Merge remote-tracking branch 'origin/v0.8.0' into ifcviewer-wgpu

src/bonsai/bonsai/bim/module/model/array.py

@@ -329,6 +329,7 @@ class _ArrayEditMixin(ParametricEditMixinBase):
         # Unhide the (possibly newly-regenerated) children so the user sees
         # the committed result. Mirrors the hide in ``_enable_one``.
         cls._set_children_visibility(element, hidden=False)
+        tool.Array.select_only_parent(obj, context)
 
     @classmethod
     def _cancel_one(cls, obj: bpy.types.Object) -> None:
@@ -421,9 +422,9 @@ class RegenerateArray(bpy.types.Operator, tool.Ifc.Operator):
         pset = ifcopenshell.util.element.get_pset(parent_element, "BBIM_Array")
         arrays = json.loads(pset["Data"])
         pset = tool.Ifc.get().by_id(pset["id"])
-        # Coalesce host recuts: the child-delete loop, the regenerate, and the
-        # per-child opening mirror all touch the same host body. Without batching,
-        # an N-child wipe-then-regen costs N+1 recuts; this collapses to one.
+        # Coalesce host recuts across the child-delete loop, the regenerate,
+        # and the per-child opening mirror: each fans out its own host body
+        # recut without the batch wrapper.
         with tool.Geometry.batch_host_recut():
             for array in arrays:
                 for child in set(array["children"]):
@@ -442,6 +443,8 @@ class RegenerateArray(bpy.types.Operator, tool.Ifc.Operator):
             tool.Model.regenerate_array(parent, arrays)
             tool.Array.constrain_children_to_parent(parent_element)
 
+        tool.Array.select_only_parent(parent, context)
+
 
 class RemoveArray(bpy.types.Operator, tool.Ifc.Operator):
     bl_idname = "bim.remove_array"

src/bonsai/bonsai/bim/module/model/mep.py

@@ -1677,6 +1677,11 @@ def _n_mep_selected(n: int) -> bool:
         element = tool.Ifc.get_entity(selected_obj)
         if element is None or not tool.System.is_mep_element(element):
             return False
+        # Array children mirror their parent's port topology. Writable MEP
+        # actions on a child get wiped by the next array regen, so gate the
+        # icons out at the visibility layer.
+        if tool.Array.is_array_child(element):
+            return False
     return True
 
 
@@ -2555,6 +2560,8 @@ def _active_is_flow_segment(obj: bpy.types.Object) -> bool:
     element = tool.Ifc.get_entity(obj)
     if element is None or not element.is_a("IfcFlowSegment"):
         return False
+    if tool.Array.is_array_child(element):
+        return False
     return tool.System.has_parametric_body(element)
 
 
@@ -2584,6 +2591,8 @@ def _active_is_bend_fitting(obj: bpy.types.Object) -> bool:
     element = tool.Ifc.get_entity(obj)
     if not _is_bend_fitting(element):
         return False
+    if tool.Array.is_array_child(element):
+        return False
     element_type = ifcopenshell.util.element.get_type(element)
     if element_type is None:
         return False

src/bonsai/bonsai/bim/module/project/operator.py

@@ -1294,6 +1294,11 @@ class LoadProjectElements(bpy.types.Operator):
             if element.IsDecomposedBy:
                 for subelement in element.IsDecomposedBy[0].RelatedObjects:
                     decomposed_elements.add(subelement)
+            # IfcSurfaceFeature (e.g. road markings) adhere to a host element
+            # via IfcRelAdheresToElement, a [1:1] hierarchical relationship in
+            # the same family as aggregation, containment and nesting (IFC4.3).
+            for rel in getattr(element, "HasSurfaceFeatures", ()):
+                decomposed_elements.update(rel.RelatedSurfaceFeatures)
         if decomposed_elements:
             self.append_decomposed_elements(decomposed_elements)
         elements.update(decomposed_elements)

src/bonsai/bonsai/tool/array.py

@@ -178,6 +178,25 @@ class Array(bonsai.core.tool.Array):
         element_root = cls.get_array_root_guid(element)
         return [o for o in occurrences if cls.get_array_root_guid(o) == element_root]
 
+    @classmethod
+    def select_only_parent(cls, parent_obj: bpy.types.Object, context: bpy.types.Context) -> None:
+        """Post-condition for the user-facing regenerate and finish-edit paths:
+        only ``parent_obj`` is selected + active. Grow and shrink otherwise
+        diverge on which objects stay selected, surfacing an inconsistency."""
+        tool.Blender.select_and_activate_single_object(context, parent_obj)
+
+    @classmethod
+    def is_array_child(cls, element: entity_instance) -> bool:
+        """True when ``element`` is a child of a parametric array — has a
+        BBIM_Array pset whose Parent GUID points to a different element.
+        Lighter than ``get_child_layer_index`` (no ``by_guid`` lookup, no
+        Data parse); suitable for per-element checks in draw handlers."""
+        pset = ifcopenshell.util.element.get_pset(element, "BBIM_Array")
+        if not pset:
+            return False
+        parent_guid = pset.get("Parent")
+        return bool(parent_guid) and parent_guid != element.GlobalId
+
     @classmethod
     def get_child_layer_index(cls, child_element: entity_instance) -> int | None:
         """Index of the layer that produced ``child_element``, or ``None``

src/bonsai/bonsai/tool/duplicate.py

@@ -248,32 +248,30 @@ class Duplicate(bonsai.core.tool.Duplicate):
         old_to_new: dict[ifcopenshell.entity_instance, list[ifcopenshell.entity_instance]],
     ) -> None:
         for element, data in relationship.items():
-            try:
-                new_relating_element = old_to_new.get(data.relating_element)[0]
-                new_related_element = old_to_new.get(data.related_element)[0]
-            except (KeyError, IndexError, TypeError):
-                continue
-            new_rel = tool.Ifc.run(
-                "geometry.connect_path",
-                relating_element=new_relating_element,
-                related_element=new_related_element,
-                relating_connection=data.relating_connection_type,
-                related_connection=data.related_connection_type,
-            )
+            new_relating_elements = old_to_new.get(data.relating_element) or []
+            new_related_elements = old_to_new.get(data.related_element) or []
             # connect_path hardcodes priorities to []; restore them post-hoc.
             priority_attrs: dict[str, Any] = {}
             if data.relating_priorities:
                 priority_attrs["RelatingPriorities"] = data.relating_priorities
             if data.related_priorities:
                 priority_attrs["RelatedPriorities"] = data.related_priorities
-            if new_rel is not None and priority_attrs:
-                try:
-                    tool.Ifc.run("attribute.edit_attributes", product=new_rel, attributes=priority_attrs)
-                except (RuntimeError, ifcopenshell.Error) as e:
-                    cls._emit_warning(
-                        f"connection priority restore failed for {new_rel}; "
-                        f"duplicate has empty RelatingPriorities/RelatedPriorities: {e}"
-                    )
+            for new_relating_element, new_related_element in zip(new_relating_elements, new_related_elements):
+                new_rel = tool.Ifc.run(
+                    "geometry.connect_path",
+                    relating_element=new_relating_element,
+                    related_element=new_related_element,
+                    relating_connection=data.relating_connection_type,
+                    related_connection=data.related_connection_type,
+                )
+                if new_rel is not None and priority_attrs:
+                    try:
+                        tool.Ifc.run("attribute.edit_attributes", product=new_rel, attributes=priority_attrs)
+                    except (RuntimeError, ifcopenshell.Error) as e:
+                        cls._emit_warning(
+                            f"connection priority restore failed for {new_rel}; "
+                            f"duplicate has empty RelatingPriorities/RelatedPriorities: {e}"
+                        )
 
     @classmethod
     def recreate_port_connections(
@@ -283,46 +281,43 @@ class Duplicate(bonsai.core.tool.Duplicate):
     ) -> None:
         """Recreate ``IfcRelConnectsPorts`` between duplicates; skip records whose duplicate's port count diverges from the snapshot."""
         for relating_element, records in snapshot.by_element.items():
+            new_relatings = old_to_new.get(relating_element) or []
+            expected_relating = snapshot.port_counts.get(relating_element)
             for record in records:
                 related_element = record.related_element
-                try:
-                    new_relating = old_to_new[relating_element][0]
-                    new_related = old_to_new[related_element][0]
-                except (KeyError, IndexError):
-                    continue
-
-                new_relating_ports = tool.System.get_ports(new_relating)
-                new_related_ports = tool.System.get_ports(new_related)
-
-                expected_relating = snapshot.port_counts.get(relating_element)
-                if expected_relating is not None and len(new_relating_ports) != expected_relating:
-                    cls._emit_warning(
-                        f"port reconnect skipped — duplicate has {len(new_relating_ports)} ports, "
-                        f"snapshot had {expected_relating}"
-                    )
-                    continue
+                new_relateds = old_to_new.get(related_element) or []
                 expected_related = snapshot.port_counts.get(related_element)
-                if expected_related is not None and len(new_related_ports) != expected_related:
-                    cls._emit_warning(
-                        f"port reconnect skipped — duplicate has {len(new_related_ports)} ports, "
-                        f"snapshot had {expected_related}"
-                    )
-                    continue
+                for new_relating, new_related in zip(new_relatings, new_relateds):
+                    new_relating_ports = tool.System.get_ports(new_relating)
+                    new_related_ports = tool.System.get_ports(new_related)
 
-                try:
-                    new_port_a = new_relating_ports[record.relating_port_index]
-                    new_port_b = new_related_ports[record.related_port_index]
-                except IndexError:
-                    cls._emit_warning(
-                        f"port reconnect skipped — record references port index past the duplicate's port list"
-                    )
-                    continue
-                try:
-                    tool.Ifc.run(
-                        "system.connect_port",
-                        port1=new_port_a,
-                        port2=new_port_b,
-                        direction=record.direction or "NOTDEFINED",
-                    )
-                except (RuntimeError, ifcopenshell.Error) as e:
-                    cls._emit_warning(f"port reconnect failed between duplicates: {e}")
+                    if expected_relating is not None and len(new_relating_ports) != expected_relating:
+                        cls._emit_warning(
+                            f"port reconnect skipped — duplicate has {len(new_relating_ports)} ports, "
+                            f"snapshot had {expected_relating}"
+                        )
+                        continue
+                    if expected_related is not None and len(new_related_ports) != expected_related:
+                        cls._emit_warning(
+                            f"port reconnect skipped — duplicate has {len(new_related_ports)} ports, "
+                            f"snapshot had {expected_related}"
+                        )
+                        continue
+
+                    try:
+                        new_port_a = new_relating_ports[record.relating_port_index]
+                        new_port_b = new_related_ports[record.related_port_index]
+                    except IndexError:
+                        cls._emit_warning(
+                            f"port reconnect skipped — record references port index past the duplicate's port list"
+                        )
+                        continue
+                    try:
+                        tool.Ifc.run(
+                            "system.connect_port",
+                            port1=new_port_a,
+                            port2=new_port_b,
+                            direction=record.direction or "NOTDEFINED",
+                        )
+                    except (RuntimeError, ifcopenshell.Error) as e:
+                        cls._emit_warning(f"port reconnect failed between duplicates: {e}")

src/bonsai/bonsai/tool/geometry.py

@@ -173,13 +173,21 @@ class Geometry(bonsai.core.tool.Geometry):
                 cls._host_update_queue = {}
                 cls._host_recut_queue = {}
                 for voided_obj in update_queue.values():
-                    if not voided_obj or not voided_obj.data:
+                    try:
+                        if not voided_obj or not voided_obj.data:
+                            continue
+                    except ReferenceError:
+                        # Blender object was deleted while the batch was open
+                        # (e.g. user removed it via the outliner mid-op).
                         continue
                     if tool.Ifc.get_entity(voided_obj) is None:
                         continue
                     bpy.ops.bim.update_representation(obj=voided_obj.name)
                 for voided_obj, _ in recut_queue.values():
-                    if not voided_obj or not voided_obj.data:
+                    try:
+                        if not voided_obj or not voided_obj.data:
+                            continue
+                    except ReferenceError:
                         continue
                     if tool.Ifc.get_entity(voided_obj) is None:
                         continue
@@ -2490,99 +2498,16 @@ class Geometry(bonsai.core.tool.Geometry):
         old_obj_name_to_new_obj_name: dict[str, str] = {}
 
