search

popsim-consortium / analysis2

Analysis for the second consortium paper.
8 stars 14 forks source link

added samples with size to dict for SLiM input deprecation warning #83

Closed stsmall closed 1 year ago

stsmall commented 1 year ago

Warning of deprecation error where previous input was vector of pop sizes. Now build dict from stdpopsim model w/ popsizes and pop names

stsmall commented 1 year ago

shoot ... forgot I also zip annotations and DFE to link them in the expand fx. Else expand creates all iterations. Seemed easier to control and returns only expected and sensible combinations.

andrewkern commented 1 year ago

@stsmall this looks fine. is the plan to push a few of these small PRs before the bigger one?

stsmall commented 1 year ago

Well ... I would rather make a big PR. @chriscrsmith and I tested the code on Friday (chris ran it on the server w/out error) and I tested the code all weekend with different params. Everything ran without error and pretty fast. Today Chris and I met to discuss how to PR the fixes and I walked him through the code modifications. Problem is that most of the code is dependent on the new {pop} dir and wildcard in the n_t.smk and that is a breaking change with the current n_t.snake. So all the methods (msmc.py, smc.py, stairway.py, gone.py, plots.py) need to be pushed along with the modified n_t.smk. So if you are OK with it, then I can make a big push.

chriscrsmith commented 1 year ago

I talked @stsmall into doing this tiny PR. I think it would be a lot easier for him/us to do a bigger PR; but maybe harder for the people reviewing the code

andrewkern commented 1 year ago

got it. so let's merge this and then move to your big PR?

chriscrsmith commented 1 year ago

checked out the pr and the sims run

andrewkern commented 1 year ago

right on. i'll squash and merge