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[python] Files re-work on io/ingest.py #2121

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johnkerl opened this issue Feb 9, 2024 · 3 comments
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[python] Files re-work on io/ingest.py #2121

johnkerl opened this issue Feb 9, 2024 · 3 comments
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@johnkerl
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johnkerl commented Feb 9, 2024

The file apis/python/src/tiledbsoma/io/ingest.py is quite large.

  • At very least split it up into io/ngest.py and io/outgest.py
  • This may entail some common symbols moved to a new io/_common.py

Possible follow-on (I prefer as a separate PR from the above):

  • io/ingest.py -> io/ingest_anndata.py (for from_anndata and from_h5ad)
  • io/outgest.py -> io/outgest_anndata.py (for to_anndata and to_h5ad)
  • io/ingest_whatevs.py and io/outgest_whatevs.py for new spatial file-format experiments

This is intended to be a warm-up issue for a new team member to be selected by @jp-dark.

Please also see
https://github.com/single-cell-data/TileDB-SOMA/wiki/Information-for-developers
and don't hesitate to contact me with any questions about TIleDB-SOMA development. :)

@johnkerl
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@ryan-williams I believe this is complete (unless you had a 2nd PR in mind) -- if I'm mistaken we can re-open -- thank you!

@ryan-williams
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Sounds good, I was thinking we can revisit the 2nd part (format-specific {ingest,outgest} files) later, if/when we support more formats…

@johnkerl
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Thanks -- I'll make a separate issue

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