Atacformer documentation updates

[nleroy917]

Megathread for tracking updates to the Atacformer documentation changes

1. Tokenizing fragments files
2. Quickly getting a UMAP from a fragments file (import, QC, etc)

[nleroy917]

can you write some docs explaining this:

batch_size = 4  # adjust based on your memory

I need to know:

what's the rough correlation of batch_size to memory? is 4 = 4Gb, so if I have 64 GB I should use 64?

clarify that this is CPU memory, or is it GPU memory if I used to.("cuda")?what is the tradeoff here? is there a downside to using lower numbers? If not, why not just set it to 1 since that uses less memoryyour recommendation for what is the ideal number, or what is a minimum, or what I should be thinking about when I decide.they seem like they're often in multiples of 12 or something. Is there a reason for that?

[nleroy917]

• Ensure that the import for AnnData is properly documented everywhere
• GPU/VRAM table?