Fix #88 move io classes to their own module

NeurodataWithoutBorders · Sep 5, 2024 · 99b5d4e · 99b5d4e
1 parent 1f3ad24
commit 99b5d4e
Show file tree

Hide file tree

Showing 27 changed files with 35 additions and 35 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -19,9 +19,9 @@ include(cmake/variables.cmake)
 
 add_library(
     aqnwb_aqnwb
-    src/BaseIO.cpp
+    src/io/BaseIO.cpp
     src/Channel.cpp
-    src/hdf5/HDF5IO.cpp
+    src/io/hdf5/HDF5IO.cpp
     src/nwb/NWBFile.cpp
     src/nwb/RecordingContainers.cpp
     src/nwb/base/TimeSeries.cpp

diff --git a/src/Utils.hpp b/src/Utils.hpp
@@ -8,9 +8,9 @@
 #include <boost/uuid/uuid_generators.hpp>
 #include <boost/uuid/uuid_io.hpp>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "boost/date_time/c_local_time_adjustor.hpp"
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 
 namespace AQNWB
 {

diff --git a/src/BaseIO.cpp → src/io/BaseIO.cpp b/src/BaseIO.cpp → src/io/BaseIO.cpp
@@ -1,4 +1,4 @@
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 
 #include "Utils.hpp"
 

diff --git a/src/BaseIO.hpp → src/io/BaseIO.hpp b/src/BaseIO.hpp → src/io/BaseIO.hpp
diff --git a/src/hdf5/HDF5IO.cpp → src/io/hdf5/HDF5IO.cpp b/src/hdf5/HDF5IO.cpp → src/io/hdf5/HDF5IO.cpp
@@ -4,7 +4,7 @@
 #include <memory>
 #include <vector>
 
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 
 #include <H5Cpp.h>
 #include <H5Fpublic.h>

diff --git a/src/hdf5/HDF5IO.hpp → src/io/hdf5/HDF5IO.hpp b/src/hdf5/HDF5IO.hpp → src/io/hdf5/HDF5IO.hpp
@@ -6,7 +6,7 @@
 
 #include <H5Opublic.h>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Types.hpp"
 
 namespace H5

diff --git a/src/nwb/NWBFile.cpp b/src/nwb/NWBFile.cpp
@@ -8,7 +8,7 @@
 
 #include "nwb/NWBFile.hpp"
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Channel.hpp"
 #include "Utils.hpp"
 #include "nwb/device/Device.hpp"

diff --git a/src/nwb/NWBFile.hpp b/src/nwb/NWBFile.hpp
@@ -7,7 +7,7 @@
 #include <string_view>
 #include <vector>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Types.hpp"
 #include "nwb/RecordingContainers.hpp"
 #include "nwb/base/TimeSeries.hpp"

diff --git a/src/nwb/base/TimeSeries.hpp b/src/nwb/base/TimeSeries.hpp
@@ -2,7 +2,7 @@
 
 #include <string>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "nwb/hdmf/base/Container.hpp"
 
 namespace AQNWB::NWB

diff --git a/src/nwb/device/Device.hpp b/src/nwb/device/Device.hpp
@@ -2,7 +2,7 @@
 
 #include <string>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "nwb/hdmf/base/Container.hpp"
 
 namespace AQNWB::NWB

diff --git a/src/nwb/ecephys/ElectricalSeries.hpp b/src/nwb/ecephys/ElectricalSeries.hpp
@@ -2,7 +2,7 @@
 
 #include <string>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Channel.hpp"
 #include "nwb/base/TimeSeries.hpp"
 

diff --git a/src/nwb/file/ElectrodeGroup.hpp b/src/nwb/file/ElectrodeGroup.hpp
@@ -2,7 +2,7 @@
 
 #include <string>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "nwb/device/Device.hpp"
 #include "nwb/hdmf/base/Container.hpp"
 

diff --git a/src/nwb/file/ElectrodeTable.hpp b/src/nwb/file/ElectrodeTable.hpp
@@ -2,7 +2,7 @@
 
 #include <string>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "nwb/hdmf/table/DynamicTable.hpp"
 #include "nwb/hdmf/table/ElementIdentifiers.hpp"
 #include "nwb/hdmf/table/VectorData.hpp"

diff --git a/src/nwb/hdmf/base/Container.hpp b/src/nwb/hdmf/base/Container.hpp
@@ -3,7 +3,7 @@
 #include <memory>
 #include <string>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 
 namespace AQNWB::NWB
 {

diff --git a/src/nwb/hdmf/base/Data.hpp b/src/nwb/hdmf/base/Data.hpp
@@ -2,7 +2,7 @@
 
 #include <memory>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 
 namespace AQNWB::NWB
 {

diff --git a/src/nwb/hdmf/table/DynamicTable.hpp b/src/nwb/hdmf/table/DynamicTable.hpp
@@ -2,7 +2,7 @@
 
