Ecosyste.ms: Issues

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

GitHub / tskit-dev/tskit issues and pull requests

#2987 - Minor fixes to error checking for pair coalescence stats

Pull Request - State: closed - Opened by nspope 16 days ago - 5 comments

#2986 - Clarification on pairwise coalescent rates

Issue - State: closed - Opened by Luker121 18 days ago - 3 comments

#2985 - Low level pair coalescence rates

Pull Request - State: closed - Opened by nspope 18 days ago - 2 comments

#2982 - "mutation" mode for statistics

Issue - State: open - Opened by petrelharp 24 days ago - 1 comment

#2980 - Relatedness matrix-vector product

Pull Request - State: open - Opened by petrelharp about 1 month ago - 17 comments

#2979 - Create C api for two-locus branch stats

Pull Request - State: closed - Opened by lkirk about 1 month ago - 4 comments

#2978 - clarify that genetic_relatedness includes self comparisons

Issue - State: open - Opened by petrelharp about 1 month ago - 1 comment

#2977 - Trivial wording change

Issue - State: open - Opened by hyanwong about 1 month ago - 1 comment

#2976 - Lowlevel pair coalescence quantiles

Pull Request - State: closed - Opened by nspope about 2 months ago - 3 comments

#2975 - Use reduction function in `pair_coalescence_stat`

Pull Request - State: closed - Opened by nspope about 2 months ago - 5 comments

#2974 - Feat : add reciprocal monophyly function to Tree class

Pull Request - State: open - Opened by Silloky 2 months ago - 5 comments

#2972 - AFS folding (polarised=False)

Issue - State: open - Opened by sunyatin 7 months ago - 6 comments

#2971 - Cannot pickle '_tskit.Tree' object

Issue - State: closed - Opened by Silloky 3 months ago - 3 comments

#2969 - Post release tasks

Pull Request - State: open - Opened by benjeffery 3 months ago - 1 comment

#2968 - Pass a numpy array of booleans to python simplify?

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

#2967 - Post release tasks

Pull Request - State: closed - Opened by benjeffery 3 months ago - 1 comment

#2966 - Fix tests for lshmm 0.0.8

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

#2965 - Drop "benchmark" CI job?

Issue - State: open - Opened by jeromekelleher 3 months ago
Labels: Infrastructure and tools

#2964 - Compile on numpy2

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

#2963 - Fix tests for numpy 2.0

Issue - State: closed - Opened by jeromekelleher 3 months ago - 1 comment

#2962 - Fixup tests for lshmm 0.0.6

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

#2961 - Post release for 0.5.7

Issue - State: closed - Opened by jeromekelleher 3 months ago - 1 comment

#2960 - Add 'mid' property to Interval class

Pull Request - State: open - Opened by currocam 3 months ago - 10 comments
Labels: AUTOMERGE-REQUESTED

#2959 - Fix CI

Pull Request - State: closed - Opened by benjeffery 3 months ago - 1 comment

#2958 - Fix CI

Pull Request - State: closed - Opened by benjeffery 4 months ago

#2957 - Pin to numpy<2

Pull Request - State: closed - Opened by benjeffery 4 months ago - 1 comment

#2956 - Document correct module for MetadataSchema

Pull Request - State: closed - Opened by hyanwong 4 months ago - 1 comment

#2955 - Correct spelling etc in pack and unpack array routines

Pull Request - State: closed - Opened by hyanwong 4 months ago - 3 comments

#2952 - Switch to ruff linting

Pull Request - State: open - Opened by benjeffery 4 months ago - 7 comments

#2951 - Split large numbers in html/cli print out.

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

#2950 - trees.c Compilation Error

Issue - State: closed - Opened by micailamarcelle 5 months ago - 2 comments

#2949 - Specify positions for branch LD matrix

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

#2948 - time windows in statistics

Pull Request - State: open - Opened by petrelharp 5 months ago - 6 comments

#2947 - Update actions versions

Pull Request - State: closed - Opened by benjeffery 5 months ago - 1 comment

#2946 - Update pre-commit

Pull Request - State: closed - Opened by benjeffery 5 months ago - 1 comment

#2945 - Drop metadata schemas on tables.

Pull Request - State: closed - Opened by jeromekelleher 5 months ago - 2 comments

#2944 - Add XTable.drop_metadata

Issue - State: closed - Opened by jeromekelleher 5 months ago - 1 comment

#2943 - Update GitHub upload/download artefacts

Issue - State: closed - Opened by jeromekelleher 5 months ago
Labels: Infrastructure and tools

#2941 - Add sample sets to the python branch LD prototype

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

#2939 - Correct typo in stats

Pull Request - State: closed - Opened by hyanwong 5 months ago

#2938 - extend path algorithm (extend_edgesV2)

