tskit-dev/tskit issues and pull requests

#2759 - Add asdict to Dataclass

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 3 comments

#2758 - Add method to compute mutation time from the mutation's node

Issue - State: closed - Opened by duncanMR over 1 year ago - 4 comments

#2757 - Mutation table

Issue - State: open - Opened by daikitag over 1 year ago - 9 comments

#2756 - 0.5.5 Release prep

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

#2754 - Fix type to Py_BuildValue

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

#2752 - add modular simplifier

Pull Request - State: open - Opened by molpopgen over 1 year ago - 13 comments

#2751 - Tracking issue: edge recording performance

Issue - State: open - Opened by molpopgen over 1 year ago
Labels: C API

#2750 - Missing data error is reported when trees converted to vcf file

Issue - State: open - Opened by Liangyy1902 over 1 year ago - 2 comments

#2749 - add_pbs and test

Pull Request - State: closed - Opened by atongsa over 1 year ago - 7 comments

#2748 - add pbs function to tree.py

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

#2746 - VCF ALT fields are non-conforming, and thus misinterpreted by bcftools

Issue - State: open - Opened by grahamgower over 1 year ago - 8 comments

#2745 - Error in handling final empty tree in stats API

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 1 comment
Labels: bug

#2742 - Fix codecov

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

#2741 - Clarify Tree.samples() behaviour w/ isolated nodes

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 4 comments

#2740 - Update docs for improved seek-from-null performance

Issue - State: open - Opened by jeromekelleher over 1 year ago - 1 comment
Labels: C API, Python API

#2739 - remove unused variable

Pull Request - State: closed - Opened by petrelharp over 1 year ago - 4 comments

#2738 - unused variable warning

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

#2737 - "invalid start byte" error accessing variant.alleles in pyodide/jupyterlite

Issue - State: closed - Opened by hyanwong over 1 year ago - 21 comments
Labels: bug

#2736 - divmat tree by tree

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 13 comments

#2735 - Fix mergify

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

#2734 - Improvement tskit treeseq from text mutations

Pull Request - State: open - Opened by lukashuebner over 1 year ago - 3 comments

#2733 - Mutation stack policy with add_mutation and "SLiM-style" mutation

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

#2732 - Require mutation parents for TreeSequence instantiation

Issue - State: open - Opened by jeromekelleher over 1 year ago - 3 comments
Labels: enhancement

#2731 - Fix mergify

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

#2730 - compute mutation parents on text input

Pull Request - State: open - Opened by petrelharp over 1 year ago - 8 comments

#2729 - Nasty gotcha in the AFS calculation

Issue - State: open - Opened by lukashuebner over 1 year ago - 3 comments

#2728 - Chromosome data in VCF

Issue - State: open - Opened by MleGhis over 1 year ago - 3 comments

#2725 - method to return span over which each node is ancestral to provided samples

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

#2724 - tskit vcf CLI not handling ploidy correctly?

Issue - State: closed - Opened by andrewkern over 1 year ago - 1 comment
Labels: bug

#2723 - Average arity of nodes in the trees

Issue - State: open - Opened by jeromekelleher over 1 year ago - 12 comments
Labels: enhancement, Python API

#2722 - Extra attribute for base time?

Issue - State: closed - Opened by hyanwong over 1 year ago - 7 comments
Labels: enhancement

#2720 - Md null schema

Pull Request - State: open - Opened by hyanwong over 1 year ago - 3 comments

#2719 - Add ``asdict()`` to util.Dataclass

Issue - State: closed - Opened by jeromekelleher over 1 year ago
Labels: good first issue, Python API

#2717 - Add 'PBS()'

Issue - State: open - Opened by atongsa over 1 year ago - 9 comments
Labels: enhancement, Python API

#2715 - Don't fail CI on codecov error

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

#2714 - CodeCov failing every PR

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 1 comment
Labels: Infrastructure and tools

#2713 - Reset CI docs cache

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 3 comments

#2712 - Docs build broken

Issue - State: closed - Opened by jeromekelleher over 1 year ago
Labels: Infrastructure and tools

#2710 - Divergence matrix

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 6 comments

#2709 - Add "Analysis/Manipulating Data" docs section

Issue - State: open - Opened by jeromekelleher over 1 year ago - 2 comments
Labels: documentation

#2708 - Documentation examples for keep_rows and id_map

Issue - State: open - Opened by jeromekelleher over 1 year ago - 1 comment
Labels: documentation, Python API

#2707 - table_collection.remap_nodes(id_map) method

Issue - State: open - Opened by jeromekelleher over 1 year ago - 1 comment
Labels: enhancement, C API

#2706 - Tree.ancestors(u) method

Issue - State: open - Opened by hyanwong over 1 year ago - 2 comments
Labels: enhancement, Python API

#2705 - Error if boolean passed as row index or slice?

