Add anndata export options (.h5ad, .zarr)

[d33bs]

Description

This PR adds the option to export data to anndata formats h5ad and zarr.

In order to reach this I felt that we should abstract the initial design of CytoTable to enable these and other export formats in the near future. To this effect, I changed _to_parquet to be _run_export_workflow (which is more true to what it does anyhow).

Please note: the anndata project is only compatible with Python <=3.11 and as a result shifts how implementation was performed.

Closes #346

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• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

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[gwaybio]

Amazing to see this functionality! Once anndata is added, it is worth a minor release IMO 🎉

[d33bs]

Thanks @gwaybio ! Merging this in after making changes.

[flying-sheep]

Zarr is a required dependency in anndata >=0.12.0, not <!

[d33bs]

Thanks for checking in on this @flying-sheep and sorry again about the version issue confusion on my part! I should have been more explicit with this particular comment; I found that I needed to manually add zarr for anndata <0.12.2 with Python 3.10 and below.

Here's an example reproducing the error I saw:

example.py

import anndata as ad
import pandas as pd

print(ad.__version__)

adata = ad.AnnData(X=pd.DataFrame({"example":[1,2,3]}))

adata.write_zarr("example.zarr")

Executed with uvx using only pandas and anndata through Python 3.10:

uvx -p 3.10 --with anndata,pandas python example.py

Yields an error: ImportError: zarr is not installed.

From this PR's standpoint I sought mostly to find a simple resolution for the many different possible versions which could be installed. Do you feel we should raise an issue about this within anndata (happy to do so)? I felt it might be due to what might have previously been treated as an optional or extra installation within the package (and perhaps not an actual error / fault of the project).

[d33bs]

I've added a minor clarification on the zarr dependency comment in #352 - thanks again for your comment!