Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / tskit-dev/msprime issues and pull requests

#2338 - Example PR for teaching

Pull Request - State: closed - Opened by benjeffery 11 days ago - 1 comment

#2334 - Update actions ubuntu version

Pull Request - State: closed - Opened by benjeffery about 1 month ago - 1 comment

#2333 - Matching recombination rates for recapitation of SLiM with msprime

Issue - State: closed - Opened by freshspaceoctopus about 1 month ago - 1 comment

#2332 - remove wrong statement

Pull Request - State: closed - Opened by petrelharp about 1 month ago - 7 comments

#2331 - Update actions ubuntu version

Pull Request - State: closed - Opened by benjeffery about 2 months ago - 1 comment

#2330 - Update GitHub Actions to latest major versions

Pull Request - State: closed - Opened by benjeffery about 2 months ago - 1 comment

#2329 - Update GitHub Actions to latest major versions

Pull Request - State: closed - Opened by benjeffery about 2 months ago - 1 comment

#2327 - ci(mergify): upgrade configuration to current format

Pull Request - State: closed - Opened by mergify[bot] 3 months ago - 1 comment

#2326 - Test_pedigree.py with internal samples

Pull Request - State: open - Opened by abureau 4 months ago - 1 comment

#2325 - Test_pedigree with internal samples

Pull Request - State: closed - Opened by abureau 4 months ago - 5 comments

#2323 - Simulate more common SNPs

Issue - State: closed - Opened by Chonghao98 4 months ago - 6 comments

#2322 - N function in pedigree sims

Pull Request - State: closed - Opened by hannesbecher 4 months ago - 5 comments

#2321 - Initial steps for internal pedigree samples

Pull Request - State: closed - Opened by jeromekelleher 5 months ago - 5 comments

#2318 - Add an example of calculating the map positions

Pull Request - State: closed - Opened by hyanwong 6 months ago - 1 comment

#2317 - removed scipy.stats.chisquared; closes #2316

Pull Request - State: closed - Opened by petrelharp 6 months ago - 2 comments

#2316 - chi square tests for mutation verification broken

Issue - State: closed - Opened by jeromekelleher 6 months ago - 1 comment
Labels: bug

#2315 - Pin to specific SLiM version

Pull Request - State: closed - Opened by jeromekelleher 6 months ago - 1 comment

#2314 - Make older msprime tests build againts numpy<2

Pull Request - State: closed - Opened by jeromekelleher 6 months ago - 1 comment

#2313 - V1.3.3 hotfix

Pull Request - State: closed - Opened by jeromekelleher 6 months ago - 2 comments

#2312 - Version 1.3.2 contains untested smc_k code

Issue - State: open - Opened by jeromekelleher 6 months ago
Labels: bug

#2311 - Update changelog for bugfix release

Pull Request - State: closed - Opened by jeromekelleher 6 months ago - 1 comment

#2310 - Multiple merger polyploid scaling

Pull Request - State: closed - Opened by jeromekelleher 6 months ago - 3 comments

#2309 - Multiple merger polyploid scaling

Pull Request - State: closed - Opened by JereKoskela 6 months ago - 2 comments

#2308 - Malloc Q rather than from stack in multi-merger

Pull Request - State: closed - Opened by jeromekelleher 6 months ago - 1 comment

#2307 - Segfault with `BetaCoalescent` and ploidy greater than diploid

Issue - State: closed - Opened by nspope 6 months ago - 9 comments
Labels: bug

#2306 - DOC: pyslim link

Pull Request - State: closed - Opened by daikitag 6 months ago - 1 comment
Labels: documentation

#2305 - Broken pyslim link in documentation

Issue - State: closed - Opened by daikitag 6 months ago - 1 comment
Labels: documentation

#2304 - add kastore to development.txt

Pull Request - State: closed - Opened by petrelharp 6 months ago - 2 comments

#2303 - Factor out distributed SMC logic

Pull Request - State: open - Opened by jeromekelleher 6 months ago - 1 comment

#2302 - No module named kastore when following Development guide

Issue - State: closed - Opened by PandaGab 6 months ago - 1 comment

#2300 - Insert merged lineage

Pull Request - State: closed - Opened by jeromekelleher 6 months ago - 2 comments

