#62 reorder cell_based registrations

Chaste · Mar 20, 2024 · 3fe4c00 · 3fe4c00
1 parent 6fb23f7
commit 3fe4c00
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Showing 4 changed files with 62 additions and 132 deletions.
diff --git a/dynamic/wrapper_generators/package_info.yaml b/dynamic/wrapper_generators/package_info.yaml
@@ -181,6 +181,7 @@ modules:
       - name: AbstractSimpleCellCycleModel
       - name: AbstractSimplePhaseBasedCellCycleModel
       - name: AbstractSimpleGenerationalCellCycleModel
+      - name: AbstractCellCycleModelOdeSolver
       - name: UniformCellCycleModel
       - name: SimpleOxygenBasedCellCycleModel
       - name: UniformG1GenerationalCellCycleModel
@@ -199,7 +200,6 @@ modules:
       - name: FixedSequenceCellCycleModel
       - name: BernoulliTrialCellCycleModel
       - name: FixedG1GenerationalCellCycleModel
-      - name: AbstractCellCycleModelOdeSolver
       ## - name: CellCycleModelOdeSolver
       - name: AbstractCellProperty
         excluded_methods:
@@ -604,28 +604,28 @@ modules:
           - AbstractCellPopulation.hpp
       - name: AbstractUpdateRule
       - name: AbstractCaUpdateRule
-      - name: DiffusionCaUpdateRule
       - name: AbstractPottsUpdateRule
+      - name: AbstractCentreBasedDivisionRule
+      - name: AbstractCaBasedDivisionRule
+      - name: AbstractCaSwitchingUpdateRule
+      - name: AbstractImmersedBoundaryDivisionRule
+      - name: AbstractVertexBasedDivisionRule
+      - name: DiffusionCaUpdateRule
       - name: VolumeConstraintPottsUpdateRule
       - name: SurfaceAreaConstraintPottsUpdateRule
       - name: AdhesionPottsUpdateRule
       - name: DifferentialAdhesionPottsUpdateRule
-      - name: AbstractVertexBasedDivisionRule
       - name: RandomDirectionVertexBasedDivisionRule
       - name: VonMisesVertexBasedDivisionRule
       - name: FixedVertexBasedDivisionRule
-      - name: AbstractCaBasedDivisionRule
       - name: ShovingCaBasedDivisionRule
       - name: ExclusionCaBasedDivisionRule
       - name: RandomDirectionCentreBasedDivisionRule
       - name: FixedCentreBasedDivisionRule
-      - name: AbstractCentreBasedDivisionRule
       - name: ShortAxisVertexBasedDivisionRule
-      - name: AbstractImmersedBoundaryDivisionRule
       - name: ShortAxisImmersedBoundaryDivisionRule
       - name: RandomCaSwitchingUpdateRule
       - name: ChemotaxisPottsUpdateRule
-      - name: AbstractCaSwitchingUpdateRule
       - name: AbstractForce
       - name: AbstractTwoBodyInteractionForce
       - name: BuskeAdhesiveForce
@@ -692,7 +692,6 @@ modules:
           - GetNodeCorrespondingToCell
           - MarkSpring
           - UnmarkSpring
-      - name: NodeBasedCellPopulationWithParticles
       - name: CaBasedCellPopulation
         excluded_methods:
           - rGetMesh
@@ -984,6 +983,45 @@ modules:
           - VertexT2SwapLocationsWriter.hpp
           - VertexT3SwapLocationsWriter.hpp
           - VoronoiDataWriter.hpp
+      - name: NodeBasedCellPopulationWithParticles
+        excluded_methods:
+          - rGetMesh
+        custom_generator: CPPWG_SOURCEROOT/projects/PyChaste/dynamic/wrapper_generators/PopulationWriter_custom.py
+        source_includes:
+          - CellAgesWriter.hpp
+          - CellAncestorWriter.hpp
+          - CellAppliedForceWriter.hpp
+          - CellCycleModelProteinConcentrationsWriter.hpp
+          - CellDataItemWriter.hpp
+          - CellDeltaNotchWriter.hpp
+          - CellDivisionLocationsWriter.hpp
+          - CellIdWriter.hpp
+          - CellLabelWriter.hpp
+          - CellLocationIndexWriter.hpp
+          - CellMutationStatesCountWriter.hpp
