
+
 UnstructuredLayout
 ##################
 

neuroml/loaders.py

@@ -3,6 +3,7 @@
 from neuroml.nml.nml import parseString as nmlparsestring
 
 import neuroml
+from neuroml import (NeuroMLDocument)
 import neuroml.utils as utils
 
 import os
@@ -18,7 +19,7 @@ class NeuroMLLoader(object):
     @classmethod
     def load(cls, src):
         doc = cls.__nml2_doc(src)
-        if isinstance(doc, neuroml.nml.nml.NeuroMLDocument):
+        if isinstance(doc, NeuroMLDocument):
             return doc
         else:
             raise TypeError(
@@ -188,7 +189,7 @@ def read_neuroml2_file(
     already_included: list = None,
     print_method: Callable = neuroml.print_,
     optimized: bool = False,
-) -> neuroml.nml.nml.NeuroMLDocument:
+) -> NeuroMLDocument:
     """
     Read a NeuroML2 file into a NeuroMLDocument object
 
@@ -234,7 +235,7 @@ def read_neuroml2_string(
     print_method: Callable = neuroml.print_,
     optimized: bool = False,
     base_path: Optional[str] = None,
-) -> neuroml.nml.nml.NeuroMLDocument:
+) -> NeuroMLDocument:
     """
     Read a NeuroML2 string into a NeuroMLDocument object
 
@@ -277,7 +278,7 @@ def _read_neuroml2(
     print_method: Callable = neuroml.print_,
     optimized: bool = False,
     base_path: Optional[str] = None,
-) -> neuroml.nml.nml.NeuroMLDocument:
+) -> NeuroMLDocument:
     """
     Read a NeuroML2 file or string into a NeuroMLDocument object.
 

neuroml/nml/gds_imports-template.py

@@ -4,6 +4,7 @@
 import inspect
 import networkx as nx
 import numpy
+import natsort
 
 import neuroml
 import neuroml.neuro_lex_ids

neuroml/nml/generatedssupersuper.py

@@ -553,3 +553,61 @@ def _check_arg_list(self, **kwargs):
                 print(err)
                 self.info()
                 raise ValueError(err)
+
+    @classmethod
+    def get_class_hierarchy(cls):
+        """Get the class hierarchy for a component classs.
+
+        Reference: https://stackoverflow.com/a/75161393/375067
+
+        See the methods in neuroml.utils to use this generated hierarchy.
+
+        :returns: nested single key dictionaries where the key of each
+            dictionary is the root node of that subtree, and keys are its
+            immediate descendents
+
+        """
+        # classes that don't have any members, like ZeroOrNone, which is an Enum
+        schema = sys.modules[cls.__module__]
+        try:
+            allmembers = cls._get_members()
+        except AttributeError:
+            return {cls.__name__: []}
+
+        retlist = []
+        for member in allmembers:
+            if member is not None:
+                # is it a complex type, which will have a corresponding class?
+                member_class = getattr(schema, member.get_data_type(), None)
+                # if it isn't a class, so a simple type, just added it with an
+                # empty list
+                if member_class is None:
+                    retlist.append({member.get_name(): []})
+                else:
+                    # if it is a class, see if it has a hierarchy
+                    try:
+                        retlist.append(member_class.get_class_hierarchy())
+                    except AttributeError:
+                        retlist.append({member_class.__name__: []})
+
+        return {cls.__name__: retlist}
+
+    @classmethod
+    def get_nml2_class_hierarchy(cls):
+        """Return the NeuroML class hierarchy.
+
+        The root here is NeuroMLDocument.
+        This is useful in calculating paths to different components to aid in
+        construction of relative paths.
+
+        This caches the value as a class variable so that it is not
+        re-calculated when used multiple times.
+        """
+        # if hierarchy exists, return
+        try:
+            return cls.__nml_hier
+        # first run
+        except AttributeError:
+            schema = sys.modules[cls.__module__]
+            cls.__nml_hier = schema.NeuroMLDocument.get_class_hierarchy()
+        return cls.__nml_hier

neuroml/nml/helper_methods.py

@@ -1772,7 +1772,8 @@ def optimise_segment_group(self, seg_group_id):
             if i not in new_includes:
                 new_includes.append(i)
         includes = set(new_includes)
-        seg_group.includes = list(includes)
+        # sorted
+        seg_group.includes = natsort.natsorted(includes, key=lambda x:x.segment_groups)
 
         # remove members that are included by included segment groups
         if len(includes) > 0 and len(members) > 0:
@@ -1782,7 +1783,8 @@ def optimise_segment_group(self, seg_group_id):
                 for i in members:
                     if i.segments not in all_segment_ids_in_group:
                         new_members.append(i)
-            seg_group.members = list(new_members)
+            # sorted
+            seg_group.members = natsort.natsorted(new_members, key=lambda x: x.segments)
 
 
     def set_spike_thresh(self, v, group_id="all"):