add nested hdf5 and schema namespaces

CMakeLists.txt

@@ -20,14 +20,14 @@ add_library(
     src/Utils.hpp
     src/io/HDF5IO.cpp
     src/io/BaseIO.cpp
-    src/hdmf/base/Data.hpp
-    src/hdmf/base/Container.cpp
-    src/hdmf/table/DynamicTable.cpp
-    src/hdmf/table/ElementIdentifiers.hpp
-    src/hdmf/table/VectorData.hpp
-    src/device/Device.cpp
-    src/file/ElectrodeGroup.cpp
-    src/file/ElectrodeTable.cpp
+    src/schema/hdmf/base/Data.hpp
+    src/schema/hdmf/base/Container.cpp
+    src/schema/hdmf/table/DynamicTable.cpp
+    src/schema/hdmf/table/ElementIdentifiers.hpp
+    src/schema/hdmf/table/VectorData.hpp
+    src/schema/nwb/device/Device.cpp
+    src/schema/nwb/file/ElectrodeGroup.cpp
+    src/schema/nwb/file/ElectrodeTable.cpp
 )
 
 target_include_directories(

src/NWBFile.cpp

@@ -9,13 +9,12 @@
 #include "NWBFile.hpp"
 
 #include "Utils.hpp"
-#include "device/Device.hpp"
-#include "file/ElectrodeGroup.hpp"
-#include "file/ElectrodeTable.hpp"
 #include "io/BaseIO.hpp"
+#include "schema/nwb/device/Device.hpp"
+#include "schema/nwb/file/ElectrodeGroup.hpp"
+#include "schema/nwb/file/ElectrodeTable.hpp"
 
-using namespace AQNWBIO;
-namespace fs = std::filesystem;
+using namespace AQNWB;
 
 // NWBFile
 
@@ -98,17 +97,19 @@ Status NWBFile::startRecording()
     std::string devicePath = "general/devices/" + groupName;
     std::string elecPath = "general/extracellular_ephys/" + groupName;
 
-    Device device = Device(devicePath, io, "description", "unknown");
+    Schema::Device device =
+        Schema::Device(devicePath, io, "description", "unknown");
     device.initialize();
 
-    ElectrodeGroup elecGroup =
-        ElectrodeGroup(elecPath, io, "description", "unknown", device);
+    Schema::ElectrodeGroup elecGroup =
+        Schema::ElectrodeGroup(elecPath, io, "description", "unknown", device);
     elecGroup.initialize();
   }
 
   // Create electrode table
   std::string electrodePath = "general/extracellular_ephys/electrodes/";
-  ElectrodeTable elecTable = ElectrodeTable(electrodePath, io, channels);
+  Schema::ElectrodeTable elecTable =
+      Schema::ElectrodeTable(electrodePath, io, channels);
   elecTable.initialize();
 
   elecTable.electrodeDataset->dataset = createRecordingData(
@@ -137,12 +138,14 @@ void NWBFile::cacheSpecifications(const std::string& specPath,
   io->createGroup("/specifications/" + specPath);
   io->createGroup("/specifications/" + specPath + versionNumber);
 
-  fs::path currentFile = __FILE__;
-  fs::path schemaDir = currentFile.parent_path().parent_path()
+  std::filesystem::path currentFile = __FILE__;
+  std::filesystem::path schemaDir = currentFile.parent_path().parent_path()
       / "resources/spec" / specPath / versionNumber;
 
-  for (auto const& entry : fs::directory_iterator {schemaDir})
-    if (fs::is_regular_file(entry) && entry.path().extension() == ".json") {
+  for (auto const& entry : std::filesystem::directory_iterator {schemaDir})
+    if (std::filesystem::is_regular_file(entry)
+        && entry.path().extension() == ".json")
+    {
       std::string specName =
           entry.path().filename().replace_extension("").string();
       if (specName.find("namespace") != std::string::npos)

src/NWBFile.hpp

@@ -4,7 +4,7 @@
 
 #include "io/BaseIO.hpp"
 
-namespace AQNWBIO
+namespace AQNWB
 {
 /**
  * @brief The NWBFile class provides an interface for setting up and managing
@@ -168,4 +168,4 @@ class NWBRecordingEngine
    */
   std::vector<int64_t> smpBuffer;
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB

src/Types.hpp

@@ -2,7 +2,7 @@
 
 #include <vector>
 
-namespace AQNWBIO
+namespace AQNWB
 {
 /**
  * @brief Provides definitions for various types used in the project.
@@ -29,4 +29,4 @@ class Types
    */
   using SizeArray = std::vector<size_t>;
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB

src/Utils.hpp

@@ -7,7 +7,7 @@
 #include <boost/uuid/uuid_generators.hpp>
 #include <boost/uuid/uuid_io.hpp>
 
