Documentation for LD matrix methods

[apragsdale]

See #3353.

This largely pulls material from an existing, open PR to complete minimal documentation for the LD matrix methods currently available in tskit. I've made edits for clarity from the original PR, and removed some material that is possibly confusing or more information than needed for a user.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.92%. Comparing base (1835ea3) to head (bae4065).

Additional details and impacted files

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##             main    #3416   +/-   ##
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  Coverage   91.92%   91.92%           
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  Files          37       37           
  Lines       32153    32153           
  Branches     5143     5143           
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  Hits        29556    29556           
  Misses       2264     2264           
  Partials      333      333           

Flag	Coverage Δ
C	82.70% <ø> (ø)
c-python	77.34% <ø> (ø)
python-tests	96.40% <ø> (ø)
python-tests-no-jit	33.22% <ø> (ø)

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Components	Coverage Δ
Python API	98.69% <ø> (ø)
Python C interface	91.23% <ø> (ø)
C library	88.86% <ø> (ø)

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[jeromekelleher]

I've had a quick read through and generally looks great. I've spotted a few typos and left a few take-it-or-leave-it comments.

I haven't thought through the details at all through, and I think it needs a careful review from @petrelharp for that.

[apragsdale]

Thanks so much for the quick review, @jeromekelleher. I agree with your suggestions and will fix things up accordingly.

[lkirk]

I think this will also need a changelog entry, since adding documentation will announce that this API is now public. Does that happen here or in a later part of the release pipeline?

[petrelharp]

That could happen here!

[jeromekelleher]

We can add to the changelog here or not, whichever is easier. We do need a review from you though @petrelharp as I'm not on top of the stats details.

[jeromekelleher]

I've created a milestone for version 1.1, which will basically be this new LD API plus the new metadata codec. Would be good to get it shipped in the next week or so if possible.