From 689b9d029e571cf456a673d550dee0e4841c4361 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 13 Aug 2024 13:53:04 +0100
Subject: [PATCH 01/21] chore: add logger to generatedssupersuper

This allows us to use it in the various helper methods for better
outputs.
---
 neuroml/nml/generatedssupersuper.py | 24 +++++++++++++++-----
 neuroml/nml/helper_methods.py       | 23 ++++++++++---------
 neuroml/nml/nml.py                  | 35 +++++++++++++++--------------
 neuroml/utils.py                    |  2 +-
 4 files changed, 50 insertions(+), 34 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index 5973f97..c3d5eb8 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -13,9 +13,6 @@
 
 from .generatedscollector import GdsCollector
 
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.INFO)
-
 
 class GeneratedsSuperSuper(object):
     """Super class for GeneratedsSuper.
@@ -23,6 +20,9 @@ class GeneratedsSuperSuper(object):
     Any bits that must go into every libNeuroML class should go here.
     """
 
+    logger = logging.getLogger(__name__)
+    logger.setLevel(logging.INFO)
+
     def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
         """Generic function to allow easy addition of a new member to a NeuroML object.
         Without arguments, when `obj=None`, it simply calls the `info()` method
@@ -97,7 +97,14 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
         if neuroml.build_time_validation.ENABLED and validate:
             self.validate()
         else:
-            logger.warning("Build time validation is disabled.")
+            if not neuroml.build_time_validation.ENABLED:
+                self.logger.warning(
+                    f"Adding new {obj.__class__.__name__}: build time validation is globally disabled."
+                )
+            else:
+                self.logger.warning(
+                    f"Adding new {obj.__class__.__name__}: build time validation is locally disabled."
+                )
         return obj
 
     @classmethod
@@ -156,7 +163,14 @@ def component_factory(cls, component_type, validate=True, **kwargs):
         if neuroml.build_time_validation.ENABLED and validate:
             comp.validate()
         else:
-            logger.warning("Build time validation is disabled.")
+            if not neuroml.build_time_validation.ENABLED:
+                cls.logger.warning(
+                    f"Creating new {comp_type_class.__name__}: build time validation is globally disabled."
+                )
+            else:
+                cls.logger.warning(
+                    f"Creating new {comp_type_class.__name__}: build time validation is locally disabled."
+                )
         return comp
 
     def __add(self, obj, member, force=False):
diff --git a/neuroml/nml/helper_methods.py b/neuroml/nml/helper_methods.py
index 37b1a94..d5da6db 100644
--- a/neuroml/nml/helper_methods.py
+++ b/neuroml/nml/helper_methods.py
@@ -1551,13 +1551,13 @@ def add_segment(
             else:
                 p = None
         except IndexError as e:
-            print("{}: prox must be a list of 4 elements".format(e))
+            raise ValueError("{}: prox must be a list of 4 elements".format(e))
         try:
             d = self.component_factory(
                 "Point3DWithDiam", x=dist[0], y=dist[1], z=dist[2], diameter=dist[3]
             )
         except IndexError as e:
-            print("{}: dist must be a list of 4 elements".format(e))
+            raise ValueError("{}: dist must be a list of 4 elements".format(e))
 
         segid = len(self.morphology.segments)
         if segid > 0 and parent is None:
@@ -1578,7 +1578,7 @@ def add_segment(
                 seg = None
                 seg = self.get_segment(seg_id)
                 if seg:
-                    raise ValueError(f"A segment with provided id {seg_id} already exists")
+                    raise ValueError(f"A segment with provided id '{seg_id}' already exists")
             except ValueError:
                 # a segment with this ID does not already exist
                 pass
@@ -1596,8 +1596,8 @@ def add_segment(
             try:
                 seg_group = self.get_segment_group(group_id)
             except ValueError as e:
-                print("Warning: {}".format(e))
-                print(f"Warning: creating Segment Group with id {group_id}")
+                self.logger.warning("{}".format(e))
+                self.logger.warning(f"Creating Segment Group with id '{group_id}'")
                 seg_group = self.add_segment_group(
                     group_id=group_id
                 )
@@ -1685,7 +1685,7 @@ def add_segment_group(self, group_id, neuro_lex_id=None, notes=None):
                 notes=notes, validate=False
             )
         else:
-            print(f"Warning: Segment group {seg_group.id} already exists.")
+            self.logger.warning(f"Segment group '{seg_group.id}' already exists.")
 
         return seg_group
 
@@ -2024,6 +2024,8 @@ def setup_default_segment_groups(self, use_convention=True, default_groups=["all
         :type default_groups: list of strings
         :returns: list of created segment groups (or empty list if none created)
         :rtype: list
+
+        :raises ValueError: if a group other than the standard groups are provided
         """
         new_groups = []
         if use_convention:
@@ -2044,8 +2046,7 @@ def setup_default_segment_groups(self, use_convention=True, default_groups=["all
                     neuro_lex_id=None
                     notes="Default segment group for all segments in the cell"
                 else:
-                    print(f"Error: only 'all', 'soma_group', 'dendrite_group', and 'axon_group' are supported. Received {grp}")
-                    return []
+                    raise ValueError(f"Only 'all', 'soma_group', 'dendrite_group', and 'axon_group' are supported. Received {grp}")
 
                 seg_group = self.add_segment_group(group_id=grp, neuro_lex_id=neuro_lex_id, notes=notes)
                 new_groups.append(seg_group)
@@ -2215,7 +2216,7 @@ def __sectionise(self, root_segment_id, seg_group, morph_tree):
         :returns: TODO
 
         """
-        # print(f"Processing element: {root_segment_id}")
+        self.logger.debug(f"Processing element: {root_segment_id}")
 
         try:
             children = morph_tree[root_segment_id]
@@ -2282,7 +2283,7 @@ def get_segment_adjacency_list(self):
                     child_lists[parent] = []
                 child_lists[parent].append(segment.id)
             except AttributeError:
-                print(f"Warning: Segment: {segment} has no parent")
+                self.logger.warning(f"Segment: {segment} has no parent")
 
         self.adjacency_list = child_lists
         return child_lists
@@ -2389,7 +2390,7 @@ def get_segments_at_distance(self, distance, src_seg = 0):
                 frac_along = ((distance - dist) / self.get_segment_length(tgt))
             except ZeroDivisionError:
                 # ignore zero length segments
-                print(f"Warning: encountered zero length segment: {tgt}")
+                self.logger.warning(f"Encountered zero length segment: {tgt}")
                 continue
 
             if frac_along > 1.0:
diff --git a/neuroml/nml/nml.py b/neuroml/nml/nml.py
index ed65129..316bf26 100644
--- a/neuroml/nml/nml.py
+++ b/neuroml/nml/nml.py
@@ -2,8 +2,8 @@
 # -*- coding: utf-8 -*-
 
