Initial outline for Trajectory refactoring

[jeromekelleher]

Here's a rough outline for what I'm thinking the low-level C will look like. I think it's worth getting things right here in the Python version before looking at the C --- it's much faster to try different things out here.

As discussed in #1803

Does this look like roughly the right design @andrewkern, @molpopgen?

Looks like we're missing quite a bit of stuff from the Python version though @andrewkern?

[codecov]

Codecov Report

❌ Patch coverage is 87.69231% with 16 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.90%. Comparing base (7a49bc6) to head (e73e8aa).
⚠️ Report is 574 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1808      +/-   ##
==========================================
- Coverage   90.92%   90.90%   -0.02%     
==========================================
  Files          20       20              
  Lines       10511    10538      +27     
  Branches     2226     2231       +5     
==========================================
+ Hits         9557     9580      +23     
- Misses        497      498       +1     
- Partials      457      460       +3     

Flag	Coverage Δ
C	90.90% <87.69%> (-0.02%)	⬇️
python	97.52% <ø> (ø)

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

Components	Coverage Δ
Python API	88.01% <ø> (-0.02%)	⬇️
Python C interface	88.98% <ø> (ø)
C library	97.28% <87.69%> (ø)

🚀 New features to boost your workflow:

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

[molpopgen]

This looks like it is on the right track. One source of confusion, for me at least, is how msprime's "new" ploidy argument gets handled here? This came up in the review of the other PR from @andrewkern -- the neutral fixation time being tested was 2n instead of 4n, and it wasn't clear (to me) why. Presumably, these trajectories should be considering an effective size of ploidy*n?

[jeromekelleher]

We don't have ploidy in the Python version @molpopgen, but we probably should. But yes, I think it would be best if we did things in the general case with arbitrary ploidy.

[molpopgen]

But yes, I think it would be best if we did things in the general case with arbitrary ploidy.

Yeah, seems prudent to iron out any wrinkles ASAP