Migrate remove_deep to remove_deep2 across API modules

remove_deep is deprecated and can silently delete elements still in use.
remove_deep2 requires zero inverses before removal, making it safer.
Also fixes a double-removal bug in remove_grid_axis and prevents
removing the last prop template from a pset template.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src/ifcopenshell-python/ifcopenshell/api/context/remove_context.py

@@ -51,8 +51,10 @@ def remove_context(file: ifcopenshell.file, context: ifcopenshell.entity_instanc
         new = context.ParentContext
         for inverse in file.get_inverse(context):
             if inverse.is_a("IfcCoordinateOperation"):
+                # Trick to make sure the coordinate operation is not referenced
+                # by a context so we can delete it safely
                 inverse.SourceCRS = inverse.TargetCRS
-                ifcopenshell.util.element.remove_deep(file, inverse)
+                ifcopenshell.util.element.remove_deep2(file, inverse)
             else:
                 ifcopenshell.util.element.replace_attribute(inverse, context, new)
         file.remove(context)

src/ifcopenshell-python/ifcopenshell/api/cost/edit_cost_value.py

@@ -59,6 +59,6 @@ def edit_cost_value(
                     value["ValueComponent"],
                 )
                 value = file.create_entity("IfcMeasureWithUnit", value_component, value["UnitComponent"])
-            if old_unit_basis and file.get_total_inverses(old_unit_basis) == 0:
-                ifcopenshell.util.element.remove_deep(file, old_unit_basis)
+            if old_unit_basis:
+                ifcopenshell.util.element.remove_deep2(file, old_unit_basis)
         setattr(cost_value, name, value)

src/ifcopenshell-python/ifcopenshell/api/grid/remove_grid_axis.py

@@ -42,7 +42,5 @@ def remove_grid_axis(file: ifcopenshell.file, axis: ifcopenshell.entity_instance
         ifcopenshell.api.grid.remove_grid_axis(model, axis=axis_2)
     """
     axis_curve = axis.AxisCurve
-    if file.get_total_inverses(axis_curve) == 1:
-        ifcopenshell.util.element.remove_deep(file, axis_curve)
-        file.remove(axis_curve)
     file.remove(axis)
+    ifcopenshell.util.element.remove_deep2(file, axis_curve)

src/ifcopenshell-python/ifcopenshell/api/pset_template/remove_prop_template.py

@@ -22,9 +22,9 @@ import ifcopenshell.util.element
 def remove_prop_template(file: ifcopenshell.file, prop_template: ifcopenshell.entity_instance) -> None:
     """Removes a property template
 
-    Note that a property set template should always have at least one
-    property template to be valid, so take care when removing property
-    templates.
+    Note that a property set template should always have at least one property
+    template to be valid. So a property set template will not be removed if it
+    is the only template ina a property ste template.
 
     :param prop_template: The IfcSimplePropertyTemplate to remove.
     :return: None
@@ -43,10 +43,8 @@ def remove_prop_template(file: ifcopenshell.file, prop_template: ifcopenshell.en
         ifcopenshell.api.pset_template.remove_prop_template(model, prop_template=prop2)
     """
     for inverse in file.get_inverse(prop_template):
-        if len(inverse.HasPropertyTemplates) == 1:
-            inverse.HasPropertyTemplates = []
-        else:
+        if len(inverse.HasPropertyTemplates) > 1:
             has_property_templates = list(inverse.HasPropertyTemplates)
             has_property_templates.remove(prop_template)
             inverse.HasPropertyTemplates = has_property_templates
-    ifcopenshell.util.element.remove_deep(file, prop_template)
+    ifcopenshell.util.element.remove_deep2(file, prop_template)

src/ifcopenshell-python/ifcopenshell/api/pset_template/remove_pset_template.py

@@ -38,4 +38,4 @@ def remove_pset_template(file: ifcopenshell.file, pset_template: ifcopenshell.en
         # Let's remove the template.
         ifcopenshell.api.pset_template.remove_pset_template(model, pset_template=template)
     """
-    ifcopenshell.util.element.remove_deep(file, pset_template)
+    ifcopenshell.util.element.remove_deep2(file, pset_template)

src/ifcopenshell-python/ifcopenshell/api/resource/add_resource_quantity.py

@@ -79,5 +79,5 @@ def add_resource_quantity(
     old_quantity = resource.BaseQuantity
     resource.BaseQuantity = quantity
     if old_quantity:
-        ifcopenshell.util.element.remove_deep(file, old_quantity)
+        ifcopenshell.util.element.remove_deep2(file, old_quantity)
     return quantity

src/ifcopenshell-python/ifcopenshell/api/resource/remove_resource_quantity.py

@@ -47,4 +47,4 @@ def remove_resource_quantity(file: ifcopenshell.file, resource: ifcopenshell.ent
     old_quantity = resource.BaseQuantity
     resource.BaseQuantity = None
     if old_quantity:
-        ifcopenshell.util.element.remove_deep(file, old_quantity)
+        ifcopenshell.util.element.remove_deep2(file, old_quantity)

src/ifcopenshell-python/ifcopenshell/api/unit/remove_unit.py

@@ -47,4 +47,5 @@ def remove_unit(file: ifcopenshell.file, unit: ifcopenshell.entity_instance) ->
             unit_assignment.Units = units
         else:
             file.remove(unit_assignment)
-    ifcopenshell.util.element.remove_deep(file, unit)
+    # TODO handle other possible unit inverses
+    ifcopenshell.util.element.remove_deep2(file, unit)