Feat: add moransi

[MxMstrmn]

Updated version of moran's I PR with pre-commits

A new approach to integrate #245

• Transfer code to new branch (based on main)
• Which preprocessing needed?
• Pytest function
• Use scanpy implementation (https://github.com/scverse/scanpy/blob/master/scanpy/metrics/_morans_i.py,. https://scanpy.readthedocs.io/en/latest/generated/scanpy.metrics.morans_i.html#scanpy-metrics-morans-i)
• Moran’s I → Moran’s I comparison
• Parameters of function
• Integrate in metrics wrapper methods

[MxMstrmn]

Hi @michalk8, do you have an idea why the checks fail here? The file locally has no syntax errors and also passes the pre-commits I added as part of this PR. Do not know how to handle this best / fix it.

[michalk8]

Done. Also, I'd seriously consider refactoring the CI to be more up-to-date.
Interestingly, AST checker pre-commit did not catch this.

[MxMstrmn]

Why does f"{variable=}" fail the parse, is that not normal python syntax?

[MxMstrmn]

I did not set the CI up, I guess @mumichae and I would be very glad for your input to improve this :)

[michalk8]

Why does f"{variable=}" fail the parse, is that not normal python syntax?

It is, just from Python 3.8 (would deprecate 3.7 since numpy support ended last December), hence the refactoring.

[MxMstrmn]

Thanks so much, @michalk8!

[mumichae]

Done. Also, I'd seriously consider refactoring the CI to be more up-to-date.
Interestingly, AST checker pre-commit did not catch this.

Are you referring to the .github/workflow content to be updated based on a newer configuration template? I wasn't aware there was an update, what consequences would the current code have of not updated?

Would be happy to update, however that would be in a separate PR.

[michalk8]

Are you referring to the .github/workflow content to be updated based on a newer configuration template? I wasn't aware there was an update, what consequences would the current code have of not updated?

Would do the following:

• remove 3.7 CI, add 3.9 (unless you need to support it)
• use pre-commits (add e.g. black) instead of running raw flake8 (this PR was)
• add tests coverage
• not sure how much work, but macOS test CI would be nice to have

The first 2 points I'd say are the one to focus on.

[mumichae]

Thanks a lot for the suggestions @michalk8 !

I think we should definitely make things more consistent, if we start using pre-commit (which we hadn't before). But I think this should be separated from Moran's I. I'll open a new issue with a description of what we'd need for pre-commit integration and would suggest we get that merged before the new metric.

[MxMstrmn]

Updated version of #303

[codecov]

Codecov Report

❌ Patch coverage is 95.94595% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 58.16%. Comparing base (b6bb778) to head (64bb73c).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
scib/metrics/morans_i.py	96.96%	2 Missing ⚠️
scib/preprocessing.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #304      +/-   ##
==========================================
+ Coverage   52.15%   58.16%   +6.01%     
==========================================
  Files          22       23       +1     
  Lines        1762     1836      +74     
==========================================
+ Hits          919     1068     +149     
+ Misses        843      768      -75     

Flag	Coverage Δ
unittests	58.16% <95.94%> (+6.01%)	⬆️

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

Files with missing lines	Coverage Δ
scib/metrics/__init__.py	100.00% <100.00%> (ø)
scib/metrics/metrics.py	82.29% <100.00%> (+0.97%)	⬆️
scib/preprocessing.py	30.80% <50.00%> (+7.44%)	⬆️
scib/metrics/morans_i.py	96.96% <96.96%> (ø)

... and 2 files with indirect coverage changes

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