 #
-# Generated Tue Jun 11 14:00:16 2024 by generateDS.py version 2.43.3.
-# Python 3.10.9 (main, Jan 11 2023, 15:21:40) [GCC 11.2.0]
+# Generated Tue Aug 13 13:52:09 2024 by generateDS.py version 2.44.1.
+# Python 3.11.9 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)]
 #
 # Command line options:
 #   ('-o', 'nml.py')
@@ -16,7 +16,7 @@
 #   NeuroML_v2.3.1.xsd
 #
 # Command line:
-#   /home/padraig/anaconda2/envs/py310//bin/generateDS -o "nml.py" --use-getter-setter="none" --user-methods="helper_methods.py" --export="write validate" --custom-imports-template="gds_imports-template.py" NeuroML_v2.3.1.xsd
+#   /home/asinha/.local/share/virtualenvs/neuroml-311-dev/bin/generateDS -o "nml.py" --use-getter-setter="none" --user-methods="helper_methods.py" --export="write validate" --custom-imports-template="gds_imports-template.py" NeuroML_v2.3.1.xsd
 #
 # Current working directory (os.getcwd()):
 #   nml
@@ -198,7 +198,7 @@ class GeneratedsSuperSuper(object):
 
     class GeneratedsSuper(GeneratedsSuperSuper):
         __hash__ = object.__hash__
-        tzoff_pattern = re_.compile(r"(\+|-)((0\d|1[0-3]):[0-5]\d|14:00)$")
+        tzoff_pattern = re_.compile("(\\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00)$")
 
         class _FixedOffsetTZ(datetime_.tzinfo):
             def __init__(self, offset, name):
@@ -704,7 +704,7 @@ def get_path_(self, node):
             path = "/".join(path_list)
             return path
 
-        Tag_strip_pattern_ = re_.compile(r"\{.*\}")
+        Tag_strip_pattern_ = re_.compile(r"{.*}")
 
         def get_path_list_(self, node, path_list):
             if node is None:
@@ -49111,13 +49111,13 @@ def add_segment(
             else:
                 p = None
         except IndexError as e:
-            print("{}: prox must be a list of 4 elements".format(e))
+            raise ValueError("{}: prox must be a list of 4 elements".format(e))
         try:
             d = self.component_factory(
                 "Point3DWithDiam", x=dist[0], y=dist[1], z=dist[2], diameter=dist[3]
             )
         except IndexError as e:
-            print("{}: dist must be a list of 4 elements".format(e))
+            raise ValueError("{}: dist must be a list of 4 elements".format(e))
 
         segid = len(self.morphology.segments)
         if segid > 0 and parent is None:
@@ -49139,7 +49139,7 @@ def add_segment(
                 seg = self.get_segment(seg_id)
                 if seg:
                     raise ValueError(
-                        f"A segment with provided id {seg_id} already exists"
+                        f"A segment with provided id '{seg_id}' already exists"
                     )
             except ValueError:
                 # a segment with this ID does not already exist
@@ -49160,8 +49160,8 @@ def add_segment(
             try:
                 seg_group = self.get_segment_group(group_id)
             except ValueError as e:
-                print("Warning: {}".format(e))
-                print(f"Warning: creating Segment Group with id {group_id}")
+                self.logger.warning("{}".format(e))
+                self.logger.warning(f"Creating Segment Group with id '{group_id}'")
                 seg_group = self.add_segment_group(group_id=group_id)
             seg_group.members.append(Member(segments=segment.id))
 
@@ -49255,7 +49255,7 @@ def add_segment_group(self, group_id, neuro_lex_id=None, notes=None):
                 validate=False,
             )
         else:
-            print(f"Warning: Segment group {seg_group.id} already exists.")
+            self.logger.warning(f"Segment group '{seg_group.id}' already exists.")
 
         return seg_group
 
@@ -49589,6 +49589,8 @@ def setup_default_segment_groups(
         :type default_groups: list of strings
         :returns: list of created segment groups (or empty list if none created)
         :rtype: list
+
+        :raises ValueError: if a group other than the standard groups are provided
         """
         new_groups = []
         if use_convention:
@@ -49609,10 +49611,9 @@ def setup_default_segment_groups(
                     neuro_lex_id = None
                     notes = "Default segment group for all segments in the cell"
                 else:
-                    print(
-                        f"Error: only 'all', 'soma_group', 'dendrite_group', and 'axon_group' are supported. Received {grp}"
+                    raise ValueError(
+                        f"Only 'all', 'soma_group', 'dendrite_group', and 'axon_group' are supported. Received {grp}"
                     )
-                    return []
 
                 seg_group = self.add_segment_group(
                     group_id=grp, neuro_lex_id=neuro_lex_id, notes=notes
@@ -49800,7 +49801,7 @@ def __sectionise(self, root_segment_id, seg_group, morph_tree):
         :returns: TODO
 
         """
-        # print(f"Processing element: {root_segment_id}")
+        self.logger.debug(f"Processing element: {root_segment_id}")
 
         try:
             children = morph_tree[root_segment_id]
@@ -49866,7 +49867,7 @@ def get_segment_adjacency_list(self):
                     child_lists[parent] = []
                 child_lists[parent].append(segment.id)
             except AttributeError:
-                print(f"Warning: Segment: {segment} has no parent")
+                self.logger.warning(f"Segment: {segment} has no parent")
 
         self.adjacency_list = child_lists
         return child_lists
@@ -49974,7 +49975,7 @@ def get_segments_at_distance(self, distance, src_seg=0):
                 frac_along = (distance - dist) / self.get_segment_length(tgt)
             except ZeroDivisionError:
                 # ignore zero length segments
-                print(f"Warning: encountered zero length segment: {tgt}")
+                self.logger.warning(f"Encountered zero length segment: {tgt}")
                 continue
 
             if frac_along > 1.0:
diff --git a/neuroml/utils.py b/neuroml/utils.py
index 3033ff7..dc3c236 100644
--- a/neuroml/utils.py
+++ b/neuroml/utils.py
@@ -234,7 +234,7 @@ def component_factory(
     Please see `GeneratedsSuperSuper.component_factory` for more information.
     """
     new_obj = schema.NeuroMLDocument().component_factory(
-        component_type, validate, **kwargs
+        component_type=component_type, validate=validate, **kwargs
     )
     return new_obj
 

From 89bd448a737ac8b36aa2ea18ea83c4dafe8376fc Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 13 Aug 2024 14:03:35 +0100
Subject: [PATCH 02/21] chore(generatedssupersuper): improve warnings

Also, use `logger.warning` instead of `warnings.warn`
---
 neuroml/nml/generatedssupersuper.py | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index c3d5eb8..b0a3ec4 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -99,11 +99,11 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
         else:
             if not neuroml.build_time_validation.ENABLED:
                 self.logger.warning(
-                    f"Adding new {obj.__class__.__name__}: build time validation is globally disabled."
+                    f"Build time validation is globally disabled: adding new {obj.__class__.__name__}."
                 )
             else:
                 self.logger.warning(
-                    f"Adding new {obj.__class__.__name__}: build time validation is locally disabled."
+                    f"Build time validation is globally disabled: adding new {obj.__class__.__name__}."
                 )
         return obj
 
