adding "generic" human DFE #1505
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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 |
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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? |
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## main #1505 +/- ##
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- Coverage 99.85% 99.68% -0.17%
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Files 121 121
Lines 4160 4178 +18
Branches 588 588
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+ Hits 4154 4165 +11
- Misses 3 6 +3
- Partials 3 7 +4
☔ View full report in Codecov by Sentry. |
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Thanks, @chriscrsmith! Merging. |
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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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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 |
chriscrsmith
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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 |
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.