tskit-dev/pyslim

Issues

• Discrepancies in diversity after recapitation and mutation overlay

  #340 opened 2 months ago by AudeCaizergues
  1

• update metadata for multichromosome

  #351 opened 2 months ago by petrelharp
  0

• :meth: is not working in documentation

  #348 opened 3 months ago by daikitag
  1

• release tasks

  #323 opened a year ago by petrelharp
  0

• Typo in `recapitate` function docstring

  #347 opened 4 months ago by daikitag
  1

• Strange warning in recapitation

  #345 opened 5 months ago by trevorcousins
  2

• Recapitation for complex demography with populations that died out

  #343 opened 5 months ago by Luker121
  11

• default sex ratio 0.0

  #339 opened 9 months ago by petrelharp
  1

• edges are lost from tree sequence after SLiM step

  #331 opened a year ago by ShyamieG
  6

• update quickreference list at top of docs

  #338 opened a year ago by petrelharp
  0

• Potential to use .frequencies() method in /tutorial.html

  #336 opened a year ago by hyanwong
  0

• AttributeError in jsonschema

  #329 opened a year ago by ans6160
  3

• Annotating tree sequence with pre-existing (node) metadata can lead to erroneous metadata

  #327 opened a year ago by clwgg
  1

• release tasks

  #312 opened a year ago by petrelharp
  0

• release tasks

  #302 opened a year ago by petrelharp
  0

• recapitation root time auto-adjust fails with root times > 1e5, resulting in an `msprime.InputError`

  #321 opened a year ago by petrelharp
  2

• test on annotating tsinfer'ed tree sequence

  #317 opened a year ago by petrelharp
  0

• provide example of annotating existing mutations

  #316 opened a year ago by petrelharp
  0

• tsinfered tree sequences don't have 'type' key in top-level metdata but `set_tree_sequence_metadata` expects they do

  #315 opened a year ago by petrelharp
  0

• recapitate has surprisingly small diversity if WF simulation is started and saved in `late`

  #307 opened a year ago by petrelharp
  7

• add VCF example to tutorial

  #306 opened a year ago by petrelharp
  0

• recapitating merged trees

  #304 opened 2 years ago by ShyamieG
  9

• Release tasks

  #292 opened 2 years ago by petrelharp
  0

• write example using `max_slim_id( )`

  #296 opened 2 years ago by petrelharp
  0

• Docs build failing

  #297 opened 2 years ago by jeromekelleher
  0

• read new section on time units

  #284 opened 2 years ago by petrelharp
  14

• Release tasks

  #260 opened 2 years ago by petrelharp
  1

• passing a rate map to `recombination_rate` does strange things

  #249 opened 2 years ago by petrelharp
  3

• deprecate unique_labels_by_group

  #287 opened 2 years ago by petrelharp
  0

• post-SLiM-v4 release tasks

  #263 opened 2 years ago by petrelharp
  1

• allow annotation of non-zero population

  #251 opened 2 years ago by petrelharp
  1

• reinstate tests after next tskit release

  #259 opened 2 years ago by petrelharp
  1

• Issues with recapitate tutorial on pyslim manual

  #271 opened 2 years ago by isadoo
  8

• first() events can now do more stuff than before

  #270 opened 2 years ago by bhaller
  1

• remove inkscape dependency for docs build

  #280 opened 2 years ago by petrelharp
  0

• say in 'installation' how to find/install other versions

  #276 opened 2 years ago by petrelharp
  0

• check for ts version in operations like pyslim.recapitate( )

  #250 opened 2 years ago by petrelharp
  2

• remove `pyslim.individual_populations`, `_times`, and `_locations`

  #255 opened 2 years ago by petrelharp
  1

• add tests of population remapping

  #256 opened 2 years ago by petrelharp
  2

• Error with pyslim.load 'AttributeError: can't set attribute'

  #266 opened 2 years ago by asadrh8
  4

• Recapitation with recent demographic events + historical sampling ?

  #264 opened 2 years ago by ChrystelleDelord
  2

• check migration table after remapping populations

  #258 opened 2 years ago by petrelharp
  1

• SLiM's multispecies branch breaks pyslim-based treeseq tests

  #246 opened 2 years ago by bhaller
  6

• catch out-of-date ts format and throw warning

  #254 opened 2 years ago by petrelharp
  0

• fixup `test_nucleotide_spectrum`

  #257 opened 2 years ago by petrelharp
  0

• Weird "pySLiM" casing on the GitHub main page

  #247 opened 2 years ago by bhaller
  0

• `modelType` has moved to community

  #252 opened 2 years ago by petrelharp
  1

• Error with recapitation with non-uniform recombination map

  #248 opened 3 years ago by ChrystelleDelord
  2

• kastore not brought in by installing pyslim

  #241 opened 3 years ago by bhaller
  10

• mixed history breaks pyslim import

  #242 opened 3 years ago by petrelharp
  0