@@ -165,11 +165,11 @@ def component_factory(cls, component_type, validate=True, **kwargs):
         else:
             if not neuroml.build_time_validation.ENABLED:
                 cls.logger.warning(
-                    f"Creating new {comp_type_class.__name__}: build time validation is globally disabled."
+                    f"Build time validation is globally disabled: creating new {comp_type_class.__name__}."
                 )
             else:
                 cls.logger.warning(
-                    f"Creating new {comp_type_class.__name__}: build time validation is locally disabled."
+                    f"Build time validation is globally disabled: creating new {comp_type_class.__name__}."
                 )
         return comp
 
@@ -184,16 +184,14 @@ def __add(self, obj, member, force=False):
         :type force: bool
 
         """
-        import warnings
-
         # A single value, not a list:
         if member.get_container() == 0:
             if force:
                 vars(self)[member.get_name()] = obj
             else:
                 if vars(self)[member.get_name()]:
-                    warnings.warn(
-                        """{} has already been assigned.  Use `force=True` to overwrite. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
+                    self.logger.warning(
+                        """Member '{}' has already been assigned. Use `force=True` to overwrite. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
                             member.get_name()
                         )
                     )
@@ -209,7 +207,7 @@ def __add(self, obj, member, force=False):
                 # There is no use case where the same child would be added
                 # twice to a component.
                 if obj in vars(self)[member.get_name()]:
-                    warnings.warn(
+                    self.logger.warning(
                         """{} already exists in {}. Use `force=True` to force readdition. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
                             obj, member.get_name()
                         )

From 3e7329ec56ce7d7e56ab421efb3f0b95c469df76 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 13 Aug 2024 14:06:36 +0100
Subject: [PATCH 03/21] test: remove testing of user warning

---
 neuroml/test/test_nml.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/neuroml/test/test_nml.py b/neuroml/test/test_nml.py
index f2ffd85..99134e2 100644
--- a/neuroml/test/test_nml.py
+++ b/neuroml/test/test_nml.py
@@ -73,10 +73,6 @@ def test_generic_add_single(self):
         # Success: returns object
         self.assertIsNotNone(doc.add(cell))
 
-        # Already added, so throw exception
-        with self.assertWarns(UserWarning):
-            doc.add(cell)
-
         # Success
         self.assertIsNotNone(doc.add(cell1))
 
@@ -164,9 +160,6 @@ def test_add_to_container(self):
 
         pop3 = neuroml.Population(id="unique")
         network.add(pop3)
-        # warning because this is already added
-        with self.assertWarns(UserWarning):
-            network.add(pop3)
 
         # Note that for Python, this is a new object
         # So we can add it again

From 737839e0e346139be919da771baaa489685dce96 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 13 Aug 2024 14:50:36 +0100
Subject: [PATCH 04/21] feat(component-factory): handle addition of "__ANY__"

Use cases:

- `component_factory(sometype, __ANY__="something")`
- `l = component_factory(sometype); l.add("something", hint="__ANY__")`

In both, we require the user to give some notion that they are trying to
add a `__ANY__` member.
---
 neuroml/nml/generatedssupersuper.py | 105 ++++++++++++++++++++--------
 1 file changed, 75 insertions(+), 30 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index b0a3ec4..c5ad619 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -58,6 +58,26 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
         if type(obj) is type or isinstance(obj, str):
             obj = self.component_factory(obj, validate=validate, **kwargs)
 
+        # if obj is still a string, it is a general string, but to confirm that
+        # this is what the user intends, ask them to provide a hint.
+        if isinstance(obj, str):
+            # no hint, no pass
+            if not hint:
+                self.logger.error("Received a text object to add.")
+                self.logger.error(
+                    'Please pass `hint="__ANY__"` to confirm that this is what you intend.'
+                )
+                self.logger.error(
+                    "I will then try to add this to an __ANY__ member in the object."
+                )
+                return None
+            # hint confirmed, try to add it below
+            else:
+                self.logger.warning("Received a text object to add.")
+                self.logger.warning(
+                    "Trying to add this to an __ANY__ member in the object."
+                )
+
         # getattr only returns the value of the provided member but one cannot
         # then use this to modify the member. Using `vars` also allows us to
         # modify the value
@@ -65,13 +85,19 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
         all_members = self._get_members()
         for member in all_members:
             # get_data_type() returns the type as a string, e.g.: 'IncludeType'
+
+            # handle "__ANY__"
+            if isinstance(obj, str) and member.get_data_type() == "__ANY__":
+                targets.append(member)
+                break
+
             if member.get_data_type() == type(obj).__name__:
                 targets.append(member)
 
         if len(targets) == 0:
             # no targets found
             e = Exception(
-                """A member object of {} type could not be found in NeuroML class {}.\n{}
+                """A member object of '{}' type could not be found in NeuroML class {}.\n{}
             """.format(type(obj).__name__, type(self).__name__, self.info())
             )
             raise e
@@ -148,11 +174,26 @@ def component_factory(cls, component_type, validate=True, **kwargs):
         module_object = sys.modules[cls.__module__]
 
         if isinstance(component_type, str):
-            comp_type_class = getattr(module_object, component_type)
+            # class names do not have spaces, so if we find a space, we treat
+            # it as a general string and just return it.
+            if " " in component_type:
+                cls.logger.warning(
+                    "Component Type appears to be a generic string: nothing to do."
+                )
+                return component_type
+            else:
+                comp_type_class = getattr(module_object, component_type)
         else:
             comp_type_class = getattr(module_object, component_type.__name__)
 
-        comp = comp_type_class(**kwargs)
+        # handle component types that support __ANY__
+        try:
+            anytypevalue = kwargs["__ANY__"]
+            # first value, so put it in a list, otherwise each element of the
+            # string is taken to be a new object
+            comp = comp_type_class(anytypeobjs_=[anytypevalue], **kwargs)
+        except KeyError:
+            comp = comp_type_class(**kwargs)
 
         # additional setups where required
         if comp_type_class.__name__ == "Cell":
@@ -184,36 +225,40 @@ def __add(self, obj, member, force=False):
         :type force: bool
 
         """
-        # A single value, not a list:
-        if member.get_container() == 0:
-            if force:
-                vars(self)[member.get_name()] = obj
-            else:
-                if vars(self)[member.get_name()]:
-                    self.logger.warning(
-                        """Member '{}' has already been assigned. Use `force=True` to overwrite. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
-                            member.get_name()
-                        )
-                    )
-                else:
-                    vars(self)[member.get_name()] = obj
-        # List
+        # handle __ANY__ which is to be stored in anytypeobjs_
+        if member.get_name() == "__ANY__":
+            vars(self)["anytypeobjs_"].append(obj)
         else:
-            if force:
-                vars(self)[member.get_name()].append(obj)
-            else:
-                # "obj in .." checks by identity and value.
-                # In XML, two children with same values are identical.
-                # There is no use case where the same child would be added
-                # twice to a component.
-                if obj in vars(self)[member.get_name()]:
-                    self.logger.warning(
-                        """{} already exists in {}. Use `force=True` to force readdition. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
-                            obj, member.get_name()
-                        )
-                    )
+            # A single value, not a list:
+            if member.get_container() == 0:
+                if force:
+                    vars(self)[member.get_name()] = obj
                 else:
+                    if vars(self)[member.get_name()]:
+                        self.logger.warning(
+                            """Member '{}' has already been assigned. Use `force=True` to overwrite. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
+                                member.get_name()
+                            )
+                        )
+                    else:
+                        vars(self)[member.get_name()] = obj
+            # List
+            else:
+                if force:
                     vars(self)[member.get_name()].append(obj)
+                else:
+                    # "obj in .." checks by identity and value.
+                    # In XML, two children with same values are identical.
+                    # There is no use case where the same child would be added
+                    # twice to a component.
+                    if obj in vars(self)[member.get_name()]:
+                        self.logger.warning(
+                            """{} already exists in {}. Use `force=True` to force readdition. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
+                                obj, member.get_name()
+                            )
+                        )
+                    else:
+                        vars(self)[member.get_name()].append(obj)
 
