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[DOCS] Explain backed is for X only

Open jeskowagner opened this issue 2 years ago • 1 comments

Added documentation to read_h5ad in backed mode, addressing #811. Let me know if you would like a more dedicated page for it!

jeskowagner avatar Sep 02 '22 07:09 jeskowagner

Codecov Report

Merging #812 (fe930fc) into master (5cb1911) will increase coverage by 0.23%. The diff coverage is n/a.

:exclamation: Current head fe930fc differs from pull request most recent head 15138cd. Consider uploading reports for the commit 15138cd to get more accurate results

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #812      +/-   ##
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+ Coverage   83.21%   83.44%   +0.23%     
==========================================
  Files          34       32       -2     
  Lines        4450     4319     -131     
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- Hits         3703     3604      -99     
+ Misses        747      715      -32     
Impacted Files Coverage Δ
anndata/_io/h5ad.py 91.98% <ø> (ø)
anndata/experimental/multi_files/_anncollection.py 70.56% <0.00%> (-0.06%) :arrow_down:
anndata/_core/merge.py 93.98% <0.00%> (-0.02%) :arrow_down:
anndata/_core/anndata.py 83.41% <0.00%> (ø)
anndata/_io/specs/methods.py 83.78% <0.00%> (ø)
anndata/__init__.py
anndata/utils.py
anndata/tests/helpers.py 95.45% <0.00%> (+0.02%) :arrow_up:
anndata/_core/aligned_mapping.py 94.14% <0.00%> (+0.20%) :arrow_up:
... and 2 more

codecov[bot] avatar Sep 02 '22 07:09 codecov[bot]

Hey, sorry for the long delay. I am now finally working on providing a longer example, probably going in fileformat-prose.rst (happy to put it elsewhere if preferred). I would like to briefly showcase what backed objects will be printed as, and saw you are making use of some files in that same documentation file (e.g. 02_processed.h5ad). Are these files available anywhere, so I can showcase file-backing on them?

jeskowagner avatar Oct 17 '22 09:10 jeskowagner

I would keep the fileformat page specific to schema.

Maybe this could be a short separate tutorial or an expansion of: https://anndata-tutorials.readthedocs.io/en/latest/getting-started.html#Partial-reading-of-large-data ?

ivirshup avatar Oct 17 '22 11:10 ivirshup

I now reference that tutorial in the docstring for better visibility. Also added the release note. In the future if time permits I may add a more complete example to the tutorial you mentioned, but unfortunately I continue to be time restricted, sorry.

jeskowagner avatar Oct 18 '22 09:10 jeskowagner

No worries about time, happy to include this as is!

ivirshup avatar Oct 18 '22 10:10 ivirshup

Sorry, I think I got a bit confused with my branch management there. But glad to hear that you're happy merging this in! Do so at your convenience.

jeskowagner avatar Oct 18 '22 10:10 jeskowagner