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[r] Add obsm, varm, obsp, and varp to SOMAExperimentAxisQuery #2351

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merged 2 commits into from
Mar 29, 2024
Merged

[r] Add obsm, varm, obsp, and varp to SOMAExperimentAxisQuery #2351

merged 2 commits into from
Mar 29, 2024

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mojaveazure
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Add support for querying *m and *p layers from SOMAExperimentAxisQuery; note, just like $X(), these methods only support layers stored as SOMASparseNDArrays

Implemented SOMA methods:

  • SOMAExperimentAxisQuery$obsm(): read an obsm layer for only the coordinates in the query
  • SOMAExperimentAxisQuery$varm(): read a varm layer for only the coordinates in the query
  • SOMAExperimentAxisQuery$obsp(): read an obsp layer for only the coordinates in the query
  • SOMAExperimentAxisQuery$varp(): read a varp layer for only the coordinates in the query

resolves #1997

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This pull request has been linked to Shortcut Story #43711: [r] Port obsm/varm for ExperimentAxisQuery from Python to R.

@johnkerl johnkerl removed the request for review from eddelbuettel March 29, 2024 16:47
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codecov bot commented Mar 29, 2024 •
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Codecov Report

Merging #2351 (f881909) into main (7eef2c6) will decrease coverage by 7.06%.
The diff coverage is 100.00%.

❗ Current head f881909 differs from pull request most recent head d56859e. Consider uploading reports for the commit d56859e to get more accurate results

Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #2351      +/-   ##
==========================================
- Coverage   82.17%   75.11%   -7.06%     
==========================================
  Files          89       52      -37     
  Lines        8226     4421    -3805     
==========================================
- Hits         6760     3321    -3439     
+ Misses       1466     1100     -366
Flag Coverage Δ
python ?
r 75.11% <100.00%> (+0.42%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components Coverage Δ
python_api ∅ <ø> (∅)
libtiledbsoma ∅ <ø> (∅)

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Maybe rebase this one more time? GH says it is 8 commits behind, 1 ahead.

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@mojaveazure
[r] Add obsm, varm, obsp, and varp to SOMAExperimentAxisQuery
f881909 
Add support for querying `*m` and `*p` layers from
`SOMAExperimentAxisQuery`; note, just like `$X()`, these methods only
support layers stored as `SOMASparseNDArrays`

Implemented SOMA methods:
 - `SOMAExperimentAxisQuery$obsm()`: read an `obsm` layer for only the
   coordinates in the query
 - `SOMAExperimentAxisQuery$varm()`: read a `varm` layer for only the
   coordinates in the query
 - `SOMAExperimentAxisQuery$obsp()`: read an `obsp` layer for only the
   coordinates in the query
 - `SOMAExperimentAxisQuery$varp()`: read a `varp` layer for only the
   coordinates in the query

resolves #1997
@mojaveazure mojaveazure force-pushed the paulhoffman/sc-43711/r-port-obsm-varm-for-experimentaxisquery branch from 7584faa to f881909 Compare March 29, 2024 17:48
@mojaveazure
Update changelog
d56859e 
Bump develop version

[ci skip]
@mojaveazure mojaveazure merged commit 6abaf66 into main Mar 29, 2024
@mojaveazure mojaveazure deleted the paulhoffman/sc-43711/r-port-obsm-varm-for-experimentaxisquery branch March 29, 2024 18:07
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johnkerl commented Apr 2, 2024 •
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@mojaveazure (just FYI, no action required on your part) the backport bot isn't running & I'm not sure why not :(

I need to debug tomorrow. For maximum neatness I'd like to backport this to release-1.9 before backporting #2188 (I prefer to run the backports in the same order as their antecedents were merged into main) ...

@johnkerl johnkerl mentioned this pull request Apr 3, 2024
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johnkerl commented Apr 3, 2024

@mojaveazure #2365 🙏

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@johnkerl johnkerl johnkerl approved these changes

@aaronwolen aaronwolen Awaiting requested review from aaronwolen

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[r] Port obsm/varm for ExperimentAxisQuery from Python to R
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@mojaveazure @eddelbuettel @johnkerl