fix(Python): add smart holder on Identified objects

.clang-tidy

@@ -8,26 +8,30 @@ Checks: >
   -fuchsia*,
   -llvmlibc*,
   -llvm-header-guard,
+  -llvm-prefer-static-over-anonymous-namespace,
   -misc-no-recursion,
+  -misc-include-cleaner,
+  -misc-const-correctness,
   -modernize-use-trailing-return-type,
+  -portability-avoid-pragma-once,
   -readability-redundant-access-specifiers,
   -readability-convert-member-functions-to-static,
   -cppcoreguidelines-avoid-const-or-ref-data-members
 
 CheckOptions:
-  - key:    misc-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic
-    value:  '1'
+  - key: misc-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic
+    value: "1"
   - key: readability-identifier-length.MinimumLoopCounterNameLength
     value: 1
   - key: readability-identifier-length.IgnoredVariableNames
-    value: '^[defijkptuvw]$'
+    value: "^[defijkptuvw]$"
   # More options here: https://clang.llvm.org/extra/clang-tidy/checks/readability/identifier-naming.html
   - key: readability-identifier-naming.NamespaceCase
     value: lower_case
   - key: readability-identifier-naming.ClassCase
-    value: CamelCase 
+    value: CamelCase
   - key: readability-identifier-naming.StructCase
-    value: CamelCase 
+    value: CamelCase
   - key: readability-identifier-naming.FunctionCase
     value: lower_case
   - key: readability-identifier-naming.VariableCase
@@ -51,14 +55,10 @@ CheckOptions:
   - key: readability-identifier-naming.GlobalFunctionCase
     value: lower_case
   - key: readability-identifier-naming.MemberConstantCase
-    value: CamelCase 
+    value: CamelCase
   - key: readability-identifier-naming.StaticConstantCase
-    value: lower_case 
+    value: lower_case
   - key: readability-function-cognitive-complexity.Threshold
     value: 10
   - key: readability-function-size.ParameterThreshold
     value: 4
-  - key: misc-include-cleaner.IgnoreHeaders
-    value:  utility;cstddef;geode/.*_export\.h;geode/.*/common\.h;geode/basic/types\.h;geode/basic/assert\.h;
-
-

bindings/python/src/explicit/mixin/core/fault.hpp

@@ -25,7 +25,8 @@
 
 #define PYTHON_FAULT( dimension )                                              \
     const auto name##dimension = "Fault" + std::to_string( dimension ) + "D";  \
-    pybind11::class_< Fault##dimension##D, Component##dimension##D >           \
+    pybind11::class_< Fault##dimension##D, Component##dimension##D,            \
+        pybind11::smart_holder >                                               \
         fault##dimension##D( module, name##dimension.c_str() );                \
                                                                                \
     pybind11::enum_< Fault##dimension##D::FAULT_TYPE >(                        \
@@ -43,9 +44,9 @@
 
 namespace geode
 {
     void define_fault( pybind11::module& module )
     {
         PYTHON_FAULT( 2 );
         PYTHON_FAULT( 3 );
     }
 } // namespace geode

bindings/python/src/explicit/mixin/core/fault_block.hpp

@@ -26,15 +26,15 @@
 #define PYTHON_FAULT_BLOCK( dimension )                                        \
     const auto name##dimension =                                               \
         "FaultBlock" + std::to_string( dimension ) + "D";                      \
-    pybind11::class_< FaultBlock##dimension##D, Component##dimension##D >(     \
-        module, name##dimension.c_str() )                                      \
+    pybind11::class_< FaultBlock##dimension##D, Component##dimension##D,       \
+        pybind11::smart_holder >( module, name##dimension.c_str() )            \
         .def( "component_id", &FaultBlock##dimension##D::component_id )
 
 namespace geode
 {
     void define_fault_block( pybind11::module& module )
     {
         PYTHON_FAULT_BLOCK( 2 );
         PYTHON_FAULT_BLOCK( 3 );
     }
 } // namespace geode

bindings/python/src/explicit/mixin/core/fault_blocks.hpp

@@ -27,7 +27,7 @@
 #define PYTHON_FAULT_BLOCKS( dimension )                                       \
     const auto name##dimension =                                               \
         "FaultBlocks" + std::to_string( dimension ) + "D";                     \
-    pybind11::class_< FaultBlocks##dimension##D >(                             \
+    pybind11::class_< FaultBlocks##dimension##D, pybind11::smart_holder >(     \
         module, name##dimension.c_str() )                                      \
         .def( "nb_fault_blocks", &FaultBlocks##dimension##D::nb_fault_blocks ) \
         .def( "fault_block", &FaultBlocks##dimension##D::fault_block,          \

