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port to slim v4 #1326

Merged
merged 1 commit into from
Aug 17, 2022
Merged

port to slim v4 #1326

merged 1 commit into from
Aug 17, 2022

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petrelharp
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With these changes, tests now pass using the new version of SLiM on my computer at least. Mostly this just required changing "generation" to "tick"; there was only one thing that was hard to track down.

@petrelharp petrelharp force-pushed the slim_v4 branch 2 times, most recently from fa6a17c to 80c805e Compare August 16, 2022 21:53
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codecov bot commented Aug 16, 2022 •
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Codecov Report

Merging #1326 (fdd2f2d) into main (7f10fe4) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main    #1326   +/-   ##
=======================================
  Coverage   99.67%   99.67%           
=======================================
  Files         111      111           
  Lines        3674     3674           
  Branches      473      473           
=======================================
  Hits         3662     3662           
  Misses          8        8           
  Partials        4        4
Impacted Files Coverage Δ
stdpopsim/slim_engine.py 100.00% <100.00%> (ø)

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@andrewkern
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okay, well to review this properly i'm going to have to start by reading the new time units section!

andrewkern
andrewkern approved these changes Aug 16, 2022
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looks like a simple enough conversion to v4, but there is definitely going to be breakage.

should average generation time be recorded in the metadata (as in the pyslim examples)? currently everything is WF so perhaps not?

stdpopsim/slim_engine.py
"inds=p"+pop+".sampleIndividuals("+n+"); " +
"sim.treeSeqRememberIndividuals(inds);}",
g, g);
if (n > 0) {
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what happens if n <= 0?

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MesserLab/SLiM#345 happens

@petrelharp
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looks like a simple enough conversion to v4, but there is definitely going to be breakage.

Where?

should average generation time be recorded in the metadata (as in the pyslim examples)? currently everything is WF so perhaps not?

No, everything is WF, so one tick = one generation. (well, actually it equals Q generations...) It's something we'll have to deal with if/when we provide nonWF recipes, but that's a hurdle for the future.

@andrewkern
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okay sounds good @petrelharp!

@andrewkern andrewkern merged commit 549a3ea into popsim-consortium:main Aug 17, 2022
@petrelharp petrelharp mentioned this pull request Aug 19, 2022
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@andrewkern andrewkern andrewkern approved these changes

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@petrelharp @andrewkern