popsim-consortium/stdpopsim issues and pull requests

#1349 - deprecate `--length-multiplier` CLI option

Issue - State: open - Opened by grahamgower about 2 years ago - 3 comments

#1347 - Mention species inclusion criteria in development docs

Issue - State: closed - Opened by nspope about 2 years ago - 2 comments

#1344 - QC for AraThal DFE

Issue - State: open - Opened by chriscrsmith about 2 years ago - 9 comments
Labels: Model QC

#1343 - require SLiM version 4.0++

Issue - State: closed - Opened by petrelharp about 2 years ago - 3 comments

#1342 - enable SLiM on Windows

Pull Request - State: open - Opened by petrelharp about 2 years ago - 17 comments

#1331 - Changelog for 0.2.0

Pull Request - State: closed - Opened by nspope about 2 years ago - 2 comments

#1321 - AraTha DFE

Issue - State: closed - Opened by chriscrsmith over 2 years ago - 2 comments
Labels: enhancement

#1319 - 0.2 release checklist

Issue - State: closed - Opened by petrelharp over 2 years ago - 7 comments

#1315 - Bump attrs from 21.4.0 to 22.1.0 in /requirements/CI

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 4 comments
Labels: dependencies

#1312 - Add pig species and published demographies (SusScr)

Issue - State: open - Opened by gregorgorjanc over 2 years ago - 4 comments
Labels: enhancement

#1305 - Enable SLiM engine on Windows

Issue - State: open - Opened by KellenRiall over 2 years ago - 1 comment
Labels: enhancement

#1292 - Dfe qc

Pull Request - State: closed - Opened by xin-huang over 2 years ago - 17 comments

#1287 - Update species.py

Pull Request - State: closed - Opened by gregorgorjanc over 2 years ago - 2 comments

#1286 - PonAbe QC and assembly update

Pull Request - State: closed - Opened by grahamgower over 2 years ago - 4 comments

#1285 - Print url when download fails

Pull Request - State: closed - Opened by grahamgower over 2 years ago - 1 comment

#1277 - Bump coverage from 6.3.3 to 6.4 in /requirements/CI

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#1276 - Bump numpy from 1.21.5 to 1.22.4 in /requirements/CI

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#1252 - Add assembly name to standard naming for annotation

Issue - State: open - Opened by petrelharp over 2 years ago - 8 comments

#1233 - Convert demographic models to Demes YAML files

Pull Request - State: open - Opened by grahamgower over 2 years ago - 11 comments

#1225 - Add recombination rate to stdpopsim.DemographicModel

Issue - State: open - Opened by gregorgorjanc over 2 years ago - 3 comments
Labels: enhancement

#1221 - 0-based counting in BosTau _HolsteinFriesian_1M13 #579

Pull Request - State: closed - Opened by gregorgorjanc over 2 years ago - 1 comment

#1220 - QC for Chimpanzee (Pan troglodytes)

Issue - State: closed - Opened by xin-huang over 2 years ago - 27 comments
Labels: Species QC

#1215 - Add PanTro

Pull Request - State: closed - Opened by xin-huang over 2 years ago - 3 comments

#1214 - Updated BosTau Holstein demography mut rate #579

Pull Request - State: closed - Opened by gregorgorjanc over 2 years ago - 1 comment

#1168 - enable slim engine tests on windows

Issue - State: open - Opened by grahamgower almost 3 years ago - 1 comment

#1089 - un-skip tests when SLiM 3.7 released

Issue - State: open - Opened by petrelharp about 3 years ago

#1085 - write "how to add a DFE" section of the development docs

Issue - State: closed - Opened by petrelharp about 3 years ago

#1057 - split catalog documentation into multiple pages

Issue - State: open - Opened by grahamgower about 3 years ago - 1 comment
Labels: docs

#1055 - implement QC for DFEs

Issue - State: closed - Opened by petrelharp about 3 years ago - 3 comments
Labels: enhancement

#992 - model.get_demography_debugger() is not working

Issue - State: open - Opened by izabelcavassim over 3 years ago - 2 comments

#944 - start selection docs

Issue - State: closed - Opened by petrelharp over 3 years ago - 2 comments
Labels: enhancement

#786 - update validation.py after demography API changes

Issue - State: closed - Opened by grahamgower over 3 years ago - 9 comments

#719 - deprecation process for old genetic maps/ids

Issue - State: open - Opened by grahamgower almost 4 years ago - 5 comments

#714 - Review externally documented Python API

Issue - State: closed - Opened by jeromekelleher almost 4 years ago - 1 comment

#670 - API for `Contig` class and `Species.get_contig()`.

Issue - State: closed - Opened by grahamgower about 4 years ago - 10 comments

#619 - Cache invalidation and naming for annotations

Issue - State: open - Opened by grahamgower about 4 years ago - 3 comments
Labels: bug, help wanted

#617 - info on slack workspace docs

Issue - State: open - Opened by agladstein about 4 years ago - 2 comments
Labels: good first issue, docs

#533 - Problems with IM Model

Issue - State: open - Opened by jeromekelleher over 4 years ago - 11 comments

#427 - Use a temp directory instead of temp files in the SLiM engine

Issue - State: open - Opened by grahamgower over 4 years ago
Labels: good first issue

#419 - the SLiM engine should print some details in the "Simulation information"

Issue - State: closed - Opened by grahamgower over 4 years ago - 1 comment
Labels: good first issue

#417 - Improve github initial user experience

Issue - State: closed - Opened by jeromekelleher over 4 years ago - 6 comments

#401 - Add option to use specific chrom region, and random region with given length

Issue - State: closed - Opened by grahamgower almost 5 years ago - 7 comments

#383 - Handling of sex chromosomes

Issue - State: open - Opened by jeromekelleher almost 5 years ago - 5 comments

#320 - Allow more flexible sampling (e.g., from past times)

Issue - State: open - Opened by jeromekelleher almost 5 years ago - 4 comments

#260 - [slim-engine-dev] Set population size to zero if there is no influence on the rest of the simulation.

Issue - State: open - Opened by grahamgower almost 5 years ago - 24 comments

#203 - Implement key-value pairs for specifying sampling

Issue - State: closed - Opened by ndukler almost 5 years ago - 4 comments

GitHub / popsim-consortium/stdpopsim issues and pull requests