restructure folders and namespace names

CMakeLists.txt

@@ -16,18 +16,17 @@ include(cmake/variables.cmake)
 
 add_library(
     aq-nwb_lib OBJECT
-    src/NWBFile.cpp
-    src/Utils.hpp
-    src/io/HDF5IO.cpp
-    src/io/BaseIO.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
+    src/BaseIO.cpp
+    src/hdf5/HDF5IO.cpp
+    src/nwb/NWBFile.cpp
+    src/nwb/hdmf/base/Data.hpp
+    src/nwb/hdmf/base/Container.cpp
+    src/nwb/hdmf/table/DynamicTable.cpp
+    src/nwb/hdmf/table/ElementIdentifiers.hpp
+    src/nwb/hdmf/table/VectorData.hpp
+    src/nwb/core/device/Device.cpp
+    src/nwb/core/file/ElectrodeGroup.cpp
+    src/nwb/core/file/ElectrodeTable.cpp
 )
 
 target_include_directories(

src/NWBFile.cpp → src/nwb/NWBFile.cpp

@@ -8,11 +8,11 @@
 
 #include "NWBFile.hpp"
 
+#include "BaseIO.hpp"
 #include "Utils.hpp"
-#include "io/BaseIO.hpp"
-#include "schema/nwb/device/Device.hpp"
-#include "schema/nwb/file/ElectrodeGroup.hpp"
-#include "schema/nwb/file/ElectrodeTable.hpp"
+#include "nwb/core/device/Device.hpp"
+#include "nwb/core/file/ElectrodeGroup.hpp"
+#include "nwb/core/file/ElectrodeTable.hpp"
 
 using namespace AQNWB;
 
@@ -97,19 +97,18 @@ Status NWBFile::startRecording()
     std::string devicePath = "general/devices/" + groupName;
     std::string elecPath = "general/extracellular_ephys/" + groupName;
 
-    Schema::Device device =
-        Schema::Device(devicePath, io, "description", "unknown");
+    NWB::Device device = NWB::Device(devicePath, io, "description", "unknown");
     device.initialize();
 
-    Schema::ElectrodeGroup elecGroup =
-        Schema::ElectrodeGroup(elecPath, io, "description", "unknown", device);
+    NWB::ElectrodeGroup elecGroup =
+        NWB::ElectrodeGroup(elecPath, io, "description", "unknown", device);
     elecGroup.initialize();
   }
 
   // Create electrode table
   std::string electrodePath = "general/extracellular_ephys/electrodes/";
-  Schema::ElectrodeTable elecTable =
-      Schema::ElectrodeTable(electrodePath, io, channels);
+  NWB::ElectrodeTable elecTable =
+      NWB::ElectrodeTable(electrodePath, io, channels);
   elecTable.initialize();
 
   elecTable.electrodeDataset->dataset = createRecordingData(
@@ -139,8 +138,9 @@ void NWBFile::cacheSpecifications(const std::string& specPath,
   io->createGroup("/specifications/" + specPath + versionNumber);
 
   std::filesystem::path currentFile = __FILE__;
-  std::filesystem::path schemaDir = currentFile.parent_path().parent_path()
-      / "resources/spec" / specPath / versionNumber;
+  std::filesystem::path schemaDir =
+      currentFile.parent_path().parent_path().parent_path() / "resources/spec"
+      / specPath / versionNumber;
 
   for (auto const& entry : std::filesystem::directory_iterator {schemaDir})
     if (std::filesystem::is_regular_file(entry)

src/NWBFile.hpp → src/nwb/NWBFile.hpp

@@ -2,7 +2,7 @@
 
 #include <cstdint>
 
-#include "io/BaseIO.hpp"
+#include "BaseIO.hpp"
 
 namespace AQNWB
 {

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

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

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

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

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

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

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

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

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

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

src/schema/nwb/file/ElectrodeTable.hpp → src/nwb/core/file/ElectrodeTable.hpp

@@ -2,12 +2,12 @@
 
 #include <string>
 
-#include "io/BaseIO.hpp"
-#include "schema/hdmf/table/DynamicTable.hpp"
-#include "schema/hdmf/table/ElementIdentifiers.hpp"
-#include "schema/hdmf/table/VectorData.hpp"
+#include "BaseIO.hpp"
+#include "nwb/hdmf/table/DynamicTable.hpp"
+#include "nwb/hdmf/table/ElementIdentifiers.hpp"
+#include "nwb/hdmf/table/VectorData.hpp"
 