         for obj in objects_to_duplicate:
-            element = tool.Ifc.get_entity(obj)
-            if element:
-                if element.is_a("IfcAnnotation") and element.ObjectType == "DRAWING":
-                    tool.Blender.deselect_object(obj)
-                    continue  # For now, don't copy drawings until we stabilise a bit more. It's tricky.
-                elif tool.Geometry.is_locked(element):
-                    tool.Blender.deselect_object(obj)
-                    continue
-            elif tool.Geometry.is_representation_item(obj):
-                cls.duplicate_ifc_item(obj)
-                continue
-
-            tracked_opening_type = tool.Model.get_tracked_opening_type(obj)
-            is_tracked_opening = bool(tracked_opening_type)
-            keep_data_linked = linked and not element and not is_tracked_opening
-
-            # Prior to duplicating, sync the object placement to make decomposition recreation more stable.
-            cls.commit_placement_if_moved(obj, apply_scale=False)
-
-            new_obj = obj.copy()
-            temp_data = None
-
-            # Currently for optimization we do not apply pending changes (scale or changed .data)
-            # to the original and duplicated objects.
-            # Keep new object edited if original is.
-            if tool.Ifc.is_edited(obj, ignore_scale=True):
-                tool.Ifc.edit(new_obj)
-
-            if obj.data and not keep_data_linked:
-                # assure root.copy_class won't replace the previous mesh globally
-                temp_data = obj.data.copy()
-                new_obj.data = temp_data
-
-                # Unlink from previous boolean element
-                # and keep object tracked for decorations.
-                if is_tracked_opening:
-                    mprops = tool.Geometry.get_mesh_props(new_obj.data)
-                    mprops.ifc_boolean_id = 0
-                    tool.Root.add_tracked_opening(new_obj, tracked_opening_type)
-
-            if obj == active_object:
-                new_active_obj = new_obj
-            for collection in obj.users_collection:
-                collection.objects.link(new_obj)
-            obj.select_set(False)
-            new_obj.select_set(True)
-            old_obj_name_to_new_obj_name[obj.name] = new_obj.name
-
-            if not element:
-                continue
-
-            # clear object's collection so it will be able to have it's own
-            tool.Blender.get_object_bim_props(new_obj).collection = None
-            # copy the actual class
-            new = bonsai.core.root.copy_class(tool.Ifc, tool.Collector, tool.Geometry, tool.Root, obj=new_obj)
-
-            # clean up the orphaned mesh with ifc id of the original object to avoid confusion
-            # IfcGridAxis keeps the same mesh data (it's pointing to ifc id 0, so it's not a problem)
-            if new and temp_data and not new.is_a("IfcGridAxis"):
-                if new.is_a("IfcRelSpaceBoundary"):
-                    surface = new.ConnectionGeometry.SurfaceOnRelatingElement
-                    temp_data.name = f"0/{surface.id()}"
-                    tool.Ifc.link(surface, temp_data)
-                else:
-                    tool.Blender.remove_data_block(temp_data)
-
-            if new:
-                # TODO: handle array data for other cases of duplication
-                array_data = arrays_to_duplicate.get(obj, None)
-                tool.Model.handle_array_on_copied_element(new, array_data)
-                if array_data:
-                    for child in tool.Array.get_all_children_objects(new):
-                        child.select_set(True)
-
-                # TODO: add new array children to recreate their decomposition too
-                old_to_new[element] = [new]
-                if new.is_a("IfcRelSpaceBoundary"):
-                    tool.Boundary.decorate_boundary(new_obj)
-                # Slab-trim booleans (from extend_walls_to_underside) belong to
-                # the source wall's connection, not the copy. Strip them so the
-                # duplicate reverts to its pre-clip extrusion — mirrors the way
-                # filling rels are dropped while manual booleans persist on copy.
-                # Reload the body when something was stripped so the viewport
-                # immediately shows the unclipped geometry; otherwise the user
-                # sees a stale mesh until they Shift+G, which is easy to miss.
-                if new.is_a("IfcWall"):
-                    if tool.Model.strip_underside_booleans(new):
-                        tool.Model.reload_body_representation(new_obj)
-                    # HasOpenings rels don't follow object duplication, so
-                    # the duplicate's body must rebuild to match its current
-                    # opening set.
-                    else:
-                        tool.Model.regenerate_wall(new_obj)
+            new_active = cls._duplicate_ifc_object_once(
+                obj,
+                active_object,
+                linked,
+                arrays_to_duplicate,
+                old_to_new,
+                old_obj_name_to_new_obj_name,
+            )
+            if new_active is not None:
+                new_active_obj = new_active
 
         # Remap Blender parent relationships for duplicated objects
         for old_obj_name, new_obj_name in old_obj_name_to_new_obj_name.items():
@@ -2610,10 +2535,211 @@ class Geometry(bonsai.core.tool.Geometry):
         # Recreate decompositions
         tool.Duplicate.recreate_decompositions(decomposition_relationships, old_to_new)
         cls.remove_linked_aggregate_data(old_to_new)
+
+        # In-loop regenerate_wall runs before recreate_connections, so any new
+        # walls that just received an IfcRelConnectsPathElements have stale
+        # junction geometry — recalculate them now that their connection graph
+        # is complete.
+        cls._recalculate_walls_with_new_connections(old_to_new)
+
         bonsai.bim.handler.refresh_ui_data()
         tool.Root.reload_grid_decorator()
         return old_to_new, new_active_obj or active_object
 
+    @classmethod
+    def duplicate_ifc_object_n_times(
+        cls, source: bpy.types.Object, count: int
+    ) -> dict[ifcopenshell.entity_instance, list[ifcopenshell.entity_instance]]:
+        """N-way duplicate of a single source.
+
+        Same per-copy semantics as duplicate_ifc_objects (IFC class copy,
+        decomposition + connection recreation, body regen for walls), but
+        bypasses the set() dedupe and the arrays_to_duplicate pre-scan so
+        callers building a fresh array don't pay per-call overhead N times.
+        Returns the same old_to_new dict shape, with the source element
+        mapping to the N new entities."""
+        if count <= 0:
+            return {}
+
+        sources = {source}
+        decomposition_relationships = tool.Duplicate.get_decomposition_relationships(sources)
+        connection_relationships = tool.Duplicate.get_connection_relationships(sources)
+        port_connection_snapshot = tool.Duplicate.get_port_connection_relationships(sources)
+        old_to_new: dict[ifcopenshell.entity_instance, list[ifcopenshell.entity_instance]] = {}
+        old_obj_name_to_new_obj_name: dict[str, str] = {}
+
+        for _ in range(count):
+            cls._duplicate_ifc_object_once(
+                source,
+                None,
+                False,
+                {},
+                old_to_new,
+                old_obj_name_to_new_obj_name,
+                keep_source_selected=True,
+            )
+
+        for old_obj_name, new_obj_name in old_obj_name_to_new_obj_name.items():
+            new_obj = bpy.data.objects.get(new_obj_name)
+            if new_obj and new_obj.parent and new_obj.parent.name in old_obj_name_to_new_obj_name:
+                world_matrix = new_obj.matrix_world.copy()
+                new_parent_name = old_obj_name_to_new_obj_name[new_obj.parent.name]
+                new_parent = bpy.data.objects.get(new_parent_name)
+                if new_parent:
+                    new_obj.parent = new_parent
+                    new_obj.matrix_world = world_matrix
+
+        for old in old_to_new.keys():
+            if old.is_a("IfcElementAssembly"):
+                tool.Root.recreate_aggregate(old_to_new)
+
+        cls.remove_old_connections(old_to_new)
+        tool.Duplicate.recreate_connections(connection_relationships, old_to_new)
+        tool.Duplicate.recreate_port_connections(port_connection_snapshot, old_to_new)
+        tool.Duplicate.recreate_decompositions(decomposition_relationships, old_to_new)
+        cls.remove_linked_aggregate_data(old_to_new)
+        cls._recalculate_walls_with_new_connections(old_to_new)
+        bonsai.bim.handler.refresh_ui_data()
+        tool.Root.reload_grid_decorator()
+        return old_to_new
+
+    @classmethod
+    def _duplicate_ifc_object_once(
+        cls,
+        obj: bpy.types.Object,
+        active_object: Optional[bpy.types.Object],
+        linked: bool,
+        arrays_to_duplicate: dict[bpy.types.Object, Any],
+        old_to_new: dict[ifcopenshell.entity_instance, list[ifcopenshell.entity_instance]],
+        old_obj_name_to_new_obj_name: dict[str, str],
+        keep_source_selected: bool = False,
+    ) -> Optional[bpy.types.Object]:
+        """Per-source body of the duplicate flow. Mutates old_to_new and
+        old_obj_name_to_new_obj_name in place. Returns new_obj when obj is
+        the active_object, else None.
+
+        keep_source_selected: when True, skip the source deselect so batched
+        callers can run N iterations without N×2 select flips and without
+        needing a post-loop restore on the source."""
+        new_active_obj: Optional[bpy.types.Object] = None
+        element = tool.Ifc.get_entity(obj)
+        if element:
+            if element.is_a("IfcAnnotation") and element.ObjectType == "DRAWING":
+                tool.Blender.deselect_object(obj)
+                return None  # For now, don't copy drawings until we stabilise a bit more. It's tricky.
+            elif tool.Geometry.is_locked(element):
+                tool.Blender.deselect_object(obj)
+                return None
+        elif tool.Geometry.is_representation_item(obj):
+            cls.duplicate_ifc_item(obj)
+            return None
+
+        tracked_opening_type = tool.Model.get_tracked_opening_type(obj)
+        is_tracked_opening = bool(tracked_opening_type)
+        keep_data_linked = linked and not element and not is_tracked_opening
+
+        # Prior to duplicating, sync the object placement to make decomposition recreation more stable.
+        cls.commit_placement_if_moved(obj, apply_scale=False)
+
+        new_obj = obj.copy()
+        temp_data = None
+
+        # Currently for optimization we do not apply pending changes (scale or changed .data)
+        # to the original and duplicated objects.
+        # Keep new object edited if original is.
+        if tool.Ifc.is_edited(obj, ignore_scale=True):
+            tool.Ifc.edit(new_obj)
+
+        if obj.data and not keep_data_linked:
+            # assure root.copy_class won't replace the previous mesh globally
+            temp_data = obj.data.copy()
+            new_obj.data = temp_data
+
+            # Unlink from previous boolean element
+            # and keep object tracked for decorations.
+            if is_tracked_opening:
+                mprops = tool.Geometry.get_mesh_props(new_obj.data)
+                mprops.ifc_boolean_id = 0
+                tool.Root.add_tracked_opening(new_obj, tracked_opening_type)
+
+        if obj == active_object:
+            new_active_obj = new_obj
+        for collection in obj.users_collection:
+            collection.objects.link(new_obj)
+        if not keep_source_selected:
+            obj.select_set(False)
+        new_obj.select_set(True)
+        old_obj_name_to_new_obj_name[obj.name] = new_obj.name
+
+        if not element:
+            return new_active_obj
+
+        # clear object's collection so it will be able to have it's own
+        tool.Blender.get_object_bim_props(new_obj).collection = None
+        # copy the actual class
+        new = bonsai.core.root.copy_class(tool.Ifc, tool.Collector, tool.Geometry, tool.Root, obj=new_obj)
+
+        # clean up the orphaned mesh with ifc id of the original object to avoid confusion
+        # IfcGridAxis keeps the same mesh data (it's pointing to ifc id 0, so it's not a problem)
+        if new and temp_data and not new.is_a("IfcGridAxis"):
+            if new.is_a("IfcRelSpaceBoundary"):
+                surface = new.ConnectionGeometry.SurfaceOnRelatingElement
+                temp_data.name = f"0/{surface.id()}"
+                tool.Ifc.link(surface, temp_data)
+            else:
+                tool.Blender.remove_data_block(temp_data)
+
+        if new:
+            # TODO: handle array data for other cases of duplication
+            array_data = arrays_to_duplicate.get(obj, None)
+            tool.Model.handle_array_on_copied_element(new, array_data)
+            if array_data:
+                for child in tool.Array.get_all_children_objects(new):
+                    child.select_set(True)
+
+            # TODO: add new array children to recreate their decomposition too
+            old_to_new.setdefault(element, []).append(new)
+            if new.is_a("IfcRelSpaceBoundary"):
+                tool.Boundary.decorate_boundary(new_obj)
+            # Slab-trim booleans (from extend_walls_to_underside) belong to
+            # the source wall's connection, not the copy. Strip them so the
+            # duplicate reverts to its pre-clip extrusion — mirrors the way
+            # filling rels are dropped while manual booleans persist on copy.
+            # Reload the body when something was stripped so the viewport
+            # immediately shows the unclipped geometry; otherwise the user
+            # sees a stale mesh until they Shift+G, which is easy to miss.
+            if new.is_a("IfcWall"):
+                if tool.Model.strip_underside_booleans(new):
+                    tool.Model.reload_body_representation(new_obj)
+                # HasOpenings rels don't follow object duplication, so
+                # the duplicate's body must rebuild to match its current
+                # opening set.
+                else:
+                    tool.Model.regenerate_wall(new_obj)
+
+        return new_active_obj
+
+    @classmethod
+    def _recalculate_walls_with_new_connections(
+        cls, old_to_new: dict[ifcopenshell.entity_instance, list[ifcopenshell.entity_instance]]
+    ) -> None:
+        """Recalculate new IfcWall duplicates that just received an
+        ``IfcRelConnectsPathElements``. The in-loop ``regenerate_wall`` runs
+        before ``recreate_connections``, so wall body geometry doesn't reflect
+        the junction until this second pass."""
+        walls_to_recalc: list[bpy.types.Object] = []
+        for new_list in old_to_new.values():
+            for new_entity in new_list:
+                if not new_entity.is_a("IfcWall"):
+                    continue
+                if not (getattr(new_entity, "ConnectedTo", None) or getattr(new_entity, "ConnectedFrom", None)):
+                    continue
+                new_obj = tool.Ifc.get_object(new_entity)
+                if new_obj is not None:
+                    walls_to_recalc.append(new_obj)
+        if walls_to_recalc:
+            tool.Model.recalculate_walls(walls_to_recalc)
+
     @classmethod
     def duplicate_ifc_item(cls, obj: bpy.types.Object) -> None:
         props = tool.Geometry.get_geometry_props()

