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bodkan / slendr

Population genetic simulations in R 🌍
https://bodkan.net/slendr
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Port slendr to SLiM 4.0 and update Python dependencies #104

Closed bodkan closed 2 years ago

bodkan commented 2 years ago

We got there and it didn't even take much time.

slendr is now locked to SLiM 4.x, and drops the 3.7.1 support going forward. Similarly, the latest versions of msprime/tskit/pyslim are also required for tree sequence analysis and are automatically installed via slendr's setup_env() function upon calling library(slendr). No additional work by the user is needed. This new slendr version will go to the main branch once automated tests in this PR pass and should appear on CRAN soon after that (no revisions will be needed this time).

I will update the manuscript soon, probably next week. I predict only 5-10 sentences will need to be changed, mostly installation instructions (CRAN instead of GitHub installation) and description of software dependencies. Basically all other changes to the R package have been internal and don't involve changes in user-facing functionality.

I would like to submit the paper to PCI for review in the first 1-2 weeks of September. I will ping all three of you (@FerRacimo, @bhaller and @petrelharp) as soon as I made those updates to the paper.

codecov-commenter commented 2 years ago

Codecov Report

Merging #104 (ea76239) into main (5a4aedb) will decrease coverage by 0.18%. The diff coverage is 60.00%.

@@            Coverage Diff             @@
##             main     #104      +/-   ##
==========================================
- Coverage   81.90%   81.71%   -0.19%     
==========================================
  Files           6        6              
  Lines        2879     2888       +9     
==========================================
+ Hits         2358     2360       +2     
- Misses        521      528       +7
Impacted Files Coverage Δ
R/tree-sequences.R 85.42% <57.89%> (-0.57%) :arrow_down:
R/compilation.R 89.71% <100.00%> (ø)

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bodkan commented 2 years ago

All CI tests passed. Merging...