Consolidate IO module under src/hydro/io and include/hydroc/io

Moves all HDF5 and simulation export code into a dedicated IO module:

- Added new public headers: include/hydroc/io/{h5_reader,h5_writer,simulation_export}.h
- Moved implementations to src/hydro/io/
- Updated all includes and CMake entries
- Removed obsolete top-level redirect headers (h5fileinfo.h, h5_writer.h, simulation_exporter.h)

Public API and behaviour unchanged. Repository IO structure is now clean, consistent, and easier to navigate.

Author: dav-og

CMakeLists.txt

@@ -335,15 +335,19 @@ endfunction()
 
 # ── Main HydroChrono Library ──
 set(HYDROCHRONO_SOURCES
-    src/h5fileinfo.cpp
+    # IO module (consolidated under src/hydro/io/)
+    src/hydro/io/h5_reader.cpp
+    src/hydro/io/h5_writer.cpp
+    src/hydro/io/simulation_export.cpp
+    src/hydro/io/hydro_config_loader.cpp
+    # Core library sources
     src/chloadaddedmass.cpp
     src/hydro_forces.cpp
     src/helper.cpp
     src/wave_types.cpp
-    # src/simulation_logging.cpp  # removed in streamlined logging
     src/hydro_yaml_parser.cpp
     src/setup_hydro_from_yaml.cpp
-    src/hydro/io/hydro_config_loader.cpp
+    # Hydro modules
     src/hydro/waves/wave_base.cpp
     src/hydro/waves/wave_utilities.cpp
     src/hydro/waves/regular_wave.cpp
@@ -359,8 +363,6 @@ set(HYDROCHRONO_SOURCES
     # logging consolidated: coordinator + CLI (logging.cpp), backend (logger_backend.cpp)
     src/utils/logger_backend.cpp
     src/utils/logging.cpp
-    src/h5_writer.cpp
-    src/simulation_exporter.cpp
 )
 
 # Create the library target and configure it

include/hydroc/chloadaddedmass.h

@@ -9,7 +9,7 @@
 
 #include <chrono/core/ChMatrix.h>
 #include <chrono/physics/ChBody.h>
-#include <hydroc/h5fileinfo.h>
+#include <hydroc/io/h5_reader.h>
 #include <vector>
 
 #include <chrono/physics/ChLoad.h>

include/hydroc/hydro_forces.h

@@ -76,7 +76,7 @@
 #include <chrono/fea/ChMeshFileLoader.h>
 
 // Hydroc library includes
-#include <hydroc/h5fileinfo.h>
+#include <hydroc/io/h5_reader.h>
 #include <hydroc/wave_types.h>
 // Note: hydro_types.h is included at the top to avoid header guard conflicts
 

include/hydroc/h5fileinfo.h include/hydroc/io/h5_reader.hinclude/hydroc/h5fileinfo.h renamed to include/hydroc/io/h5_reader.h

@@ -1,13 +1,14 @@
-#ifndef H5FILEINFO_H
-#define H5FILEINFO_H
 /*********************************************************************
- * @file  h5fileinfo.h
+ * @file  h5_reader.h
  *
- * @brief header file of HydroData main class and helper class \
- * H5FileInfo.
+ * @brief HDF5 reader for hydrodynamic data (HydroData and H5FileInfo).
+ *
+ * This header provides the public API for reading BEMIO-formatted HDF5
+ * hydrodynamic data files. HydroData holds the parsed coefficients and
+ * H5FileInfo handles file loading.
  *********************************************************************/
-// TODO: clean up include statements
-#pragma once
+#ifndef HYDROC_IO_H5_READER_H
+#define HYDROC_IO_H5_READER_H
 
 #include <limits>
 #include <optional>
@@ -29,9 +30,7 @@ class H5File;
 
 class H5FileInfo;
 