src/bonsai/bonsai/tool/model.py

@@ -1247,6 +1247,35 @@ class Model(bonsai.core.tool.Model):
         with tool.Geometry.batch_host_recut():
             cls._regenerate_array_body(parent_obj, data, array_layers_to_apply)
 
+    @classmethod
+    def _prune_orphan_array_children(cls, array: dict[str, Any]) -> None:
+        """Drop GUIDs from ``array['children']`` whose IFC entity or Blender
+        object is no longer alive, and cascade-remove the orphan IFC entity
+        if it still exists. Outliner / keyboard delete of a Bonsai-managed
+        object bypasses ``bim.delete``'s cascade, leaving dangling opening
+        and filling references that later confuse regen and crash the
+        ``batch_host_recut`` drain."""
+        live_guids: list[str] = []
+        ifc_file = tool.Ifc.get()
+        for guid in array["children"]:
+            try:
+                element = ifc_file.by_guid(guid)
+            except RuntimeError:
+                continue
+            obj = tool.Ifc.get_object(element)
+            try:
+                is_live = obj is not None and obj.data is not None
+            except ReferenceError:
+                is_live = False
+            if is_live:
+                live_guids.append(guid)
+                continue
+            try:
+                ifcopenshell.api.root.remove_product(ifc_file, product=element)
+            except (RuntimeError, ifcopenshell.Error):
+                pass
+        array["children"] = live_guids
+
     @classmethod
     def _regenerate_array_body(
         cls, parent_obj: bpy.types.Object, data: list[dict[str, Any]], array_layers_to_apply: Iterable[int]
@@ -1262,6 +1291,7 @@ class Model(bonsai.core.tool.Model):
         obj_stack = [parent_obj]
 
         for array_i, array in enumerate(data):
+            cls._prune_orphan_array_children(array)
             child_i = 0
             existing_children = set(array["children"])
             total_existing_children = len(array["children"])
@@ -1275,6 +1305,14 @@ class Model(bonsai.core.tool.Model):
             else:
                 base_offset = Vector([array["x"], array["y"], array["z"]]) * unit_scale
 
+            target_new_in_this_layer = (array["count"] - 1) * len(obj_stack)
+            missing_count = max(0, target_new_in_this_layer - total_existing_children)
+            new_entities_pool: list[ifcopenshell.entity_instance] = []
+            if missing_count > 0:
+                batch_old_to_new = tool.Geometry.duplicate_ifc_object_n_times(parent_obj, missing_count)
+                new_entities_pool = batch_old_to_new.get(parent_element, [])
+            new_entities_iter = iter(new_entities_pool)
+
             for i in range(array["count"]):
                 if i == 0:
                     continue
@@ -1292,8 +1330,13 @@ class Model(bonsai.core.tool.Model):
                         child_obj = tool.Ifc.get_object(child_element)
                         assert child_obj
                     except (IndexError, RuntimeError, AssertionError):
-                        old_to_new, _ = tool.Geometry.duplicate_ifc_objects([parent_obj])
-                        child_element = next(iter(old_to_new.values()))[0]
+                        try:
+                            child_element = next(new_entities_iter)
+                        except StopIteration:
+                            # Stale-GUID mid-list left the pool exhausted; fall back
+                            # to a one-off duplicate so the layer can still complete.
+                            old_to_new, _ = tool.Geometry.duplicate_ifc_objects([parent_obj])
+                            child_element = next(iter(old_to_new.values()))[0]
                         child_obj = tool.Ifc.get_object(child_element)
 
                     # add child pset
@@ -1361,14 +1404,7 @@ class Model(bonsai.core.tool.Model):
             tool.Ifc.get(), pset=pset, properties={"Data": json_data, "Parent": parent_element.GlobalId}
         )
 
-        # Post-condition: parent is selected on return. duplicate_ifc_objects
-        # deselects the source on every call inside the regen loop; without
-        # this restore, callers get a deselected parent for arrays with N >= 2.
-        # TODO: batch the per-child duplicate_ifc_objects([parent]) calls into
-        # a single N-way duplicate — N depsgraph churns + N select/deselect
-        # flips is wasteful, and a batched duplicate would also remove the
-        # need for this restore.
-        parent_obj.select_set(True)
+        tool.Blender.set_object_selection(parent_obj, True)
 
     @classmethod
     def mirror_parent_void_fillings_to_children(

src/bonsai/bonsai/tool/root.py

@@ -373,35 +373,37 @@ class Root(bonsai.core.tool.Root):
                 try:
                     new_aggregate = old_to_new[old_aggregate]
                 except:
-                    bonsai.core.aggregate.unassign_object(
-                        tool.Ifc,
-                        tool.Aggregate,
-                        tool.Collector,
-                        relating_obj=tool.Ifc.get_object(old_aggregate),
-                        related_obj=tool.Ifc.get_object(new[0]),
-                    )
-                    continue
-
-                bonsai.core.aggregate.assign_object(
-                    tool.Ifc,
-                    tool.Aggregate,
-                    tool.Collector,
-                    relating_obj=tool.Ifc.get_object(new_aggregate[0]),
-                    related_obj=tool.Ifc.get_object(new[0]),
-                )
-
-                # Make sure that the array children also get reassigned to the correct aggregate
-                pset = ifcopenshell.util.element.get_pset(new[0], "BBIM_Array")
-                if pset:
-                    array_children = tool.Array.get_all_children_objects(new[0])
-                    for obj in array_children:
-                        bonsai.core.aggregate.assign_object(
+                    for new_entity in new:
+                        bonsai.core.aggregate.unassign_object(
                             tool.Ifc,
                             tool.Aggregate,
                             tool.Collector,
-                            relating_obj=tool.Ifc.get_object(new_aggregate[0]),
-                            related_obj=tool.Ifc.get_object(tool.Ifc.get_entity(obj)),
+                            relating_obj=tool.Ifc.get_object(old_aggregate),
+                            related_obj=tool.Ifc.get_object(new_entity),
                         )
+                    continue
+
+                for new_entity in new:
+                    bonsai.core.aggregate.assign_object(
+                        tool.Ifc,
+                        tool.Aggregate,
+                        tool.Collector,
+                        relating_obj=tool.Ifc.get_object(new_aggregate[0]),
+                        related_obj=tool.Ifc.get_object(new_entity),
+                    )
+
+                    # Make sure that the array children also get reassigned to the correct aggregate
+                    pset = ifcopenshell.util.element.get_pset(new_entity, "BBIM_Array")
+                    if pset:
+                        array_children = tool.Array.get_all_children_objects(new_entity)
+                        for obj in array_children:
+                            bonsai.core.aggregate.assign_object(
+                                tool.Ifc,
+                                tool.Aggregate,
+                                tool.Collector,
+                                relating_obj=tool.Ifc.get_object(new_aggregate[0]),
+                                related_obj=tool.Ifc.get_object(tool.Ifc.get_entity(obj)),
+                            )
 
         if new_aggregate is None:
             return

src/bonsai/bonsai/tool/system.py

@@ -357,6 +357,13 @@ class System(bonsai.core.tool.System):
             if not cls.is_mep_element(element):
                 continue
 
+            # Array children inherit port topology from their parent's IFC
+            # entity, but their positions are derived — drawing ports on every
+            # copy of an arrayed segment doubles up markers and misleads the
+            # user into thinking each copy has its own port network.
+            if tool.Array.is_array_child(element):
+                continue
+
             selected_element = element in connected_elements
             verts_pos = []
 

