feat(Attribute): add uuid to attributes changes

.clang-format

@@ -1,5 +1,3 @@
-# DO NOT MODIFY DIRECTLY THIS FILE
-# LOOK AT https://github.com/Geode-solutions/actions
 AccessModifierOffset: -4
 AlignAfterOpenBracket: DontAlign
 AlignConsecutiveAssignments: false

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

@@ -30,11 +30,11 @@
 #include <geode/geosciences/implicit/representation/core/stratigraphic_model.hpp>
 #include <geode/geosciences/implicit/representation/core/stratigraphic_section.hpp>
 
 namespace geode
 {
     namespace detail
     {
         void define_implicit_model_helpers( pybind11::module& module )
         {
             module
                 .def( "rescale_model_implicit_value",
@@ -67,15 +67,14 @@
                 .def( "horizon_id_from_name_2d", &horizon_id_from_name< 2 > )
                 .def( "horizon_id_from_name_3d", &horizon_id_from_name< 3 > )
                 .def( "implicit_section_from_cross_section_scalar_field",
-                    []( CrossSection& model, std::string_view attribute_name ) {
+                    []( CrossSection& model, const uuid& attribute_id ) {
                         return implicit_section_from_cross_section_scalar_field(
-                            model.clone(), attribute_name );
+                            model.clone(), attribute_id );
                     } )
                 .def( "implicit_model_from_structural_model_scalar_field",
-                    []( StructuralModel& model,
-                        std::string_view attribute_name ) {
+                    []( StructuralModel& model, const uuid& attribute_id ) {
                         return implicit_model_from_structural_model_scalar_field(
-                            model.clone(), attribute_name );
+                            model.clone(), attribute_id );
                     } )
                 .def( "stratigraphic_model_from_implicit_model_and_coords",
                     []( ImplicitStructuralModel& implicit_model,

bindings/python/tests/implicit/test-py-stratigraphic-section.py

@@ -43,9 +43,12 @@ def import_section_with_stratigraphy():
 
     for surface in stratigraphic_section.surfaces():
         mesh = surface.mesh()
-        scalar_attribute = mesh.vertex_attribute_manager().find_attribute_double(
+        scalar_attributes = mesh.vertex_attribute_manager().attribute_ids_matching_name(
             "curvature_min"
         )
+        scalar_attribute = mesh.vertex_attribute_manager().find_read_only_attribute_double(
+            scalar_attributes[0]
+        )
         for vertex_id in range(mesh.nb_vertices()):
             model_builder.set_stratigraphic_coordinates(
                 surface,

include/geode/geosciences/explicit/geometry/geographic_coordinate_system.hpp

@@ -36,7 +36,7 @@
 
 namespace geode
 {
     struct opengeode_geosciences_explicit_api GeographicCoordinateSystemInfo
     {
         GeographicCoordinateSystemInfo( std::string authority_in,
             std::string code_in,
@@ -59,7 +59,7 @@
         {
             archive.ext( *this,
                 Growable< Archive, GeographicCoordinateSystemInfo >{
                     { []( Archive& a, GeographicCoordinateSystemInfo& info ) {
                         a.text1b( info.authority, info.authority.max_size() );
                         a.text1b( info.code, info.code.max_size() );
                         a.text1b( info.name, info.name.max_size() );
@@ -72,7 +72,7 @@
     };
 
     template < index_t dimension >
     class GeographicCoordinateSystem
         : public AttributeCoordinateReferenceSystem< dimension >
     {
         friend class bitsery::Access;
@@ -80,6 +80,11 @@
     public:
         GeographicCoordinateSystem(
             AttributeManager& manager, GeographicCoordinateSystemInfo info );
+
+        GeographicCoordinateSystem( AttributeManager& manager,
+            const geode::uuid& uuid,
+            GeographicCoordinateSystemInfo info );
+
         ~GeographicCoordinateSystem();
 