-// TODO separate these 2 classes into 2 files? (and corresponding .cpp)
-
-// contains "chunked" data from the h5 file, generated from H5FileInfor class
+// contains "chunked" data from the h5 file, generated from H5FileInfo class
 class HydroData {
   public:
     struct BodyInfo {
@@ -45,7 +44,6 @@ class HydroData {
         Eigen::MatrixXd lin_matrix;
         Eigen::MatrixXd inf_added_mass;
         Eigen::Tensor<double, 3> rirf_matrix;
-        // Eigen::Tensor<double, 3> radiation_damping_matrix;
     };
     struct SimulationParameters {
         std::string h5_file_name;
@@ -59,15 +57,11 @@ class HydroData {
         Eigen::Tensor<double, 3> excitation_phase_matrix;
     };
     struct IrregularWaveInfo {
-        // Eigen::Tensor<double,3> excitation_re_matrix;
-        // Eigen::Vector3i re_dims;
-        // Eigen::Tensor<double, 3> excitation_im_matrix;
-        // Eigen::Vector3i im_dims;
         Eigen::VectorXd excitation_irf_time;
-        Eigen::MatrixXd excitation_irf_matrix;  // TODO needs to be tensor?
+        Eigen::MatrixXd excitation_irf_matrix;
 
         // see std::optional documentation for how to use
-        std::optional<Eigen::MatrixXd> excitation_irf_resampled;  // TODO needs to be tensor?
+        std::optional<Eigen::MatrixXd> excitation_irf_resampled;
         std::optional<Eigen::MatrixXd> excitation_irf_time_resampled;
     };
 
@@ -160,8 +154,8 @@ class HydroData {
      */
     Eigen::VectorXd GetCBVector(int b) const { return body_data_[b].cb; }
 
-    double GetExcitationIRFVal(int b, int dof, int s) const;  // TODO if this isn't used get rid of it
-    Eigen::MatrixXd GetExcitationIRF(int b) const;            // TODO if this isn't used get rid of it
+    double GetExcitationIRFVal(int b, int dof, int s) const;
+    Eigen::MatrixXd GetExcitationIRF(int b) const;
 
     // things that are the same no matter the body, don't need body argument
     /**
@@ -225,11 +219,14 @@ class HydroData {
     std::vector<IrregularWaveInfo>& GetIrregularWaveInfos() { return irreg_wave_data_; }
 };
 
-// TODO change name to LoadH5File or ReadH5File or H5Init or something similar to give better description of
-// functionality used only to initialize everything in HydroData from the h5 file
+/**
+ * @brief HDF5 file reader for hydrodynamic data.
+ *
+ * Reads BEMIO-formatted HDF5 files and produces a HydroData object.
+ */
 class H5FileInfo {
   public:
-    bool printed = false;  // TODO remove this, dont use here
+    bool printed = false;
 
     /**
      * @brief prepares for h5 file reading, checks file exists.
@@ -257,7 +254,7 @@ class H5FileInfo {
      *
      * @return newly initialized HydroData object
      */
-    HydroData ReadH5Data();  // TODO: eventually pass user input struct here? instead of making it in function?
+    HydroData ReadH5Data();
 
   private:
     std::string h5_file_name_;
@@ -299,7 +296,7 @@ class H5FileInfo {
      * @param[in] data_name data name within file to extract value from
      * @param[out] var variable to be set from h5 info
      */
-    void Init3D(H5::H5File& file, std::string data_name, Eigen::Tensor<double, 3>& var /*, std::vector<int>& dims*/);
+    void Init3D(H5::H5File& file, std::string data_name, Eigen::Tensor<double, 3>& var);
 
     /**
      * @brief helper function for readH5Data() to remove the middle index of 3D data if that index is 1.
@@ -314,4 +311,4 @@ class H5FileInfo {
     Eigen::MatrixXd SqueezeMid(Eigen::Tensor<double, 3>& to_be_squeezed);
 };
 
-#endif
+#endif  // HYDROC_IO_H5_READER_H

include/hydroc/h5_writer.h include/hydroc/io/h5_writer.hinclude/hydroc/h5_writer.h renamed to include/hydroc/io/h5_writer.h

