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API: Major refactoring of all codes to use a strict Interface/AbstractBaseClass, Concrete style of naming #1537

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API: Major refactoring of all codes to use a strict Interface/AbstractBaseClass, Concrete style of naming #1537

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418 changes: 418 additions & 0 deletions CLAUDE.md
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81 changes: 53 additions & 28 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -369,13 +369,13 @@ set(SIMPLNX_HDRS
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/CoreDataIOManager.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/DataIOCollection.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/IDataFactory.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/IDataIOManager.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/AbstractDataIOManager.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/IOConstants.hpp

${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/DataIOManager.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/DataStructureReader.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/DataStructureWriter.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/IDataIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractDataIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/IOUtilities.hpp

${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/DataStoreIO.hpp
Expand All @@ -390,12 +390,12 @@ set(SIMPLNX_HDRS
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/GridMontageIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/HexahedralGeomIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/ImageGeomIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/IGeometryIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/IGridGeometryIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/INodeGeom0dIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/INodeGeom1dIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/INodeGeom2dIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/INodeGeom3dIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractGeometryIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractGridGeometryIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractNodeGeom0dIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractNodeGeom1dIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractNodeGeom2dIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractNodeGeom3dIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/NeighborListIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/QuadGeomIO.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/RectGridGeomIO.hpp
Expand All @@ -422,6 +422,13 @@ set(SIMPLNX_HDRS
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/TriangleGeom.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/VertexGeom.hpp

${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractGeometry.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractGridGeometry.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractNodeGeometry0D.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractNodeGeometry1D.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractNodeGeometry2D.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractNodeGeometry3D.hpp

${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/IGeometry.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/IGridGeometry.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/INodeGeometry0D.hpp
Expand All @@ -433,6 +440,7 @@ set(SIMPLNX_HDRS
${SIMPLNX_SOURCE_DIR}/DataStructure/EmptyDataStore.hpp

${SIMPLNX_SOURCE_DIR}/Plugin/AbstractPlugin.hpp
${SIMPLNX_SOURCE_DIR}/Plugin/IPlugin.hpp
${SIMPLNX_SOURCE_DIR}/Plugin/PluginLoader.hpp

${SIMPLNX_SOURCE_DIR}/DataStructure/Montage/AbstractMontage.hpp
Expand All @@ -442,24 +450,26 @@ set(SIMPLNX_HDRS

${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractDataStore.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractListStore.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractStringStore.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IStringStore.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AttributeMatrix.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/BaseGroup.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataArray.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataGroup.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataMap.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataObject.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractDataObject.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IDataObject.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataPath.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataStore.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataStructure.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IDataStructure.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DynamicListArray.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/EmptyDataStore.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/EmptyListStore.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IArray.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IDataArray.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractArray.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractDataArray.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IDataStore.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IListStore.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/INeighborList.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractNeighborList.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/LinkedPath.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Metadata.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/NeighborList.hpp
Expand All @@ -468,6 +478,7 @@ set(SIMPLNX_HDRS
${SIMPLNX_SOURCE_DIR}/DataStructure/StringArray.hpp
${SIMPLNX_SOURCE_DIR}/DataStructure/StringStore.hpp

${SIMPLNX_SOURCE_DIR}/Filter/AbstractFilter.hpp
${SIMPLNX_SOURCE_DIR}/Filter/AbstractParameter.hpp
${SIMPLNX_SOURCE_DIR}/Filter/AnyCloneable.hpp
${SIMPLNX_SOURCE_DIR}/Filter/Arguments.hpp
Expand Down Expand Up @@ -510,6 +521,7 @@ set(SIMPLNX_HDRS

${SIMPLNX_SOURCE_DIR}/Pipeline/AbstractPipelineFilter.hpp
${SIMPLNX_SOURCE_DIR}/Pipeline/AbstractPipelineNode.hpp
${SIMPLNX_SOURCE_DIR}/Pipeline/IPipelineNode.hpp
${SIMPLNX_SOURCE_DIR}/Pipeline/Pipeline.hpp
${SIMPLNX_SOURCE_DIR}/Pipeline/PipelineFilter.hpp
${SIMPLNX_SOURCE_DIR}/Pipeline/PlaceholderFilter.hpp
Expand All @@ -527,11 +539,13 @@ set(SIMPLNX_HDRS
${SIMPLNX_SOURCE_DIR}/Pipeline/Messaging/RenamedMessage.hpp

${SIMPLNX_SOURCE_DIR}/Plugin/AbstractPlugin.hpp
${SIMPLNX_SOURCE_DIR}/Plugin/IPlugin.hpp
${SIMPLNX_SOURCE_DIR}/Plugin/PluginLoader.hpp