         [[nodiscard]] static GeographicCoordinateSystem< dimension >

include/geode/geosciences/explicit/representation/core/cross_section.hpp

@@ -24,6 +24,7 @@
 #pragma once
 
 #include <geode/basic/algorithm.hpp>
+#include <geode/basic/bitsery_archive.hpp>
 
 #include <geode/model/mixin/core/corner.hpp>
 #include <geode/model/mixin/core/corner_collection.hpp>
@@ -51,7 +52,7 @@
      * A Cross Section is a Section composed of Faults and Horizons (as Lines)
      * and FaultBlocks and StratigraphicUnits (as Surfaces).
      */
     class opengeode_geosciences_explicit_api CrossSection
         : public Section,
           public Faults2D,
           public Horizons2D,
@@ -59,7 +60,7 @@
           public StratigraphicUnits2D
     {
     public:
         class opengeode_geosciences_explicit_api HorizonItemRange
             : public Relationships::ItemRangeIterator
         {
         public:
@@ -78,7 +79,7 @@
             const CrossSection& cross_section_;
         };
 
         class opengeode_geosciences_explicit_api FaultItemRange
             : public Relationships::ItemRangeIterator
         {
         public:
@@ -97,7 +98,7 @@
             const CrossSection& cross_section_;
         };
 
         class opengeode_geosciences_explicit_api FaultBlockItemRange
             : public Relationships::ItemRangeIterator
         {
         public:
@@ -116,7 +117,7 @@
             const CrossSection& cross_section_;
         };
 
         class opengeode_geosciences_explicit_api StratigraphicUnitItemRange
             : public Relationships::ItemRangeIterator
         {
         public:
@@ -147,6 +148,7 @@
         using Components = tuple_cat< MeshComponents, CollectionComponents >;
 
         CrossSection() = default;
+        CrossSection( BITSERY );
         CrossSection( CrossSection&& ) noexcept = default;
         explicit CrossSection( Section&& section ) noexcept;
         CrossSection( const CrossSection& initial_model,

include/geode/geosciences/explicit/representation/core/structural_model.hpp

@@ -24,6 +24,7 @@
 #pragma once
 
 #include <geode/basic/algorithm.hpp>
+#include <geode/basic/bitsery_archive.hpp>
 
 #include <geode/model/mixin/core/block.hpp>
 #include <geode/model/mixin/core/block_collection.hpp>
@@ -150,6 +151,7 @@ namespace geode
         using Components = tuple_cat< MeshComponents, CollectionComponents >;
 
         StructuralModel() = default;
+        StructuralModel( BITSERY );
         StructuralModel( StructuralModel&& ) noexcept = default;
         explicit StructuralModel( BRep&& brep ) noexcept;
         StructuralModel( const StructuralModel& initial_model,

include/geode/geosciences/implicit/mixin/core/stratigraphic_relationships.hpp

@@ -54,6 +54,7 @@ namespace geode
 
     public:
         StratigraphicRelationships();
+        StratigraphicRelationships( BITSERY );
         ~StratigraphicRelationships();
 
         [[nodiscard]] bool is_above(

include/geode/geosciences/implicit/representation/core/detail/helpers.hpp

@@ -71,13 +71,11 @@ namespace geode
 
         [[nodiscard]] ImplicitCrossSection opengeode_geosciences_implicit_api
             implicit_section_from_cross_section_scalar_field(
-                CrossSection&& section,
-                std::string_view scalar_attribute_name );
+                CrossSection&& section, const uuid& scalar_attribute_id );
 
         [[nodiscard]] ImplicitStructuralModel opengeode_geosciences_implicit_api
             implicit_model_from_structural_model_scalar_field(
-                StructuralModel&& model,
-                std::string_view scalar_attribute_name );
+                StructuralModel&& model, const uuid& scalar_attribute_id );
 
         [[nodiscard]] StratigraphicModel opengeode_geosciences_implicit_api
             stratigraphic_model_from_implicit_model_and_coords(

include/geode/geosciences/implicit/representation/core/horizons_stack.hpp

@@ -23,6 +23,7 @@
 
 #pragma once
 
+#include <geode/basic/bitsery_archive.hpp>
 #include <geode/basic/identifier.hpp>
 #include <geode/basic/pimpl.hpp>
 
@@ -134,6 +135,7 @@ namespace geode
         using Components = tuple_cat< MeshComponents, CollectionComponents >;
 
         HorizonsStack();
+        HorizonsStack( BITSERY );
         HorizonsStack( HorizonsStack< dimension >&& horizons_stack ) noexcept;
         ~HorizonsStack();
 

include/geode/geosciences/implicit/representation/core/implicit_cross_section.hpp