Issue - State: open - Opened by benjeffery over 1 year ago - 3 comments
Labels: enhancement

#2704 - Argument mismatch between c code and python code in TableCollection.simplify() leads to TypeError

Issue - State: closed - Opened by General-Solution over 1 year ago - 4 comments

#2702 - Correct doc typo

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

#2701 - Post release version update

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

#2700 - Table subset

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 19 comments

#2699 - Returning node x,y locations in a plotted tree

Issue - State: open - Opened by hyanwong over 1 year ago - 7 comments
Labels: Visualisation

#2698 - Add missing changelog

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

#2697 - Freeze docs environment

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 5 comments

#2696 - Implement Tree.seek_index using C code

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

#2695 - implementing Variant.repr

Pull Request - State: closed - Opened by chriscrsmith over 1 year ago - 8 comments

#2694 - Implement Variant.repr

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 7 comments
Labels: enhancement, good first issue, Python API

#2693 - Add 311 changelog

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

#2692 - Fix wheel building for 3.11

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

#2691 - 0.5.4 Release prep

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 3 comments

#2690 - Update linting action

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

#2689 - Lint failing, maybe due to removed package archive

Issue - State: closed - Opened by benjeffery over 1 year ago - 1 comment
Labels: Infrastructure and tools

#2688 - Clear docs CI cache

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

#2687 - Doc build failure

Issue - State: closed - Opened by benjeffery over 1 year ago - 2 comments

#2686 - Add codecov token

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 3 comments

#2685 - Implement edge differences from table collections.

Pull Request - State: closed - Opened by molpopgen over 1 year ago - 12 comments

#2684 - Improve error messages for legacy and compressed formats

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 6 comments

#2683 - `nose` tests being removed from pytest

Issue - State: closed - Opened by benjeffery over 1 year ago - 3 comments
Labels: Infrastructure and tools

#2682 - Detect `tszip`ed files and give a helpful error.

Issue - State: closed - Opened by benjeffery over 1 year ago - 6 comments
Labels: Python API

#2681 - Shorthand filter_all argument for simplify

Pull Request - State: open - Opened by hyanwong over 1 year ago - 4 comments

#2680 - Codecov 404ing

Issue - State: closed - Opened by benjeffery over 1 year ago - 5 comments
Labels: Infrastructure and tools

#2679 - Document RateMap etc

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

#2678 - Port over intervals

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 12 comments

#2672 - Release 0.5.4?

Issue - State: closed - Opened by benjeffery over 1 year ago - 8 comments
Labels: Infrastructure and tools

#2671 - Method or attribute for start and end of tree sequence data

Issue - State: closed - Opened by hyanwong over 1 year ago - 14 comments

#2669 - Implement is_root

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 1 comment

#2666 - Method to in-place subset a table

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 3 comments
Labels: enhancement, C API

#2665 - Multichrom example

Pull Request - State: open - Opened by jeromekelleher almost 2 years ago - 20 comments

#2663 - Don't update sample flags in simplify

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago - 16 comments

#2662 - Add TSK_SIMPLIFY_NO_UPDATE_SAMPLE_FLAGS

Issue - State: closed - Opened by jeromekelleher almost 2 years ago
Labels: C API

#2661 - Efficient seeking to trees.

Pull Request - State: closed - Opened by molpopgen almost 2 years ago - 41 comments

#2659 - Add tsk_tree_seek_index

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 3 comments
Labels: C API

#2651 - extend edges method

Pull Request - State: closed - Opened by petrelharp almost 2 years ago - 35 comments

#2643 - Add unweighted_rf_distance (symmetric_distance) function and tests

Pull Request - State: open - Opened by Billyzhang1229 almost 2 years ago - 11 comments

#2637 - Metadata size in tables

Issue - State: open - Opened by hyanwong almost 2 years ago - 6 comments
Labels: enhancement, Python API

#2636 - Put intervals.py into tskit

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 19 comments

#2631 - Mutation's "inherited" state

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 4 comments
Labels: enhancement, Python API

#2625 - Make tqdm(ts.variants()) work better

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 6 comments
Labels: enhancement, Python API

#2624 - Support Py3.11

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 4 comments

#2621 - Use recursive updates for weights in ``CoalescenceTimeDistribution``

Pull Request - State: closed - Opened by nspope almost 2 years ago - 9 comments

#2618 - Add Tree.siblings()

Pull Request - State: closed - Opened by szhan almost 2 years ago - 32 comments
Labels: enhancement, Python API

#2617 - Add `states()` method to return actual genotype states as characters

Pull Request - State: open - Opened by hyanwong almost 2 years ago - 9 comments

#2616 - Add Tree.siblings(u) method

Issue - State: closed - Opened by jeromekelleher almost 2 years ago
Labels: enhancement, good first issue, Python API

#2614 - Redesign weight functions for `CoalescenceTimeDistribution` to ensure correctness when propagating weights up trees

Issue - State: closed - Opened by nspope almost 2 years ago

GitHub / tskit-dev/tskit issues and pull requests