make random state argument handling more consistent

[ilia-kats]

• always default to non-None random_state (consistent within muon and with scanpy)
• fix condition before setting random state in .tl.leiden (closes random_state=0 does not set seed in muon.tl.leiden, either a bug or unclear documentation #154, closes fix: handle random_state=0 correctly in leiden clustering #184, closes Fix leiden/louvain ignoring random_state=0 #218)

[ilan-gold]

How is this not a breaking change for reproducibility given that you're changing the default? If you didn't set the random seed by default now in each of these, you're setting it every time now to 0. I think handling random state this way is a separate issue

[ilia-kats]

We already weren't reproducible before, unless someone set their global random seed at the very beginning of the analysis, which very few people do. I would think this improves reproducibility. But I guess we can defer that change to muon 0.2 or something, with an explicit warning in the release notes.

[ilan-gold]

Up to you! If the goal is to just "fix the issue" I think checking is not None is sufficient but otherwise this change seems reasonable

[grst]

Maybe worth fully adhering to https://scientific-python.org/specs/spec-0007/ while you are at it?

[codecov]

Codecov Report

❌ Patch coverage is 0% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 26.27%. Comparing base (76ee541) to head (87903c5).

Files with missing lines	Patch %	Lines
src/muon/tl.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #166   +/-   ##
=======================================
  Coverage   26.27%   26.27%           
=======================================
  Files          16       16           
  Lines        2299     2299           
=======================================
  Hits          604      604           
  Misses       1695     1695           

Files with missing lines	Coverage Δ
src/muon/atac/tl.py	12.73% <ø> (ø)
src/muon/prot/pp.py	10.29% <ø> (ø)
src/muon/tl.py	40.90% <0.00%> (ø)

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[ilia-kats]

Maybe worth fully adhering to https://scientific-python.org/specs/spec-0007/ while you are at it?

yeah, that was my thought as well.

[ilia-kats]

@grst turns out we can't adhere to SPEC007 yet: muon itself does not do any random sampling, the random_state argument is always passed to an upstream package, none of which (scanpy, scikit-learn, pandas, umap-learn) currently support SPEC007 (meaning they all accept a random_state argument typed as int | RandomState | None.

[grst]

I see, thanks for investigating!