tskit-dev/pyslim issues and pull requests

#240 - `unique_labels_by_group` returns False for unused groups

Issue - State: closed - Opened by petrelharp almost 3 years ago - 1 comment

#239 - adding magic

Pull Request - State: closed - Opened by andrewkern almost 3 years ago

#238 - Redirect for docs object.inv

Issue - State: closed - Opened by benjeffery almost 3 years ago - 1 comment

#237 - inconsistent time scaling after calling pyslim.recapitate

Issue - State: closed - Opened by bguo068 almost 3 years ago - 1 comment

#235 - Error in VCF output: More than 9 alleles not currently supported

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

#234 - docs update (closes #139)

Pull Request - State: closed - Opened by petrelharp almost 3 years ago

#233 - use samples(time=) for individuals_alive_at sometimes (closes #208)

Pull Request - State: closed - Opened by petrelharp almost 3 years ago

#232 - clean up requirements and test with windows?

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

#230 - deprecate SlimTreeSequence

Pull Request - State: closed - Opened by petrelharp almost 3 years ago - 1 comment

#225 - add `mutation_rate` to recapitate

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

#223 - fixup XY annotation example

Issue - State: open - Opened by petrelharp almost 3 years ago
Labels: enhancement, documentation

#222 - mention time units

Issue - State: closed - Opened by petrelharp almost 3 years ago - 2 comments
Labels: documentation, priority

#220 - test running `.py` files in SLiM recipes

Issue - State: open - Opened by petrelharp almost 3 years ago - 2 comments
Labels: tests

#218 - change `generate_nucleotides` to use reference sequence if present

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

#214 - Release tasks

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

#211 - monitor memory and do gc

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

#209 - use `table.metadata_vector( )` in docs

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

#208 - switch to using `ts.samples(time=X)` in examples?

Issue - State: closed - Opened by petrelharp about 3 years ago - 1 comment

#203 - add `samples_only` argument to `individuals_alive_at`

Issue - State: closed - Opened by petrelharp about 3 years ago - 1 comment
Labels: enhancement

#202 - add _X and _Y tests

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

#188 - add citation.cff

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

#185 - individual_populations gives birth locations, not sampling locations

Issue - State: closed - Opened by petrelharp over 3 years ago - 1 comment

#179 - add method to get the largest SLiM mutation ID

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

#178 - add example of converting to nucleotides for VCF output

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

#173 - migration to being functional

Issue - State: closed - Opened by petrelharp over 3 years ago - 4 comments

#171 - write example of finding the realised DFE

Issue - State: closed - Opened by petrelharp over 3 years ago - 1 comment
Labels: enhancement, documentation

#170 - deal with `first()` stages

Issue - State: closed - Opened by petrelharp over 3 years ago - 3 comments
Labels: bug, priority

#169 - wrap union to deal with SLiM metadata

Issue - State: open - Opened by mufernando over 3 years ago - 4 comments

#167 - annotate fails on empty tree sequence

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

#166 - deal appropriately when annotating with existing mutations

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

#139 - make reference page for what's in the metadata

Issue - State: closed - Opened by petrelharp almost 4 years ago

#138 - Define attributes in Sphinx to allow linking

Issue - State: closed - Opened by hyanwong almost 4 years ago - 1 comment
Labels: documentation

#121 - tutorial feature: loading a coalescent sim with overlaid mutations into SLiM

Issue - State: closed - Opened by bhaller almost 4 years ago - 1 comment
Labels: documentation

#111 - add CI step that runs stdpopsim tests

Issue - State: open - Opened by grahamgower almost 4 years ago - 2 comments
Labels: tests

#103 - annotate_mutations

Issue - State: open - Opened by petrelharp about 4 years ago - 2 comments
Labels: enhancement

#62 - a tree-sequence-validation feature inside pyslim would be useful

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

#60 - write method to emit SLiM reload script

Issue - State: open - Opened by petrelharp almost 5 years ago - 1 comment

#56 - give example of matching individuals to something written to metadata

Issue - State: open - Opened by petrelharp about 5 years ago - 2 comments
Labels: documentation

#53 - add multiple population recapitation example

Issue - State: closed - Opened by petrelharp about 5 years ago - 1 comment
Labels: documentation

#44 - Document recapitation with generation_time for a nonWF model

Issue - State: closed - Opened by petrelharp over 5 years ago - 3 comments
Labels: documentation

#23 - provide subset argument to recapitate

Issue - State: closed - Opened by petrelharp almost 6 years ago - 5 comments

#8 - provide method for assigning individuals to populations

Issue - State: closed - Opened by petrelharp over 6 years ago - 3 comments
Labels: annotation

#7 - provide method for setting individuals and remembered nodes in annotation

Issue - State: closed - Opened by petrelharp over 6 years ago - 1 comment

#6 - pyslim could provide further help in decoding mutations

Issue - State: open - Opened by bhaller over 6 years ago
Labels: enhancement

GitHub / tskit-dev/pyslim issues and pull requests