[python] Outgest additional X layers to AnnData

[johnkerl]

Issue and/or context: Issue #2079

[codecov]

Codecov Report

Merging #2119 (33e5679) into main (5647fb4) will increase coverage by 4.72%.
The diff coverage is n/a.

❗ Current head 33e5679 differs from pull request most recent head d8aa814. Consider uploading reports for the commit d8aa814 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2119      +/-   ##
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+ Coverage   67.05%   71.77%   +4.72%     
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  Files          49      101      +52     
  Lines        2577     6920    +4343     
  Branches      211      211              
==========================================
+ Hits         1728     4967    +3239     
- Misses        747     1851    +1104     
  Partials      102      102              

Flag	Coverage Δ
libtiledbsoma	66.97% <ø> (-0.08%)	⬇️
r	74.62% <ø> (?)

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Components	Coverage Δ
python_api	∅ <ø> (∅)
libtiledbsoma	48.34% <ø> (ø)

[johnkerl]

@aaronwolen @mojaveazure ping 🙏

[johnkerl]

@aaronwolen @mojaveazure ping 🙏

[aaronwolen]

Limiting the user's export options to either all or none of the X layers may be too inflexible. Ideally, they should be able to specify any subset of the layers they want.

[johnkerl]

@aaronwolen thanks!

To avoid length iteration cycles, please take a minute or two to simply offer a candidate method signature, and I will do what you ask

Thank you in advance!

[johnkerl]

I don't know why this is suddenly failing CI in files I did not touch (Python 3.7 only).

I am actively debugging.

[aaronwolen]

Thanks for the productive discussions. Tested it out and it works great.

[johnkerl]

I don't know why this is now failing Python 3.7 CI on tests which I did not touch. It passes tests for me on my laptop. I will iteratively debug on #2137.

[ihnorton]

This needs to be typing.KeysView for 3.7 compatibility.

[johnkerl]

Thank you @ihnorton !!!!!

Requested changes were made

[github-actions]

The backport to release-1.7 failed:

The process '/usr/bin/git' failed with exit code 1

To backport manually, run these commands in your terminal:

# Fetch latest updates from GitHub
git fetch
# Create a new working tree
git worktree add .worktrees/backport-release-1.7 release-1.7
# Navigate to the new working tree
cd .worktrees/backport-release-1.7
# Create a new branch
git switch --create backport-2119-to-release-1.7
# Cherry-pick the merged commit of this pull request and resolve the conflicts
git cherry-pick --mainline 1 d9c4e07eb8e05a99218df3876244a2de025f5ae5
# Push it to GitHub
git push --set-upstream origin backport-2119-to-release-1.7
# Go back to the original working tree
cd ../..
# Delete the working tree
git worktree remove .worktrees/backport-release-1.7

Then, create a pull request where the base branch is release-1.7 and the compare/head branch is backport-2119-to-release-1.7.

[aaronwolen]

[sc-40032]

[shortcut-integration]

This pull request has been linked to Shortcut Story #40032: Support exporting additional X layers to anndata.