do not use h5py on restarts

[PhilipDeegan]

prevent hdf5 header/lib mismatch

eg: https://stackoverflow.com/q/45411700/795574

Summary by CodeRabbit

• New Features

  • Introduced new methods for retrieving patch data IDs and serialized simulation strings directly from the restart file.
  • Added a new method to read attributes from HDF5 files, enhancing data handling capabilities.

• Improvements

  • Enhanced clarity of function parameters, improving readability and understanding of intended use.
  • Streamlined internal logic to reduce dependencies on external libraries, potentially improving performance.

[coderabbitai]

Walkthrough

Walkthrough

The recent changes enhance clarity and performance in the codebase by renaming parameters for better readability, streamlining internal logic, and introducing new methods for handling data. Key functions now utilize a more direct approach to retrieve information, reducing reliance on external libraries. These modifications not only simplify the code but also improve maintainability and extend functionality in attribute reading and data processing.

Changes

Files	Change Summary
pyphare/pyphare/pharein/__init__.py	Renamed parameters in _patch_data_ids and _serialized_simulation_string from path to restart_file_dir, streamlining logic and removing h5py dependency.
src/hdf5/detail/h5/h5_file.hpp	Reformatted file() method for readability; added a new template method read_attribute for reading attributes from HDF5 files.
src/python3/cpp_etc.cpp	Introduced a lambda function samrai_restart_file to handle path retrieval, added new functions patch_data_ids and serialized_simulation_string for improved modularity.

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[coderabbitai]

Actionable comments posted: 0

Review details

Configuration used: .coderabbit.yaml
Review profile: CHILL

Commits

Files that changed from the base of the PR and between a233cc7 and 07b697a.

Files selected for processing (3)

• pyphare/pyphare/pharein/init.py (1 hunks)
• src/hdf5/detail/h5/h5_file.hpp (2 hunks)
• src/python3/cpp_etc.cpp (2 hunks)

Additional context used

Path-based instructions (1)

src/hdf5/detail/h5/h5_file.hpp (1)

Pattern **/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.

Additional comments not posted (7)

src/python3/cpp_etc.cpp (3)

36-38: LGTM!

The lambda function samrai_restart_file is clear and correctly encapsulates the call to PHARE::amr::HierarchyRestarter::getRestartFileFullPath(path).

---

60-69: LGTM!

The function patch_data_ids correctly retrieves patch data IDs from the restart file using the HighFive library and handles the case where HighFive support is not available.

---

70-79: LGTM!

The function serialized_simulation_string correctly retrieves the serialized simulation string from the restart file using the HighFive library and handles the case where HighFive support is not available.

src/hdf5/detail/h5/h5_file.hpp (2)

72-75: LGTM!

The reformatting of the file method enhances readability without altering functionality.

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241-248: LGTM!

The method read_attribute is well-implemented and correctly retrieves the attribute using the getGroup and getAttribute methods.

pyphare/pyphare/pharein/__init__.py (2)

73-80: LGTM!

The function _patch_data_ids correctly replaces the use of h5py with cpp_etc_lib, enhancing clarity and reducing dependencies.

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83-86: LGTM!

The function _serialized_simulation_string correctly replaces the use of h5py with cpp_etc_lib, enhancing clarity and reducing dependencies.