+          - CellMutationStatesWriter.hpp
+          - CellPopulationAdjacencyMatrixWriter.hpp
+          - CellPopulationAreaWriter.hpp
+          - CellPopulationElementWriter.hpp
+          - CellProliferativePhasesCountWriter.hpp
+          - CellProliferativePhasesWriter.hpp
+          - CellProliferativeTypesCountWriter.hpp
+          - CellProliferativeTypesWriter.hpp
+          - CellRadiusWriter.hpp
+          - CellRemovalLocationsWriter.hpp
+          - CellRosetteRankWriter.hpp
+          - CellVolumesWriter.hpp
+          - HeterotypicBoundaryLengthWriter.hpp
+          - LegacyCellProliferativeTypesWriter.hpp
+          - NodeLocationWriter.hpp
+          - NodeVelocityWriter.hpp
+          - PottsMeshWriter.hpp
+          - RadialCellDataDistributionWriter.hpp
+          - VertexIntersectionSwapLocationsWriter.hpp
+          - VertexT1SwapLocationsWriter.hpp
+          - VertexT2SwapLocationsWriter.hpp
+          - VertexT3SwapLocationsWriter.hpp
+          - VoronoiDataWriter.hpp
       - name: NodeBasedCellPopulationWithBuskeUpdate
         excluded_methods:
           - rGetMesh

diff --git a/dynamic/wrappers/cell_based/cell_based.main.cpp b/dynamic/wrappers/cell_based/cell_based.main.cpp
@@ -388,6 +388,7 @@ PYBIND11_MODULE(_chaste_project_PyChaste_cell_based, m)
     register_AbstractSimpleCellCycleModel_class(m);
     register_AbstractSimplePhaseBasedCellCycleModel_class(m);
     register_AbstractSimpleGenerationalCellCycleModel_class(m);
+    register_AbstractCellCycleModelOdeSolver_class(m);
     register_UniformCellCycleModel_class(m);
     register_SimpleOxygenBasedCellCycleModel_class(m);
     register_UniformG1GenerationalCellCycleModel_class(m);
@@ -401,12 +402,11 @@ PYBIND11_MODULE(_chaste_project_PyChaste_cell_based, m)
     register_GammaG1CellCycleModel_class(m);
     register_ExponentialG1GenerationalCellCycleModel_class(m);
     register_AbstractOdeBasedPhaseBasedCellCycleModel_class(m);
-    register_TysonNovakCellCycleModel_class(m);
     register_Alarcon2004OxygenBasedCellCycleModel_class(m);
     register_FixedSequenceCellCycleModel_class(m);
     register_BernoulliTrialCellCycleModel_class(m);
     register_FixedG1GenerationalCellCycleModel_class(m);
-    register_AbstractCellCycleModelOdeSolver_class(m);
+    register_TysonNovakCellCycleModel_class(m);
     register_AbstractCellProperty_class(m);
     register_CellPropertyCollection_class(m);
     register_AbstractCellProliferativeType_class(m);
@@ -591,10 +591,20 @@ PYBIND11_MODULE(_chaste_project_PyChaste_cell_based, m)
     register_AbstractUpdateRule3_class(m);
     register_AbstractCaUpdateRule2_class(m);
     register_AbstractCaUpdateRule3_class(m);
-    register_DiffusionCaUpdateRule2_class(m);
-    register_DiffusionCaUpdateRule3_class(m);
     register_AbstractPottsUpdateRule2_class(m);
     register_AbstractPottsUpdateRule3_class(m);
+    register_AbstractCentreBasedDivisionRule2_2_class(m);
+    register_AbstractCentreBasedDivisionRule3_3_class(m);
+    register_AbstractCaBasedDivisionRule2_class(m);
+    register_AbstractCaBasedDivisionRule3_class(m);
+    register_AbstractCaSwitchingUpdateRule2_class(m);
+    register_AbstractCaSwitchingUpdateRule3_class(m);
+    register_AbstractImmersedBoundaryDivisionRule2_class(m);
+    register_AbstractImmersedBoundaryDivisionRule3_class(m);
+    register_AbstractVertexBasedDivisionRule2_class(m);
+    register_AbstractVertexBasedDivisionRule3_class(m);
+    register_DiffusionCaUpdateRule2_class(m);
+    register_DiffusionCaUpdateRule3_class(m);
     register_VolumeConstraintPottsUpdateRule2_class(m);
