boundary conditions from python3 to hdf5

[PhilipDeegan]

https://github.com/PHAREHUB/PHARE/issues/165 https://github.com/PHAREHUB/PHARE/issues/166

Summary by CodeRabbit

• New Features

  • Added support for specifying boundary conditions for different simulation dimensions.
  • Enhanced the diagnostic tools to include boundary condition information in output files.

• Bug Fixes

  • Corrected loop declaration syntax for improved code consistency.
  • Improved handling of string data types in MPI utilities.

• Documentation

  • Updated documentation to reflect new methods and functionality related to boundary conditions.

• Refactor

  • Streamlined attribute writing in HDF5 files with new utility functions and error handling.
  • Refactored diagnostic model to include boundary conditions as part of patch properties.

• Tests

  • Implemented new tests to verify the correct setting and output of boundary conditions in diagnostics.

[coderabbitai[bot]]

Walkthrough

Walkthrough

The recent changes in the pyphare codebase focus on enhancing boundary conditions and attribute management. The updates include configuring boundary types based on simulation dimensions in pharein, initializing boundary conditions in the Hierarchy class, handling std::string data types in mpi_utils, improving attribute management in h5writer classes, and adding support for std::vector<std::string> for boundary conditions in diagnostics, with corresponding testing.

Changes

File Path	Change Summary
pyphare/pyphare/pharein/__init__.py	Added conditional string declarations for grid boundary types based on simulation dimensions.
src/amr/wrappers/hierarchy.hpp src/diagnostic/diagnostic_model_view.hpp	Added member functions for boundary conditions; updated constructor for Hierarchy.
src/core/data/grid/gridlayout.hpp	Minor syntax change in loop declaration.
src/core/utilities/mpi_utils.hpp	Added handling for std::string data type.
src/diagnostic/detail/h5typewriter.hpp src/diagnostic/detail/h5writer.hpp src/hdf5/detail/h5/h5_file.hpp	Enhanced attribute handling with new methods and error checking; modified existing methods to handle global attributes.
tests/diagnostic/test_diagnostics.hpp	Added testing for new std::vector<std::string> boundary condition attributes.

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[PhilipDeegan]

I figured it was a safe assumption that there wouldn't be different boundary conditions per level / model or solver type

[nicolasaunai]

caution about globals attributes considered in this PR that may be per rank from python