fix formatting

NeurodataWithoutBorders · Sep 10, 2024 · cd2d098 · cd2d098
1 parent 3d32106
commit cd2d098
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Showing 6 changed files with 40 additions and 35 deletions.
diff --git a/src/BaseIO.hpp b/src/BaseIO.hpp
@@ -293,7 +293,8 @@ class BaseIO
       const std::string& path) = 0;
 
   /**
-   * @brief Checks whether a Dataset, Group, or Link already exists at the location in the file.
+   * @brief Checks whether a Dataset, Group, or Link already exists at the
+   * location in the file.
    * @param path The location of the object in the file.
    * @return Whether the object exists.
    */

diff --git a/src/hdf5/HDF5IO.hpp b/src/hdf5/HDF5IO.hpp
@@ -235,7 +235,8 @@ class HDF5IO : public BaseIO
       const std::string& path) override;
 
   /**
-   * @brief Checks whether a Dataset, Group, or Link already exists at the location in the file.
+   * @brief Checks whether a Dataset, Group, or Link already exists at the
+   * location in the file.
    * @param path The location of the object in the file.
    * @return Whether the object exists.
    */

diff --git a/src/nwb/NWBFile.cpp b/src/nwb/NWBFile.cpp
@@ -127,13 +127,14 @@ Status NWBFile::createElectricalSeries(
     std::string electrodePath = "/general/extracellular_ephys/" + sourceName;
     std::string electricalSeriesPath = acquisitionPath + "/" + groupName;
 
-    // Check if device exists for groupName, create device and electrode group if not
-    if (!io->objectExists(devicePath)){
+    // Check if device exists for groupName, create device and electrode group
+    // if not
+    if (!io->objectExists(devicePath)) {
       Device device = Device(devicePath, io, "description", "unknown");
       device.initialize();
 
       ElectrodeGroup elecGroup =
-        ElectrodeGroup(electrodePath, io, "description", "unknown", device);
+          ElectrodeGroup(electrodePath, io, "description", "unknown", device);
       elecGroup.initialize();
     }
 
@@ -192,13 +193,14 @@ Status NWBFile::createSpikeEventSeries(
     std::string electrodePath = "/general/extracellular_ephys/" + sourceName;
     std::string spikeEventSeriesPath = acquisitionPath + "/" + groupName;
 
-    // Check if device exists for groupName, create device and electrode group if not
-    if (!io->objectExists(devicePath)){
+    // Check if device exists for groupName, create device and electrode group
+    // if not
+    if (!io->objectExists(devicePath)) {
       Device device = Device(devicePath, io, "description", "unknown");
       device.initialize();
 
       ElectrodeGroup elecGroup =
-        ElectrodeGroup(electrodePath, io, "description", "unknown", device);
+          ElectrodeGroup(electrodePath, io, "description", "unknown", device);
       elecGroup.initialize();
     }
 

diff --git a/tests/testEcephys.cpp b/tests/testEcephys.cpp
@@ -172,9 +172,9 @@ TEST_CASE("SpikeEventSeries", "[ecephys]")
     // setup mock data
     SizeType numChannels = 4;
     std::vector<Types::ChannelVector> mockArrays =
-      getMockChannelArrays(numChannels);
+        getMockChannelArrays(numChannels);
     std::vector<std::vector<float>> mockData =
-      getMockData2D(numSamples * numChannels, numEvents); 
+        getMockData2D(numSamples * numChannels, numEvents);
 
     // setup io object
     std::string path = getTestFilePath("SpikeEventSeries3D.h5");
@@ -188,14 +188,14 @@ TEST_CASE("SpikeEventSeries", "[ecephys]")
     elecTable.initialize();
 
     // setup electrical series
-    NWB::SpikeEventSeries ses = NWB::SpikeEventSeries(
-        dataPath,
-        io,
-        dataType,
-        mockArrays[0],
-        "no description",
-        SizeArray {0, numChannels, numSamples},
-        SizeArray {8, 1, 1});
+    NWB::SpikeEventSeries ses =
+        NWB::SpikeEventSeries(dataPath,
+                              io,
+                              dataType,
+                              mockArrays[0],
+                              "no description",
+                              SizeArray {0, numChannels, numSamples},
+                              SizeArray {8, 1, 1});
     ses.initialize();
 