src/bonsai/test/bim/module/model/test_array_duplicate_batched.py

@@ -0,0 +1,714 @@
+# Bonsai - OpenBIM Blender Add-on
+# Copyright (C) 2026
+#
+# This file is part of Bonsai.
+#
+# Bonsai is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Bonsai is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Bonsai.  If not, see <http://www.gnu.org/licenses/>.
+#
+# This file was generated with the assistance of an AI coding tool.
+
+"""Tests for the batched array-duplicate path.
+
+`tool.Geometry.duplicate_ifc_object_n_times` lifts the per-call overhead of
+`duplicate_ifc_objects` (snapshot, UI refresh, decorator reload, select
+flips) out of the per-child loop in `_regenerate_array_body`. These tests
+pin three contracts:
+
+1. N-way batched duplicate produces N distinct entities mapped from the
+   source under `old_to_new[source_element]`, and the source object stays
+   selected throughout (no per-iteration deselect).
+2. Per-layer batching collapses the N independent UI refreshes into one.
+3. End-to-end array regen still yields the same number and shape of
+   children as the per-call baseline."""
+
+import json
+from unittest.mock import patch
+
+import bpy
+import ifcopenshell
+import pytest
+
+import bonsai.tool as tool
+from test.bim.bootstrap import NewFile
+
+pytestmark = pytest.mark.model
+
+
+def _build_actuator(name: str = "Actuator") -> tuple[bpy.types.Object, ifcopenshell.entity_instance]:
+    """Minimal IfcActuator + cube — matches the test_array_batch_recut.py shape."""
+    bpy.ops.bim.create_project()
+    bpy.ops.mesh.primitive_cube_add()
+    obj = bpy.context.active_object
+    obj.name = name
+    rprops = tool.Root.get_root_props()
+    rprops.ifc_product = "IfcElement"
+    bpy.ops.bim.assign_class(ifc_class="IfcActuator", predefined_type="ELECTRICACTUATOR", userdefined_type="")
+    element = tool.Ifc.get_entity(obj)
+    return obj, element
+
+
+def _build_actuator_with_array_pset(
+    count: int, x: float = 1.0
+) -> tuple[bpy.types.Object, ifcopenshell.entity_instance, list[dict]]:
+    obj, element = _build_actuator()
+    parent_data = [
+        {
+            "children": [],
+            "count": count,
+            "method": "OFFSET",
+            "x": x,
+            "y": 0.0,
+            "z": 0.0,
+            "use_local_space": False,
+            "sync_children": False,
+        }
+    ]
+    pset = ifcopenshell.api.pset.add_pset(tool.Ifc.get(), product=element, name="BBIM_Array")
+    ifcopenshell.api.pset.edit_pset(
+        tool.Ifc.get(),
+        pset=pset,
+        properties={"Data": json.dumps(parent_data), "Parent": element.GlobalId},
+    )
+    return obj, element, parent_data
+
+
+class TestDuplicateIfcObjectNTimes(NewFile):
+    def test_returns_empty_dict_for_zero_count(self):
+        obj, _ = _build_actuator()
+        result = tool.Geometry.duplicate_ifc_object_n_times(obj, 0)
+        assert result == {}
+
+    def test_returns_empty_dict_for_negative_count(self):
+        obj, _ = _build_actuator()
+        result = tool.Geometry.duplicate_ifc_object_n_times(obj, -3)
+        assert result == {}
+
+    def test_produces_n_distinct_entities(self):
+        obj, element = _build_actuator()
+        result = tool.Geometry.duplicate_ifc_object_n_times(obj, 5)
+        new_entities = result.get(element)
+        assert new_entities is not None
+        assert len(new_entities) == 5
+        assert len({e.id() for e in new_entities}) == 5
+        for new_entity in new_entities:
+            assert new_entity.is_a("IfcActuator")
+            assert new_entity.GlobalId != element.GlobalId
+
+    def test_source_stays_selected_after_batch(self):
+        obj, _ = _build_actuator()
+        obj.select_set(True)
+        tool.Geometry.duplicate_ifc_object_n_times(obj, 4)
+        assert obj in bpy.context.selected_objects, "source object must remain selected across batched duplicates"
+
+    def test_each_new_entity_has_blender_object(self):
+        obj, element = _build_actuator()
+        result = tool.Geometry.duplicate_ifc_object_n_times(obj, 3)
+        for new_entity in result[element]:
+            new_obj = tool.Ifc.get_object(new_entity)
+            assert new_obj is not None
+            assert new_obj is not obj
+
+
+class TestBatchedRefreshUIDataCallCount(NewFile):
+    def test_n_times_calls_refresh_ui_data_once(self):
+        obj, _ = _build_actuator()
+        with patch("bonsai.bim.handler.refresh_ui_data") as refresh_mock:
+            tool.Geometry.duplicate_ifc_object_n_times(obj, 8)
+        assert (
+            refresh_mock.call_count == 1
+        ), f"batched 8-way duplicate must call refresh_ui_data once, got {refresh_mock.call_count}"
+
+    def test_n_times_calls_reload_grid_decorator_once(self):
+        obj, _ = _build_actuator()
+        with patch.object(tool.Root, "reload_grid_decorator") as reload_mock:
+            tool.Geometry.duplicate_ifc_object_n_times(obj, 8)
+        assert reload_mock.call_count == 1
+
+
+class TestRegenerateArrayEndToEnd(NewFile):
+    def test_regenerate_array_creates_expected_children(self):
+        obj, element, parent_data = _build_actuator_with_array_pset(count=8)
+        bpy.context.view_layer.objects.active = obj
+        tool.Model.regenerate_array(obj, parent_data)
+
+        layer = parent_data[0]
+        assert len(layer["children"]) == 7, "8-element array means 7 new children (parent + 7)"
+        for child_guid in layer["children"]:
+            child_element = tool.Ifc.get().by_guid(child_guid)
+            assert child_element is not None
+            assert child_element.is_a("IfcActuator")
+            child_pset = ifcopenshell.util.element.get_pset(child_element, "BBIM_Array")
+            assert child_pset is not None
+            assert child_pset["Parent"] == element.GlobalId
+
+    def test_regenerate_array_parent_stays_selected(self):
+        obj, element, parent_data = _build_actuator_with_array_pset(count=4)
+        bpy.context.view_layer.objects.active = obj
+        obj.select_set(True)
+        tool.Model.regenerate_array(obj, parent_data)
+        assert (
+            obj in bpy.context.selected_objects
+        ), "regenerate_array must leave parent_obj selected on return (post-condition)"
+
+    def test_regen_operator_leaves_only_parent_selected_and_active(self):
+        """Post-condition parity between grow and shrink for the user-facing
+        ``bim.regenerate_array`` operator: only the parent is selected + active;
+        every child is deselected. Pre-fix the grow path left new children
+        selected, creating inconsistency with the shrink path.
+
+        Scoped to the operator, not the tool method — ``remove_array`` and
+        ``apply_array`` also invoke ``tool.Model.regenerate_array`` internally
+        but expect a different post-selection state (children stay selected
+        for user follow-up work)."""
+        obj, element, parent_data = _build_actuator_with_array_pset(count=6)
+        bpy.context.view_layer.objects.active = obj
+        obj.select_set(True)
+        bpy.ops.bim.regenerate_array()
+
+        assert obj in bpy.context.selected_objects
+        assert bpy.context.view_layer.objects.active is obj
+        parent_pset = ifcopenshell.util.element.get_pset(element, "BBIM_Array")
+        parent_data_after = json.loads(parent_pset["Data"])
+        for child_guid in parent_data_after[0]["children"]:
+            child_element = tool.Ifc.get().by_guid(child_guid)
+            child_obj = tool.Ifc.get_object(child_element)
+            assert (
+                child_obj not in bpy.context.selected_objects
+            ), f"child {child_obj.name} must be deselected on regenerate_array return"
+
+    def test_regen_operator_after_shrink_still_leaves_only_parent_selected(self):
+        obj, element, parent_data = _build_actuator_with_array_pset(count=6)
+        bpy.context.view_layer.objects.active = obj
+        bpy.ops.bim.regenerate_array()
+
+        parent_pset = ifcopenshell.util.element.get_pset(element, "BBIM_Array")
+        arrays = json.loads(parent_pset["Data"])
+        arrays[0]["count"] = 3
+        pset_entity = tool.Ifc.get().by_id(parent_pset["id"])
+        ifcopenshell.api.pset.edit_pset(tool.Ifc.get(), pset=pset_entity, properties={"Data": json.dumps(arrays)})
+        bpy.ops.bim.regenerate_array()
+
+        assert obj in bpy.context.selected_objects
+        assert bpy.context.view_layer.objects.active is obj
+        parent_pset = ifcopenshell.util.element.get_pset(element, "BBIM_Array")
+        arrays_after = json.loads(parent_pset["Data"])
+        for child_guid in arrays_after[0]["children"]:
+            child_element = tool.Ifc.get().by_guid(child_guid)
+            child_obj = tool.Ifc.get_object(child_element)
+            assert child_obj not in bpy.context.selected_objects
+
+    def test_regenerate_array_child_positions_match_offset(self):
+        obj, element, parent_data = _build_actuator_with_array_pset(count=4, x=2.5)
+        bpy.context.view_layer.objects.active = obj
+        parent_x = obj.matrix_world.translation.x
+        tool.Model.regenerate_array(obj, parent_data)
+
+        layer = parent_data[0]
+        for i, child_guid in enumerate(layer["children"], start=1):
+            child_element = tool.Ifc.get().by_guid(child_guid)
+            child_obj = tool.Ifc.get_object(child_element)
+            expected_x = parent_x + 2.5 * i
+            assert child_obj.matrix_world.translation.x == pytest.approx(
+                expected_x
+            ), f"child {i}: expected x≈{expected_x}, got {child_obj.matrix_world.translation.x}"
+
+
+class TestRegenerateArrayUIRefreshCoalesces(NewFile):
+    def test_n_children_grow_calls_refresh_ui_data_once_per_layer(self):
+        obj, element, parent_data = _build_actuator_with_array_pset(count=8)
+        bpy.context.view_layer.objects.active = obj
+        with patch("bonsai.bim.handler.refresh_ui_data") as refresh_mock:
+            tool.Model.regenerate_array(obj, parent_data)
+        assert refresh_mock.call_count == 1, (
+            "growing an array layer from 0 to 7 children must call refresh_ui_data once, "
+            f"got {refresh_mock.call_count}"
+        )
+
+    def test_n_children_grow_calls_reload_grid_decorator_once_per_layer(self):
+        obj, element, parent_data = _build_actuator_with_array_pset(count=8)
+        bpy.context.view_layer.objects.active = obj
+        with patch.object(tool.Root, "reload_grid_decorator") as reload_mock:
+            tool.Model.regenerate_array(obj, parent_data)
+        assert reload_mock.call_count == 1
+
+
+class TestRecreateAggregateIteratesAllNew(NewFile):
+    """Pins the [0]-indexing sweep in tool/root.py recreate_aggregate. When the
+    new-list has N>1 entries (the batched-duplicate shape), every entry must be
+    aggregate-assigned, not just new[0]."""
+
+    def test_iterates_assign_object_per_new_entity_when_old_has_aggregate(self):
+        from unittest.mock import Mock
+
+        old_assembly = Mock()
+        old_assembly.is_a = lambda c: c == "IfcElementAssembly"
+        old_parent_aggregate = Mock()
+        old_parent_aggregate.is_a = lambda c: False
+
+        new_assemblies = [Mock(), Mock(), Mock()]
+        new_parent_aggregate = [Mock()]
+
+        old_to_new = {old_assembly: new_assemblies, old_parent_aggregate: new_parent_aggregate}
+
+        with patch(
+            "ifcopenshell.util.element.get_aggregate",
+            side_effect=lambda e: old_parent_aggregate if e is old_assembly else None,
+        ), patch("bonsai.core.aggregate.assign_object") as assign_mock, patch(
+            "ifcopenshell.util.element.get_pset", return_value=None
+        ), patch.object(
+            tool.Ifc, "get_object", side_effect=lambda e: Mock(spec=bpy.types.Object)
+        ), patch.object(
+            tool.Blender, "select_and_activate_single_object"
+        ):
+            tool.Root.recreate_aggregate(old_to_new)
+
+        assert (
+            assign_mock.call_count == 3
+        ), f"recreate_aggregate must assign each of N new entities (not just new[0]); got {assign_mock.call_count}"
+
+    def test_iterates_unassign_object_per_new_entity_when_aggregate_missing(self):
+        from unittest.mock import Mock
+
+        old_assembly = Mock()
+        old_assembly.is_a = lambda c: c == "IfcElementAssembly"
+        old_parent_aggregate = Mock()
+
+        new_assemblies = [Mock(), Mock(), Mock()]
+        old_to_new = {old_assembly: new_assemblies}  # parent aggregate NOT in old_to_new
+
+        with patch(
+            "ifcopenshell.util.element.get_aggregate",
+            side_effect=lambda e: old_parent_aggregate if e is old_assembly else None,
+        ), patch("bonsai.core.aggregate.unassign_object") as unassign_mock, patch.object(
+            tool.Ifc, "get_object", side_effect=lambda e: Mock(spec=bpy.types.Object)
+        ):
+            tool.Root.recreate_aggregate(old_to_new)
+
+        assert unassign_mock.call_count == 3, (
+            f"recreate_aggregate must unassign each of N new entities when parent aggregate is missing; "
+            f"got {unassign_mock.call_count}"
+        )
+
+
+class TestRecreateConnectionsZipsPairs(NewFile):
+    """Pins the [0]-indexing sweep in tool/duplicate.py recreate_connections. When
+    both sides of a connection are duplicated N times, zip-pair the N new
+    relating with N new related; when only one side is duplicated, skip."""
+
+    def _make_connection_data(self):
+        from unittest.mock import Mock
+
+        from bonsai.tool.duplicate import ConnectionRecord
+
+        return ConnectionRecord(
+            type="path",
+            relating_element=Mock(),
+            related_element=Mock(),
+            relating_connection_type="ATSTART",
+            related_connection_type="ATEND",
+            relating_priorities=[],
+            related_priorities=[],
+        )
+
+    def test_zips_n_pairs_when_both_sides_duplicated(self):
+        from unittest.mock import Mock
+
+        data = self._make_connection_data()
+        old_to_new = {
+            data.relating_element: [Mock(), Mock(), Mock()],
+            data.related_element: [Mock(), Mock(), Mock()],
+        }
+        relationship = {Mock(): data}
+
+        with patch.object(tool.Ifc, "run", return_value=None) as run_mock:
+            tool.Duplicate.recreate_connections(relationship, old_to_new)
+
+        connect_calls = [c for c in run_mock.call_args_list if c.args and c.args[0] == "geometry.connect_path"]
+        assert (
+            len(connect_calls) == 3
+        ), f"zip-pair must create 3 connect_path calls for 3-vs-3 batched duplicate; got {len(connect_calls)}"
+
+    def test_skips_when_other_side_not_duplicated(self):
+        from unittest.mock import Mock
+
+        data = self._make_connection_data()
+        # Only relating side is in old_to_new; related side was NOT duplicated.
+        old_to_new = {data.relating_element: [Mock(), Mock(), Mock()]}
+        relationship = {Mock(): data}
+
+        with patch.object(tool.Ifc, "run", return_value=None) as run_mock:
+            tool.Duplicate.recreate_connections(relationship, old_to_new)
+
+        connect_calls = [c for c in run_mock.call_args_list if c.args and c.args[0] == "geometry.connect_path"]
+        assert (
+            connect_calls == []
+        ), "when only one side of a connection is in old_to_new, no connections should be recreated"
+
+    def test_single_pair_case_unchanged(self):