     register_VolumeConstraintPottsUpdateRule3_class(m);
     register_SurfaceAreaConstraintPottsUpdateRule2_class(m);
@@ -603,16 +613,12 @@ PYBIND11_MODULE(_chaste_project_PyChaste_cell_based, m)
     register_AdhesionPottsUpdateRule3_class(m);
     register_DifferentialAdhesionPottsUpdateRule2_class(m);
     register_DifferentialAdhesionPottsUpdateRule3_class(m);
-    register_AbstractVertexBasedDivisionRule2_class(m);
-    register_AbstractVertexBasedDivisionRule3_class(m);
     register_RandomDirectionVertexBasedDivisionRule2_class(m);
     register_RandomDirectionVertexBasedDivisionRule3_class(m);
     register_VonMisesVertexBasedDivisionRule2_class(m);
     register_VonMisesVertexBasedDivisionRule3_class(m);
     register_FixedVertexBasedDivisionRule2_class(m);
     register_FixedVertexBasedDivisionRule3_class(m);
-    register_AbstractCaBasedDivisionRule2_class(m);
-    register_AbstractCaBasedDivisionRule3_class(m);
     register_ShovingCaBasedDivisionRule2_class(m);
     register_ShovingCaBasedDivisionRule3_class(m);
     register_ExclusionCaBasedDivisionRule2_class(m);
@@ -621,20 +627,14 @@ PYBIND11_MODULE(_chaste_project_PyChaste_cell_based, m)
     register_RandomDirectionCentreBasedDivisionRule3_3_class(m);
     register_FixedCentreBasedDivisionRule2_2_class(m);
     register_FixedCentreBasedDivisionRule3_3_class(m);
-    register_AbstractCentreBasedDivisionRule2_2_class(m);
-    register_AbstractCentreBasedDivisionRule3_3_class(m);
     register_ShortAxisVertexBasedDivisionRule2_class(m);
     register_ShortAxisVertexBasedDivisionRule3_class(m);
-    register_AbstractImmersedBoundaryDivisionRule2_class(m);
-    register_AbstractImmersedBoundaryDivisionRule3_class(m);
     register_ShortAxisImmersedBoundaryDivisionRule2_class(m);
     register_ShortAxisImmersedBoundaryDivisionRule3_class(m);
     register_RandomCaSwitchingUpdateRule2_class(m);
     register_RandomCaSwitchingUpdateRule3_class(m);
     register_ChemotaxisPottsUpdateRule2_class(m);
     register_ChemotaxisPottsUpdateRule3_class(m);
-    register_AbstractCaSwitchingUpdateRule2_class(m);
-    register_AbstractCaSwitchingUpdateRule3_class(m);
     register_AbstractForce2_2_class(m);
     register_AbstractForce3_3_class(m);
     register_AbstractTwoBodyInteractionForce2_2_class(m);
@@ -711,8 +711,6 @@ PYBIND11_MODULE(_chaste_project_PyChaste_cell_based, m)
     register_AbstractCentreBasedCellPopulation3_3_class(m);
     register_AbstractOnLatticeCellPopulation2_class(m);
     register_AbstractOnLatticeCellPopulation3_class(m);
-    register_NodeBasedCellPopulationWithParticles2_class(m);
-    register_NodeBasedCellPopulationWithParticles3_class(m);
     register_CaBasedCellPopulation2_class(m);
     register_CaBasedCellPopulation3_class(m);
     register_ImmersedBoundaryCellPopulation2_class(m);
@@ -727,6 +725,8 @@ PYBIND11_MODULE(_chaste_project_PyChaste_cell_based, m)
     register_PottsBasedCellPopulation3_class(m);
     register_NodeBasedCellPopulation2_class(m);
     register_NodeBasedCellPopulation3_class(m);
+    register_NodeBasedCellPopulationWithParticles2_class(m);
+    register_NodeBasedCellPopulationWithParticles3_class(m);
     register_NodeBasedCellPopulationWithBuskeUpdate2_class(m);
     register_NodeBasedCellPopulationWithBuskeUpdate3_class(m);
     register_AbstractTargetAreaModifier2_class(m);

diff --git a/dynamic/wrappers/pde/AbstractCellCycleModelOdeSolver.cppwg.cpp b/dynamic/wrappers/pde/AbstractCellCycleModelOdeSolver.cppwg.cpp
diff --git a/dynamic/wrappers/pde/AbstractCellCycleModelOdeSolver.cppwg.hpp b/dynamic/wrappers/pde/AbstractCellCycleModelOdeSolver.cppwg.hpp