     @classmethod
     def _get_members(cls):

From c575dbebf9e85c1a915eda934440cdb1f9e4b240 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 13 Aug 2024 16:10:31 +0100
Subject: [PATCH 05/21] chore(component-factory): simplify code

---
 neuroml/nml/generatedssupersuper.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index c5ad619..a455325 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -186,14 +186,15 @@ def component_factory(cls, component_type, validate=True, **kwargs):
         else:
             comp_type_class = getattr(module_object, component_type.__name__)
 
+        comp = comp_type_class(**kwargs)
+
         # handle component types that support __ANY__
         try:
             anytypevalue = kwargs["__ANY__"]
-            # first value, so put it in a list, otherwise each element of the
-            # string is taken to be a new object
-            comp = comp_type_class(anytypeobjs_=[anytypevalue], **kwargs)
+            # append value to anytypeobjs_ list
+            comp.anytypeobjs_.append(anytypevalue)
         except KeyError:
-            comp = comp_type_class(**kwargs)
+            pass
 
         # additional setups where required
         if comp_type_class.__name__ == "Cell":

From 09117fc34648398f33e32a4edd10d08f686631ef Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 13 Aug 2024 16:16:00 +0100
Subject: [PATCH 06/21] chore: revert to raising exception

---
 neuroml/nml/generatedssupersuper.py | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index a455325..c0655af 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -63,14 +63,12 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
         if isinstance(obj, str):
             # no hint, no pass
             if not hint:
-                self.logger.error("Received a text object to add.")
-                self.logger.error(
-                    'Please pass `hint="__ANY__"` to confirm that this is what you intend.'
+                e = Exception(
+                    "Received a text object to add. "
+                    + 'Please pass `hint="__ANY__"` to confirm that this is what you intend. '
+                    + "I will then try to add this to an __ANY__ member in the object."
                 )
-                self.logger.error(
-                    "I will then try to add this to an __ANY__ member in the object."
-                )
-                return None
+                raise e
             # hint confirmed, try to add it below
             else:
                 self.logger.warning("Received a text object to add.")

From 843d5df7ba32131d200b979e19f8ba0aa5887540 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 14 Aug 2024 18:15:15 +0100
Subject: [PATCH 07/21] chore: correct warning string

---
 neuroml/nml/generatedssupersuper.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index c0655af..f577804 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -127,7 +127,7 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
                 )
             else:
                 self.logger.warning(
-                    f"Build time validation is globally disabled: adding new {obj.__class__.__name__}."
+                    f"Build time validation is locally disabled: adding new {obj.__class__.__name__}."
                 )
         return obj
 
@@ -209,7 +209,7 @@ def component_factory(cls, component_type, validate=True, **kwargs):
                 )
             else:
                 cls.logger.warning(
-                    f"Build time validation is globally disabled: creating new {comp_type_class.__name__}."
+                    f"Build time validation is locally disabled: creating new {comp_type_class.__name__}."
                 )
         return comp
 

From 0e1e62e0e217b91030e6098755dcac9bba23ad93 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Thu, 15 Aug 2024 10:31:21 +0100
Subject: [PATCH 08/21] chore: make validation disabled messages into debugs

Otherwise the output is too verbose.
---
 neuroml/nml/generatedssupersuper.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index f577804..c26e38c 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -122,11 +122,11 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
             self.validate()
         else:
             if not neuroml.build_time_validation.ENABLED:
-                self.logger.warning(
+                self.logger.debug(
                     f"Build time validation is globally disabled: adding new {obj.__class__.__name__}."
                 )
             else:
-                self.logger.warning(
+                self.logger.debug(
                     f"Build time validation is locally disabled: adding new {obj.__class__.__name__}."
                 )
         return obj
@@ -204,11 +204,11 @@ def component_factory(cls, component_type, validate=True, **kwargs):
             comp.validate()
         else:
             if not neuroml.build_time_validation.ENABLED:
-                cls.logger.warning(
+                cls.logger.debug(
                     f"Build time validation is globally disabled: creating new {comp_type_class.__name__}."
                 )
             else:
-                cls.logger.warning(
+                cls.logger.debug(
                     f"Build time validation is locally disabled: creating new {comp_type_class.__name__}."
                 )
         return comp

From e8d4b8a65455df111ccb140cdc56faa5d9e0216d Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Thu, 15 Aug 2024 11:33:51 +0100
Subject: [PATCH 09/21] feat(generatedssuper): reduce warnings, improve when
 they're called

---
 neuroml/nml/generatedssupersuper.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index c26e38c..58b60b9 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -226,15 +226,20 @@ def __add(self, obj, member, force=False):
         """
         # handle __ANY__ which is to be stored in anytypeobjs_
         if member.get_name() == "__ANY__":
+            self.logger.debug("__ANY__ member, appending to anytypeobjs_.")
             vars(self)["anytypeobjs_"].append(obj)
         else:
             # A single value, not a list:
+            self.logger.debug("Not a container member, assigning.")
             if member.get_container() == 0:
                 if force:
                     vars(self)[member.get_name()] = obj
+                    self.logger.warning(
+                        """Overwriting member '{}'.""".format(member.get_name())
+                    )
                 else:
                     if vars(self)[member.get_name()]:
-                        self.logger.warning(
+                        self.logger.debug(
                             """Member '{}' has already been assigned. Use `force=True` to overwrite. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
                                 member.get_name()
                             )
@@ -243,8 +248,12 @@ def __add(self, obj, member, force=False):
                         vars(self)[member.get_name()] = obj
             # List
             else:
+                self.logger.debug("Container member, appending.")
                 if force:
                     vars(self)[member.get_name()].append(obj)
+                    self.logger.warning(
+                        """Force appending to member '{}'""".format(member.get_name())
+                    )
                 else:
                     # "obj in .." checks by identity and value.
                     # In XML, two children with same values are identical.
@@ -252,7 +261,7 @@ def __add(self, obj, member, force=False):
                     # twice to a component.
                     if obj in vars(self)[member.get_name()]:
                         self.logger.warning(
-                            """{} already exists in {}. Use `force=True` to force readdition. Hint: you can make changes to the already added object as required without needing to re-add it because only references to the objects are added, not their values.""".format(
+                            """{} already exists in {}. Use `force=True` to force readdition.""".format(
                                 obj, member.get_name()
                             )
                         )

