fix formatting

src/BaseIO.cpp

@@ -32,7 +32,7 @@ const BaseDataType BaseDataType::DSTR = BaseDataType(T_STR, DEFAULT_STR_SIZE);
 // BaseIO
 
 BaseIO::BaseIO()
-    : readyToOpen(true) 
+    : readyToOpen(true)
     , opened(false)
 {
 }
@@ -78,7 +78,10 @@ Status BaseIO::createDataAttributes(const std::string& path,
 Status BaseIO::createTimestampsAttributes(const std::string& path)
 {
   int interval = 1;
-  createAttribute(BaseDataType::I32, static_cast<const void*>(&interval), path + "/timestamps", "interval");
+  createAttribute(BaseDataType::I32,
+                  static_cast<const void*>(&interval),
+                  path + "/timestamps",
+                  "interval");
   createAttribute("seconds", path + "/timestamps", "unit");
 
   return Status::Success;

src/Channel.hpp

@@ -19,7 +19,8 @@ class Channel
           int globalIndex,
           float conversion = 1e6f,  // uV to V
           float samplingRate = 30000.f,
-          float bitVolts = 0.000002f,  // least significant bit needed to convert 16-bit int to volts
+          float bitVolts = 0.000002f,  // least significant bit needed to
+                                       // convert 16-bit int to volts
           std::vector<float> position = {0.f, 0.f, 0.f})
       : name(name)
       , groupName(groupName)

src/Utils.hpp

@@ -7,9 +7,9 @@
 #include <boost/uuid/uuid.hpp>
 #include <boost/uuid/uuid_generators.hpp>
 #include <boost/uuid/uuid_io.hpp>
-#include "boost/date_time/c_local_time_adjustor.hpp"
 
 #include "BaseIO.hpp"
+#include "boost/date_time/c_local_time_adjustor.hpp"
 #include "hdf5/HDF5IO.hpp"
 
 namespace AQNWB
@@ -58,11 +58,13 @@ inline std::string getCurrentTime()
  * @brief Factory method to create an IO object.
  * @return A pointer to a BaseIO object
  */
-inline std::unique_ptr<BaseIO> createIO(const std::string& type, const std::string& filename) {
-    if (type == "HDF5") {
-        return std::make_unique<HDF5::HDF5IO>(filename);
-    } else {
-        throw std::invalid_argument("Invalid IO type");
-    }
+inline std::unique_ptr<BaseIO> createIO(const std::string& type,
+                                        const std::string& filename)
+{
+  if (type == "HDF5") {
+    return std::make_unique<HDF5::HDF5IO>(filename);
+  } else {
+    throw std::invalid_argument("Invalid IO type");
+  }
 }
 }  // namespace AQNWB

src/hdf5/HDF5IO.cpp

@@ -685,4 +685,4 @@ Status HDF5RecordingData::writeDataRow(const SizeType& xDataSize,
   }
 
   return Status::Success;
-};
+}

src/nwb/NWBFile.cpp

@@ -178,7 +178,8 @@ Status NWBFile::startRecording(std::vector<Types::ChannelGroup> recordingArrays)
 
     timeseriesData.push_back(std::move(electricalSeries));
 
-    // Add electrode information to electrode table (does not write to datasets yet)
+    // Add electrode information to electrode table (does not write to datasets
+    // yet)
     elecTable.addElectrodes(channelGroup);
   }
 
@@ -191,9 +192,9 @@ Status NWBFile::startRecording(std::vector<Types::ChannelGroup> recordingArrays)
 void NWBFile::stopRecording() {}
 
 Status NWBFile::writeTimeseriesTimestamps(int datasetInd,
-                                    int numSamples,
-                                    BaseDataType type,
-                                    const void* data)
+                                          int numSamples,
+                                          BaseDataType type,
+                                          const void* data)
 {
   if (!timeseriesData[datasetInd])
     return Status::Failure;

src/nwb/NWBFile.hpp

@@ -55,9 +55,7 @@ class NWBFile
    * @brief Starts a recording.
    * @return Status The status of the recording operation.
    */
-  Status startRecording(
-      std::vector<Types::ChannelGroup>
-          recordingArrays);
+  Status startRecording(std::vector<Types::ChannelGroup> recordingArrays);
 
