Ecosyste.ms: Issues

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

GitHub / tskit-dev/pyslim issues and pull requests

#359 - do not simulate null ancestry; closes #357

Pull Request - State: open - Opened by petrelharp 23 days ago - 1 comment

#358 - pyslim.recapitate error

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

#357 - recapitation attempts to use null genomes

Issue - State: open - Opened by Hongjinwu about 1 month ago - 12 comments

#356 - Update actions ubuntu version

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

#355 - Update GitHub Actions to latest major versions

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

#352 - TSK_ERR_MUTATION_TIME_OLDER_THAN_PARENT_NODE

Issue - State: closed - Opened by steinrue 4 months ago - 9 comments

#351 - update metadata for multichromosome

Issue - State: open - Opened by petrelharp 4 months ago

#349 - Update documentation

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

#348 - :meth: is not working in documentation

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

#347 - Typo in `recapitate` function docstring

Issue - State: closed - Opened by daikitag 7 months ago - 1 comment

#346 - Update methods.py

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

#345 - Strange warning in recapitation

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

#344 - Fix mutation rate in time units example

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

#343 - Recapitation for complex demography with populations that died out

Issue - State: closed - Opened by Luker121 8 months ago - 11 comments

#342 - Fix codecov

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

#340 - Discrepancies in diversity after recapitation and mutation overlay

Issue - State: closed - Opened by AudeCaizergues 12 months ago - 1 comment

#339 - default sex ratio 0.0

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

#338 - update quickreference list at top of docs

Issue - State: open - Opened by petrelharp about 1 year ago

#337 - Update vignette_space.md

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

#336 - Potential to use .frequencies() method in /tutorial.html

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

#335 - fix navigation with keys warning

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

#333 - Suggesting an edit for vignette_space.slim

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

#332 - Suggestion for vignette: a spatial simulation

Pull Request - State: closed - Opened by jiseonmin over 1 year ago - 2 comments

#331 - edges are lost from tree sequence after SLiM step

Issue - State: closed - Opened by ShyamieG over 1 year ago - 6 comments

#330 - Update docs deps and theme

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

#329 - AttributeError in jsonschema

Issue - State: closed - Opened by ans6160 over 1 year ago - 3 comments

#328 - typo fix metdadata

Pull Request - State: closed - Opened by Tatianabellagio over 1 year ago - 2 comments

#326 - add new methods to the API docs

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

#324 - Upgrade docs

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

#323 - release tasks

Issue - State: open - Opened by petrelharp over 1 year ago

#322 - removes allclose, closes #321

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

#320 - Update time_units.md

Pull Request - State: closed - Opened by petrelharp over 1 year ago - 2 comments

#319 - explain no adjustment needed for WF sims

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

#317 - test on annotating tsinfer'ed tree sequence

Issue - State: open - Opened by petrelharp over 1 year ago

#316 - provide example of annotating existing mutations

Issue - State: open - Opened by petrelharp over 1 year ago

#314 - Bump cache number

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

#313 - copy over tskit dependencies DO NOT MERGE

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

#312 - release tasks

Issue - State: closed - Opened by petrelharp over 1 year ago

#311 - This *actually* fixes the bug.

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

#310 - version bump

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

#309 - docs for convert alleles (closes #178)

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

#308 - deal with varying root times in recapitate (closes #307)

Pull Request - State: closed - Opened by petrelharp over 1 year ago - 9 comments

#306 - add VCF example to tutorial

Issue - State: closed - Opened by petrelharp over 1 year ago

#305 - Test CI for codecov issues

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 2 comments

#304 - recapitating merged trees

Issue - State: closed - Opened by ShyamieG almost 2 years ago - 9 comments

#302 - release tasks

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

#301 - updates to demo use of meanParentAge

Pull Request - State: closed - Opened by silastittes over 2 years ago - 8 comments

#300 - document using next_slim_id (closes #296)

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

#299 - use metadata vector

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

#298 - Fix deps for new pip

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

#297 - Docs build failing

Issue - State: closed - Opened by jeromekelleher over 2 years ago

#296 - write example using `max_slim_id( )`

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

#295 - edits

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

#294 - refactor of GH test action workflow

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

#293 - edits to time units docs

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

#292 - Release tasks

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

#291 - added slim clone and compile to GH actions

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

#290 - max_slim_mutation_id function

Pull Request - State: closed - Opened by mufernando over 2 years ago - 10 comments

#289 - deprecate unique labels by group

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

#288 - how to migrate code

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

#287 - deprecate unique_labels_by_group

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

#286 - annotate empty ts

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

#285 - warn if overwriting mutation metadata

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

#284 - read new section on time units

Issue - State: closed - Opened by petrelharp over 2 years ago - 14 comments

#283 - use extant reference sequence (closes #218)

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

#282 - mention how to install other versions, closes #276

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

#281 - don't always do inkscape; closes #280

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

#280 - remove inkscape dependency for docs build

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

#279 - Time units: closes #222

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

#278 - time units docs: closes #222

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

#277 - deal with `first` stage

Pull Request - State: closed - Opened by petrelharp over 2 years ago - 5 comments

#276 - say in 'installation' how to find/install other versions

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

#275 - remove individual_{populations,times,locations} (closes #255)

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

#274 - conda slim v4

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

#273 - more testing of population remapping

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

#272 - run missing recipe

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

#271 - Issues with recapitate tutorial on pyslim manual

Issue - State: closed - Opened by isadoo over 2 years ago - 8 comments

#270 - first() events can now do more stuff than before

Issue - State: closed - Opened by bhaller over 2 years ago - 1 comment

#266 - Error with pyslim.load 'AttributeError: can't set attribute'

Issue - State: closed - Opened by asadrh8 over 2 years ago - 4 comments

#264 - Recapitation with recent demographic events + historical sampling ?

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

#263 - post-SLiM-v4 release tasks

Issue - State: closed - Opened by petrelharp over 2 years ago - 1 comment

#262 - separate docs CI

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

#261 - version bump

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

#260 - Release tasks

Issue - State: closed - Opened by petrelharp over 2 years ago - 1 comment

#259 - reinstate tests after next tskit release

Issue - State: closed - Opened by petrelharp over 2 years ago - 1 comment

#258 - check migration table after remapping populations

Issue - State: closed - Opened by petrelharp over 2 years ago - 1 comment

#257 - fixup `test_nucleotide_spectrum`

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

#256 - add tests of population remapping

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

#255 - remove `pyslim.individual_populations`, `_times`, and `_locations`

Issue - State: closed - Opened by petrelharp over 2 years ago - 1 comment

#254 - catch out-of-date ts format and throw warning

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

#253 - Slim v4

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

#252 - `modelType` has moved to community

Issue - State: closed - Opened by petrelharp over 2 years ago - 1 comment

#251 - allow annotation of non-zero population

Issue - State: closed - Opened by petrelharp over 2 years ago - 1 comment

#250 - check for ts version in operations like pyslim.recapitate( )

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

#249 - passing a rate map to `recombination_rate` does strange things

Issue - State: closed - Opened by petrelharp almost 3 years ago - 3 comments
Labels: bug

#248 - Error with recapitation with non-uniform recombination map

Issue - State: closed - Opened by ChrystelleDelord almost 3 years ago - 2 comments