New layout

[jeromekelleher]

This is a work in progress - I'll have to see how SLiM fits in to the general workflows. The diff is noisy, but it's mainly just ruff updates which are harmless.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 98.27586% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.74%. Comparing base (137ae17) to head (636d283).

Files with missing lines	Patch %	Lines
pyslim/spatial.py	75.00%	1 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #411      +/-   ##
==========================================
- Coverage   96.83%   96.74%   -0.09%     
==========================================
  Files           8        8              
  Lines         789      769      -20     
  Branches      146      146              
==========================================
- Hits          764      744      -20     
  Misses         15       15              
  Partials       10       10              

Flag	Coverage Δ
python-tests	96.74% <98.27%> (?)

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[jeromekelleher]

This would generally be a lot easier if we could separate running tests and docs from running SLiM. Would you be up for restructuring things here so that tests and docs depend on known paths to tree sequence files, rather than running slim inline @petrelharp? If we did that I think we could use the general workflows for documentation and tests fairly straightforwardly (which would be good in the long run).

[petrelharp]

This would generally be a lot easier if we could separate running tests and docs from running SLiM. Would you be up for restructuring things here so that tests and docs depend on known paths to tree sequence files, rather than running slim inline @petrelharp?

I'm okay with that restructuring in principle! But, one issue here is that something we test a fair bit is, for instance, "can pyslim do manipulations to tree sequences that are then readable by SLiM". So, either I misunderstand, or we'll still need to run slim inline in the tests?

[jeromekelleher]

I think this is ready to go. I didn't end up making any real changes, as the SLiM invocations are pretty deeply embedded, and just updated the docs workflow to optionally install SLiM. The tests workflow is bespoke enough that it's not worth refactoring right now.

I had to skip some tests because of failures, but they've been broken for a while (#412).

It would be good to merge this ASAP @petrelharp as I'm trying to get a coordinated set of releases out so that the ecosystem is up to date and the top-level website build can be simplified.

[jeromekelleher]

OK, I'm going to go ahead and merge this as no one has objected.