Single or multiple packages?

[grst]

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.

[grst]

One observation here is that already for a package for transcriptomics only, we would have optional dependencies, e.g. for loom or excel (see https://github.com/scverse/scverse-io/issues/5).

So we anyway need a mechanism for dealing with that and I don't think it's a good argument against a single package.

[Zethson]

Added one pro for multiple packages (edited) but I really think that a single package will be easier for everyone. scanpy also isn't shipping leidenalg and it hasn't really been an issue. Nor PAGA or some others.