Switch to ruff linting

[benjeffery]

trafficstars

For numpy2 checks etc.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 86.65%. Comparing base (998d710) to head (54dabad).

:exclamation: Current head 54dabad differs from pull request most recent head 872880c

Please upload reports for the commit 872880c to get more accurate results.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2952      +/-   ##
==========================================
- Coverage   89.63%   86.65%   -2.99%     
==========================================
  Files          29       11      -18     
  Lines       30189    22932    -7257     
  Branches     5877     4254    -1623     
==========================================
- Hits        27061    19872    -7189     
+ Misses       1789     1754      -35     
+ Partials     1339     1306      -33     

Flag	Coverage Δ
c-tests	86.20% <ø> (ø)
lwt-tests	80.78% <ø> (ø)
python-c-tests	88.72% <ø> (ø)
python-tests	?

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

see 18 files with indirect coverage changes

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 98.95833% with 1 line in your changes missing coverage. Please review.

Project coverage is 89.63%. Comparing base (998d710) to head (d9256d9). Report is 148 commits behind head on main.

Files with missing lines	Patch %	Lines
python/tskit/trees.py	95.45%	1 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2952      +/-   ##
==========================================
- Coverage   89.63%   89.63%   -0.01%     
==========================================
  Files          29       29              
  Lines       30189    30173      -16     
  Branches     5877     5877              
==========================================
- Hits        27061    27045      -16     
  Misses       1789     1789              
  Partials     1339     1339              

Flag	Coverage Δ
c-tests	86.20% <ø> (ø)
lwt-tests	80.78% <ø> (ø)
python-c-tests	88.72% <ø> (ø)
python-tests	99.03% <98.95%> (-0.01%)	:arrow_down:

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

Files with missing lines	Coverage Δ
python/tskit/cli.py	96.96% <100.00%> (ø)
python/tskit/combinatorics.py	99.36% <100.00%> (ø)
python/tskit/drawing.py	99.23% <100.00%> (-0.01%)	:arrow_down:
python/tskit/exceptions.py	100.00% <100.00%> (ø)
python/tskit/formats.py	99.46% <100.00%> (ø)
python/tskit/genotypes.py	99.07% <100.00%> (ø)
python/tskit/intervals.py	100.00% <100.00%> (ø)
python/tskit/metadata.py	99.04% <100.00%> (-0.01%)	:arrow_down:
python/tskit/provenance.py	100.00% <ø> (ø)
python/tskit/stats.py	100.00% <100.00%> (ø)
... and 5 more

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

[benjeffery]

Well this was a lot noisier than I was expecting, although it did show up a couple of actual errors.

[jeromekelleher]

Ruff is quite opinionated about getting people to use f strings etc isn't it?

What were the errors?

LGTM though, happy to switch.

Given the noisiness we may want to try and flush a few open PRs through first.

[benjeffery]

If we don't want to enforce f-strings we can switch that off - they do generally read better though.

The errors were: A test where a subsequent pytest.raises was nested inside the first, such that the second didn't run. An ibd test that was missing an assert so the value was evaluated, but not checked.

[petrelharp]

I'm happy with whatevery you all think, but I did find two places I wished it was less opinionated (see comments).

[hyanwong]

I've been using ruff and it's much quicker than our previous linter, which makes development a little slicker and more palatable, so I would be happy with switching over.

[benjeffery]

Still planning to do this - waiting till the number of in-flight PRs is a bit lower.

[benjeffery]

I've just tried to bring this up-to-date and while doing so noticed quite a few new changes that weren't in this original PR as ruff had added new checks. As such I don't think we want to switch as our usual PR's moving forward will have lint changes in, black has been relatively stable. I'm open to ruff once/if things have settled down in a year or two, but right now I think it will be too noisey.