@@ -25,6 +25,7 @@
 
 #include <optional>
 
+#include <geode/basic/bitsery_archive.hpp>
 #include <geode/basic/pimpl.hpp>
 
 #include <geode/geosciences/explicit/representation/core/cross_section.hpp>
@@ -56,6 +57,7 @@ namespace geode
             "geode_implicit_attribute";
         using implicit_attribute_type = double;
         ImplicitCrossSection();
+        ImplicitCrossSection( BITSERY );
         ImplicitCrossSection( ImplicitCrossSection&& implicit_model ) noexcept;
         explicit ImplicitCrossSection( CrossSection&& cross_section ) noexcept;
         ImplicitCrossSection( const ImplicitCrossSection& initial_model,

include/geode/geosciences/implicit/representation/core/implicit_structural_model.hpp

@@ -25,6 +25,7 @@
 
 #include <optional>
 
+#include <geode/basic/bitsery_archive.hpp>
 #include <geode/basic/pimpl.hpp>
 
 #include <geode/geosciences/explicit/representation/core/structural_model.hpp>
@@ -63,6 +64,7 @@ namespace geode
             "geode_implicit_attribute";
         using implicit_attribute_type = double;
         ImplicitStructuralModel();
+        ImplicitStructuralModel( BITSERY );
         ImplicitStructuralModel(
             ImplicitStructuralModel&& implicit_model ) noexcept;
         explicit ImplicitStructuralModel(
@@ -87,6 +89,9 @@ namespace geode
             return native_extension_static();
         }
 
+        [[nodiscard]] uuid block_implicit_function_attribute_id(
+            const uuid& block_id ) const;
+
         /*!
          * Return the implicit value at the given vertex of the given block.
          */

include/geode/geosciences/implicit/representation/core/stratigraphic_model.hpp

@@ -23,6 +23,7 @@
 
 #pragma once
 
+#include <geode/basic/bitsery_archive.hpp>
 #include <geode/basic/pimpl.hpp>
 
 #include <geode/geosciences/implicit/common.hpp>
@@ -59,6 +60,7 @@ namespace geode
                 "geode_associated_block_polyhedron_facet";
         using stratigraphic_location_type = Point2D;
         StratigraphicModel();
+        StratigraphicModel( BITSERY );
         StratigraphicModel( StratigraphicModel&& implicit_model ) noexcept;
         explicit StratigraphicModel(
             ImplicitStructuralModel&& structural_model ) noexcept;
@@ -142,6 +144,9 @@ namespace geode
 
         [[nodiscard]] BoundingBox3D stratigraphic_bounding_box() const;
 
+        [[nodiscard]] uuid block_stratigraphic_location_attribute_id(
+            const uuid& block_id ) const;
+
     public:
         void initialize_stratigraphic_query_trees(
             StratigraphicModelBuilderKey );

include/geode/geosciences/implicit/representation/core/stratigraphic_section.hpp

@@ -25,6 +25,7 @@
 
 #include <optional>
 
+#include <geode/basic/bitsery_archive.hpp>
 #include <geode/basic/pimpl.hpp>
 
 #include <geode/geosciences/implicit/common.hpp>
@@ -62,6 +63,7 @@ namespace geode
 
         using stratigraphic_location_type = Point1D;
         StratigraphicSection();
+        StratigraphicSection( BITSERY );
         StratigraphicSection(
             StratigraphicSection&& stratigraphic_section ) noexcept;
         explicit StratigraphicSection(
@@ -145,6 +147,9 @@ namespace geode
 
         [[nodiscard]] BoundingBox2D stratigraphic_bounding_box() const;
 
+        [[nodiscard]] uuid surface_stratigraphic_location_attribute_id(
+            const uuid& surface ) const;
+
     public:
         void initialize_stratigraphic_query_trees(
             StratigraphicSectionBuilderKey );

src/geode/geosciences/explicit/geometry/geographic_coordinate_system.cpp

@@ -122,6 +122,16 @@ namespace geode
     {
     }
 
+    template < index_t dimension >
+    GeographicCoordinateSystem< dimension >::GeographicCoordinateSystem(
+        AttributeManager& manager,
+        const uuid& uuid,
+        GeographicCoordinateSystemInfo info )
+        : AttributeCoordinateReferenceSystem< dimension >{ manager, uuid },
+          impl_{ std::move( info ) }
+    {
+    }
+
     template < index_t dimension >
     GeographicCoordinateSystem< dimension >::~GeographicCoordinateSystem() =
         default;