-namespace AQNWBIO
+namespace AQNWB
 {
 /**
  * @brief Generates a UUID (Universally Unique Identifier) as a string.
@@ -40,4 +40,4 @@ inline std::string getCurrentTime()
 
   return oss.str();
 }
-}  // namespace AQNWBIO
+}  // namespace AQNWB

src/io/BaseIO.cpp

@@ -2,7 +2,7 @@
 
 #include "Utils.hpp"
 
-using namespace AQNWBIO;
+using namespace AQNWB;
 
 // BaseDataType
 

src/io/BaseIO.hpp

@@ -10,11 +10,11 @@
 #define DEFAULT_STR_SIZE 256
 #define DEFAULT_ARRAY_SIZE 1
 
-using Status = AQNWBIO::Types::Status;
-using SizeArray = AQNWBIO::Types::SizeArray;
-using SizeType = AQNWBIO::Types::SizeType;
+using Status = AQNWB::Types::Status;
+using SizeArray = AQNWB::Types::SizeArray;
+using SizeType = AQNWB::Types::SizeType;
 
-namespace AQNWBIO
+namespace AQNWB
 {
 
 class BaseRecordingData;
@@ -372,4 +372,4 @@ class BaseRecordingData
   std::vector<uint32_t> rowXPos;
 };
 
-}  // namespace AQNWBIO
+}  // namespace AQNWB

src/io/HDF5IO.cpp

@@ -11,7 +11,7 @@
 #include "Utils.hpp"
 
 using namespace H5;
-using namespace AQNWBIO;
+using namespace AQNWB::HDF5;
 
 // HDF5IO
 
@@ -342,7 +342,7 @@ Status HDF5IO::createStringDataSet(const std::string& path,
   return Status::Success;
 }
 
-BaseRecordingData* HDF5IO::getDataSet(const std::string& path)
+AQNWB::BaseRecordingData* HDF5IO::getDataSet(const std::string& path)
 {
   std::unique_ptr<DataSet> data;
 
@@ -364,10 +364,10 @@ BaseRecordingData* HDF5IO::getDataSet(const std::string& path)
   }
 }
 
-BaseRecordingData* HDF5IO::createDataSet(const BaseDataType& type,
-                                         const SizeArray& size,
-                                         const SizeArray& chunking,
-                                         const std::string& path)
+AQNWB::BaseRecordingData* HDF5IO::createDataSet(const BaseDataType& type,
+                                                const SizeArray& size,
+                                                const SizeArray& chunking,
+                                                const std::string& path)
 {
   std::unique_ptr<DataSet> data;
   DSetCreatPropList prop;

src/io/HDF5IO.hpp

@@ -14,7 +14,7 @@ class DataType;
 class Exception;
 }  // namespace H5
 
-namespace AQNWBIO
+namespace AQNWB::HDF5
 {
 class HDF5RecordingData;  // declare here because gets used in HDF5IO class
 
@@ -275,4 +275,4 @@ class HDF5RecordingData : public BaseRecordingData
    */
   Status checkStatus(int status);
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB::HDF5

src/hdmf/base/Container.cpp → src/schema/hdmf/base/Container.cpp

@@ -1,6 +1,6 @@
-#include "Container.hpp"
+#include "schema/hdmf/base/Container.hpp"
 
-using namespace AQNWBIO;
+using namespace AQNWB::Schema;
 
 // Container
 

src/hdmf/base/Container.hpp → src/schema/hdmf/base/Container.hpp

@@ -5,7 +5,7 @@
 
 #include "io/BaseIO.hpp"
 
-namespace AQNWBIO
+namespace AQNWB::Schema
 {
 /**
  * @brief Abstract data type for a group storing collections of data and
@@ -48,4 +48,4 @@ class Container
    */
   std::shared_ptr<BaseIO> io;
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB::Schema

src/hdmf/base/Data.hpp → src/schema/hdmf/base/Data.hpp

@@ -4,7 +4,7 @@
 
 #include "io/BaseIO.hpp"
 
-namespace AQNWBIO
+namespace AQNWB::Schema
 {
 /**
  * @brief An abstract data type for a dataset.
@@ -27,4 +27,4 @@ class Data
    */
   std::unique_ptr<BaseRecordingData> dataset;
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB::Schema

src/hdmf/table/DynamicTable.cpp → src/schema/hdmf/table/DynamicTable.cpp

@@ -1,6 +1,6 @@
-#include "DynamicTable.hpp"
+#include "schema/hdmf/table/DynamicTable.hpp"
 
-using namespace AQNWBIO;
+using namespace AQNWB::Schema;
 
