Migrate all data formats from parquet to h5ad and other major improvements

[rcannood]

Describe your changes

• Adds cell obs to de_train.uns["single_cell_obs"]
• Changes inputs and outputs of methods and metrics all to AnnData
• Adds --layer input parameter to methods and metrics (default sign_log10_pval).
• Stability analysis workflow
• Split up LSTM-GRU-CNN method into a workflow of [prepare, train, predict] components.

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality (new method, new metric, ...)
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI Tests succeed and look good!