#2298 - Add lineage tail

Pull Request - State: closed - Opened by jeromekelleher 6 months ago - 2 comments

#2297 - Move segment attrs to lineage

Pull Request - State: closed - Opened by jeromekelleher 7 months ago - 2 comments

#2296 - Simpler lineage struct

Pull Request - State: closed - Opened by jeromekelleher 7 months ago - 3 comments

#2295 - Add lineage struct

Pull Request - State: closed - Opened by jeromekelleher 7 months ago - 2 comments

#2294 - Add Lineage/lineage_t concept

Issue - State: open - Opened by jeromekelleher 7 months ago - 1 comment

#2293 - Multiple model simulation is not accurately capturing demography model

Issue - State: closed - Opened by daikitag 7 months ago - 6 comments
Labels: bug

#2291 - Fix doc refs and CircleCI

Pull Request - State: closed - Opened by benjeffery 7 months ago - 1 comment

#2290 - Changelog

Pull Request - State: closed - Opened by benjeffery 7 months ago - 2 comments

#2289 - Coalescent rate trajectory ignores a population's activation time

Issue - State: open - Opened by apragsdale 7 months ago - 2 comments

#2288 - Python 3.12 wheels

Issue - State: closed - Opened by fcooper8472 7 months ago - 3 comments

#2287 - Upgrade actions and use numpy2

Pull Request - State: closed - Opened by benjeffery 7 months ago - 8 comments

#2286 - Support numpy >= 2, drop Python 3.8

Pull Request - State: closed - Opened by jeromekelleher 8 months ago - 2 comments

#2285 - MacOS ARM wheels packages broken

Issue - State: closed - Opened by jeromekelleher 9 months ago - 3 comments
Labels: bug

#2284 - stat verification gc smck

Pull Request - State: closed - Opened by GertjanBisschop 9 months ago - 2 comments

#2283 - update installation docs

Pull Request - State: closed - Opened by GertjanBisschop 9 months ago - 1 comment

#2282 - Smc(k) gene conversion

Pull Request - State: closed - Opened by GertjanBisschop 9 months ago - 3 comments

#2281 - merge

Pull Request - State: closed - Opened by agushin101 9 months ago

#2280 - Enable gene conversion for SMC_K model

Issue - State: closed - Opened by GertjanBisschop 9 months ago - 1 comment

#2277 - Fix OSX tests

Pull Request - State: closed - Opened by benjeffery 10 months ago - 7 comments

#2276 - add tree fixation using newick string and TreeSequence object

Pull Request - State: open - Opened by not-a-feature 10 months ago - 5 comments

#2275 - Fix codecov

Pull Request - State: closed - Opened by benjeffery 10 months ago - 1 comment

#2273 - add record_provenance argument to sim_mutations; closes #2272

Pull Request - State: closed - Opened by petrelharp 10 months ago - 1 comment

#2272 - no `record_provenance` argument to sim_mutations

Issue - State: closed - Opened by petrelharp 11 months ago

#2271 - Clarify the meaning of the mutation rate when a matrix is used

Pull Request - State: closed - Opened by hyanwong 11 months ago - 3 comments

#2270 - Hulls

Pull Request - State: closed - Opened by GertjanBisschop 11 months ago - 2 comments

#2269 - AFS folding (polarised=False)

Issue - State: open - Opened by sunyatin 11 months ago - 6 comments

#2267 - Disallow unstable beta coalescents

Pull Request - State: closed - Opened by JereKoskela 12 months ago - 5 comments

#2266 - multiallelic sites within the VCF

Issue - State: open - Opened by LuisGFdez 12 months ago - 1 comment

#2265 - Verification kdeplot

Pull Request - State: closed - Opened by daikitag 12 months ago - 1 comment

#2264 - Docs versioning no longer working

Issue - State: open - Opened by jeromekelleher 12 months ago - 2 comments
Labels: documentation