Pull Request - State: open - Opened by hfr1tz3 5 months ago - 9 comments

#2937 - Drop codecov target for lwt to 80%

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

#2935 - Fix osx tests

Pull Request - State: closed - Opened by benjeffery 5 months ago - 3 comments

#2934 - Two locus branch stats python prototype

Pull Request - State: closed - Opened by lkirk 5 months ago - 11 comments

#2933 - remove 1/2 in branch AFS: closes #2925

Pull Request - State: closed - Opened by petrelharp 5 months ago - 11 comments

#2932 - Low level pair coalescence counts

Pull Request - State: closed - Opened by nspope 6 months ago - 30 comments

#2931 - Codecov upload issues

Issue - State: open - Opened by benjeffery 6 months ago - 1 comment

#2930 - Fix codecov paths

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

#2929 - edges lost after merging two trees

Issue - State: closed - Opened by ShyamieG 6 months ago - 20 comments

#2928 - Set explict paths for codecov

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

#2927 - another try at #2915

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

#2925 - Folded AFS between branch and site modes differs by factor of two

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

#2924 - Test coverage report

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

#2923 - Bug assertion in `ts.allele_frequency_spectrum`

Issue - State: open - Opened by nspope 6 months ago - 8 comments
Labels: bug

#2922 - Test codecov

Pull Request - State: closed - Opened by benjeffery 6 months ago - 10 comments

#2921 - Update codecov action

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

#2920 - Add `pair_coalescence_counts` method

Pull Request - State: closed - Opened by nspope 6 months ago - 8 comments

#2919 - TreeSequence.f2 is not symmetric with multiallelic sites

Issue - State: open - Opened by BenjaminPeter 6 months ago - 3 comments

#2918 - Fix codecov yml

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

#2917 - Add node_is_sample array

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

#2916 - Update development.md

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

#2915 - API for counting coalescing pairs

Pull Request - State: closed - Opened by nspope 6 months ago - 31 comments

#2914 - Error pip install tskit on Windows

Issue - State: closed - Opened by LauraBertola 6 months ago - 2 comments

#2913 - Use reusable workflows across repos?

Issue - State: open - Opened by jeromekelleher 6 months ago - 2 comments
Labels: Infrastructure and tools

#2912 - Two locus branch stats python prototype

Pull Request - State: closed - Opened by lkirk 6 months ago - 10 comments

#2911 - Implement efficient seeking from non-null trees using tree_pos

Pull Request - State: open - Opened by duncanMR 7 months ago - 4 comments

#2910 - Installing tskit on Windows

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

#2909 - Add note about creating a reverse node map

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

#2908 - Dividing by zero should be NaN

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

#2907 - Should 2-locus ratio statistics return NaN on 0/0?

Issue - State: closed - Opened by lkirk 7 months ago - 4 comments

#2906 - Two locus user-facing python ld matrix API

Pull Request - State: closed - Opened by lkirk 7 months ago - 4 comments

#2905 - clarity on use of tskit.union()

Issue - State: closed - Opened by ShyamieG 8 months ago - 4 comments

#2904 - Simpler, more efficient interface for pair coalescence rates

Issue - State: open - Opened by nspope 8 months ago - 6 comments
Labels: enhancement

#2903 - Add 'mid' property to Interval class

Issue - State: open - Opened by jeromekelleher 8 months ago
Labels: enhancement, good first issue, Python API

#2902 - Python LD Matrix API

Pull Request - State: closed - Opened by lkirk 8 months ago - 15 comments

#2901 - Error when the VCF will have a zero position site

Pull Request - State: closed - Opened by benjeffery 8 months ago - 10 comments

#2900 - Testing CI

Pull Request - State: closed - Opened by benjeffery 8 months ago - 1 comment

#2899 - Number of variable sites (not just num_sites)

Issue - State: open - Opened by hyanwong 8 months ago - 1 comment

#2897 - Documentation for IBD segments

Issue - State: open - Opened by jeromekelleher 8 months ago
Labels: documentation

#2896 - Add support for MRCA based IBD

Issue - State: open - Opened by jeromekelleher 8 months ago - 2 comments
Labels: enhancement

#2894 - Numpy 2.0 Python

Issue - State: closed - Opened by jeromekelleher 8 months ago - 5 comments

#2893 - C API for numpy 2.0

Issue - State: open - Opened by jeromekelleher 8 months ago - 4 comments
Labels: C API, Infrastructure and tools

#2890 - Document divergence_matrix

Issue - State: open - Opened by jeromekelleher 9 months ago
Labels: documentation

#2889 - Document genetic_relatedness_matrix

Issue - State: open - Opened by jeromekelleher 9 months ago
Labels: documentation

#2888 - Sample_sets incorrect in genetic_relatedness_matrix

Issue - State: closed - Opened by jeromekelleher 9 months ago - 16 comments
Labels: bug

#2887 - Add direct links to Python and C APIs from README

Pull Request - State: open - Opened by hyanwong 9 months ago - 1 comment

#2884 - extend edges misses some extendable edges

Issue - State: open - Opened by petrelharp 9 months ago

#2882 - Can I get a list of descendants of a branch (edge)?

Issue - State: open - Opened by hanbin973 10 months ago - 11 comments

#2880 - Add c/CMakeLists.txt

Pull Request - State: open - Opened by lukashuebner 10 months ago - 8 comments

#2878 - Reinstate check for chromosome name in read_hapmap

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

#2877 - Add IO methods for RateMap

Issue - State: open - Opened by jeromekelleher over 3 years ago
Labels: enhancement

#2876 - Add RateMap.zip(other1, other2,...) method

Issue - State: open - Opened by jeromekelleher over 3 years ago - 6 comments
Labels: enhancement