Add Harmony to scanpy

[Intron7]

After recent changes from Harmonypy its necessary to move HarmonyBatchcorrection to scanpy. This function is based on harmony-pytorch and rapids-singlecell

[codecov]

Codecov Report

❌ Patch coverage is 94.40000% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.31%. Comparing base (af57cff) to head (88dca09).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/scanpy/preprocessing/_harmony/__init__.py	96.06%	9 Missing ⚠️
src/scanpy/preprocessing/_harmony_integrate.py	75.00%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3953      +/-   ##
==========================================
+ Coverage   77.96%   78.31%   +0.35%     
==========================================
  Files         118      119       +1     
  Lines       12517    12749     +232     
==========================================
+ Hits         9759     9985     +226     
- Misses       2758     2764       +6     

Flag	Coverage Δ
hatch-test.low-vers	77.61% <94.40%> (+0.36%)	⬆️
hatch-test.pre	77.27% <94.40%> (+0.37%)	⬆️

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

Files with missing lines	Coverage Δ
src/scanpy/external/pp/__init__.py	100.00% <ø> (ø)
src/scanpy/preprocessing/__init__.py	100.00% <100.00%> (ø)
src/scanpy/preprocessing/_harmony_integrate.py	75.00% <75.00%> (ø)
src/scanpy/preprocessing/_harmony/__init__.py	96.06% <96.06%> (ø)

[flying-sheep]

Looks good! I fixed the docs and made the code a bit nicer, but the reference tests have been failing from the start. Any idea why? You said they work locally for you?

[Intron7]

so 0.05 for L2 was way to low harmony-pytorch is at 0.0511. we were at 0.0501. I also ran harmoypy once and it was at 0.063. so I set L2 to 0.1