Single or multiple packages?

Option 1: one package that contains functions for multiple modalities (e.g. transcriptomics, AIRR, ATAC, ...).
Option 2: one package per modality, e.g. gex-io, airr-io, epigenetics-io

Pro one package

• joint maintenance -> reduced overhead and bus factor
• central place for users to look for IO functions
• potential for multimodal IO functions that generate MuData objects directly

Pro multiple packages

• clear who's responsible for releasing the package
• no need to deal with optional dependencies
• Can release packages independently more quickly

Optional dependencies

• Could be handled with dependency groups.

  pip install scverse-io
  

  installs only the basic functions.

  then there's e.g.

  scverse-io[airr]
  

  and

  scverse-io[all]
  

  The latter would be broadly advertised in the README.

• Maybe it's not as bad after all. Most IO functions should get away the same packages reading csv/mtx/json/h5.

• @flying-sheep made the point that if an optional dependency is not installed, the error message should be just a plain
  message with installation instructions rather than a full stack-trace that will be intimidating for beginners.

Review the README and the discussion of single-package versus per-modality packaging, including optional dependency groups and missing-dependency messages. Done means reaching and documenting a project decision; the issue does not name implementation files or tests to run.