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Added BosTau demographies from Boitard et al. (2016) #1593

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merged 2 commits into from
Dec 13, 2024

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gregorgorjanc
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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

@gregorgorjanc
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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 bot commented Dec 12, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.81%. Comparing base (6740b88) to head (9f28b6e).
Report is 4 commits behind head on main.

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1593   +/-   ##
=======================================
  Coverage   99.81%   99.81%           
=======================================
  Files         130      130           
  Lines        4376     4408   +32     
  Branches      603      603           
=======================================
+ Hits         4368     4400   +32     
  Misses          3        3           
  Partials        5        5           

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@petrelharp petrelharp left a comment

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Looks good to me! Minor suggestions.

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@petrelharp
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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]>
@gregorgorjanc
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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

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Looks good - thanks! Now if we can get this QC'ed very soon (a week?) it'll go in the next release!

@petrelharp petrelharp merged commit 16497b3 into popsim-consortium:main Dec 13, 2024
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2 participants