 #include <string>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "nwb/hdmf/base/Container.hpp"
 #include "nwb/hdmf/table/ElementIdentifiers.hpp"
 #include "nwb/hdmf/table/VectorData.hpp"

diff --git a/tests/examples/testWorkflowExamples.cpp b/tests/examples/testWorkflowExamples.cpp
@@ -1,11 +1,11 @@
 
 #include <catch2/catch_test_macros.hpp>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Channel.hpp"
 #include "Types.hpp"
 #include "Utils.hpp"
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 #include "nwb/NWBFile.hpp"
 #include "nwb/RecordingContainers.hpp"
 #include "nwb/file/ElectrodeTable.hpp"

diff --git a/tests/examples/test_HDF5IO_examples.cpp b/tests/examples/test_HDF5IO_examples.cpp
@@ -9,7 +9,7 @@
 
 #include <catch2/catch_test_macros.hpp>
 
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 #include "nwb/NWBFile.hpp"
 #include "nwb/file/ElectrodeTable.hpp"
 #include "testUtils.hpp"

diff --git a/tests/examples/test_ecephys_data_read.cpp b/tests/examples/test_ecephys_data_read.cpp
@@ -2,11 +2,11 @@
 #include <catch2/catch_test_macros.hpp>
 #include <catch2/matchers/catch_matchers_all.hpp>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Channel.hpp"
 #include "Types.hpp"
 #include "Utils.hpp"
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 #include "nwb/NWBFile.hpp"
 #include "nwb/RecordingContainers.hpp"
 #include "nwb/device/Device.hpp"

diff --git a/tests/examples/test_example.cpp b/tests/examples/test_example.cpp
@@ -1,7 +1,7 @@
 // [example_all]
 #include <catch2/catch_test_macros.hpp>
 
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 #include "testUtils.hpp"
 
 TEST_CASE("SimpleExamples", "[hdf5io]")

diff --git a/tests/testBase.cpp b/tests/testBase.cpp
@@ -1,7 +1,7 @@
 #include <catch2/catch_test_macros.hpp>
 #include <catch2/matchers/catch_matchers_all.hpp>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Types.hpp"
 #include "Utils.hpp"
 #include "nwb/base/TimeSeries.hpp"

diff --git a/tests/testEcephys.cpp b/tests/testEcephys.cpp
@@ -2,11 +2,11 @@
 #include <catch2/catch_test_macros.hpp>
 #include <catch2/matchers/catch_matchers_all.hpp>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Channel.hpp"
 #include "Types.hpp"
 #include "Utils.hpp"
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 #include "nwb/device/Device.hpp"
 #include "nwb/ecephys/ElectricalSeries.hpp"
 #include "nwb/file/ElectrodeGroup.hpp"

diff --git a/tests/testFile.cpp b/tests/testFile.cpp
@@ -1,9 +1,9 @@
 #include <catch2/catch_test_macros.hpp>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Channel.hpp"
 #include "Types.hpp"
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 #include "nwb/file/ElectrodeTable.hpp"
 #include "testUtils.hpp"
 

diff --git a/tests/testHDF5IO.cpp b/tests/testHDF5IO.cpp
@@ -8,10 +8,10 @@
 
 #include <catch2/catch_test_macros.hpp>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Channel.hpp"
 #include "Types.hpp"
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 #include "nwb/NWBFile.hpp"
 #include "nwb/file/ElectrodeTable.hpp"
 #include "testUtils.hpp"

diff --git a/tests/testNWBFile.cpp b/tests/testNWBFile.cpp
@@ -1,8 +1,8 @@
 #include <catch2/catch_test_macros.hpp>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Utils.hpp"
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 #include "nwb/NWBFile.hpp"
 #include "nwb/RecordingContainers.hpp"
 #include "nwb/base/TimeSeries.hpp"

diff --git a/tests/testRecordingWorkflow.cpp b/tests/testRecordingWorkflow.cpp
@@ -3,11 +3,11 @@
 #include <catch2/catch_test_macros.hpp>
 #include <catch2/matchers/catch_matchers_all.hpp>
 
-#include "BaseIO.hpp"
+#include "io/BaseIO.hpp"
 #include "Channel.hpp"
 #include "Types.hpp"
 #include "Utils.hpp"
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 #include "nwb/NWBFile.hpp"
 #include "nwb/RecordingContainers.hpp"
 #include "nwb/file/ElectrodeTable.hpp"

diff --git a/tests/testUtils.hpp b/tests/testUtils.hpp
@@ -9,7 +9,7 @@
 
 #include "Channel.hpp"
 #include "Types.hpp"
-#include "hdf5/HDF5IO.hpp"
+#include "io/hdf5/HDF5IO.hpp"
 
 using namespace AQNWB;
 namespace fs = std::filesystem;