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Added BosTau demographies from Boitard et al. (2016) #1593
Added BosTau demographies from Boitard et al. (2016) #1593
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Test fail because I have specified recombination rate specific to inferred demographic models - this functionality is available in PR #1591 |
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1593 +/- ##
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Coverage 99.81% 99.81%
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Files 130 130
Lines 4376 4408 +32
Branches 603 603
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+ Hits 4368 4400 +32
Misses 3 3
Partials 5 5 ☔ View full report in Codecov by Sentry. |
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Looks good to me! Minor suggestions.
Don't worry about the pre-commit or failing macos tests; I think if you fix up those things in my review, and test it locally (as in the docs) then we can merge this and you'll open QC issues. Hm - QC will be a bit tricky here because of the "personal communication"; so, the personal communication should probably be pasted into the QC issue? |
Added BosTau Boitard et al. (2016) parameter tables for docs Update stdpopsim/catalog/BosTau/demographic_models.py Co-authored-by: Peter Ralph <[email protected]> Update stdpopsim/catalog/BosTau/demographic_models.py Co-authored-by: Peter Ralph <[email protected]> Update stdpopsim/catalog/BosTau/demographic_models.py Co-authored-by: Peter Ralph <[email protected]> Update stdpopsim/catalog/BosTau/demographic_models.py Co-authored-by: Peter Ralph <[email protected]>
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@petrelharp I have now went over all the suggested changes, done the testing in Python, so I think this is ready for a merge. Should I open 4 QC issues (I added 4 models from one publication) or 1 QC issue for the 4 models? I will add personal communication note in there ... I have made Simon Boitard (author of the publication) aware as well. I created one issue here #1598 |
Looks good - thanks! Now if we can get this QC'ed very soon (a week?) it'll go in the next release! |
I have added four BosTau demographies from Boitard et al. (2016) https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005877 to complement the one from MacLeod et al. (2013) https://doi.org/10.1093/molbev/mst125