Include generated files in repo

.gitignore

@@ -1,6 +1,4 @@
-/cpp/generated/
 /cpp/build/
-/python/petsird/
 __pycache__/
 
 # Common editor backups

cpp/CMakeLists.txt

@@ -16,3 +16,19 @@ add_executable(petsird_analysis petsird_analysis.cpp)
 target_link_libraries(petsird_analysis petsird_generated)
 
 add_subdirectory(generated)
+
+# PETSIRD Library (libpetsird)
+add_library(petsird SHARED $<TARGET_OBJECTS:petsird_generated>)
+target_link_libraries(petsird petsird_generated)
+install(TARGETS petsird DESTINATION lib)
+
+# Set the target include directory where headers will be installed
+set(INSTALL_INCLUDE_DIR "include/petsird")
+
+# Collect all header files in the current directory and subdirectories
+file(GLOB_RECURSE HEADER_FILES "*.h")
+
+# Specify the installation directory for header files
+install(FILES ${HEADER_FILES}
+    DESTINATION ${INSTALL_INCLUDE_DIR}
+)

cpp/generated/CMakeLists.txt

@@ -0,0 +1,40 @@
+# This file was generated by the "yardl" tool. DO NOT EDIT.
+
+# To opt out of generating this file, set cpp.generateCMakeLists to false in the _package.yml file.
+
+# To use the object library defined in this file, add the following to your CMakeLists.txt file:
+# target_link_libraries(<your target> petsird_generated)
+# add_subdirectory(<path to this directory>)
+
+set(HOWARD_HINNANT_DATE_MINIMUM_VERSION "3.0.0")
+find_package(date ${HOWARD_HINNANT_DATE_MINIMUM_VERSION} REQUIRED)
+
+if(VCPKG_TARGET_TRIPLET)
+  set(HDF5_CXX_LIBRARIES hdf5::hdf5_cpp-shared)
+else()
+  set(HDF5_CXX_LIBRARIES hdf5::hdf5_cpp)
+endif()
+
+set(HDF5_MINIMUM_VERSION "1.10.5")
+find_package(HDF5 ${HDF5_MINIMUM_VERSION} REQUIRED COMPONENTS C CXX)
+
+set(XTENSOR_MINIMUM_VERSION "0.21.10")
+find_package(xtensor ${XTENSOR_MINIMUM_VERSION} REQUIRED)
+
+set(NLOHMANN_JSON_MINIMUM_VERSION "3.11.1")
+find_package(nlohmann_json ${NLOHMANN_JSON_MINIMUM_VERSION} REQUIRED)
+add_library(petsird_generated OBJECT
+  protocols.cc
+  types.cc
+  ndjson/protocols.cc
+  binary/protocols.cc
+  hdf5/protocols.cc
+)
+
+target_link_libraries(petsird_generated
+  PUBLIC ${HDF5_C_LIBRARIES}
+  PUBLIC ${HDF5_CXX_LIBRARIES}
+  PUBLIC xtensor
+  PUBLIC date::date
+  PUBLIC nlohmann_json::nlohmann_json
+)

cpp/generated/binary/protocols.h

@@ -0,0 +1,61 @@
+// This file was generated by the "yardl" tool. DO NOT EDIT.
+
+#pragma once
+#include <array>
+#include <complex>
+#include <memory>
+#include <optional>
+#include <variant>
+#include <vector>
+
+#include "../protocols.h"
+#include "../yardl/detail/binary/reader_writer.h"
+
+namespace petsird::binary {
+// Binary writer for the PETSIRD protocol.
+// Definition of the stream of data
+class PETSIRDWriter : public petsird::PETSIRDWriterBase, yardl::binary::BinaryWriter {
+  public:
+  PETSIRDWriter(std::ostream& stream, Version version = Version::Current)
+      : yardl::binary::BinaryWriter(stream, petsird::PETSIRDWriterBase::SchemaFromVersion(version)), version_(version) {}
+
+  PETSIRDWriter(std::string file_name, Version version = Version::Current)
+      : yardl::binary::BinaryWriter(file_name, petsird::PETSIRDWriterBase::SchemaFromVersion(version)), version_(version) {}
+
+  void Flush() override;
+
+  protected:
+  void WriteHeaderImpl(petsird::Header const& value) override;
+  void WriteTimeBlocksImpl(petsird::TimeBlock const& value) override;
+  void WriteTimeBlocksImpl(std::vector<petsird::TimeBlock> const& values) override;
+  void EndTimeBlocksImpl() override;
+  void CloseImpl() override;
+
+  Version version_;
+};
+
+// Binary reader for the PETSIRD protocol.
+// Definition of the stream of data
+class PETSIRDReader : public petsird::PETSIRDReaderBase, yardl::binary::BinaryReader {
+  public:
+  PETSIRDReader(std::istream& stream)
+      : yardl::binary::BinaryReader(stream), version_(petsird::PETSIRDReaderBase::VersionFromSchema(schema_read_)) {}
+
+  PETSIRDReader(std::string file_name)
+      : yardl::binary::BinaryReader(file_name), version_(petsird::PETSIRDReaderBase::VersionFromSchema(schema_read_)) {}
+
+  Version GetVersion() { return version_; }
+
+  protected:
+  void ReadHeaderImpl(petsird::Header& value) override;
+  bool ReadTimeBlocksImpl(petsird::TimeBlock& value) override;
+  bool ReadTimeBlocksImpl(std::vector<petsird::TimeBlock>& values) override;
+  void CloseImpl() override;
+
+  Version version_;
+
+  private:
+  size_t current_block_remaining_ = 0;
+};
+
+} // namespace petsird::binary