+        """Pre-sweep behavior (1 source -> 1 new) must still work — zip with two 1-element lists."""
+        from unittest.mock import Mock
+
+        data = self._make_connection_data()
+        old_to_new = {
+            data.relating_element: [Mock()],
+            data.related_element: [Mock()],
+        }
+        relationship = {Mock(): data}
+
+        with patch.object(tool.Ifc, "run", return_value=None) as run_mock:
+            tool.Duplicate.recreate_connections(relationship, old_to_new)
+
+        connect_calls = [c for c in run_mock.call_args_list if c.args and c.args[0] == "geometry.connect_path"]
+        assert len(connect_calls) == 1
+
+
+class TestRecalculateWallsWithNewConnections(NewFile):
+    """Pins the post-connection wall recalc: after ``recreate_connections``
+    wires new IfcRelConnectsPathElements onto duplicated walls, the wall
+    bodies must be re-recalculated because the in-loop ``regenerate_wall``
+    fired before the connections existed. Otherwise the junction geometry
+    stays stale and the user has to manually regen."""
+
+    def test_walls_with_new_connections_are_recalculated(self):
+        from unittest.mock import Mock
+
+        wall_new = Mock()
+        wall_new.is_a = lambda c: c == "IfcWall"
+        wall_new.ConnectedTo = [Mock()]
+        wall_new.ConnectedFrom = []
+
+        wall_obj = Mock(spec=bpy.types.Object)
+        old_to_new = {Mock(): [wall_new]}
+
+        with patch.object(tool.Ifc, "get_object", return_value=wall_obj), patch.object(
+            tool.Model, "recalculate_walls"
+        ) as recalc_mock:
+            tool.Geometry._recalculate_walls_with_new_connections(old_to_new)
+
+        assert recalc_mock.call_count == 1
+        assert recalc_mock.call_args.args[0] == [wall_obj]
+
+    def test_walls_without_connections_are_skipped(self):
+        from unittest.mock import Mock
+
+        wall_new = Mock()
+        wall_new.is_a = lambda c: c == "IfcWall"
+        wall_new.ConnectedTo = []
+        wall_new.ConnectedFrom = []
+
+        old_to_new = {Mock(): [wall_new]}
+
+        with patch.object(tool.Ifc, "get_object", return_value=Mock(spec=bpy.types.Object)), patch.object(
+            tool.Model, "recalculate_walls"
+        ) as recalc_mock:
+            tool.Geometry._recalculate_walls_with_new_connections(old_to_new)
+
+        assert recalc_mock.call_count == 0, "walls with no new connections must not trigger a recalc pass"
+
+    def test_non_wall_entities_are_skipped(self):
+        from unittest.mock import Mock
+
+        actuator_new = Mock()
+        actuator_new.is_a = lambda c: c == "IfcActuator"
+        actuator_new.ConnectedTo = [Mock()]
+
+        old_to_new = {Mock(): [actuator_new]}
+
+        with patch.object(tool.Ifc, "get_object", return_value=Mock(spec=bpy.types.Object)), patch.object(
+            tool.Model, "recalculate_walls"
+        ) as recalc_mock:
+            tool.Geometry._recalculate_walls_with_new_connections(old_to_new)
+
+        assert recalc_mock.call_count == 0
+
+    def test_multiple_new_walls_collected_into_one_call(self):
+        from unittest.mock import Mock
+
+        wall_a_new = Mock()
+        wall_a_new.is_a = lambda c: c == "IfcWall"
+        wall_a_new.ConnectedTo = [Mock()]
+        wall_a_new.ConnectedFrom = []
+        wall_b_new = Mock()
+        wall_b_new.is_a = lambda c: c == "IfcWall"
+        wall_b_new.ConnectedTo = []
+        wall_b_new.ConnectedFrom = [Mock()]
+
+        objs = {wall_a_new: Mock(spec=bpy.types.Object), wall_b_new: Mock(spec=bpy.types.Object)}
+        old_to_new = {Mock(): [wall_a_new], Mock(): [wall_b_new]}
+
+        with patch.object(tool.Ifc, "get_object", side_effect=lambda e: objs.get(e)), patch.object(
+            tool.Model, "recalculate_walls"
+        ) as recalc_mock:
+            tool.Geometry._recalculate_walls_with_new_connections(old_to_new)
+
+        assert recalc_mock.call_count == 1
+        assert set(recalc_mock.call_args.args[0]) == {objs[wall_a_new], objs[wall_b_new]}
+
+
+class TestMEPActionGuardsAgainstArrayChildren(NewFile):
+    """Pins the array-child guards on the three MEP-action visibility helpers.
+    Writable MEP actions (add fitting, remove terminal, join, re-edit bend)
+    applied to an array child get wiped by the next regen — gating the icons
+    at the visibility layer prevents that footgun."""
+
+    def test_active_is_flow_segment_returns_false_for_array_child(self):
+        from unittest.mock import Mock
+
+        from bonsai.bim.module.model.mep import _active_is_flow_segment
+
+        obj = Mock(spec=bpy.types.Object)
+        element = Mock()
+        element.is_a = lambda c: c == "IfcFlowSegment"
+
+        with patch.object(tool.Ifc, "get_entity", return_value=element), patch.object(
+            tool.Array, "is_array_child", return_value=True
+        ), patch.object(tool.System, "has_parametric_body", return_value=True):
+            assert _active_is_flow_segment(obj) is False
+
+    def test_active_is_flow_segment_true_for_non_array_parent(self):
+        from unittest.mock import Mock
+
+        from bonsai.bim.module.model.mep import _active_is_flow_segment
+
+        obj = Mock(spec=bpy.types.Object)
+        element = Mock()
+        element.is_a = lambda c: c == "IfcFlowSegment"
+
+        with patch.object(tool.Ifc, "get_entity", return_value=element), patch.object(
+            tool.Array, "is_array_child", return_value=False
+        ), patch.object(tool.System, "has_parametric_body", return_value=True):
+            assert _active_is_flow_segment(obj) is True
+
+    def test_active_is_bend_fitting_returns_false_for_array_child(self):
+        from unittest.mock import Mock
+
+        from bonsai.bim.module.model.mep import _active_is_bend_fitting
+
+        obj = Mock(spec=bpy.types.Object)
+        element = Mock()
+
+        with patch.object(tool.Ifc, "get_entity", return_value=element), patch(
+            "bonsai.bim.module.model.mep._is_bend_fitting", return_value=True
+        ), patch.object(tool.Array, "is_array_child", return_value=True):
+            assert _active_is_bend_fitting(obj) is False
+
+    def test_n_mep_selected_returns_false_when_any_selected_is_array_child(self):
+        from unittest.mock import Mock
+
+        from bonsai.bim.module.model.mep import _n_mep_selected
+
+        obj_a = Mock(spec=bpy.types.Object)
+        obj_b = Mock(spec=bpy.types.Object)
+        element_a = Mock()
+        element_b = Mock()
+
+        def is_array_child(el):
+            return el is element_b
+
+        with patch.object(tool.Blender, "get_selected_objects", return_value=[obj_a, obj_b]), patch.object(
+            tool.Ifc, "get_entity", side_effect=lambda o: element_a if o is obj_a else element_b
+        ), patch.object(tool.System, "is_mep_element", return_value=True), patch.object(
+            tool.Array, "is_array_child", side_effect=is_array_child
+        ):
+            assert _n_mep_selected(2) is False
+
+
+class TestSelectOnlyParent(NewFile):
+    """Pins ``tool.Array.select_only_parent`` — the shared helper wired into
+    both ``bim.regenerate_array`` and ``bim.finish_editing_array`` so the
+    grow / shrink / edit-commit paths converge on the same post-condition:
+    only the parent is selected + active."""
+
+    def test_deselects_children_selects_and_activates_parent(self):
+        obj, element, parent_data = _build_actuator_with_array_pset(count=4)
+        bpy.context.view_layer.objects.active = obj
+        obj.select_set(True)
+        tool.Model.regenerate_array(obj, parent_data)
+        for child_guid in parent_data[0]["children"]:
+            child_element = tool.Ifc.get().by_guid(child_guid)
+            child_obj = tool.Ifc.get_object(child_element)
+            child_obj.select_set(True)
+
+        tool.Array.select_only_parent(obj, bpy.context)
+
+        assert obj in bpy.context.selected_objects
+        assert bpy.context.view_layer.objects.active is obj
+        for child_guid in parent_data[0]["children"]:
+            child_element = tool.Ifc.get().by_guid(child_guid)
+            child_obj = tool.Ifc.get_object(child_element)
+            assert child_obj not in bpy.context.selected_objects
+
+
+class TestIsArrayChild(NewFile):
+    """Pins ``tool.Array.is_array_child`` — the light helper used by the port
+    decorator (and any future per-element guard) to skip array children."""
+
+    def test_returns_false_when_no_bbim_array_pset(self):
+        from unittest.mock import Mock
+
+        element = Mock()
+        with patch("ifcopenshell.util.element.get_pset", return_value=None):
+            assert tool.Array.is_array_child(element) is False
+
+    def test_returns_false_on_the_array_parent_itself(self):
+        from unittest.mock import Mock
+
+        element = Mock()
+        element.GlobalId = "PARENT_GUID"
+        with patch("ifcopenshell.util.element.get_pset", return_value={"Parent": "PARENT_GUID"}):
+            assert tool.Array.is_array_child(element) is False
+
+    def test_returns_true_when_parent_guid_points_elsewhere(self):
+        from unittest.mock import Mock
+
+        element = Mock()
+        element.GlobalId = "CHILD_GUID"
+        with patch("ifcopenshell.util.element.get_pset", return_value={"Parent": "PARENT_GUID"}):
+            assert tool.Array.is_array_child(element) is True
+
+
+class TestOrphanArrayChildPrune(NewFile):
+    """Outliner / keyboard delete of a Bonsai-managed array child bypasses
+    ``bim.delete``'s cascade, leaving the IFC entity and its opening / filling
+    refs behind. Regen must prune these orphans before the main loop or the
+    stale registry entry corrupts the ``batch_host_recut`` drain."""
+
+    def test_orphan_ifc_entity_pruned_from_children_list(self):
+        obj, element, parent_data = _build_actuator_with_array_pset(count=4)
+        bpy.context.view_layer.objects.active = obj
+        tool.Model.regenerate_array(obj, parent_data)
+        assert len(parent_data[0]["children"]) == 3
+
+        orphan_guid = parent_data[0]["children"][1]
+        orphan_element = tool.Ifc.get().by_guid(orphan_guid)
+        orphan_obj = tool.Ifc.get_object(orphan_element)
+        assert orphan_obj is not None
+        bpy.data.objects.remove(orphan_obj, do_unlink=True)
+
+        tool.Model.regenerate_array(obj, parent_data)
+
+        assert (
+            orphan_guid not in parent_data[0]["children"]
+        ), "orphan GUID must be pruned from array['children'] once its Blender object is dead"
+        try:
+            still_there = tool.Ifc.get().by_guid(orphan_guid)
+        except RuntimeError:
+            still_there = None
+        assert still_there is None, "orphan IFC entity must be cascade-removed, not left as a leak"
+
+    def test_regen_completes_when_child_deleted_outside_bim_cascade(self):
+        obj, element, parent_data = _build_actuator_with_array_pset(count=6)
+        bpy.context.view_layer.objects.active = obj
+        tool.Model.regenerate_array(obj, parent_data)
+
+        victim_guid = parent_data[0]["children"][2]
+        victim_element = tool.Ifc.get().by_guid(victim_guid)
+        victim_obj = tool.Ifc.get_object(victim_element)
+        bpy.data.objects.remove(victim_obj, do_unlink=True)
+
+        tool.Model.regenerate_array(obj, parent_data)
+
+        assert len(parent_data[0]["children"]) == 5, "regen must rebuild to the target count after pruning the orphan"
+        for guid in parent_data[0]["children"]:
+            child = tool.Ifc.get().by_guid(guid)
+            child_obj = tool.Ifc.get_object(child)
+            assert child_obj is not None, "every surviving child must have a live Blender object"
+
+
+class TestRecreatePortConnectionsZipsPairs(NewFile):
+    """Pins the [0]-indexing sweep in tool/duplicate.py recreate_port_connections.
+    When both sides of a port-to-port connection are duplicated N times, the
+    connection must be recreated on every pair of new siblings — not just the
+    first. Matters for arrayed MEP segments (pipes / ducts / cables) where each
+    child in the array should stay connected to its neighbour after regen."""
+
+    def _make_snapshot(self, relating_element, records, port_counts):
+        from bonsai.tool.duplicate import PortConnectionSnapshot
+
+        return PortConnectionSnapshot(
+            by_element={relating_element: records},
+            port_counts=port_counts,
+        )
+
+    def _make_record(self, related_element, relating_port_index=0, related_port_index=0, direction="SOURCE"):
+        from bonsai.tool.duplicate import PortConnectionRecord
+
+        return PortConnectionRecord(
+            relating_port_index=relating_port_index,
+            related_element=related_element,
+            related_port_index=related_port_index,
+            direction=direction,
+        )
+
+    def test_zips_n_pairs_when_both_sides_duplicated(self):
+        from unittest.mock import Mock
+
+        relating_old = Mock()
+        related_old = Mock()
+        record = self._make_record(related_old)
+        snapshot = self._make_snapshot(relating_old, [record], port_counts={})
+
+        old_to_new = {
+            relating_old: [Mock(), Mock(), Mock()],
+            related_old: [Mock(), Mock(), Mock()],
+        }
+
+        fake_ports = [Mock(), Mock()]
+        with patch.object(tool.System, "get_ports", return_value=fake_ports), patch.object(
+            tool.Ifc, "run", return_value=None
+        ) as run_mock:
+            tool.Duplicate.recreate_port_connections(snapshot, old_to_new)
+
+        connect_calls = [c for c in run_mock.call_args_list if c.args and c.args[0] == "system.connect_port"]
+        assert (
+            len(connect_calls) == 3
+        ), f"zip-pair must create 3 connect_port calls for 3-vs-3 batched MEP duplicate; got {len(connect_calls)}"
+
+    def test_skips_when_other_side_not_duplicated(self):
+        from unittest.mock import Mock
+
+        relating_old = Mock()
+        related_old = Mock()
+        record = self._make_record(related_old)
+        snapshot = self._make_snapshot(relating_old, [record], port_counts={})
+
+        # Only relating side is in old_to_new.
+        old_to_new = {relating_old: [Mock(), Mock(), Mock()]}
+
+        with patch.object(tool.System, "get_ports", return_value=[Mock()]), patch.object(
+            tool.Ifc, "run", return_value=None
+        ) as run_mock:
+            tool.Duplicate.recreate_port_connections(snapshot, old_to_new)
+
+        connect_calls = [c for c in run_mock.call_args_list if c.args and c.args[0] == "system.connect_port"]
+        assert connect_calls == [], "when only one side is in old_to_new, no port connections should be recreated"
+
+    def test_single_pair_case_unchanged(self):
+        """Pre-sweep behavior (1 source -> 1 new) must still work — zip with two 1-element lists."""
+        from unittest.mock import Mock
+
+        relating_old = Mock()
+        related_old = Mock()
+        record = self._make_record(related_old)
+        snapshot = self._make_snapshot(relating_old, [record], port_counts={})
+
+        old_to_new = {relating_old: [Mock()], related_old: [Mock()]}
+
+        with patch.object(tool.System, "get_ports", return_value=[Mock()]), patch.object(
+            tool.Ifc, "run", return_value=None
+        ) as run_mock:
+            tool.Duplicate.recreate_port_connections(snapshot, old_to_new)
+
+        connect_calls = [c for c in run_mock.call_args_list if c.args and c.args[0] == "system.connect_port"]
+        assert len(connect_calls) == 1