   /**
    * @brief Closes the relevant datasets.
@@ -72,9 +70,9 @@ class NWBFile
    * @param data The data to write.
    */
   Status writeTimeseriesTimestamps(int datasetInd,
-                             int numSamples,
-                             BaseDataType type,
-                             const void* data);
+                                   int numSamples,
+                                   BaseDataType type,
+                                   const void* data);
 
   /**
    * @brief Write a row of timeseries data to the NWB file.

src/nwb/NWBRecording.cpp

@@ -32,14 +32,12 @@ Status NWBRecording::openFiles(const std::string& rootFolder,
       rootFolder + baseName + std::to_string(experimentNumber) + ".nwb";
 
   // initialize nwbfile object and create base structure
-  nwbfile = std::make_unique<NWB::NWBFile>(
-      generateUuid(),
-      createIO(IOType, filename));
+  nwbfile = std::make_unique<NWB::NWBFile>(generateUuid(),
+                                           createIO(IOType, filename));
   nwbfile->initialize();
 
   // start the new recording
-  return nwbfile->startRecording(
-      recordingArrays);
+  return nwbfile->startRecording(recordingArrays);
 }
 
 void NWBRecording::closeFiles()
@@ -62,12 +60,12 @@ void NWBRecording::writeTimeseriesData(int timeseriesInd,
                  [multFactor](float value) { return value * multFactor; });
 
   // convert float to int16
-  std::transform(scaledBuffer.get(),
-                 scaledBuffer.get() + numSamples,
-                 intBuffer.get(),
-                 [](float value) {
-                   return static_cast<int16_t>(std::clamp(value, -32768.0f, 32767.0f));
-                 });
+  std::transform(
+      scaledBuffer.get(),
+      scaledBuffer.get() + numSamples,
+      intBuffer.get(),
+      [](float value)
+      { return static_cast<int16_t>(std::clamp(value, -32768.0f, 32767.0f)); });
 
   // write intBuffer data to dataset
   nwbfile->writeTimeseriesData(timeseriesInd,
@@ -79,4 +77,4 @@ void NWBRecording::writeTimeseriesData(int timeseriesInd,
     nwbfile->writeTimeseriesTimestamps(
         timeseriesInd, numSamples, BaseDataType::F64, timestampBuffer);
   }
-}
+}

src/nwb/file/ElectrodeTable.cpp

@@ -30,7 +30,7 @@ void ElectrodeTable::addElectrodes(std::vector<Channel> channels)
     groupNames.push_back(ch.groupName);
     electrodeNumbers.push_back(ch.globalIndex);
     locationNames.push_back("unknown");
-  } 
+  }
 }
 
 void ElectrodeTable::finalize()

src/nwb/hdmf/table/DynamicTable.cpp

@@ -79,4 +79,4 @@ std::string DynamicTable::getDescription() const
 const std::vector<std::string>& DynamicTable::getColNames()
 {
   return colNames;
-}
+}

src/nwb/hdmf/table/DynamicTableRegion.hpp

@@ -10,8 +10,7 @@ namespace AQNWB::NWB
 /**
  * @brief An n-dimensional dataset representing a column of a DynamicTable.
  */
-class DynamicTableRegion
-    : public VectorData
+class DynamicTableRegion : public VectorData
 {
 public:
   /**

tests/testHDF5IO.cpp

@@ -27,25 +27,25 @@ TEST_CASE("writeGroup", "[hdf5io]")
     hdf5io.close();
   }
 
-  SECTION("try initializing group that already exists") 
+  SECTION("try initializing group that already exists")
   {
     // TODO
   }
 
-  SECTION("try initializing group without parent group") 
+  SECTION("try initializing group without parent group")
   {
     // TODO
   }
 }
 
 TEST_CASE("writeDataset", "[hdf5io]")
 {
-  SECTION("create dataset and write data row") 
+  SECTION("create dataset and write data row")
   {
     // TODO
   }
 