From ebb2f8cae93faf858c66fd4f5222e4c4a112d524 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 16 Aug 2024 16:50:55 +0100
Subject: [PATCH 10/21] feat: generalise get_by_id

---
 neuroml/nml/generatedssupersuper.py | 28 ++++++++++++
 neuroml/nml/helper_methods.py       | 71 ++---------------------------
 2 files changed, 33 insertions(+), 66 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index 58b60b9..ad3d099 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -681,3 +681,31 @@ def get_nml2_class_hierarchy(cls):
             schema = sys.modules[cls.__module__]
             cls.__nml_hier = schema.NeuroMLDocument.get_class_hierarchy()
         return cls.__nml_hier
+
+    def get_by_id(self, id_):
+        """Get a component or attribute by its ID
+
+        :param id_: ID of component or name of attribute to find
+        :type id_: str
+        :returns:  component with specified ID, or attribute, or None if neither found
+        """
+        all_ids = []
+        all_members = self._get_members()
+        for member in all_members:
+            if member.get_container() == 0:
+                if member.get_name() == id_:
+                    return member
+                else:
+                    all_ids.append(member.get_name())
+            else:
+                contents = getattr(self, member.get_name(), None)
+                for m in contents:
+                    if hasattr(m, "id"):
+                        if m.id == id_:
+                            return m
+                    else:
+                        all_ids.append(m.id)
+
+        self.logger.warning(f"Id '{id_}' not found in {self.__name__}")
+        self.logger.warning(f"All ids: {sorted(all_ids)}")
+        return None
diff --git a/neuroml/nml/helper_methods.py b/neuroml/nml/helper_methods.py
index d5da6db..83035c6 100644
--- a/neuroml/nml/helper_methods.py
+++ b/neuroml/nml/helper_methods.py
@@ -877,39 +877,6 @@ def summary(self, show_includes=True, show_non_network=True):
 
         return info
 
-    warn_count = 0
-
-    def get_by_id(self, id: str) -> typing.Optional[typing.Any]:
-        """Get a component by specifying its ID.
-
-        :param id: id of Component to get
-        :type id: str
-        :returns: Component with given ID or None if no Component with provided ID was found
-        """
-        if len(id)==0:
-            callframe = inspect.getouterframes(inspect.currentframe(), 2)
-            print('Method: '+ callframe[1][3] + ' is asking for an element with no id...')
-
-            return None
-        all_ids = []
-        for ms in self.member_data_items_:
-            mlist = getattr(self, ms.get_name())
-            # TODO: debug why this is required
-            if mlist is None:
-                continue
-            for m in mlist:
-                if hasattr(m,"id"):
-                    if m.id == id:
-                        return m
-                    else:
-                        all_ids.append(m.id)
-        if self.warn_count<10:
-            neuroml.print_("Id "+id+" not found in <neuroml> element. All ids: "+str(sorted(all_ids)))
-            self.warn_count+=1
-        elif self.warn_count==10:
-            neuroml.print_(" - Suppressing further warnings about id not found...")
-        return None
-
     def append(self, element):
         """Append an element
 
@@ -924,47 +891,19 @@ def append(self, element):
 
 METHOD_SPECS += (nml_doc_summary,)
 
-network_get_by_id = MethodSpec(
-    name="get_by_id",
-    source='''\
-
-    warn_count = 0
-    def get_by_id(self, id: str) -> typing.Optional[typing.Any]:
-        """Get a component by its ID
-
-        :param id: ID of component to find
-        :type id: str
-        :returns:  component with specified ID or None if no component with specified ID found
-        """
-        all_ids = []
-        for ms in self.member_data_items_:
-            mlist = getattr(self, ms.get_name())
-            # TODO: debug why this is required
-            if mlist is None:
-                continue
-            for m in mlist:
-                if hasattr(m,"id"):
-                    if m.id == id:
-                        return m
-                    else:
-                        all_ids.append(m.id)
-        if self.warn_count<10:
-            neuroml.print_("Id "+id+" not found in <network> element. All ids: "+str(sorted(all_ids)))
-            self.warn_count+=1
-        elif self.warn_count==10:
-            neuroml.print_(" - Suppressing further warnings about id not found...")
-        return None
-
+network_str = MethodSpec(
+    name="str",
+    source="""\
 
     def __str__(self):
 
         return "Network "+str(self.id)+" with "+str(len(self.populations))+" population(s)"
 
-    ''',
+    """,
     class_names=("Network"),
 )
 
-METHOD_SPECS += (network_get_by_id,)
+METHOD_SPECS += (network_str,)
 
 
 cell_methods = MethodSpec(

From fb7d15d1a3ff87dd624f4f9a959a310296a351d7 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 16 Aug 2024 16:57:47 +0100
Subject: [PATCH 11/21] fix(nml): return member value

---
 neuroml/nml/generatedssupersuper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index ad3d099..f7e7276 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -694,7 +694,7 @@ def get_by_id(self, id_):
         for member in all_members:
             if member.get_container() == 0:
                 if member.get_name() == id_:
-                    return member
+                    return getattr(self, member.get_name())
                 else:
                     all_ids.append(member.get_name())
             else:

From a440a28c13ce7bd29304f1525b48aee66431e026 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 16 Aug 2024 16:58:56 +0100
Subject: [PATCH 12/21] chore(nml): regenerate

---
 neuroml/nml/nml.py | 75 +---------------------------------------------
 1 file changed, 1 insertion(+), 74 deletions(-)

diff --git a/neuroml/nml/nml.py b/neuroml/nml/nml.py
index 316bf26..13b30b9 100644
--- a/neuroml/nml/nml.py
+++ b/neuroml/nml/nml.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 #
-# Generated Tue Aug 13 13:52:09 2024 by generateDS.py version 2.44.1.
+# Generated Fri Aug 16 16:50:58 2024 by generateDS.py version 2.44.1.
 # Python 3.11.9 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)]
 #
 # Command line options:
@@ -12468,39 +12468,6 @@ def _buildChildren(
             obj_.original_tagname_ = "inputList"
         super(Network, self)._buildChildren(child_, node, nodeName_, True)
 
-    warn_count = 0
-
-    def get_by_id(self, id: str) -> typing.Optional[typing.Any]:
-        """Get a component by its ID
-
-        :param id: ID of component to find
-        :type id: str
-        :returns:  component with specified ID or None if no component with specified ID found
-        """
-        all_ids = []
-        for ms in self.member_data_items_:
-            mlist = getattr(self, ms.get_name())
-            # TODO: debug why this is required
-            if mlist is None:
-                continue
-            for m in mlist:
-                if hasattr(m, "id"):
-                    if m.id == id:
-                        return m
-                    else:
-                        all_ids.append(m.id)
-        if self.warn_count < 10:
-            neuroml.print_(
-                "Id "
-                + id
-                + " not found in <network> element. All ids: "
-                + str(sorted(all_ids))
-            )
-            self.warn_count += 1
-        elif self.warn_count == 10:
-            neuroml.print_(" - Suppressing further warnings about id not found...")
-        return None
-
     def __str__(self):
         return (
             "Network "
@@ -42532,46 +42499,6 @@ def summary(self, show_includes=True, show_non_network=True):
 