src/bonsai/test/bim/module/model/test_mep_actions_visibility.py

@@ -346,7 +346,9 @@ def test_active_is_flow_segment_classifies_segment_vs_fitting():
     fitting_elem.is_a = lambda c: c == "IfcFlowFitting"
 
     plain = Mock()
-    with patch("bonsai.bim.module.model.mep.tool.System.has_parametric_body", return_value=True):
+    with patch("bonsai.bim.module.model.mep.tool.System.has_parametric_body", return_value=True), patch(
+        "bonsai.bim.module.model.mep.tool.Array.is_array_child", return_value=False
+    ):
         with patch("bonsai.bim.module.model.mep.tool.Ifc.get_entity", return_value=segment_elem):
             assert _active_is_flow_segment(plain) is True
         with patch("bonsai.bim.module.model.mep.tool.Ifc.get_entity", return_value=fitting_elem):

src/bonsai/test/tool/test_geometry_batch_host_recut.py

@@ -164,6 +164,62 @@ def test_stale_element_skipped_at_drain():
     assert recut.call_count == 0
 
 
+class _DeadStructRNA:
+    """Simulates a Blender object whose StructRNA has been removed — every
+    attribute access raises ReferenceError. Enqueue this as voided_obj to
+    reproduce the outliner-mid-batch-delete crash."""
+
+    def __getattr__(self, name):
+        raise ReferenceError("StructRNA of type Object has been removed")
+
+    def __bool__(self):
+        raise ReferenceError("StructRNA of type Object has been removed")
+
+
+def test_dead_structrna_recut_skipped_at_drain():
+    """Blender object is deleted while the batch is open (outliner delete +
+    manual DEL bypass the bim.delete cascade). The drain must skip it silently
+    — not raise — so unrelated hosts in the same batch still get their recut."""
+    from bonsai import tool
+
+    dead_obj = _DeadStructRNA()
+    live_obj = _mock_voided_obj("LiveWall")
+    rep = Mock()
+
+    def get_entity(obj):
+        # Called only when the guard clears — for the dead ref, guard short-circuits first.
+        return _mock_element(2)
+
+    with patch("bonsai.core.geometry.switch_representation") as recut, patch.object(
+        tool.Ifc, "get_entity", side_effect=get_entity
+    ), patch.object(tool.Geometry, "get_active_representation", return_value=rep):
+        with tool.Geometry.batch_host_recut():
+            tool.Geometry._host_recut_queue[999] = (dead_obj, rep)
+            tool.Geometry.recut_host(live_obj, rep)
+
+    assert recut.call_count == 1, "live host must still get its recut despite a dead sibling in the queue"
+    drained_obj = recut.call_args.kwargs["obj"]
+    assert drained_obj is live_obj
+
+
+def test_dead_structrna_update_skipped_at_drain():
+    """Same guarantee for update_representation drain path."""
+    from bonsai import tool
+
+    dead_obj = _DeadStructRNA()
+    live_obj = _mock_voided_obj("LiveWall")
+    bpy_ops_mock = Mock()
+
+    with patch("bonsai.tool.geometry.bpy.ops", new=bpy_ops_mock), patch.object(
+        tool.Ifc, "get_entity", return_value=_mock_element(42)
+    ), patch.object(tool.Geometry, "get_active_representation", return_value=Mock()):
+        with tool.Geometry.batch_host_recut():
+            tool.Geometry._host_update_queue[999] = dead_obj
+            tool.Geometry.update_host_representation(live_obj)
+
+    assert bpy_ops_mock.bim.update_representation.call_count == 1
+
+
 def test_exception_inside_batch_still_resets_state():
     from bonsai import tool
 

src/bonsai/test/tool/test_model.py

@@ -630,15 +630,15 @@ class TestUsingArrays(NewFile):
     def test_remove_array_first_to_last(self):
         self.setup_array(add_second_layer=True)
         bpy.ops.bim.remove_array(item=0)
-        assert len(bpy.context.selected_objects) == 3
+        assert len(self._array_objects()) == 3
         bpy.ops.bim.remove_array(item=0)
-        assert len(bpy.context.selected_objects) == 1
+        assert len(self._array_objects()) == 1
 
     def test_apply_array_1_layer(self):
         self.setup_array()
         bpy.ops.bim.apply_array()
 
-        objs = bpy.context.selected_objects
+        objs = self._array_objects()
         assert len(objs) == 4
         # check BBIM_Array psets are removed
         for obj in objs:
@@ -664,7 +664,7 @@ class TestUsingArrays(NewFile):
         self.setup_array(sync_children=True)
         bpy.ops.bim.apply_array()
 
-        objs = bpy.context.selected_objects
+        objs = self._array_objects()
         assert len(objs) == 4
         # check BBIM_Array psets are removed
         for obj in objs:

src/ifcopenshell-python/ifcopenshell/api/alignment/__init__.py

@@ -49,6 +49,7 @@ Future versions of this API may support:
 
 from ._get_segment_start_point_label import register_referent_name_callback
 from .add_stationing_referent import add_stationing_referent
+from .add_positioning_referent import add_positioning_referent
 from .add_vertical_layout import add_vertical_layout
 from .add_zero_length_segment import add_zero_length_segment
 from .create import create
@@ -94,6 +95,7 @@ from .util import *
 
 __all__ = [
     "add_stationing_referent",
+    "add_positioning_referent",
     "add_vertical_layout",
     "add_zero_length_segment",
     "create",

src/ifcopenshell-python/ifcopenshell/api/alignment/add_positioning_referent.py

@@ -0,0 +1,113 @@
+# IfcOpenShell - IFC toolkit and geometry engine
+# Copyright (C) 2025 Thomas Krijnen <thomas@aecgeeks.com>
+#
+# This file is part of IfcOpenShell.
+#
+# IfcOpenShell is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# IfcOpenShell is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with IfcOpenShell.  If not, see <http://www.gnu.org/licenses/>.
+
+import ifcopenshell
+import ifcopenshell.api.alignment
+from ifcopenshell.api.alignment.update_fallback_position import update_fallback_position
+import ifcopenshell.api.pset
+import ifcopenshell.guid
+from ifcopenshell import entity_instance
+
+
+def add_positioning_referent(
+    file: ifcopenshell.file,
+    name: str,
+    alignment: entity_instance,
+    distance_along: float,
+    station: float,
+    positioned_product: entity_instance,
+) -> entity_instance:
+    """
+    Semantically defines the position of a product along an alignment by adding an IfcReferent to the alignment that defines the stationing system.
+
+    :param alignment: the alignment to receive the referent
+    :param distance_along: distance along the alignment basis curve
+    :param station: station value
+    :param name: name to assign to IfcReferent.Name, typically a stringized version of the station value
+    :param positioned_product: the product whose position is informed by the referent
+    :return: referent
+
+    Example:
+
+    .. code:: python
+
+        alignment = model.by_type("IfcAlignment")[0]
+        pier = model.by_type("IfcBridgePart")[0]
+        ifcopenshell.api.alignment.add_positioning_referent(model,name="Pier 1 Sta 1+00",alignment=alignment,distance_along=0.0,station=100.0,positioned_product=pier)
+    """
+
+    basis_curve = ifcopenshell.api.alignment.get_basis_curve(alignment)
+
+    object_placement = None
+    representation = None
+    if basis_curve and basis_curve.is_a("IfcCompositeCurve") and 0 < len(basis_curve.Segments):
+        object_placement = file.createIfcLinearPlacement(
+            RelativePlacement=file.createIfcAxis2PlacementLinear(
+                Location=file.createIfcPointByDistanceExpression(
+                    DistanceAlong=file.createIfcLengthMeasure(distance_along),
+                    OffsetLateral=None,
+                    OffsetVertical=None,
+                    OffsetLongitudinal=None,
+                    BasisCurve=basis_curve,
+                )
+            ),
+        )
+
+        update_fallback_position(file, object_placement)
+    else:
+        object_placement = file.createIfcLocalPlacement(
+            PlacementRelTo=None,
+            RelativePlacement=file.createIfcAxis2Placement2D(
+                Location=file.createIfcCartesianPoint(alignment.ObjectPlacement.RelativePlacement.Location.Coordinates)
+            ),
+        )
+
+    # this commented out code is what you would do to add a geometric representation of the referent
+    # the example is a circle. a better way would be to pass a representation into the function
+    #    representation = file.create_entity(
+    #        name="IfcCircle",
+    #        position=file.createIfcAxis2Placement2D(Location=file.createIfcCartesianPoint(Coordinates=(0.0, 0.0)),
+    #        radius=1.0)
+    #    )
+
+    # create referent for the station
+    referent = file.createIfcReferent(
+        GlobalId=ifcopenshell.guid.new(),
+        OwnerHistory=None,
+        Name=name,
+        Description=None,
+        ObjectType=None,
+        ObjectPlacement=object_placement,
+        Representation=representation,
+        PredefinedType="POSITION",
+    )
+    pset_stationing = ifcopenshell.api.pset.add_pset(file, product=referent, name="Pset_Stationing")
+    ifcopenshell.api.pset.edit_pset(file, pset=pset_stationing, properties={"Station": station})
+
+    if len(referent.Positions) == 0:
+        rel_positions = file.createIfcRelPositions(
+            GlobalId=ifcopenshell.guid.new(),
+            RelatingPositioningElement=referent,
+            RelatedProducts=[
+                positioned_product,
+            ],
+        )
+    else:
+        referent.Positions[0].RelatedProducts += (positioned_product,)
+
+    return referent

src/ifcopenshell-python/ifcopenshell/api/alignment/add_stationing_referent.py

@@ -16,35 +16,33 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with IfcOpenShell.  If not, see <http://www.gnu.org/licenses/>.
 
