Description

This PR makes two important changes in our depletion_results.h5 files:

1. Reaction rates are no longer written by default. In most cases, users probably do not need the reaction rates that are computed during depletion and they can consume a lot of disk space (see anecdote in Depletion Results File Lite: Suppress Reaction Rates #3602). To get reaction rates written, you need to call integrator.integrate(..., write_rates=True)
2. For integrators that use multiple "stages" (transport solves/matrix exponentials), we no longer write the intermediate solutions, which are really of no use for the vast majority of users. This removes a dimension from some of the datasets in depletion_results.h5; I've preserved the ability to load old files that still have the extra dimension.

Fixes #3602

Checklist

• I have performed a self-review of my own code
• I have run clang-format (version 15) on any C++ source files (if applicable)
• I have followed the style guidelines for Python source files (if applicable)
• I have made corresponding changes to the documentation (if applicable)
• I have added tests that prove my fix is effective or that my feature works (if applicable)