     // write channel data
@@ -230,13 +230,12 @@ TEST_CASE("SpikeEventSeries", "[ecephys]")
     REQUIRE_THAT(dataOut[1], Catch::Matchers::Approx(mockData[1]).margin(1));
   }
 
-SECTION("test writing events - events x samples")
+  SECTION("test writing events - events x samples")
   {
     // setup mock data
-    std::vector<Types::ChannelVector> mockArrays =
-      getMockChannelArrays(1);
+    std::vector<Types::ChannelVector> mockArrays = getMockChannelArrays(1);
     std::vector<std::vector<float>> mockData =
-      getMockData2D(numSamples, numEvents); 
+        getMockData2D(numSamples, numEvents);
 
     // setup io object
     std::string path = getTestFilePath("SpikeEventSeries2D.h5");
@@ -250,14 +249,13 @@ SECTION("test writing events - events x samples")
     elecTable.initialize();
 
     // setup electrical series
-    NWB::SpikeEventSeries ses = NWB::SpikeEventSeries(
-        dataPath,
-        io,
-        dataType,
-        mockArrays[0],
-        "no description",
-        SizeArray {0, numSamples},
-        SizeArray {8, 1});
+    NWB::SpikeEventSeries ses = NWB::SpikeEventSeries(dataPath,
+                                                      io,
+                                                      dataType,
+                                                      mockArrays[0],
+                                                      "no description",
+                                                      SizeArray {0, numSamples},
+                                                      SizeArray {8, 1});
     ses.initialize();
 
     // write channel data
@@ -272,8 +270,8 @@ SECTION("test writing events - events x samples")
         std::make_unique<H5::H5File>(path, H5F_ACC_RDONLY);
     std::unique_ptr<H5::DataSet> dataset =
         std::make_unique<H5::DataSet>(file->openDataSet(dataPath + "/data"));
-    std::vector<std::vector<float>> dataOut(
-        numEvents, std::vector<float>(numSamples));
+    std::vector<std::vector<float>> dataOut(numEvents,
+                                            std::vector<float>(numSamples));
     float* buffer = new float[numEvents * numSamples];
 
     H5::DataSpace fSpace = dataset->getSpace();

diff --git a/tests/testNWBFile.cpp b/tests/testNWBFile.cpp
@@ -75,12 +75,13 @@ TEST_CASE("createMultipleEcephysDatasets", "[nwb]")
   std::unique_ptr<NWB::RecordingContainers> recordingContainers =
       std::make_unique<NWB::RecordingContainers>();
   Status resultCreateES = nwbfile.createElectricalSeries(
-      mockArrays, BaseDataType::F32, recordingContainers.get());   
+      mockArrays, BaseDataType::F32, recordingContainers.get());
   REQUIRE(resultCreateES == Status::Success);
 
   // create SpikeEventSeries
   SizeType numSamples = 5;
-  std::vector<Types::ChannelVector> mockSpikeArrays = getMockChannelArrays(1, 2, "spikedata");
+  std::vector<Types::ChannelVector> mockSpikeArrays =
+      getMockChannelArrays(1, 2, "spikedata");
   Status resultCreateSES = nwbfile.createSpikeEventSeries(
       mockSpikeArrays, BaseDataType::F32, recordingContainers.get());
 

diff --git a/tests/testUtils.hpp b/tests/testUtils.hpp
@@ -33,7 +33,9 @@ inline std::string getTestFilePath(std::string filename)
 }
 
 inline std::vector<Types::ChannelVector> getMockChannelArrays(
-    SizeType numChannels = 2, SizeType numArrays = 2, std::string groupName = "esdata")
+    SizeType numChannels = 2,
+    SizeType numArrays = 2,
+    std::string groupName = "esdata")
 {
   std::vector<Types::ChannelVector> arrays(numArrays);
   for (SizeType i = 0; i < numArrays; i++) {