-import numpy as np
+from typing import Optional
 
 import ifcopenshell
 import ifcopenshell.api.alignment
 from ifcopenshell.api.alignment.update_fallback_position import update_fallback_position
 import ifcopenshell.api.pset
-import ifcopenshell.geom
 import ifcopenshell.guid
 import ifcopenshell.util.element
-import ifcopenshell.util.unit
-from ifcopenshell import entity_instance, ifcopenshell_wrapper
+from ifcopenshell import entity_instance
 
 
 def add_stationing_referent(
     file: ifcopenshell.file,
+    name: str,
     alignment: entity_instance,
     distance_along: float,
     station: float,
-    name: str,
-    positioned_product: entity_instance,
+    incoming_station: Optional[float] = None,
 ) -> entity_instance:
     """
-    Adds an IfcReferent to the alignment with the Pset_Stationing property set.
+    Adds an IfcReferent to the alignment that defines the stationing system.
 
+    :param name: name to assign to IfcReferent.Name, typically a stringized version of the station value
     :param alignment: the alignment to receive the referent
     :param distance_along: distance along the alignment basis curve
     :param station: station value
-    :param name: name to assign to IfcReferent.Name, typically a stringized version of the station value
-    :param positioned_product: the product whose position is informed by the referent
+    :param incoming_station: station value of the incoming segment, only set to specify a station equation
     :return: referent
 
     Example:
@@ -52,7 +50,7 @@ def add_stationing_referent(
     .. code:: python
 
         alignment = model.by_type("IfcAlignment")[0]
-        ifcopenshell.api.alignment.add_stationing_referent(model,alignment=alignment,distance_along=0.0,station=100.0)
+        ifcopenshell.api.alignment.add_stationing_referent(model,name="1+00.0",alignment=alignment,distance_along=0.0,station=100.0)
     """
 
     basis_curve = ifcopenshell.api.alignment.get_basis_curve(alignment)
@@ -100,8 +98,12 @@ def add_stationing_referent(
         Representation=representation,
         PredefinedType="STATION",
     )
+    properties = {"Station": station}
+    if incoming_station is not None:
+        properties["IncomingStation"] = incoming_station
+
     pset_stationing = ifcopenshell.api.pset.add_pset(file, product=referent, name="Pset_Stationing")
-    ifcopenshell.api.pset.edit_pset(file, pset=pset_stationing, properties={"Station": station})
+    ifcopenshell.api.pset.edit_pset(file, pset=pset_stationing, properties=properties)
 
     nest = ifcopenshell.api.alignment.get_referent_nest(file, alignment)
     if nest is None:
@@ -115,15 +117,4 @@ def add_stationing_referent(
         nest.RelatedObjects, key=lambda x: ifcopenshell.util.element.get_pset(x, name="Pset_Stationing", prop="Station")
     )
 
-    if len(referent.Positions) == 0:
-        rel_positions = file.createIfcRelPositions(
-            GlobalId=ifcopenshell.guid.new(),
-            RelatingPositioningElement=referent,
-            RelatedProducts=[
-                positioned_product,
-            ],
-        )
-    else:
-        referent.Positions[0].RelatedProducts += (positioned_product,)
-
     return referent

src/ifcopenshell-python/ifcopenshell/api/alignment/add_vertical_layout.py

@@ -51,18 +51,6 @@ def _move_vertical_layout_to_child_alignment(
     # aggregate the child alignment to the parent alignment
     ifcopenshell.api.aggregate.assign_object(file, products=[child_alignment], relating_object=parent_alignment)
 
-    # move all referents positioning segments of the vertical layout to the referent nest of the child alignment
-    child_referent_nest = ifcopenshell.api.alignment.get_referent_nest(file, child_alignment)
-    parent_referent_nest = ifcopenshell.api.alignment.get_referent_nest(file, parent_alignment)
-    for referent in parent_referent_nest.RelatedObjects:
-        for product in referent.Positions[0].RelatedProducts:
-            if product.is_a("IfcAlignmentSegment") and product.Nests[0].RelatingObject == vertical_layout:
-                # ifcopenshell.api.nest.change_nest(file,referent,child_alignment) - this doesn't work because referent is assigned to child_alignment.IsNestedBy[0].RelatedObjects
-                # and it needs to be assigned to child_alignment.IsNestedBy[1].RelatedObjects
-                # move the referent manually - unassign it and add it to the child alignment's referent nest
-                ifcopenshell.api.nest.unassign_object(file, [referent])
-                child_referent_nest.RelatedObjects += (referent,)
-
     # if the parent alignment has a representation, move the Axis/Curve3D represention to the child alignment
     base_curve = ifcopenshell.api.alignment.get_basis_curve(parent_alignment)
     if base_curve:

src/ifcopenshell-python/ifcopenshell/api/alignment/create.py

@@ -88,7 +88,7 @@ def create(
 
     referent_name = ifcopenshell.util.alignment.station_as_string(file, start_station)
     referent = ifcopenshell.api.alignment.add_stationing_referent(
-        file, alignment, 0.0, start_station, referent_name, alignment
+        file, referent_name, alignment, 0.0, start_station
     )
 
     for layout in alignment_layouts:

src/ifcopenshell-python/ifcopenshell/api/alignment/create_as_polyline.py

@@ -141,7 +141,7 @@ def create_as_polyline(
 
     # define stationing
     name = ifcopenshell.util.alignment.station_as_string(file, start_station)
-    referent = ifcopenshell.api.alignment.add_stationing_referent(file, alignment, 0.0, start_station, name, alignment)
+    referent = ifcopenshell.api.alignment.add_stationing_referent(file, name, alignment, 0.0, start_station)
 
     # IFC 4.1.4.1.1 Alignment Aggregation To Project
     project = file.by_type("IfcProject")[0]

src/ifcopenshell-python/ifcopenshell/api/alignment/distance_along_from_station.py

@@ -16,23 +16,47 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with IfcOpenShell.  If not, see <http://www.gnu.org/licenses/>.
 
+from typing import Optional
+
 import ifcopenshell
 import ifcopenshell.api.alignment
+import ifcopenshell.util.element
 from ifcopenshell import entity_instance
 
 
-def distance_along_from_station(file: ifcopenshell.file, alignment: entity_instance, station: float) -> float:
+def _distance_along_of_referent(referent: entity_instance) -> float:
+    placement = referent.ObjectPlacement
+    if placement.is_a("IfcLinearPlacement"):
+        return placement.RelativePlacement.Location.DistanceAlong.wrappedValue
+    # IfcLocalPlacement fallback (e.g. semantic-only alignment, or the placement could not yet
+    # be expressed relative to a basis curve) carries no DistanceAlong; it is only ever used for
+    # the starting referent, at distance 0.0.
+    return 0.0
+
+
+def distance_along_from_station(file: ifcopenshell.file, alignment: entity_instance, station: float) -> Optional[float]:
     """
     Given a station, returns the distance along the horizontal alignment.
 
     If the alignment does not have stationing defined with an IfcReferent, the start of the alignment is assumed
     to be at station 0.0. That is, the station is the distance along.
 
-    .. note:: The current implementation does not account for station equations and assumes stationing is increasing along the alignment.
+    Station equations (where Pset_Stationing.IncomingStation is set on a referent) are taken into account.
+    For each STATION referent nested to the alignment, DistanceAlong (D) and the outgoing station (S, i.e.
+    Pset_Stationing.Station) are read off, sorted by DistanceAlong. The requested station is located within
+    the segment defined by the last referent whose outgoing station is less than or equal to it, and the
+    distance along is computed as D + (station - S) for that referent.
+
+    If the station falls within a gap introduced by a forward (gap) station equation - that is, it was skipped
+    over by the equation - there is no distance along that corresponds to it, and None is returned.
+
+    Note that an overlap (backward) station equation causes a range of stations to correspond to two distinct
+    distances along the alignment, one on either side of the equation. This implementation returns the distance
+    along in the segment following the equation (i.e. the outgoing side).
 
     :param alignment: the alignment
     :param station: station value
-    :return: distance along the horizontal alignment
+    :return: distance along the horizontal alignment, or None if the station falls inside a station equation gap
 
     Example:
 
@@ -43,6 +67,33 @@ def distance_along_from_station(file: ifcopenshell.file, alignment: entity_insta
         print(dist_along) # 100.00
     """
 
-    start_station = ifcopenshell.api.alignment.get_alignment_start_station(file, alignment)
-    dist_along = station - start_station
-    return dist_along
+    referent_nest = ifcopenshell.api.alignment.get_referent_nest(file, alignment)
+    if referent_nest is None:
+        start_station = ifcopenshell.api.alignment.get_alignment_start_station(file, alignment)
+        return station - start_station
+
+    stations = [
+        (_distance_along_of_referent(referent), ifcopenshell.util.element.get_pset(referent, name="Pset_Stationing", prop="Station"))
+        for referent in referent_nest.RelatedObjects
+    ]
+    stations.sort(key=lambda entry: entry[0])
+
+    index = None
+    for i, (distance_along, outgoing_station) in enumerate(stations):
+        if outgoing_station <= station:
+            index = i
+
+    if index is None:
+        # station precedes the alignment's starting station; extrapolate from the first referent
+        distance_along, outgoing_station = stations[0]
+        return distance_along + (station - outgoing_station)
+
+    distance_along, outgoing_station = stations[index]
+
+    if index + 1 < len(stations):
+        next_distance_along, _ = stations[index + 1]
+        if station - outgoing_station > next_distance_along - distance_along:
+            # the station was skipped over by a forward (gap) station equation
+            return None
+
+    return distance_along + (station - outgoing_station)

src/ifcopenshell-python/ifcopenshell/api/alignment/update_fallback_position.py

@@ -36,9 +36,12 @@ def update_fallback_position(file: ifcopenshell.file, lp: entity_instance):
 
     p = ifcopenshell.util.placement.get_local_placement(lp)
 
-    x = float(p[0, 3])
-    y = float(p[1, 3])
-    z = float(p[2, 3])
+
+    unit_scale = ifcopenshell.util.unit.calculate_unit_scale(file)
+
+    x = float(p[0, 3])*unit_scale
+    y = float(p[1, 3])*unit_scale
+    z = float(p[2, 3])*unit_scale
 
     rx = float(p[0, 0])
     ry = float(p[1, 0])

src/ifcopenshell-python/ifcopenshell/util/element.py

@@ -1125,7 +1125,8 @@ def get_decomposition(element: ifcopenshell.entity_instance, is_recursive=True)
     """
     Retrieves all subelements of an element based on the spatial decomposition
     hierarchy. This includes all subspaces and elements contained in subspaces,
-    parts of an aggregate, all openings, and all fills of any openings.
+    parts of an aggregate, all openings, all fills of any openings, and any
+    surface features adhering to an element (IFC4.3 and above).
 
