Refac hierarchies

[nicolasaunai]

• [x] run particle count

• [x] refactoring hierarchy.py in separate files

• [x] partial Patch Hierarchies with selection box

• [x] refactoring of hierarchy_fromh5 into separate functions

  • [x] new from H5, add time, add data (same time same patch layout)
  • [x] use new functions to replace hierarchy_fromh5
  • [x] run.Getters can be given a list of times

• [x] ScarlarField, VectorField and operators

• [x] Run convenience methods for getting times

• [x] hierarchy.patch_levels not strictly required anymore

  • [x] replaced usage by time_hier instead

• [x] PatchHierarchy unit tests

    run = Run(path)
    pc = run.GetParticleCount(0)
    for ilvl, lvl in pc.levels().items():
        c = [p.attrs["particle_count"] for p in lvl.patches]
        print(f"there are {sum(c)} particles on level {ilvl}")

there are 32000000.0 particles on level 0
there are 20478022.0 particles on level 1
there are 40959036.0 particles on level 2

Also some refractory to split hierarchy.py in different files.

Summary by CodeRabbit

• Refactor

  • Improved parameter naming in box classes for clarity.
  • Enhanced consistency in error handling and import statements.
  • Streamlined import structure in multiple modules.

• New Features

  • Introduced various mathematical operations for hierarchical data structures.
  • Added functions and classes for managing patch hierarchies from HDF5 files and simulation data.
  • Introduced comprehensive PatchHierarchy class for efficient multi-dimensional data management and visualization.

• Bug Fixes

  • Fixed typos and improved error message consistency.
  • Corrected comparison logic to follow best practices.
  • Updated test functions with skip annotations for pending changes.

[coderabbitai[bot]]

Walkthrough

## Walkthrough The recent updates to the `pyphare` project enhance code clarity through parameter renaming, streamline import management, and standardize error messaging. New functions and classes have been introduced for managing hierarchical data, while various refinements across the codebase aim to boost efficiency and maintainability. Additionally, test cases have been updated to reflect changes in function parameters and import paths, with some tests marked to be skipped pending further updates. ## Changes | File(s) | Change Summary | |---------|----------------| | `pyphare/.../box.py` | Renamed parameters in `nDBox`, `Box1D`, `Box2D`, and `Box3D`'s `__init__` methods from `l` and `u` to `lower` and `upper` for clarity. | | `pyphare/.../operators.py` | Introduced functions for computing dot products, cross products, square roots, gradients, and moduli for hierarchical data structures. | | `pyphare/.../phare_utilities.py` | Modified `print_trace()` to import `traceback` separately from `sys`. | | `pyphare/.../cpp/__init__.py` | Simplified exception handling by removing the specific error variable `err`. | | `pyphare/.../pharein/__init__.py` | Consolidated imports and updated the `__all__` list for public entities. | | `pyphare/.../pharein/diagnostics.py` | Corrected a comment typo and removed an empty line in the `_setSubTypeAttributes` method. | | `pyphare/.../pharein/examples/job.py` | Refactored imports to utilize the `pyphare.pharein` module via the alias `ph`. | | `pyphare/.../pharein/maxwellian_fluid_model.py` | Removed unused import of `yee_element_is_primal`. | | `pyphare/.../pharein/restarts.py` | Updated error messages to use standard strings for consistency. | | `pyphare/.../pharein/simulation.py` | Enhanced checks and updated variable names for clarity. | | `pyphare/.../pharesee/geometry.py` | Modified import statements for `FieldData` and `is_root_lvl`. | | `pyphare/.../pharesee/hierarchy/__init__.py` | Introduced functions for managing hierarchical structures for scalar and vector fields. | | `pyphare/.../pharesee/hierarchy/fromh5.py` | Added functions for creating patch hierarchies from HDF5 files. | | `pyphare/.../pharesee/hierarchy/fromsim.py` | Introduced `hierarchy_from_sim` for constructing patch hierarchies from simulation data. | | `pyphare/.../pharesee/hierarchy/hierarchy.py` | Enhanced `PatchHierarchy` class with new methods for data handling and management. | | `pyphare/.../pharesee/hierarchy/patch.py` | Added a new `Patch` class with methods for initialization and data manipulation. | | `tools/python3/phloping.py` | Refactored logic for extracting particle counts per timestep per level, improving efficiency. | | `tests/simulator/test_load_balancing.py` | Updated import for `hierarchy_compare` and renamed parameter `time` to `times`; added skip annotations for some tests. |

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