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QC for GAS_1A17 (AnoGam) #1279

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merged 1 commit into from
May 26, 2022
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petrelharp
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Closes #1278.

I've renamed the model GabonAg1000G_1A17, since the string is supposed to be "descriptive", and "GAS" is just the internal code used for Gabon. I've also decided not to put all 110 epoch times and demographic sizes in the summary table. I ran into no problems!

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codecov bot commented May 25, 2022

Codecov Report

Merging #1279 (09fd16a) into main (a98b3f0) will increase coverage by 0.20%.
The diff coverage is 100.00%.

❗ Current head 09fd16a differs from pull request most recent head 997ff8b. Consider uploading reports for the commit 997ff8b to get more accurate results

@@            Coverage Diff             @@
##             main    #1279      +/-   ##
==========================================
+ Coverage   99.45%   99.65%   +0.20%     
==========================================
  Files         110      111       +1     
  Lines        3503     3523      +20     
  Branches      436      438       +2     
==========================================
+ Hits         3484     3511      +27     
+ Misses         15        8       -7     
  Partials        4        4              
Impacted Files Coverage Δ
stdpopsim/catalog/AnoGam/demographic_models.py 100.00% <100.00%> (+58.33%) ⬆️
stdpopsim/qc/AnoGam.py 100.00% <100.00%> (ø)
stdpopsim/qc/__init__.py 100.00% <100.00%> (ø)

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@petrelharp
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So - I got the same model, but then I tried to remove the "epochs" in the model in which nothing changes - i.e., the zero-length epochs and the ones where the population size is the same as before. Now, things don't pass, and someone else ought to fix up the original model. Might you be able to have a go at this, @andrewkern?

@petrelharp
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Never mind! I got it! Simplified the model in the code by some careful hand editing, and it agrees with the programatic solution in QC. I think tihs is ready to go!

@andrewkern
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right on. i'm going to merge this

fixup qc model

simplified model

allow fractional values of generation time
@petrelharp
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wait let me squash it first

@petrelharp petrelharp merged commit 77f9663 into popsim-consortium:main May 26, 2022
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QC for GAS_1A17 (AnoGam)
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