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adding "generic" human DFE #1505

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merged 6 commits into from
Aug 19, 2023
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chriscrsmith
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@chriscrsmith chriscrsmith commented Aug 5, 2023

For #1494 .

Adding human DFE from Kyriazis et al. Will need to finish this once the h-s relationship PR (#1498) is in, for now this is only half finished but the values are in place at least.

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Ok this PR is ready for a review. Started a QC issue #1507

Tests failing with error "EnvironmentNameNotFound: Could not find conda environment: stdpopsim"

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try bumping the cache number

@petrelharp petrelharp mentioned this pull request Aug 15, 2023
@chriscrsmith
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Updated with new prop deleterious.

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Looks good, other than some minor suggestions/comments!

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Thanks @petrelharp . How's it look now?

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codecov bot commented Aug 18, 2023

Codecov Report

Patch coverage: 100.00% and project coverage change: -0.17% ⚠️

Comparison is base (d923127) 99.85% compared to head (8cd2e59) 99.68%.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1505      +/-   ##
==========================================
- Coverage   99.85%   99.68%   -0.17%     
==========================================
  Files         121      121              
  Lines        4160     4178      +18     
  Branches      588      588              
==========================================
+ Hits         4154     4165      +11     
- Misses          3        6       +3     
- Partials        3        7       +4     
Files Changed Coverage Δ
stdpopsim/catalog/HomSap/dfes.py 100.00% <100.00%> (ø)

... and 2 files with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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Thanks, @chriscrsmith! Merging.

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LGTM!

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Wait, not merging - what's up with the failing tests?

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Looks like you need to run pre-commit to format the code yet, @chriscrsmith - can you do that (and squash down the commits while you're about it)? I guess the cache didn't fix the other CI errors, though. Hm - any clues what's going on there?

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chriscrsmith commented Aug 18, 2023

I changed two lines in tests.py according to some posts I found online and the test pass now. What do you think?

Doh. Now it's failing yet again

got proportion

added dom coefficients

almost finished

added lethal mutations

Update dfes.py

add uniform DFE (closes popsim-consortium#1481)

h-s relationship (closes popsim-consortium#1488)

formatting

test dominance coeffs actually in there

remove deprecated set-output (see https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/ )
and bump cache

package version bumps

remove python 3.7 as it is end-of-life and creates install problems for scikit-allel

make sure the tests are testing what they're supposed to test

chris comments

changelog

clarify manual

more chris comments

bump cache?!?!

using homsap mu

using homsap mu

flake8

delete stray print

different neutral prop

Update stdpopsim/catalog/HomSap/dfes.py

Co-authored-by: Peter Ralph <petrel.harp@gmail.com>

Update stdpopsim/catalog/HomSap/dfes.py

Co-authored-by: Peter Ralph <petrel.harp@gmail.com>

Update stdpopsim/catalog/HomSap/dfes.py

Co-authored-by: Peter Ralph <petrel.harp@gmail.com>

updates to new dfe

Apply suggestions from code review

reduce cache num again

fixxxxxxxxxxxxxxxxxxxxxxxxx

bump cache

trying changeing tests.yml

trying changeing tests.yml

reduce cache num again
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This has passed: https://github.com/popsim-consortium/stdpopsim/actions/runs/5908022482
... the CI issues are not due to this PR. (same with codecov) Merging.

@petrelharp petrelharp merged commit d89010f into popsim-consortium:main Aug 19, 2023
6 of 11 checks passed
@chriscrsmith chriscrsmith deleted the generic_dfe branch August 19, 2023 13:17
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2 participants