bindings/python/src/explicit/mixin/core/faults.hpp

@@ -26,7 +26,7 @@
 
 #define PYTHON_FAULTS( dimension )                                             \
     const auto name##dimension = "Faults" + std::to_string( dimension ) + "D"; \
-    pybind11::class_< Faults##dimension##D >(                                  \
+    pybind11::class_< Faults##dimension##D, pybind11::smart_holder >(          \
         module, name##dimension.c_str() )                                      \
         .def( "nb_faults", &Faults##dimension##D::nb_faults )                  \
         .def( "fault", &Faults##dimension##D::fault,                           \

bindings/python/src/explicit/mixin/core/horizon.hpp

@@ -26,7 +26,8 @@
 #define PYTHON_HORIZON( dimension )                                            \
     const auto name##dimension =                                               \
         "Horizon" + std::to_string( dimension ) + "D";                         \
-    pybind11::class_< Horizon##dimension##D, Component##dimension##D >         \
+    pybind11::class_< Horizon##dimension##D, Component##dimension##D,          \
+        pybind11::smart_holder >                                               \
         horizon##dimension##D( module, name##dimension.c_str() );              \
                                                                                \
     pybind11::enum_< Horizon##dimension##D::CONTACT_TYPE >(                    \
@@ -48,7 +49,7 @@
 {
     void define_horizon( pybind11::module& module )
     {
         PYTHON_HORIZON( 2 );
         PYTHON_HORIZON( 3 );
     }
 } // namespace geode

bindings/python/src/explicit/mixin/core/horizons.hpp

@@ -27,7 +27,7 @@
 #define PYTHON_HORIZONS( dimension )                                           \
     const auto name##dimension =                                               \
         "Horizons" + std::to_string( dimension ) + "D";                        \
-    pybind11::class_< Horizons##dimension##D >(                                \
+    pybind11::class_< Horizons##dimension##D, pybind11::smart_holder >(        \
         module, name##dimension.c_str() )                                      \
         .def( "nb_horizons", &Horizons##dimension##D::nb_horizons )            \
         .def( "horizon", &Horizons##dimension##D::horizon,                     \

bindings/python/src/explicit/mixin/core/stratigraphic_unit.hpp

@@ -27,14 +27,15 @@
     const auto name##dimension =                                               \
         "StratigraphicUnit" + std::to_string( dimension ) + "D";               \
     pybind11::class_< StratigraphicUnit##dimension##D,                         \
-        Component##dimension##D >( module, name##dimension.c_str() )           \
+        Component##dimension##D, pybind11::smart_holder >(                     \
+        module, name##dimension.c_str() )                                      \
         .def( "component_id", &StratigraphicUnit##dimension##D::component_id )
 
 namespace geode
 {
     void define_stratigraphic_unit( pybind11::module& module )
     {
         PYTHON_STRATIGRAPHIC_UNIT( 2 );
         PYTHON_STRATIGRAPHIC_UNIT( 3 );
     }
 } // namespace geode

bindings/python/src/explicit/mixin/core/stratigraphic_units.hpp

@@ -27,8 +27,8 @@
 #define PYTHON_STRATIGRAPHIC_UNITS( dimension )                                \
     const auto name##dimension =                                               \
         "StratigraphicUnits" + std::to_string( dimension ) + "D";              \
-    pybind11::class_< StratigraphicUnits##dimension##D >(                      \
-        module, name##dimension.c_str() )                                      \
+    pybind11::class_< StratigraphicUnits##dimension##D,                        \
+        pybind11::smart_holder >( module, name##dimension.c_str() )            \
         .def( "nb_stratigraphic_units",                                        \
             &StratigraphicUnits##dimension##D::nb_stratigraphic_units )        \
         .def( "stratigraphic_unit",                                            \

bindings/python/src/explicit/representation/core/cross_section.hpp

@@ -30,7 +30,8 @@ namespace geode
     void define_cross_section( pybind11::module& module )
     {
         pybind11::class_< CrossSection, Section, Faults2D, Horizons2D,
-            FaultBlocks2D, StratigraphicUnits2D >( module, "CrossSection" )
+            FaultBlocks2D, StratigraphicUnits2D, pybind11::smart_holder >(
+            module, "CrossSection" )
             .def( pybind11::init<>() )
             .def( pybind11::init( []( Section& section ) {
                 return CrossSection{ section.clone() };

