normalize_total with numba

[Intron7]

Fixes #3135

This also removes the deprecated functions out

[selmanozleyen]

so this part can be in fast-array-utils under the name elem_mult @flying-sheep right? This is what I understood from our discussions. Should we first implement elem_mult then come back to this issue?

[flying-sheep]

Generally I wouldn’t stop scanpy improvements for fast_array_utils.

But if part of this can be replaced with a mult helper, we could do that now!

[codecov]

Codecov Report

Attention: Patch coverage is 95.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 76.74%. Comparing base (e6e86f2) to head (862f786).
Report is 1 commits behind head on main.

✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/scanpy/preprocessing/_normalization.py	95.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3571      +/-   ##
==========================================
+ Coverage   76.68%   76.74%   +0.05%     
==========================================
  Files         113      113              
  Lines       12709    12703       -6     
==========================================
+ Hits         9746     9749       +3     
+ Misses       2963     2954       -9     

Files with missing lines	Coverage Δ
src/scanpy/preprocessing/_normalization.py	89.41% <95.00%> (+9.19%)	⬆️

[flying-sheep]

@Intron7 you have to write Fixes #3135 to link the issue.

[flying-sheep]

Also this needs a release note!

[Intron7]

@flying-sheep of course

[flying-sheep]

Release note please

[lumberbot-app]

Owee, I'm MrMeeseeks, Look at me.

There seem to be a conflict, please backport manually. Here are approximate instructions:

1. Checkout backport branch and update it.

git checkout 1.11.x
git pull

2. Cherry pick the first parent branch of the this PR on top of the older branch:

git cherry-pick -x -m1 55bfe348619fec1b800aae9086f6a1edddd5444e

3. You will likely have some merge/cherry-pick conflict here, fix them and commit:

git commit -am 'Backport PR #3571: `normalize_total` with numba'

4. Push to a named branch:

git push YOURFORK 1.11.x:auto-backport-of-pr-3571-on-1.11.x

5. Create a PR against branch 1.11.x, I would have named this PR:

"Backport PR #3571 on branch 1.11.x (normalize_total with numba)"

And apply the correct labels and milestones.

Congratulations — you did some good work! Hopefully your backport PR will be tested by the continuous integration and merged soon!

Remember to remove the Still Needs Manual Backport label once the PR gets merged.

If these instructions are inaccurate, feel free to suggest an improvement.