src/geode/geosciences/explicit/geometry/geographic_coordinate_system_helper.cpp

@@ -115,13 +115,17 @@
             const geode::AttributeCoordinateReferenceSystem< Mesh::dim >& >(
             crs_manager.find_coordinate_reference_system( old_crs_name ) );
         auto& attribute_manager = mesh.vertex_attribute_manager();
-        attribute_manager.rename_attribute(
-            attribute_crs.attribute_name(), info.name );
+        auto attribute =
+            attribute_manager.template find_attribute< geode::VariableAttribute,
+                geode::Point< Mesh::dim > >( attribute_crs.attribute_id() );
+        geode::IdentifierBuilder attribute_identifier_builder{ *attribute };
+        attribute_identifier_builder.set_name( info.name );
         auto crs_builder =
             builder.main_coordinate_reference_system_manager_builder();
         crs_builder.register_coordinate_reference_system( crs_name,
             std::make_shared< geode::GeographicCoordinateSystem< Mesh::dim > >(
-                attribute_manager, std::move( info ) ) );
+                attribute_manager, attribute_crs.attribute_id(),
+                std::move( info ) ) );
         crs_builder.delete_coordinate_reference_system( old_crs_name );
         crs_builder.set_active_coordinate_reference_system( crs_name );
     }

src/geode/geosciences/explicit/representation/core/cross_section.cpp

@@ -191,6 +191,8 @@ namespace geode
         return { *this, stratigraphic_unit };
     }
 
+    CrossSection::CrossSection( BITSERY bitsery ) : Section{ bitsery } {}
+
     CrossSection::CrossSection( Section&& section ) noexcept
         : Section{ std::move( section ) }
     {

src/geode/geosciences/explicit/representation/core/structural_model.cpp

@@ -197,6 +197,8 @@ namespace geode
         return { *this, stratigraphic_unit };
     }
 
+    StructuralModel::StructuralModel( BITSERY bitery ) : BRep{ bitery } {}
+
     StructuralModel::StructuralModel( BRep&& brep ) noexcept
         : BRep{ std::move( brep ) }
     {

src/geode/geosciences/explicit/representation/io/geode/geode_cross_section_input.cpp

@@ -54,7 +54,7 @@ namespace geode
     {
         const UnzipFile zip_reader{ filename(), uuid{}.string() };
         zip_reader.extract_all();
-        CrossSection cross_section;
+        CrossSection cross_section{ BITSERY::constructor };
         detail::load_cross_section_files(
             cross_section, zip_reader.directory() );
         return cross_section;

src/geode/geosciences/explicit/representation/io/geode/geode_structural_model_input.cpp

@@ -56,7 +56,7 @@ namespace geode
     {
         const UnzipFile zip_reader{ filename(), uuid{}.string() };
         zip_reader.extract_all();
-        StructuralModel structural_model;
+        StructuralModel structural_model{ BITSERY::constructor };
         detail::load_structural_model_files(
             structural_model, zip_reader.directory() );
         return structural_model;

src/geode/geosciences/implicit/mixin/core/stratigraphic_relationships.cpp

@@ -54,6 +54,8 @@ namespace geode
             initialize_relation_attributes();
         }
 
+        Impl( BITSERY bitsery ) : RelationshipsImpl( bitsery ) {}
+
         bool is_above( const uuid& above_id, const uuid& under_id ) const
         {
             auto current = under_id;
@@ -202,10 +204,24 @@ namespace geode
     private:
         void initialize_relation_attributes()
         {
-            above_relations_ =
+            const auto ids =
+                relation_attribute_manager().attribute_ids_matching_name(
+                    "geode_above_relations" );
+            if( ids.has_value() )
+            {
+                above_relations_ = relation_attribute_manager()
+                                       .find_attribute< SparseAttribute, bool >(
+                                           ids.value()[0] );
+                return;
+            }
+            const auto above_relations_id =
                 relation_attribute_manager()
-                    .find_or_create_attribute< SparseAttribute, bool >(
-                        "geode_above_relations", false );
+                    .create_attribute< SparseAttribute, bool >(
+                        "geode_above_relations", false,
+                        geode::AttributeProperties{} );
+            above_relations_ = relation_attribute_manager()
+                                   .find_attribute< SparseAttribute, bool >(
+                                       above_relations_id );
         }
 
         std::optional< index_t > relation_edge(
@@ -284,6 +300,10 @@ namespace geode
     };
 
     StratigraphicRelationships::StratigraphicRelationships() = default;
+    StratigraphicRelationships::StratigraphicRelationships( BITSERY bitsery )
+        : impl_( bitsery )
+    {
+    }
     StratigraphicRelationships::StratigraphicRelationships(
         StratigraphicRelationships&& ) noexcept = default;
     StratigraphicRelationships& StratigraphicRelationships::operator=(