Add Zarr support

[keller-mark]

Fixes #91

These changes are from both me and @Artur-man

The main public-facing changes here are:

• The ZarrAnnData class
• read_zarr and write_zarr top-level functions
• Support for from_Seurat(output_class="ZarrAnnData")
• Support for from_SingleCellExperiment(output_class="ZarrAnnData")

Internally:

• read_zarr_helpers.R is the zarr analog of read_h5ad_helpers.R
• write_zarr_helpers.R is the zarr analog of write_h5ad_helpers.R
• Test fixtures within inst/extdata/example.zarr (this makes the diff noisy, apologies)
• Lots of tests:
  • test-Zarr-read.R (35 new tests)
  • test-Zarr-write.R (70)
  • test-ZarrAnnData.R (26)
  • test-h5ad-zarr.R (17)

A number of these functions generate warnings in the R console that are intended to be followed up on to improve the code (and should probably be resolved as end users may not appreciate them), but the tests still pass despite these warnings.

Known things that are not implemented here:

• support for recarrays
• usage of mode = c("r", "r+", "a", "w", "w-", "x") parameter value

[rcannood]

Fantastic work @keller-mark and @Artur-man !

I went through the PR for a first time and left some minor comments. I will review the code by running it a couple of times next :)

[Artur-man]

@lazappi I think I did not check before finishing the hackathon. Do you set the default zarr version for write methods now ? or do you write only zarr v2 or v3 ?

Again here is the parameter from anndata to set the default behaviour:
https://github.com/keller-mark/anndataR/blob/528eff0024f73b39c5147d5eb15e7ad8b9b7bade/inst/scripts/example_files.py#L142

would be nice to do that too if we are not rushing bioc release.

[Artur-man]

Ok I took another look at it. The roundtrip tests and write tests do not have zarr v3 tests but thats fine for now I think. What is more important is that we can read both versions. Since this is gonna stay as the devel branch for another 6 months I can throw another PR later. Lets not overdo it.

UPDATE: I wrote a version of test-Zarr-write.R loops over both v2 and v3 ... looks like its working.

[lazappi]

I thought there was something that was missing from {Rarr} that was blocking writing v3 but I forgot to open an issue and come back to it. If you think the extra tests are passing do you want to push them here?