Documentation/Consistency Review#3329
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benjeffery merged 8 commits intotskit-dev:mainfrom Nov 24, 2025
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #3329 +/- ##
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Coverage 89.72% 89.72%
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Files 29 29
Lines 31181 31192 +11
Branches 5720 5722 +2
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+ Hits 27976 27988 +12
Misses 1796 1796
+ Partials 1409 1408 -1
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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.
docs/stats.md
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| statistics, isolated samples without mutations directly above them are treated | ||
| as carrying the ancestral allele rather than as missing. Future versions of | ||
| tskit may expose options to treat missing data differently in statistics; for | ||
| now, if you need explicit control over how missing data are handled you should |
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| 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 |
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IBD extracted to #3330 |
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I'll wait for @petrelharp before merging. |
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This all looks good, but see comments/suggestions? |
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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.