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Vaquita species add #1514

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merged 1 commit into from
Oct 10, 2023
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igronau
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@igronau igronau commented Sep 13, 2023

Initial version of the Vaquita species model. We still need to figure out the recombination rate. See #1508.

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codecov bot commented Sep 13, 2023

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (d89010f) 99.85% compared to head (357bf42) 99.85%.
Report is 7 commits behind head on main.

❗ Current head 357bf42 differs from pull request most recent head 262ad39. Consider uploading reports for the commit 262ad39 to get more accurate results

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1514   +/-   ##
=======================================
  Coverage   99.85%   99.85%           
=======================================
  Files         121      124    +3     
  Lines        4178     4191   +13     
  Branches      588      588           
=======================================
+ Hits         4172     4185   +13     
  Misses          3        3           
  Partials        3        3           
Files Coverage Δ
stdpopsim/catalog/PhoSin/__init__.py 100.00% <100.00%> (ø)
stdpopsim/catalog/PhoSin/genome_data.py 100.00% <100.00%> (ø)
stdpopsim/catalog/PhoSin/species.py 100.00% <100.00%> (ø)

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@igronau igronau force-pushed the vaquita_species_add branch from 789bbdb to a2091db Compare September 14, 2023 08:55
@chriscrsmith chriscrsmith mentioned this pull request Oct 9, 2023
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@petrelharp petrelharp left a comment

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LGTM; some minor changes.

README.md Outdated Show resolved Hide resolved
stdpopsim/catalog/PhoSin/species.py Outdated Show resolved Hide resolved
stdpopsim/catalog/PhoSin/species.py Outdated Show resolved Hide resolved
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Let's make sure I didn't mess this up, then merge.

Implemented PhoSin species (Vaquita). First version (before QC)

now also adding the test file

added explanation for recombination rate and fixed issues in docs

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Update stdpopsim/catalog/PhoSin/species.py

cache bump
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I ran the tests locally, and they're wroking, so even if this doesn't work after the cache bump I'm going to merge this with or without the CI.

@petrelharp petrelharp mentioned this pull request Oct 10, 2023
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Okay - everything passed except for the tests as reported in #1523, unrelated to this PR. I will merge.

@petrelharp petrelharp merged commit 5f2e528 into popsim-consortium:main Oct 10, 2023
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igronau commented Oct 11, 2023

Looks good. Thanks, @petrelharp

@igronau igronau mentioned this pull request Oct 12, 2023
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2 participants