         return info
 
-    warn_count = 0
-
-    def get_by_id(self, id: str) -> typing.Optional[typing.Any]:
-        """Get a component by specifying its ID.
-
-        :param id: id of Component to get
-        :type id: str
-        :returns: Component with given ID or None if no Component with provided ID was found
-        """
-        if len(id) == 0:
-            callframe = inspect.getouterframes(inspect.currentframe(), 2)
-            print(
-                "Method: " + callframe[1][3] + " is asking for an element with no id..."
-            )
-
-            return None
-        all_ids = []
-        for ms in self.member_data_items_:
-            mlist = getattr(self, ms.get_name())
-            # TODO: debug why this is required
-            if mlist is None:
-                continue
-            for m in mlist:
-                if hasattr(m, "id"):
-                    if m.id == id:
-                        return m
-                    else:
-                        all_ids.append(m.id)
-        if self.warn_count < 10:
-            neuroml.print_(
-                "Id "
-                + id
-                + " not found in <neuroml> element. All ids: "
-                + str(sorted(all_ids))
-            )
-            self.warn_count += 1
-        elif self.warn_count == 10:
-            neuroml.print_(" - Suppressing further warnings about id not found...")
-        return None
-
     def append(self, element):
         """Append an element
 

From 3a9f3e5aaccb465c3f5b365ce73dea949f05cc5b Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 16 Aug 2024 16:59:17 +0100
Subject: [PATCH 13/21] test(nml): add another test for get_by_id

---
 neuroml/test/test_nml.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/neuroml/test/test_nml.py b/neuroml/test/test_nml.py
index 99134e2..c4bad93 100644
--- a/neuroml/test/test_nml.py
+++ b/neuroml/test/test_nml.py
@@ -192,6 +192,18 @@ def test_get_by_id(self):
         test_pop = network.get_by_id("pop0")
         self.assertIs(test_pop, pop)
 
+    def test_get_by_id2(self):
+        """Test the get_by_id method, but for attribute"""
+        channel = neuroml.IonChannel(id="test", species="k", conductance="10pS")
+        species = channel.get_by_id("species")
+        self.assertEqual(species, "k")
+        conductance = channel.get_by_id("conductance")
+        self.assertEqual(conductance, "10pS")
+
+        # can now be edited
+        conductance = "20pS"
+        self.assertEqual(conductance, "20pS")
+
     def test_component_validate(self):
         """Test validate function"""
         network = neuroml.Network()

From d2bba990ce1fb6eaf53a4ef7a4c2293fee0a258e Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 16 Aug 2024 17:31:24 +0100
Subject: [PATCH 14/21] fix(nml): correctly append to all ids

---
 neuroml/nml/generatedssupersuper.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index f7e7276..9776423 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -692,19 +692,20 @@ def get_by_id(self, id_):
         all_ids = []
         all_members = self._get_members()
         for member in all_members:
+            # not a list
             if member.get_container() == 0:
                 if member.get_name() == id_:
                     return getattr(self, member.get_name())
                 else:
                     all_ids.append(member.get_name())
             else:
-                contents = getattr(self, member.get_name(), None)
+                contents = getattr(self, member.get_name(), [])
                 for m in contents:
                     if hasattr(m, "id"):
                         if m.id == id_:
                             return m
-                    else:
-                        all_ids.append(m.id)
+                        else:
+                            all_ids.append(m.id)
 
         self.logger.warning(f"Id '{id_}' not found in {self.__name__}")
         self.logger.warning(f"All ids: {sorted(all_ids)}")

From a60ae01d4100211753e92c64b1378f8e7f9ac083 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Mon, 19 Aug 2024 16:48:28 +0100
Subject: [PATCH 15/21] feat(get_member): also return objects if type or
 attribute are given

---
 neuroml/nml/generatedssupersuper.py | 37 +++++++++++++++++++++++------
 1 file changed, 30 insertions(+), 7 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index 9776423..dd61b9f 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -682,23 +682,43 @@ def get_nml2_class_hierarchy(cls):
             cls.__nml_hier = schema.NeuroMLDocument.get_class_hierarchy()
         return cls.__nml_hier
 
-    def get_by_id(self, id_):
-        """Get a component or attribute by its ID
+    def get_member(self, id_):
+        """Get a component or attribute by its ID, or type, or attribute name
+
+        :param id_: id of component ("biophys"), or its type
+            ("BiophysicalProperties"), or its attribute name
+            ("biophysical_properties")
+
+
+            When the attribute name or type are given, this simply returns the
+            associated object, which could be a list.
 
-        :param id_: ID of component or name of attribute to find
         :type id_: str
-        :returns:  component with specified ID, or attribute, or None if neither found
+        :returns:  component if found, else None
         """
         all_ids = []
         all_members = self._get_members()
         for member in all_members:
+            # check name: biophysical_properties
+            if member.get_name() == id_:
+                return getattr(self, member.get_name())
+            # check type: BiophysicalProperties
+            elif member.get_data_type() == id_:
+                return getattr(self, member.get_name())
+
+            # check contents
+
             # not a list
             if member.get_container() == 0:
-                if member.get_name() == id_:
-                    return getattr(self, member.get_name())
+                # check contents for id: biophysical_properties.id
+                contents = getattr(self, member.get_name(), None)
+                if hasattr(contents, "id"):
+                    if contents.id == id_:
+                        return contents
                 else:
                     all_ids.append(member.get_name())
             else:
+                # container: iterate over each item
                 contents = getattr(self, member.get_name(), [])
                 for m in contents:
                     if hasattr(m, "id"):
@@ -707,6 +727,9 @@ def get_by_id(self, id_):
                         else:
                             all_ids.append(m.id)
 
-        self.logger.warning(f"Id '{id_}' not found in {self.__name__}")
+        try:
+            self.logger.warning(f"Id '{id_}' not found in {self.__name__}")
+        except AttributeError:
+            self.logger.warning(f"Id '{id_}' not found in {self.id}")
         self.logger.warning(f"All ids: {sorted(all_ids)}")
         return None

From 704483ae74afd8839cf3c95b9ccf064f50085492 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 21 Aug 2024 11:38:46 +0100
Subject: [PATCH 16/21] fix(fix_external_morphs/biophys): add checks for
 missing attributes

---
 neuroml/utils.py | 57 +++++++++++++++++++++++++++++++++---------------
 1 file changed, 40 insertions(+), 17 deletions(-)

diff --git a/neuroml/utils.py b/neuroml/utils.py
index dc3c236..5855882 100644
--- a/neuroml/utils.py
+++ b/neuroml/utils.py
@@ -316,7 +316,10 @@ def get_relative_component_path(
 
 
 def fix_external_morphs_biophys_in_cell(
-    nml2_doc: NeuroMLDocument, overwrite: bool = True
+    nml2_doc: NeuroMLDocument,
+    overwrite: bool = True,
+    load_morphology: bool = True,
+    load_biophysical_properties: bool = True,
 ) -> NeuroMLDocument:
     """Handle externally referenced morphologies and biophysics in cells.
 