@@ -1,8 +1,5 @@
-#ifndef HYDROC_H5_WRITER_H
-#define HYDROC_H5_WRITER_H
-
-/**
- * @file h5_writer.h
+/*********************************************************************
+ * @file  h5_writer.h
  * @brief Lightweight RAII writer over the HDF5 C++ API (H5Cpp.h).
  *
  * Provides a compact, easy-to-use interface to write groups, attributes, and
@@ -13,7 +10,9 @@
  * @note Types: strings are written as variable-length UTF-8; numeric datasets use native double.
  * @note Errors: global HDF5 error printing is disabled; failures surface as HDF5 exceptions or std::runtime_error on open.
  * @note Thread-safety: not thread-safe; synchronize externally if shared across threads.
- */
+ *********************************************************************/
+#ifndef HYDROC_IO_H5_WRITER_H
+#define HYDROC_IO_H5_WRITER_H
 
 #include <H5Cpp.h>
 #include <string>
@@ -148,4 +147,5 @@ class H5Writer {
 
 } // namespace hydroc
 
-#endif // HYDROC_H5_WRITER_H
+#endif // HYDROC_IO_H5_WRITER_H
+

include/hydroc/simulation_exporter.h include/hydroc/io/simulation_export.hinclude/hydroc/simulation_exporter.h renamed to include/hydroc/io/simulation_export.h

@@ -1,5 +1,5 @@
 /**
- * @file simulation_exporter.h
+ * @file simulation_export.h
  * @brief Public interface for exporting HydroChrono simulations to HDF5.
  *
  * Provides a thin, high-level API to record inputs, model description, and
@@ -10,8 +10,8 @@
  * @note Encoding & units: strings are UTF-8; time in seconds, distances in meters,
  *       angles in radians unless documented otherwise in attribute names.
  */
-#ifndef HYDROC_SIMULATION_EXPORTER_H
-#define HYDROC_SIMULATION_EXPORTER_H
+#ifndef HYDROC_IO_SIMULATION_EXPORT_H
+#define HYDROC_IO_SIMULATION_EXPORT_H
 
 #include <memory>
 #include <vector>
@@ -169,6 +169,5 @@ class SimulationExporter {
 
 } // namespace hydroc
 
-#endif // HYDROC_SIMULATION_EXPORTER_H
-
+#endif // HYDROC_IO_SIMULATION_EXPORT_H
 

src/hydro/force_components/hydrostatics_component.cpp

@@ -4,7 +4,7 @@
  *********************************************************************/
 
 #include "hydrostatics_component.h"
-#include <hydroc/h5fileinfo.h>
+#include <hydroc/io/h5_reader.h>
 
 #include <Eigen/Dense>
 #include <cassert>

src/hydro/force_components/radiation_component.cpp

@@ -4,7 +4,7 @@
  *********************************************************************/
 
 #include "radiation_component.h"
-#include <hydroc/h5fileinfo.h>
+#include <hydroc/io/h5_reader.h>
 
 #include <Eigen/Dense>
 #include <cassert>

src/h5fileinfo.cpp src/hydro/io/h5_reader.cppsrc/h5fileinfo.cpp renamed to src/hydro/io/h5_reader.cpp

@@ -6,7 +6,7 @@
  *********************************************************************/
 // TODO: this include statement list looks good
 #include <H5Cpp.h>
-#include <hydroc/h5fileinfo.h>
+#include <hydroc/io/h5_reader.h>
 #include <filesystem>  // std::filesystem::absolute
 #include <hydroc/logging.h>
 

src/h5_writer.cpp src/hydro/io/h5_writer.cppsrc/h5_writer.cpp renamed to src/hydro/io/h5_writer.cpp

@@ -10,7 +10,7 @@
  * @note Future: chunking/compression and additional data types can be added if needed.
  */
 
-#include <hydroc/h5_writer.h>
+#include <hydroc/io/h5_writer.h>
 
 #include <stdexcept>
 #include <sstream>