Documentation/Consistency Review

[benjeffery]

I thought it wise before 1.0 to do a full (automated) review that documentation lines up with the code we're running. Several hours of token crunching and 45min of human review/improvement resulted in these commits, which are best viewed as separate diffs as it's a bit of a grab-bag. I think these are all worth merging though - even if they are things we weren't planning to get to.

That there wasn't more than this to find is very reassuring, but then a lot of effort has been put in to ensure tskit's quality.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.72%. Comparing base (1e2ccb6) to head (f50727f).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3329   +/-   ##
=======================================
  Coverage   89.72%   89.72%           
=======================================
  Files          29       29           
  Lines       31181    31192   +11     
  Branches     5720     5722    +2     
=======================================
+ Hits        27976    27988   +12     
  Misses       1796     1796           
+ Partials     1409     1408    -1     

Flag	Coverage Δ
c-tests	86.71% <100.00%> (+<0.01%)	⬆️
lwt-tests	80.38% <ø> (ø)
python-c-tests	87.05% <ø> (ø)
python-tests	98.84% <100.00%> (+<0.01%)	⬆️
python-tests-no-jit	33.51% <7.69%> (-0.05%)	⬇️
python-tests-numpy1	50.16% <92.30%> (+0.05%)	⬆️

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

Files with missing lines	Coverage Δ
c/tskit/tables.c	83.08% <100.00%> (+0.01%)	⬆️
python/tskit/trees.py	98.89% <100.00%> (+<0.01%)	⬆️

🚀 New features to boost your workflow:

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

[jeromekelleher]

I've gone through and it all looks good to me except for the IBDsegments stuff, which I'd have to spend more time on. I'd suggest pulling this commit out into it's own PR, and get the rest merged.

[jeromekelleher]

Suggested change

	now, if you need explicit control over how missing data are handled you should
	now, if you need explicit control over how missing data is handled you should

[benjeffery]

:D

[benjeffery]

95bad61

[benjeffery]

IBD extracted to #3330

[benjeffery]

I'll wait for @petrelharp before merging.

[petrelharp]

This all looks good, but see comments/suggestions?