@@ -338,6 +341,10 @@ def fix_external_morphs_biophys_in_cell(
     :param overwrite: toggle whether the document is overwritten or a deep copy
         created
     :type overwrite: bool
+    :param load_morphology: whether morphologies should be loaded
+    :type load_morphology: bool
+    :param load_biophysical_properties: whether biophysical_properties should be loaded
+    :type load_biophysical_properties: bool
     :returns: neuroml document
     :raises KeyError: if referenced morphologies/biophysics cannot be found
     """
@@ -349,7 +356,7 @@ def fix_external_morphs_biophys_in_cell(
     # get a list of morph/biophys ids being referred to by cells
     referenced_ids = []
     for cell in newdoc.cells:
-        if cell.morphology_attr is not None:
+        if load_morphology is True and cell.morphology_attr is not None:
             if cell.morphology is None:
                 referenced_ids.append(cell.morphology_attr)
             else:
@@ -357,7 +364,10 @@ def fix_external_morphs_biophys_in_cell(
                     f"Cell ({cell}) already contains a Morphology, ignoring reference."
                 )
                 logger.warning("Please check/correct your cell description")
-        if cell.biophysical_properties_attr is not None:
+        if (
+            load_biophysical_properties is True
+            and cell.biophysical_properties_attr is not None
+        ):
             if cell.biophysical_properties is None:
                 referenced_ids.append(cell.biophysical_properties_attr)
             else:
@@ -369,27 +379,39 @@ def fix_external_morphs_biophys_in_cell(
     # load referenced ids from included files and store them in dicts
     ext_morphs = {}
     ext_biophys = {}
-    for inc in newdoc.includes:
-        incdoc = loaders.read_neuroml2_file(inc.href, verbose=False, optimized=True)
-        for morph in incdoc.morphology:
+    # includes/morphology/biophysical_properties should generally be empty
+    # lists and not None, but there may be cases where these have been removed
+    # after the document was loaded
+    if newdoc.includes:
+        for inc in newdoc.includes:
+            incdoc = loaders.read_neuroml2_file(inc.href, verbose=False, optimized=True)
+            if load_morphology is True and incdoc.morphology:
+                for morph in incdoc.morphology:
+                    if morph.id in referenced_ids:
+                        ext_morphs[morph.id] = morph
+            if load_biophysical_properties is True and incdoc.biophysical_properties:
+                for biophys in incdoc.biophysical_properties:
+                    if biophys.id in referenced_ids:
+                        ext_biophys[biophys.id] = biophys
+
+    if load_morphology is True and newdoc.morphology:
+        for morph in newdoc.morphology:
             if morph.id in referenced_ids:
                 ext_morphs[morph.id] = morph
-        for biophys in incdoc.biophysical_properties:
+
+    if load_biophysical_properties is True and newdoc.biophysical_properties:
+        for biophys in newdoc.biophysical_properties:
             if biophys.id in referenced_ids:
                 ext_biophys[biophys.id] = biophys
 
-    # also include morphs/biophys that are in the same document
-    for morph in newdoc.morphology:
-        if morph.id in referenced_ids:
-            ext_morphs[morph.id] = morph
-    for biophys in newdoc.biophysical_properties:
-        if biophys.id in referenced_ids:
-            ext_biophys[biophys.id] = biophys
-
     # update cells by placing the morphology/biophys in them:
     # if referenced ids are not found, throw errors
     for cell in newdoc.cells:
-        if cell.morphology_attr is not None and cell.morphology is None:
+        if (
+            load_morphology is True
+            and cell.morphology_attr is not None
+            and cell.morphology is None
+        ):
             try:
                 # TODO: do we need a deepcopy here?
                 cell.morphology = copy.deepcopy(ext_morphs[cell.morphology_attr])
@@ -401,7 +423,8 @@ def fix_external_morphs_biophys_in_cell(
                 raise e
 
         if (
-            cell.biophysical_properties_attr is not None
+            load_biophysical_properties is True
+            and cell.biophysical_properties_attr is not None
             and cell.biophysical_properties is None
         ):
             try:

From 86e89150cae33fb1f8c8496f84e9cce5386e2e65 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 21 Aug 2024 15:30:06 +0100
Subject: [PATCH 17/21] feat(fix-morph-bio): only bother reading include files
 if anything is referenced

---
 neuroml/utils.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/neuroml/utils.py b/neuroml/utils.py
index 5855882..5e97600 100644
--- a/neuroml/utils.py
+++ b/neuroml/utils.py
@@ -376,6 +376,10 @@ def fix_external_morphs_biophys_in_cell(
                 )
                 logger.warning("Please check/correct your cell description")
 
+    if len(referenced_ids) == 0:
+        logger.debug("No externally referenced morphologies or biophysics")
+        return newdoc
+
     # load referenced ids from included files and store them in dicts
     ext_morphs = {}
     ext_biophys = {}

From 124eefe1507c2a1b1040efe4a47ebcb3b5d966ab Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 21 Aug 2024 15:46:34 +0100
Subject: [PATCH 18/21] feat(fix-morph): optimise further to only load stuff if
 required

---
 neuroml/utils.py | 66 +++++++++++++++++++++++++++++++++---------------
 1 file changed, 46 insertions(+), 20 deletions(-)

diff --git a/neuroml/utils.py b/neuroml/utils.py
index 5e97600..af26761 100644
--- a/neuroml/utils.py
+++ b/neuroml/utils.py
@@ -15,7 +15,7 @@
 import networkx
 
 import neuroml.nml.nml as schema
-from neuroml import NeuroMLDocument
+from neuroml import BiophysicalProperties, Morphology, NeuroMLDocument
 
 from . import loaders
 
@@ -348,14 +348,9 @@ def fix_external_morphs_biophys_in_cell(
     :returns: neuroml document
     :raises KeyError: if referenced morphologies/biophysics cannot be found
     """
-    if overwrite is False:
-        newdoc = copy.deepcopy(nml2_doc)
-    else:
-        newdoc = nml2_doc
-
     # get a list of morph/biophys ids being referred to by cells
     referenced_ids = []
-    for cell in newdoc.cells:
+    for cell in nml2_doc.cells:
         if load_morphology is True and cell.morphology_attr is not None:
             if cell.morphology is None:
                 referenced_ids.append(cell.morphology_attr)
@@ -378,35 +373,66 @@ def fix_external_morphs_biophys_in_cell(
 
     if len(referenced_ids) == 0:
         logger.debug("No externally referenced morphologies or biophysics")
-        return newdoc
+        return nml2_doc
+
+    if overwrite is False:
+        newdoc = copy.deepcopy(nml2_doc)
+    else:
+        newdoc = nml2_doc
 
