Add data read

.github/workflows/codespell.yml

@@ -6,8 +6,8 @@ on:
     - main
 
   pull_request:
-    branches:
-    - main
+    #branches:
+    #- main
   workflow_dispatch:
 
 jobs:

.github/workflows/doxygen-build.yml

@@ -2,8 +2,8 @@ name: Doxygen build test
 
 on:
   pull_request:
-    branches:
-    - main
+    #branches:
+    #- main
 
 jobs:
   test:
@@ -17,7 +17,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: "true"
-      
+
       - name: Install dependencies - macos
         run: brew install hdf5 boost catch2 doxygen graphviz
 

.github/workflows/lint.yml

@@ -6,8 +6,8 @@ on:
     - main
 
   pull_request:
-    branches:
-    - main
+    #branches:
+    #- main
   workflow_dispatch:
 
 jobs:

.github/workflows/tests.yml

@@ -6,8 +6,8 @@ on:
     - main
 
   pull_request:
-    branches:
-    - main
+    #branches:
+    #- main
   workflow_dispatch:
 
 jobs:
@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest, ubuntu-latest]
-    
+
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -39,7 +39,7 @@ jobs:
         git checkout "v3.5.3"
         cmake -Bbuild -H. -DBUILD_TESTING=OFF
         sudo cmake --build build/ --target install
-    
+
     - name: Install dependencies - macos
       if: matrix.os == 'macos-latest'
       run: brew install hdf5 boost catch2
@@ -67,7 +67,7 @@ jobs:
 
   sanitize:
     needs: test
-    
+
     runs-on: ubuntu-latest
 
     steps:

CMakeLists.txt

@@ -19,9 +19,10 @@ 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/io/hdf5/HDF5RecordingData.cpp
     src/nwb/NWBFile.cpp
     src/nwb/RecordingContainers.cpp
     src/nwb/base/TimeSeries.cpp

docs/Doxyfile.in

@@ -14,6 +14,10 @@ EXTRACT_ALL = YES
 RECURSIVE = YES
 OUTPUT_DIRECTORY = "@DOXYGEN_OUTPUT_DIRECTORY@"
 
+# Also show private members in the docs,
+EXTRACT_PRIVATE = YES
+# HIDE_UNDOC_MEMBERS = YES
+
 # Enable Markdown support
 MARKDOWN_SUPPORT = YES
 

docs/pages/1_userdocs.dox

@@ -7,4 +7,5 @@
  * - \subpage user_install_page
  * - \subpage workflow
  * - \subpage hdf5io
+ * - \subpage read_page
  */

docs/pages/devdocs/documentation.dox

@@ -69,7 +69,7 @@
  *
  *  To display a code snippet from our example in the documentation we can use the
  *  ``\snippet <file> <label>`` Doxygen command in our ``*.dox`` documentation file.
- *  For example to just show the line where we create the \ref AQNWB::HDF5::HDF5IO "HDF5IO
+ *  For example to just show the line where we create the \ref AQNWB::IO::HDF5::HDF5IO "HDF5IO"
  *  object we use:
  *
  * \code{.sh}

docs/pages/userdocs/hdf5io.dox

@@ -96,7 +96,7 @@
  *
  * \section hdf5io_swmr Single-Writer Multiple-Reader (SWMR) Mode
  *
- * The \ref AQNWB::HDF5::HDF5IO "HDF5IO" I/O backend uses by default SWMR mode while recording data.
+ * The \ref AQNWB::IO::HDF5::HDF5IO "HDF5IO" I/O backend uses by default SWMR mode while recording data.
  * Using SWMR, one process can write to the HDF5 file and multiple other processes can read
  * from the file concurrently while ensuring that the readers see a consistent view of the data.
  *
@@ -106,7 +106,7 @@
  *     node [shape=box, style=filled];
  *
  *     // Define the writer node with light blue fill color
- *     writer [label="AqNWB HDF5IO\n(SWMR Write)", fillcolor=lightblue, URL="\ref AQNWB::HDF5::HDF5IO"];
+ *     writer [label="AqNWB HDF5IO\n(SWMR Write)", fillcolor=lightblue, URL="\ref AQNWB::IO::HDF5::HDF5IO"];
  *     // Define the HDF5 file node with a distinct shape
  *     hdf5_file [label="\n.nwb\n(HDF5 File)\n ", shape=folder, fillcolor=lightgray, URL="\ref AQNWB::NWB::NWBFile"];
  *     // Define reader nodes with light green fill color
@@ -148,11 +148,11 @@
  * \note
  * While SWMR mode ensures data integrity, some data loss may still occur if the application crashes.
  * Only data that has been completely written and flushed to disk will be readable. To manually
- * flush data to disk use \ref AQNWB::HDF5::HDF5IO::flush  "HDF5IO::flush".
+ * flush data to disk use \ref AQNWB::IO::HDF5::HDF5IO::flush  "HDF5IO::flush".
  *
  * \subsection  hdf5io_swmr_workflow Writing an NWB file with SWMR mode
  *
- * SWMR mode is enabled when calling \ref AQNWB::HDF5::HDF5IO::startRecording "HDF5IO::startRecording".
+ * SWMR mode is enabled when calling \ref AQNWB::IO::HDF5::HDF5IO::startRecording "HDF5IO::startRecording".
  * Once SWMR mode is enabled, no new data objects (Datasets, Groups, Attributes etc.)
  * can be created, but we can only add and set values to existing data objects. Since other
  * processes may read from the HDF5 file, it is not possible to intermittently disable
@@ -168,7 +168,7 @@
  * This workflow is applicable to a wide range of data acquisition use-cases. However,
  * for use cases that require creation of new Groups and Datasets during acquisition,
  * you can disable the use of SWMR mode by setting `disableSWMRMode=true` when
- * constructing the \ref AQNWB::HDF5::HDF5IO object.
+ * constructing the \ref AQNWB::IO::HDF5::HDF5IO object.
  *
  * \warning
  * While disabling SWMR mode allows Groups and Datasets to be created during and after