-  SECTION("create dataset and write data block") 
+  SECTION("create dataset and write data block")
   {
     // TODO
   }

tests/testNWBFile.cpp

@@ -36,9 +36,11 @@ TEST_CASE("startRecording", "[nwb]")
   std::vector<float> mockData = {1.0, 2.0, 3.0, 4.0, 5.0};
   std::vector<float> mockTimestamps = {0.1, 0.2, 0.3, 0.4, 0.5};
   nwbfile.writeTimeseriesData(0, 0, 5, BaseDataType::F32, mockData.data());
-  nwbfile.writeTimeseriesTimestamps(0, 5, BaseDataType::F32, mockTimestamps.data());
+  nwbfile.writeTimeseriesTimestamps(
+      0, 5, BaseDataType::F32, mockTimestamps.data());
   nwbfile.writeTimeseriesData(1, 0, 5, BaseDataType::F32, mockData.data());
-  nwbfile.writeTimeseriesTimestamps(1, 5, BaseDataType::F32, mockTimestamps.data());
+  nwbfile.writeTimeseriesTimestamps(
+      1, 5, BaseDataType::F32, mockTimestamps.data());
 
   nwbfile.finalize();
 

tests/testNWBRecording.cpp

@@ -48,7 +48,8 @@ TEST_CASE("writeContinuousData", "[recording]")
         for (const auto& channel : channelGroup) {
           // copy data into buffer
           std::copy(mockData[channel.globalIndex].begin() + samplesRecorded,
-                    mockData[channel.globalIndex].begin() + samplesRecorded + numSamples / 10,
+                    mockData[channel.globalIndex].begin() + samplesRecorded
+                        + numSamples / 10,
                     dataBuffer.begin());
           std::copy(mockTimestamps.begin() + samplesRecorded,
                     mockTimestamps.begin() + samplesRecorded + numSamples / 10,
@@ -60,7 +61,6 @@ TEST_CASE("writeContinuousData", "[recording]")
                                            dataBuffer.data(),
                                            timestampsBuffer.data(),
                                            dataBuffer.size());
-
         }
       }
       // check if recording is done
@@ -71,18 +71,18 @@ TEST_CASE("writeContinuousData", "[recording]")
     }
   }
 
-  SECTION("check contents of data and timestamps", "[recording]") 
+  SECTION("check contents of data and timestamps", "[recording]")
   {
-    // TODO 
+    // TODO
   }
 
-  SECTION("test if more samples than buffer size", "[recording]") 
+  SECTION("test if more samples than buffer size", "[recording]")
   {
-    // TODO 
+    // TODO
   }
 
-  SECTION("add a new recording number to the same file", "[recording]") 
+  SECTION("add a new recording number to the same file", "[recording]")
   {
-    // TODO 
+    // TODO
   }
-}
+}

tests/testUtils.hpp

@@ -36,9 +36,8 @@ inline std::vector<Types::ChannelGroup> getMockChannelArrays()
   Channel ch1 = Channel("ch1", "array1", 1, 1);
   Channel ch2 = Channel("ch2", "array2", 0, 2);
   Channel ch3 = Channel("ch3", "array2", 1, 3);
-  std::vector<Types::ChannelGroup> arrays = {
-      Types::ChannelGroup {ch0, ch1},
-      Types::ChannelGroup {ch2, ch3}};  
+  std::vector<Types::ChannelGroup> arrays = {Types::ChannelGroup {ch0, ch1},
+                                             Types::ChannelGroup {ch2, ch3}};
   return arrays;
 }
 
@@ -50,7 +49,7 @@ inline std::vector<std::vector<float>> getMockData(int numChannels = 4,
 
   std::random_device rd;
   std::mt19937 rng(rd());  // random number generator
-  std::uniform_real_distribution<> dis(-1.0, 1.0);  //range of floats
+  std::uniform_real_distribution<> dis(-1.0, 1.0);  // range of floats
 
   for (auto& channelData : mockData) {
     for (auto& data : channelData) {
@@ -73,4 +72,4 @@ inline std::vector<double> getMockTimestamps(int numSamples = 1000,
   }
 
   return mockTimestamps;
-}
+}