ParticleGroup.from_hdf5

[electronsandstuff]

Per discussion with @ChristopherMayes, this PR adds a new method .from_hdf5 to ParticleGroup with a time_offset argument. Additional cleanup is performed.

• Add pre-commit to conda env
• Add .vscode to .gitignore
• Add unit tests for all existing input types for __init__ argument h5
  • Path, h5py.File, h5py.Group, "legacy" group with no species
• New exceptions.py with custom BeamPhysics exceptions for HDF5 file load errors
• load_bunch_data and __init__ are broken into methods to handle each atomic part of loading the only species in the only iteration of a particle group.
  • load_species_data gets the array dict from one species
  • _only_species_group loads the only species in the OpenPMD iteration passed to it (or passes through to handle "legacy" version w/o species)
  • _only_iteration_group gets the only iteration, raising on none or multiple. Handles files, groups, paths.
  • _only_iteration_only_species_group handles the file loading, existing behavior of passing through raw species group.
• Move load_bunch_data to readers.py and keep import there for legacy support
• Time offset loading methods
  • load_time_offset to load from an open species group
  • load_only_time_offset loads from only species from only iteration with same input semantics as .from_hdf5
• Add t_offset to ParticleGroupt.write
• Updated documentation
  • docs/examples/write_examples.ipynb updated to use read w/o time offset
  • docs/examples/read_examples.ipynb demostrates .from_hdf5 and time offset methods
  • New docs/api/readers.md

Note: this PR also includes the changes noted in #152. It was intended as a stacked PR, but due to working out of a fork is set up to target main instead and will supersede it.