     # load referenced ids from included files and store them in dicts
-    ext_morphs = {}
-    ext_biophys = {}
+    found = False
+    ext_morphs: Dict[str, Morphology] = {}
+    ext_biophys: Dict[str, BiophysicalProperties] = {}
+
+    # first check the same document
+    if not found and load_morphology is True and newdoc.morphology:
+        for morph in newdoc.morphology:
+            if morph.id in referenced_ids:
+                ext_morphs[morph.id] = morph
+
+            if (len(ext_morphs) + len(ext_biophys)) == len(referenced_ids):
+                logger.debug("Found all references")
+                found = True
+                break
+
+    if (
+        not found
+        and load_biophysical_properties is True
+        and newdoc.biophysical_properties
+    ):
+        for biophys in newdoc.biophysical_properties:
+            if biophys.id in referenced_ids:
+                ext_biophys[biophys.id] = biophys
+
+            if (len(ext_morphs) + len(ext_biophys)) == len(referenced_ids):
+                logger.debug("Found all references")
+                found = True
+                break
+
+    # now check included files (they need to be loaded and parsed, so this can
+    # be computationally intensive)
     # includes/morphology/biophysical_properties should generally be empty
     # lists and not None, but there may be cases where these have been removed
     # after the document was loaded
-    if newdoc.includes:
+    if not found and newdoc.includes:
         for inc in newdoc.includes:
             incdoc = loaders.read_neuroml2_file(inc.href, verbose=False, optimized=True)
+
             if load_morphology is True and incdoc.morphology:
                 for morph in incdoc.morphology:
                     if morph.id in referenced_ids:
                         ext_morphs[morph.id] = morph
+
             if load_biophysical_properties is True and incdoc.biophysical_properties:
                 for biophys in incdoc.biophysical_properties:
                     if biophys.id in referenced_ids:
                         ext_biophys[biophys.id] = biophys
 
-    if load_morphology is True and newdoc.morphology:
-        for morph in newdoc.morphology:
-            if morph.id in referenced_ids:
-                ext_morphs[morph.id] = morph
-
-    if load_biophysical_properties is True and newdoc.biophysical_properties:
-        for biophys in newdoc.biophysical_properties:
-            if biophys.id in referenced_ids:
-                ext_biophys[biophys.id] = biophys
+            if (len(ext_morphs) + len(ext_biophys)) == len(referenced_ids):
+                logger.debug("Found all references")
+                found = True
+                break
 
     # update cells by placing the morphology/biophys in them:
     # if referenced ids are not found, throw errors

From db7e44258c2579e129490b3cade74583e4381f19 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 21 Aug 2024 16:27:39 +0100
Subject: [PATCH 19/21] chore: revert method name to `get_by_id`

I was breaking API here!
---
 neuroml/nml/generatedssupersuper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index dd61b9f..5254024 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -682,7 +682,7 @@ def get_nml2_class_hierarchy(cls):
             cls.__nml_hier = schema.NeuroMLDocument.get_class_hierarchy()
         return cls.__nml_hier
 
-    def get_member(self, id_):
+    def get_by_id(self, id_):
         """Get a component or attribute by its ID, or type, or attribute name
 
         :param id_: id of component ("biophys"), or its type

From 5b63e125c669ed1f0142fd9e43f501f9a236da12 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 23 Aug 2024 11:42:29 +0100
Subject: [PATCH 20/21] test(nml): add test for addition of "__ANY__" elements

---
 neuroml/nml/generatedssupersuper.py | 15 +++++++++++++--
 neuroml/test/test_nml.py            | 15 +++++++++++++++
 2 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/neuroml/nml/generatedssupersuper.py b/neuroml/nml/generatedssupersuper.py
index 5254024..5fa4e1b 100644
--- a/neuroml/nml/generatedssupersuper.py
+++ b/neuroml/nml/generatedssupersuper.py
@@ -37,7 +37,14 @@ def add(self, obj=None, hint=None, force=False, validate=True, **kwargs):
         calling (parent) component type object.
 
         :param obj: member object or class type (neuroml.NeuroMLDocument) or
-            name of class type ("NeuroMLDocument"), or None
+            name of class type ("NeuroMLDocument"), a string, or None
+
+            If the string that is passed is not the name of a NeuroML
+            component type, it will be added as a string if the parent
+            component type allows "any" elements. This does not mean that one
+            can add anything, since it must still be valid XML/LEMS. The
+            only usecase for this currently is to add RDF strings to the
+            Annotation component type.
         :type obj: str or type or None
         :param hint: member name to add to when there are multiple members that `obj` can be added to
         :type hint: string
@@ -159,12 +166,16 @@ def component_factory(cls, component_type, validate=True, **kwargs):
             Note that when providing the class type, one will need to import it,
             e.g.: `import NeuroMLDocument`, to ensure that it is defined, whereas
             this will not be required when using the string.
+
+            If the value passed for component_type is a general string (with
+            spaces), it is simply returned
         :type component_type: str/type
         :param validate: toggle validation (default: True)
         :type validate: bool
         :param kwargs: named arguments to be passed to ComponentType constructor
         :type kwargs: named arguments
-        :returns: new Component (object) of provided ComponentType
+        :returns: new Component (object) of provided ComponentType, or
+            unprocessed string with spaces if given for component_type
         :rtype: object
         :raises ValueError: if validation/checks fail
 
diff --git a/neuroml/test/test_nml.py b/neuroml/test/test_nml.py
index c4bad93..29d12a1 100644
--- a/neuroml/test/test_nml.py
+++ b/neuroml/test/test_nml.py
@@ -841,6 +841,21 @@ def test_class_hierarchy(self):
         print()
         print_hierarchy(hier)
 
+    def test_adding_any(self):
+        """Test adding things to __ANY__ attributes"""
+        newdoc = neuroml.NeuroMLDocument(id="lol")
+        annotation = newdoc.add(neuroml.Annotation)
+        # valid NeuroML, but not valid LEMS
+        # space required to distinguish it from the name of a component type,
+        # which will not have spaces
+        annotation.add(" some_string", hint="__ANY__")
+
+        # remove all spaces to test the string
+        annotation_text = str(annotation)
+        annotation_text = "".join(annotation_text.split())
+        print(annotation_text)
+        self.assertEqual("<Annotation>some_string</Annotation>", annotation_text)
+
 
 if __name__ == "__main__":
     ta = TestNML()

From 5e36a9f31c8a769dfe9e0c164d0a2df24c88a6e0 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 23 Aug 2024 11:47:53 +0100
Subject: [PATCH 21/21] test(nml): test addition of __ANY__

---
 neuroml/test/test_nml.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/neuroml/test/test_nml.py b/neuroml/test/test_nml.py
index 29d12a1..6c71041 100644
--- a/neuroml/test/test_nml.py
+++ b/neuroml/test/test_nml.py
@@ -841,6 +841,20 @@ def test_class_hierarchy(self):
         print()
         print_hierarchy(hier)
 
+    def test_adding_any_exception(self):
+        """Test adding things to __ANY__ attributes exception raise"""
+        newdoc = neuroml.NeuroMLDocument(id="lol")
+        annotation = newdoc.add(neuroml.Annotation)
+
+        # without hint="__ANY__", we raise an exception
+        with self.assertRaises(Exception) as cm:
+            annotation.add(" some_string")
+
+        self.assertEqual(
+            """Received a text object to add. Please pass `hint="__ANY__"` to confirm that this is what you intend. I will then try to add this to an __ANY__ member in the object.""",
+            str(cm.exception),
+        )
+
     def test_adding_any(self):
         """Test adding things to __ANY__ attributes"""
         newdoc = neuroml.NeuroMLDocument(id="lol")