Refactor from/to Seurat conversion

[rcannood]

• Redesigned the from_Seurat / to_Seurat conversion functions

[rcannood]

Note: Could use https://satijalab.github.io/seurat-object/reference/UpdateSeuratObject.html to update a Seurat <v5 object to v5 in from_Seurat().

[lazappi]

Mostly adding suggestions for accessing stuff from a Seurat object. I didn't comment on every line but I think there should be an example for each slot.

[lazappi]

These instructions won't work for Bioconductor packages. Fixing that should probably be a separate issue. And/or maybe one about updating all messages/warning/errors to use {cli} if we are going to depend on it anyway?

[rcannood]

These instructions won't work for Bioconductor packages.

Fixed!

updating all messages/warning/errors to use {cli} if we are going to depend on it anyway?

I'd like that, but let's do this in a separate PR 😅

[rcannood]

Phew. I think I addressed most of the comments, except:

• Wherever SeuratObject had functions for accessing certain data, these functions were used (e.g. changed names(obj@layers) for SeuratObject::Layers(obj)). However, I didn't change code when the alternative was less specific (e.g. changing obj@assays[[assay_name]] for obj[[assay_name]]) or readable (e.g. changing [email protected] for obj[[]]) to avoid accidental bugs.
• Changing all stop(), warning(), cat(), etc.. to use {cli} sounds great, but let's do that in a separate PR

Also,

• I tried to clean up with cleanup_HDF5AnnData when an error occurs while converting to HDF5AnnData. @lazappi Can you take a look?

[lazappi]

I think I'm happy with this now

[lazappi]

Just something like what's in the documentation. I guess it depends what's in the example object.

[lazappi]

Should this be outside the error part so the cleanup is still run if one of the later steps fails?

[rcannood]

I think there is no code after this call in the function. The SCE converter is simply a bit limited at this stage