${SIMPLNX_SOURCE_DIR}/Utilities/ArrayCreationUtilities.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/AlignSections.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/ArrayThreshold.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/IArrayThreshold.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/DataArrayUtilities.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/DataGroupUtilities.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/DataObjectUtilities.hpp
Expand All @@ -549,13 +563,14 @@ set(SIMPLNX_HDRS
${SIMPLNX_SOURCE_DIR}/Utilities/StringUtilities.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/StringInterpretationUtilities.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/IntersectionUtilities.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/IParallelAlgorithm.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelAlgorithm.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelDataAlgorithm.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelData2DAlgorithm.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelData3DAlgorithm.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelTaskAlgorithm.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/SamplingUtils.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/SegmentFeatures.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/ISegmentFeatures.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/AbstractSegmentFeatures.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/TimeUtilities.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/TooltipGenerator.hpp
${SIMPLNX_SOURCE_DIR}/Utilities/TooltipRowItem.hpp
Expand Down Expand Up @@ -619,13 +634,13 @@ set(SIMPLNX_SRCS
${SIMPLNX_SOURCE_DIR}/DataStructure/Observers/AbstractDataStructureObserver.cpp

${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/DataIOCollection.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/IDataIOManager.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/AbstractDataIOManager.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/Generic/CoreDataIOManager.cpp

${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/DataIOManager.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/DataStructureReader.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/DataStructureWriter.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/IDataIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractDataIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/IOUtilities.cpp

${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/IDataStoreIO.cpp
Expand All @@ -637,19 +652,25 @@ set(SIMPLNX_SRCS
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/GridMontageIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/HexahedralGeomIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/ImageGeomIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/IGeometryIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/IGridGeometryIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/INodeGeom0dIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/INodeGeom1dIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/INodeGeom2dIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/INodeGeom3dIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractGeometryIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractGridGeometryIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractNodeGeom0dIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractNodeGeom1dIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractNodeGeom2dIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/AbstractNodeGeom3dIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/QuadGeomIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/RectGridGeomIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/StringArrayIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/TetrahedralGeomIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/TriangleGeomIO.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IO/HDF5/VertexGeomIO.cpp

${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractGeometry.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractGridGeometry.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractNodeGeometry0D.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractNodeGeometry1D.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractNodeGeometry2D.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/AbstractNodeGeometry3D.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/IGeometry.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/IGridGeometry.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Geometry/INodeGeometry0D.cpp
Expand All @@ -670,22 +691,24 @@ set(SIMPLNX_SRCS
${SIMPLNX_SOURCE_DIR}/DataStructure/Montage/GridMontage.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Montage/GridTileIndex.cpp

${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractStringStore.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IStringStore.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AttributeMatrix.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/BaseGroup.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataGroup.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataMap.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataObject.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractDataObject.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataPath.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataStructure.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/INeighborList.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/IDataStructure.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/AbstractNeighborList.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/LinkedPath.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/Metadata.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/NeighborList.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/DataArray.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/StringArray.cpp
${SIMPLNX_SOURCE_DIR}/DataStructure/StringStore.cpp

${SIMPLNX_SOURCE_DIR}/Filter/AbstractFilter.cpp
${SIMPLNX_SOURCE_DIR}/Filter/AbstractParameter.cpp
${SIMPLNX_SOURCE_DIR}/Filter/Arguments.cpp
${SIMPLNX_SOURCE_DIR}/Filter/ConstDataParameter.cpp
Expand Down Expand Up @@ -719,6 +742,7 @@ set(SIMPLNX_SRCS

${SIMPLNX_SOURCE_DIR}/Pipeline/AbstractPipelineFilter.cpp
${SIMPLNX_SOURCE_DIR}/Pipeline/AbstractPipelineNode.cpp
${SIMPLNX_SOURCE_DIR}/Pipeline/IPipelineNode.cpp
${SIMPLNX_SOURCE_DIR}/Pipeline/Pipeline.cpp
${SIMPLNX_SOURCE_DIR}/Pipeline/PipelineFilter.cpp
${SIMPLNX_SOURCE_DIR}/Pipeline/PlaceholderFilter.cpp
Expand All @@ -736,6 +760,7 @@ set(SIMPLNX_SRCS
${SIMPLNX_SOURCE_DIR}/Pipeline/Messaging/RenamedMessage.cpp

${SIMPLNX_SOURCE_DIR}/Plugin/AbstractPlugin.cpp
${SIMPLNX_SOURCE_DIR}/Plugin/IPlugin.cpp
${SIMPLNX_SOURCE_DIR}/Plugin/PluginLoader.cpp

${SIMPLNX_SOURCE_DIR}/Utilities/ArrayCreationUtilities.cpp
Expand All @@ -752,12 +777,12 @@ set(SIMPLNX_SRCS
${SIMPLNX_SOURCE_DIR}/Utilities/MaskCompareUtilities.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/MemoryUtilities.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/MessageHelper.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/IParallelAlgorithm.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelAlgorithm.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelDataAlgorithm.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelData2DAlgorithm.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelData3DAlgorithm.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/ParallelTaskAlgorithm.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/SegmentFeatures.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/AbstractSegmentFeatures.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/StringInterpretationUtilities.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/AlignSections.cpp
${SIMPLNX_SOURCE_DIR}/Utilities/OStreamUtilities.cpp
Expand Down
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