Question: Future of anndata-rs with continuing anndata development?

[mtvector]

Hi there,

Thanks for your help so far! I'm wondering about the future of anndata-rs as anndata is continuously changing, especially through integration with RAPIDS. (https://anndata.readthedocs.io/en/latest/#id5) This implementation of an out-of-core anndata is extremely cool, but I have a few questions about the long term.

I'm wondering if you have plans or have discussed with the scverse team about the SnapATAC2 anndata-rs being merged in with the anndata package? This would be very nice to know that there will not be interoperability issues as both SnapATAC and anndata continue development. A number of people at the institute had this concern in the switch from ArchR, and I imagine other users have this question as well.

On the other hand, (this might be a naive question), is it possible to run everything in memory by converting (or loading an anndata-rs h5ad using scanpy.read) to the standard anndata.AnnData and save back to the standard anndata, meaning snapatac2 will always be usable with the standard anndata?

Thanks so much!
Matthew

[kaizhang]

Thank you for these excellent questions! First of all, anndata-rs is written in Rust and hence is difficult to be merged into the Python anndata package. The Python anndata package has a plan for implementing fully backed AnnData object just like anndata-rs. But the progress seems to be slow and that's the motivation for starting the anndata-rs project in the first place -- I really need fully backed AnnData object in SnapATAC2.

Rest assured SnapATAC2 is fully compatible with standard/in-memory AnnData structure by design, and will continue to be so. If you use a standard AnnData object with SnapATAC2 and find problems, then that's a bug and please open an issue.