#2263 - Update docs copyright year

Issue - State: closed - Opened by jeromekelleher 12 months ago
Labels: documentation

#2262 - Update installation docs for minimum python version

Issue - State: closed - Opened by jeromekelleher 12 months ago
Labels: documentation

#2261 - Document no pip install on Windows

Issue - State: closed - Opened by daikitag 12 months ago - 1 comment
Labels: documentation

#2258 - update changelog

Pull Request - State: closed - Opened by GertjanBisschop 12 months ago - 1 comment

#2257 - Numerical stability of beta model

Pull Request - State: closed - Opened by JereKoskela about 1 year ago - 6 comments

#2249 - issue with replicates using "num_replicates"

Issue - State: closed - Opened by yzliu01 about 1 year ago - 4 comments

#2248 - global stop condition

Pull Request - State: open - Opened by GertjanBisschop about 1 year ago - 1 comment

#2247 - Syncing sweeps implementation in algorithms.py

Pull Request - State: open - Opened by GertjanBisschop about 1 year ago - 1 comment

#2246 - Update pypi release package

Pull Request - State: closed - Opened by benjeffery about 1 year ago

#2245 - Update changelog date

Pull Request - State: closed - Opened by benjeffery about 1 year ago

#2244 - Remove research notice

Pull Request - State: closed - Opened by jeromekelleher about 1 year ago - 1 comment

#2243 - Save information about sweep in SweepGenicSelection model

Issue - State: open - Opened by jeromekelleher about 1 year ago - 6 comments
Labels: enhancement

#2242 - Illogical Lineage Counts in algorithms.py

Issue - State: open - Opened by agushin101 about 1 year ago - 7 comments

#2241 - Additional stats tests microsats

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 1 comment

#2240 - Update demography tests to stdpopsim 0.2

Issue - State: open - Opened by GertjanBisschop about 1 year ago - 1 comment
Labels: Infrastructure and tools

#2239 - pin stdpopsim

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 2 comments

#2238 - avoid negative probs, closes #2237

Pull Request - State: closed - Opened by petrelharp about 1 year ago - 1 comment

#2237 - TPM microsats model transition matrix error

Issue - State: closed - Opened by GertjanBisschop about 1 year ago - 6 comments

#2236 - verification.py updates

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 1 comment

#2235 - Computing likelihood for decapitated ARGs.

Issue - State: open - Opened by GertjanBisschop about 1 year ago
Labels: enhancement

#2234 - make verfication.py compatible with latest pyslim

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 1 comment

#2233 - Tests fail with stdpopsim 0.2.0

Issue - State: open - Opened by benjeffery about 1 year ago - 7 comments
Labels: Infrastructure and tools

#2232 - modify checks arg lik

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 8 comments

#2231 - remove ll_representation argument

Pull Request - State: open - Opened by GertjanBisschop about 1 year ago - 2 comments

#2230 - fix msmssweeps verification

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 1 comment

#2229 - AttributeErrors in verification.py: MsmsSweeps

Issue - State: closed - Opened by GertjanBisschop about 1 year ago - 5 comments

#2228 - remove tests/data folder

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 3 comments

#2227 - update changelog

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 1 comment

#2226 - 1.3.0 Release

Issue - State: closed - Opened by jeromekelleher about 1 year ago - 2 comments

#2225 - dtwf/ped stats tests

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 1 comment

#2224 - fix sorting bug pedigrees

Pull Request - State: closed - Opened by GertjanBisschop about 1 year ago - 1 comment

#2223 - Island model - migration rate definition

Issue - State: closed - Opened by JaneeshBansal about 1 year ago - 1 comment

#2222 - Update development.md

Pull Request - State: closed - Opened by daikitag about 1 year ago - 1 comment

#2221 - CpG mutation models

Issue - State: open - Opened by hyanwong about 1 year ago - 4 comments

#2220 - Update DOI msprime 1.0 paper CITATION.md

Pull Request - State: closed - Opened by GertjanBisschop over 1 year ago - 1 comment