 // DynamicTable
 

src/hdmf/table/DynamicTable.hpp → src/schema/hdmf/table/DynamicTable.hpp

@@ -2,12 +2,12 @@
 
 #include <string>
 
-#include "hdmf/base/Container.hpp"
-#include "hdmf/table/ElementIdentifiers.hpp"
-#include "hdmf/table/VectorData.hpp"
 #include "io/BaseIO.hpp"
+#include "schema/hdmf/base/Container.hpp"
+#include "schema/hdmf/table/ElementIdentifiers.hpp"
+#include "schema/hdmf/table/VectorData.hpp"
 
-namespace AQNWBIO
+namespace AQNWB::Schema
 {
 /**
  * @brief Represents a group containing multiple datasets that are aligned on
@@ -94,4 +94,4 @@ class DynamicTable : public Container
    */
   std::vector<std::string> colNames;
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB::Schema

src/hdmf/table/ElementIdentifiers.hpp → src/schema/hdmf/table/ElementIdentifiers.hpp

@@ -1,8 +1,8 @@
 #pragma once
 
-#include "hdmf/base/Data.hpp"
+#include "schema/hdmf/base/Data.hpp"
 
-namespace AQNWBIO
+namespace AQNWB::Schema
 {
 /**
  * @brief A list of unique identifiers for values within a dataset, e.g. rows of
@@ -11,4 +11,4 @@ namespace AQNWBIO
 class ElementIdentifiers : public Data
 {
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB::Schema

src/hdmf/table/VectorData.cpp → src/schema/hdmf/table/VectorData.cpp

@@ -1,6 +1,6 @@
-#include "VectorData.hpp"
+#include "schema/hdmf/table/VectorData.hpp"
 
-using namespace AQNWBIO;
+using namespace AQNWB::Schema;
 
 // VectorData
 std::string VectorData::getDescription() const

src/hdmf/table/VectorData.hpp → src/schema/hdmf/table/VectorData.hpp

@@ -2,9 +2,9 @@
 
 #include <string>
 
-#include "hdmf/base/Data.hpp"
+#include "schema/hdmf/base/Data.hpp"
 
-namespace AQNWBIO
+namespace AQNWB::Schema
 {
 /**
  * @brief An n-dimensional dataset representing a column of a DynamicTable.
@@ -24,4 +24,4 @@ class VectorData : public Data
    */
   std::string description;
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB::Schema

src/device/Device.cpp → src/schema/nwb/device/Device.cpp

@@ -1,6 +1,6 @@
-#include "Device.hpp"
+#include "schema/nwb/device/Device.hpp"
 
-using namespace AQNWBIO;
+using namespace AQNWB::Schema;
 
 // Device
 /** Constructor */

src/device/Device.hpp → src/schema/nwb/device/Device.hpp

@@ -2,10 +2,10 @@
 
 #include <string>
 
-#include "hdmf/base/Container.hpp"
 #include "io/BaseIO.hpp"
+#include "schema/hdmf/base/Container.hpp"
 
-namespace AQNWBIO
+namespace AQNWB::Schema
 {
 /**
  * @brief Metadata about a data acquisition device, e.g., recording system,
@@ -60,4 +60,4 @@ class Device : public Container
    */
   std::string manufacturer;
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB::Schema

src/file/ElectrodeGroup.cpp → src/schema/nwb/file/ElectrodeGroup.cpp

@@ -1,6 +1,6 @@
-#include "ElectrodeGroup.hpp"
+#include "schema/nwb/file/ElectrodeGroup.hpp"
 
-using namespace AQNWBIO;
+using namespace AQNWB::Schema;
 
 // ElectrodeGroup
 

src/file/ElectrodeGroup.hpp → src/schema/nwb/file/ElectrodeGroup.hpp

@@ -2,11 +2,11 @@
 
 #include <string>
 
-#include "device/Device.hpp"
-#include "hdmf/base/Container.hpp"
 #include "io/BaseIO.hpp"
+#include "schema/hdmf/base/Container.hpp"
+#include "schema/nwb/device/Device.hpp"
 
-namespace AQNWBIO
+namespace AQNWB::Schema
 {
 /**
  * @brief The ElectrodeGroup class represents a physical grouping of electrodes,
@@ -78,4 +78,4 @@ class ElectrodeGroup : public Container
    */
   Device device;
 };
-}  // namespace AQNWBIO
+}  // namespace AQNWB::Schema

src/file/ElectrodeTable.cpp → src/schema/nwb/file/ElectrodeTable.cpp

@@ -1,6 +1,6 @@
-#include "ElectrodeTable.hpp"
+#include "schema/nwb/file/ElectrodeTable.hpp"
 
-using namespace AQNWBIO;
+using namespace AQNWB::Schema;
 
 // ElectrodeTable