-namespace AQNWB::Schema
+namespace AQNWB::NWB
 {
 /**
  * @brief Represents a table containing electrode metadata.
@@ -115,4 +115,4 @@ class ElectrodeTable : public DynamicTable
    */
   std::string groupPath = "/general/extracellular_ephys/array1";
 };
-}  // namespace AQNWB::Schema
+}  // namespace AQNWB::NWB

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

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

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

@@ -3,9 +3,9 @@
 #include <memory>
 #include <string>
 
-#include "io/BaseIO.hpp"
+#include "BaseIO.hpp"
 
-namespace AQNWB::Schema
+namespace AQNWB::NWB
 {
 /**
  * @brief Abstract data type for a group storing collections of data and
@@ -48,4 +48,4 @@ class Container
    */
   std::shared_ptr<BaseIO> io;
 };
-}  // namespace AQNWB::Schema
+}  // namespace AQNWB::NWB

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

@@ -2,9 +2,9 @@
 
 #include <memory>
 
-#include "io/BaseIO.hpp"
+#include "BaseIO.hpp"
 
-namespace AQNWB::Schema
+namespace AQNWB::NWB
 {
 /**
  * @brief An abstract data type for a dataset.
@@ -27,4 +27,4 @@ class Data
    */
   std::unique_ptr<BaseRecordingData> dataset;
 };
-}  // namespace AQNWB::Schema
+}  // namespace AQNWB::NWB

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

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

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

@@ -2,12 +2,12 @@
 
 #include <string>
 
-#include "io/BaseIO.hpp"
-#include "schema/hdmf/base/Container.hpp"
-#include "schema/hdmf/table/ElementIdentifiers.hpp"
-#include "schema/hdmf/table/VectorData.hpp"
+#include "BaseIO.hpp"
+#include "nwb/hdmf/base/Container.hpp"
+#include "nwb/hdmf/table/ElementIdentifiers.hpp"
+#include "nwb/hdmf/table/VectorData.hpp"
 
-namespace AQNWB::Schema
+namespace AQNWB::NWB
 {
 /**
  * @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 AQNWB::Schema
+}  // namespace AQNWB::NWB

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

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

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

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

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

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

tests/aq-nwb_test.cpp

@@ -3,10 +3,10 @@
 
 #include <catch2/catch_test_macros.hpp>
 
-#include "NWBFile.hpp"
-#include "io/BaseIO.hpp"
-#include "io/HDF5IO.hpp"
-#include "schema/nwb/file/ElectrodeTable.hpp"
+#include "BaseIO.hpp"
+#include "hdf5/HDF5IO.hpp"
+#include "nwb/NWBFile.hpp"
+#include "nwb/core/file/ElectrodeTable.hpp"
 
 using namespace AQNWB;
 namespace fs = std::filesystem;
@@ -105,7 +105,7 @@ TEST_CASE("ElectrodeTable", "[datatypes]")
     std::shared_ptr<BaseIO> io = std::make_unique<HDF5::HDF5IO>(filename);
     io->open();
     io->createGroup("array1");
-    Schema::ElectrodeTable electrodeTable(path, io, channels);
+    NWB::ElectrodeTable electrodeTable(path, io, channels);
     electrodeTable.initialize();
     electrodeTable.setGroupPath("array1");
     electrodeTable.electrodeDataset->dataset =
@@ -136,7 +136,7 @@ TEST_CASE("ElectrodeTable", "[datatypes]")
     std::string filename = getTestFilePath("electrodeTableNoData.h5");
     std::shared_ptr<BaseIO> io = std::make_unique<HDF5::HDF5IO>(filename);
     io->open();
-    Schema::ElectrodeTable electrodeTable(path, io, std::vector<int>(), "none");
+    NWB::ElectrodeTable electrodeTable(path, io, std::vector<int>(), "none");
     electrodeTable.initialize();
   }
 }