bindings/python/src/explicit/representation/core/structural_model.hpp

@@ -30,7 +30,8 @@ namespace geode
     void define_structural_model( pybind11::module& module )
     {
         pybind11::class_< StructuralModel, BRep, Faults3D, Horizons3D,
-            FaultBlocks3D, StratigraphicUnits3D >( module, "StructuralModel" )
+            FaultBlocks3D, StratigraphicUnits3D, pybind11::smart_holder >(
+            module, "StructuralModel" )
             .def( pybind11::init<>() )
             .def( pybind11::init( []( BRep& model ) {
                 return StructuralModel{ model.clone() };

bindings/python/src/implicit/mixin/core/stratigraphic_relationships.hpp

@@ -27,7 +27,7 @@ namespace geode
 {
     void define_stratigraphic_relationships( pybind11::module& module )
     {
-        pybind11::class_< StratigraphicRelationships >(
+        pybind11::class_< StratigraphicRelationships, pybind11::smart_holder >(
             module, "StratigraphicRelationships" )
             .def( pybind11::init<>() )
             .def( "is_above", &StratigraphicRelationships::is_above )

bindings/python/src/implicit/representation/core/horizons_stack.hpp

@@ -29,8 +29,8 @@
     const auto name##dimension =                                               \
         "HorizonsStack" + std::to_string( dimension ) + "D";                   \
     pybind11::class_< HorizonsStack##dimension##D, StratigraphicRelationships, \
-        Horizons##dimension##D, StratigraphicUnits##dimension##D,              \
-        Identifier >( module, name##dimension.c_str() )                        \
+        Horizons##dimension##D, StratigraphicUnits##dimension##D, Identifier,  \
+        pybind11::smart_holder >( module, name##dimension.c_str() )            \
         .def( pybind11::init<>() )                                             \
         .def( "native_extension",                                              \
             &HorizonsStack##dimension##D::native_extension )                   \
@@ -90,6 +90,6 @@
 {
     void define_horizons_stack( pybind11::module& module )
     {
         PYTHON_HORIZONS_STACK( 2 );
         PYTHON_HORIZONS_STACK( 3 );
     }

bindings/python/src/implicit/representation/core/implicit_cross_section.hpp

@@ -29,8 +29,8 @@ namespace geode
 {
     void define_implicit_cross_section( pybind11::module& module )
     {
-        pybind11::class_< ImplicitCrossSection, CrossSection >(
-            module, "ImplicitCrossSection" )
+        pybind11::class_< ImplicitCrossSection, CrossSection,
+            pybind11::smart_holder >( module, "ImplicitCrossSection" )
             .def( pybind11::init<>() )
             .def( pybind11::init( []( CrossSection& cross_section ) {
                 return ImplicitCrossSection{ cross_section.clone() };

bindings/python/src/implicit/representation/core/implicit_structural_model.hpp

@@ -31,8 +31,8 @@ namespace geode
 {
     void define_implicit_structural_model( pybind11::module& module )
     {
-        pybind11::class_< ImplicitStructuralModel, StructuralModel >(
-            module, "ImplicitStructuralModel" )
+        pybind11::class_< ImplicitStructuralModel, StructuralModel,
+            pybind11::smart_holder >( module, "ImplicitStructuralModel" )
             .def( pybind11::init<>() )
             .def( pybind11::init( []( StructuralModel& model ) {
                 return ImplicitStructuralModel{ model.clone() };

bindings/python/src/implicit/representation/core/stratigraphic_model.hpp

@@ -35,8 +35,8 @@ namespace geode
 {
     void define_stratigraphic_model( pybind11::module& module )
     {
-        pybind11::class_< StratigraphicModel, ImplicitStructuralModel >(
-            module, "StratigraphicModel" )
+        pybind11::class_< StratigraphicModel, ImplicitStructuralModel,
+            pybind11::smart_holder >( module, "StratigraphicModel" )
             .def( pybind11::init<>() )
             .def( pybind11::init( []( ImplicitStructuralModel& model ) {
                 return StratigraphicModel{ model.clone() };

bindings/python/src/implicit/representation/core/stratigraphic_section.hpp

@@ -35,8 +35,8 @@ namespace geode
 {
     void define_stratigraphic_section( pybind11::module& module )
     {
-        pybind11::class_< StratigraphicSection, ImplicitCrossSection >(
-            module, "StratigraphicSection" )
+        pybind11::class_< StratigraphicSection, ImplicitCrossSection,
+            pybind11::smart_holder >( module, "StratigraphicSection" )
             .def( pybind11::init<>() )
             .def( pybind11::init( []( ImplicitCrossSection& cross_section ) {
                 return StratigraphicSection{ cross_section.clone() };