     :param element: The IFC element
     :return: The decomposition of the element
@@ -1161,6 +1162,10 @@ def get_decomposition(element: ifcopenshell.entity_instance, is_recursive=True)
             related = rel.RelatedObjects
             queue.extend(related)
             results.update(related)
+        for rel in getattr(element, "HasSurfaceFeatures", []):
+            related = rel.RelatedSurfaceFeatures
+            queue.extend(related)
+            results.update(related)
         if not is_recursive:
             break
     return results
@@ -1251,6 +1256,8 @@ def get_parent(
     - Nesting: components are attached to a host parent
     - Filling: the physical element fills an opening, such as a window filling a hole
     - Voiding: the opening voids another physical element, such as a hole in a wall
+    - Adherence: a surface feature adheres to a host element, such as a road
+      marking adhering to a road course (IFC4.3 and above)
 
     :param element: Any physical or spatial element in the tree
     :param ifc_class: Optionally filter the type of parent you're after. For
@@ -1270,6 +1277,7 @@ def get_parent(
         or get_nest(element)
         or get_filled_void(element)
         or get_voided_element(element)
+        or get_adhered_element(element)
     )
 
     if not ifc_class:
@@ -1321,6 +1329,28 @@ def get_voided_element(element: ifcopenshell.entity_instance) -> Union[ifcopensh
         return rel[0].RelatingBuildingElement
 
 
+def get_adhered_element(element: ifcopenshell.entity_instance) -> Union[ifcopenshell.entity_instance, None]:
+    """If the element is a surface feature, get the element it adheres to
+
+    In IFC4.3 an IfcSurfaceFeature (such as a road marking) adheres to a host
+    element through the IfcRelAdheresToElement relationship. This is a [1:1]
+    cardinality hierarchical relationship, in the same family as aggregation,
+    containment and nesting.
+
+    :param element: The IfcSurfaceFeature
+    :return: The host element that the surface feature adheres to
+
+    Example:
+
+    .. code:: python
+
+        marking = file.by_type("IfcSurfaceFeature")[0]
+        host = ifcopenshell.util.element.get_adhered_element(marking)
+    """
+    if rel := getattr(element, "AdheresToElement", None):
+        return rel[0].RelatingElement
+
+
 def get_aggregate(element: ifcopenshell.entity_instance) -> Union[ifcopenshell.entity_instance, None]:
     """
     Retrieves the aggregate parent of an element.
@@ -1415,6 +1445,29 @@ def get_contained(element: ifcopenshell.entity_instance) -> list[ifcopenshell.en
     return objects
 
 
+def get_surface_features(element: ifcopenshell.entity_instance) -> list[ifcopenshell.entity_instance]:
+    """Retrieves the surface features that adhere to an element.
+
+    In IFC4.3 an IfcSurfaceFeature (such as a road marking) adheres to a host
+    element through the IfcRelAdheresToElement relationship.
+
+    :param element: The IFC element
+    :return: The surface features adhering to the element
+
+    Example:
+
+    .. code:: python
+
+        element = file.by_type("IfcCourse")[0]
+        markings = ifcopenshell.util.element.get_surface_features(element)
+    """
+    objects: list[ifcopenshell.entity_instance] = []
+    if has_surface_features := getattr(element, "HasSurfaceFeatures", ()):
+        for rel in has_surface_features:
+            objects.extend(rel.RelatedSurfaceFeatures)
+    return objects
+
+
 def get_components(
     element: ifcopenshell.entity_instance, include_ports: bool = False
 ) -> list[ifcopenshell.entity_instance]:

src/ifcopenshell-python/test/api/alignment/test_add_positioning_referent.py

@@ -0,0 +1,100 @@
+# IfcOpenShell - IFC toolkit and geometry engine
+# Copyright (C) 2025 Thomas Krijnen <thomas@aecgeeks.com>
+#
+# This file is part of IfcOpenShell.
+#
+# IfcOpenShell is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# IfcOpenShell is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with IfcOpenShell.  If not, see <http://www.gnu.org/licenses/>.
+
+
+import ifcopenshell.api.alignment
+import ifcopenshell.api.context
+import ifcopenshell.api.unit
+import ifcopenshell.util.element
+
+
+def test_add_positioning_referent():
+    file = ifcopenshell.file(schema="IFC4X3")
+    project = file.createIfcProject(GlobalId=ifcopenshell.guid.new(), Name="Test")
+    length = ifcopenshell.api.unit.add_si_unit(file, unit_type="LENGTHUNIT")
+    ifcopenshell.api.unit.assign_unit(file, units=[length])
+    geometric_representation_context = ifcopenshell.api.context.add_context(file, context_type="Model")
+    axis_model_representation_subcontext = ifcopenshell.api.context.add_context(
+        file,
+        context_type="Model",
+        context_identifier="Axis",
+        target_view="MODEL_VIEW",
+        parent=geometric_representation_context,
+    )
+
+    alignment = ifcopenshell.api.alignment.create(file, "TestAlignment", start_station=2000.0)
+
+    horizontal_layout = ifcopenshell.api.alignment.get_horizontal_layout(alignment)
+    segment = ifcopenshell.api.alignment.get_layout_segments(horizontal_layout)[0]
+
+    referent = ifcopenshell.api.alignment.add_positioning_referent(
+        file, "P.C.", alignment, distance_along=0.0, station=2000.0, positioned_product=segment
+    )
+
+    assert referent.is_a("IfcReferent")
+    assert referent.PredefinedType == "POSITION"
+    assert referent.Name == "P.C."
+    assert ifcopenshell.util.element.get_pset(element=referent, name="Pset_Stationing")
+    assert ifcopenshell.util.element.get_pset(element=referent, name="Pset_Stationing", prop="Station") == 2000.0
+    assert referent.ObjectPlacement != None
+
+    assert len(referent.Positions) == 1
+    rel_positions = referent.Positions[0]
+    assert rel_positions.is_a("IfcRelPositions")
+    assert rel_positions.RelatingPositioningElement == referent
+    assert rel_positions.RelatedProducts == (segment,)
+
+
+def test_add_positioning_referent_creates_separate_referent_per_call():
+    file = ifcopenshell.file(schema="IFC4X3")
+    project = file.createIfcProject(GlobalId=ifcopenshell.guid.new(), Name="Test")
+    length = ifcopenshell.api.unit.add_si_unit(file, unit_type="LENGTHUNIT")
+    ifcopenshell.api.unit.assign_unit(file, units=[length])
+    geometric_representation_context = ifcopenshell.api.context.add_context(file, context_type="Model")
+    axis_model_representation_subcontext = ifcopenshell.api.context.add_context(
+        file,
+        context_type="Model",
+        context_identifier="Axis",
+        target_view="MODEL_VIEW",
+        parent=geometric_representation_context,
+    )
+
+    alignment = ifcopenshell.api.alignment.create(file, "TestAlignment", start_station=2000.0)
+
+    horizontal_layout = ifcopenshell.api.alignment.get_horizontal_layout(alignment)
+    segment = ifcopenshell.api.alignment.get_layout_segments(horizontal_layout)[0]
+
+    first_referent = ifcopenshell.api.alignment.add_positioning_referent(
+        file, "P.C.", alignment, distance_along=0.0, station=2000.0, positioned_product=segment
+    )
+
+    other_product = file.createIfcBuildingElementProxy(GlobalId=ifcopenshell.guid.new(), Name="Sign")
+    second_referent = ifcopenshell.api.alignment.add_positioning_referent(
+        file, "P.C.", alignment, distance_along=0.0, station=2000.0, positioned_product=other_product
+    )
+
+    # each call creates its own IfcReferent, each with its own IfcRelPositions to the product passed in
+    assert first_referent != second_referent
+    assert len(first_referent.Positions) == 1
+    assert first_referent.Positions[0].RelatedProducts == (segment,)
+    assert len(second_referent.Positions) == 1
+    assert second_referent.Positions[0].RelatedProducts == (other_product,)
+
+
+test_add_positioning_referent()
+test_add_positioning_referent_creates_separate_referent_per_call()

src/ifcopenshell-python/test/api/alignment/test_add_stationing_to_alignment.py

@@ -57,3 +57,27 @@ def test_add_stationing_to_alignment():
     assert ifcopenshell.util.element.get_pset(element=referent, name="Pset_Stationing")
     assert ifcopenshell.util.element.get_pset(element=referent, name="Pset_Stationing", prop="Station") == 2000.0
     assert referent.ObjectPlacement != None
+
+    # add a station equation at 1000 distance along. this is station 3+000 in coming and 4+000 outgoing.
+    # this is a gap equation.
+    second_referent = ifcopenshell.api.alignment.add_stationing_referent(
+        file, "4+000.000", alignment, distance_along=1000.0, station=4000.0, incoming_station=3000.0
+    )
+
+    referent_nest = ifcopenshell.api.alignment.get_referent_nest(file, alignment)
+    assert len(referent_nest.RelatedObjects) == 2
+
+    assert second_referent == referent_nest.RelatedObjects[1]
+
+    assert second_referent.PredefinedType == "STATION"
+    assert second_referent.Name == "4+000.000"
+    assert ifcopenshell.util.element.get_pset(element=second_referent, name="Pset_Stationing")
+    assert ifcopenshell.util.element.get_pset(element=second_referent, name="Pset_Stationing", prop="Station") == 4000.0
+    assert (
+        ifcopenshell.util.element.get_pset(element=second_referent, name="Pset_Stationing", prop="IncomingStation")
+        == 3000.0
+    )
+    assert second_referent.ObjectPlacement != None
+
+
+test_add_stationing_to_alignment()

src/ifcopenshell-python/test/api/alignment/test_distance_along_from_station.py

@@ -59,3 +59,58 @@ def test_distance_along_from_station():
 
     # Station 175+25.36
     assert ifcopenshell.api.alignment.distance_along_from_station(file, alignment, 17525.36) == pytest.approx(7525.36)
+
+
+def test_distance_along_from_station_with_station_equations():
+    # Reproduces the worked example from the IFC Alignment Geometry Implementation Guide, chapter 9.2.6:
+    # a gap equation (P3: incoming 14+00.00, outgoing 17+00.00) and an overlap equation
+    # (P4: incoming 19+00.00, outgoing 18+50.00).
+    file = ifcopenshell.file(schema="IFC4X3")
+    project = file.createIfcProject(GlobalId=ifcopenshell.guid.new(), Name="Test")
+    length = ifcopenshell.api.unit.add_conversion_based_unit(file, name="foot")
+    ifcopenshell.api.unit.assign_unit(file, units=[length])
+    geometric_representation_context = ifcopenshell.api.context.add_context(file, context_type="Model")
+    axis_model_representation_subcontext = ifcopenshell.api.context.add_context(
+        file,
+        context_type="Model",
+        context_identifier="Axis",
+        target_view="MODEL_VIEW",
+        parent=geometric_representation_context,
+    )
+
+    coordinates = [(500.0, 2500.0), (3340.0, 660.0), (4340.0, 5000.0), (7600.0, 4560.0), (8480.0, 2010.0)]
+    radii = [(1000.0), (1250.0), (950.0)]
+    vpoints = [(0.0, 100.0), (2000.0, 135.0), (5000.0, 105.0), (7400.0, 153.0), (9800.0, 105.0), (12800.0, 90.0)]
+    lengths = [(1600.0), (1200.0), (2000.0), (800.0)]
+
+    alignment = ifcopenshell.api.alignment.create_by_pi_method(
+        file, "TestAlignment", coordinates, radii, vpoints, lengths, start_station=1000.0
+    )
+
+    ifcopenshell.api.alignment.add_stationing_referent(
+        file, "P3", alignment, distance_along=400.0, station=1700.0, incoming_station=1400.0
+    )
+    ifcopenshell.api.alignment.add_stationing_referent(
+        file, "P4", alignment, distance_along=600.0, station=1850.0, incoming_station=1900.0
+    )
+
+    distance_along_from_station = ifcopenshell.api.alignment.distance_along_from_station
+
+    # between P2 and P3: Sta. 13+00.00
+    assert distance_along_from_station(file, alignment, 1300.0) == pytest.approx(300.0)
+
+    # between P3 and P4: Sta. 18+00.00
+    assert distance_along_from_station(file, alignment, 1800.0) == pytest.approx(500.0)
+
+    # between P4 and P5: Sta. 19+25.00
+    assert distance_along_from_station(file, alignment, 1925.0) == pytest.approx(675.0)
+
+    # Sta. 15+00.00 falls inside the gap opened by the equation at P3 and has no corresponding distance along
+    assert distance_along_from_station(file, alignment, 1500.0) is None
+
+    # Sta. 18+75.00 falls inside the overlap zone at P4; the post-equation (outgoing) match is returned
+    assert distance_along_from_station(file, alignment, 1875.0) == pytest.approx(625.0)
+
+
+test_distance_along_from_station()
+test_distance_along_from_station_with_station_equations()