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
#2988 - provide feedback on `max_iter` for `extend_haplotypes`
Issue -
State: open - Opened by petrelharp 12 days ago
#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
#2984 - wrong output for genetic_relatedness(... indexes=None, proportion=True)
Issue -
State: closed - Opened by petrelharp 22 days ago
#2983 - inconsistent handling of non-ancestral material in non-strict, unpolarised branch stats
Issue -
State: closed - Opened by petrelharp 23 days ago
- 2 comments
#2982 - "mutation" mode for statistics
Issue -
State: open - Opened by petrelharp 24 days ago
- 1 comment
#2981 - set default for genetic_relatedness to polarised=True and remove a factor of 1/2
Issue -
State: open - Opened by petrelharp about 1 month ago
#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
#2936 - keep_intervals() giving _tskit.LibraryError: Can't squash, flush, simplify or link ancestors...
Issue -
State: closed - Opened by TymekPieszko 5 months ago
- 7 comments
#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
#2898 - write_vcf should use the reference sequence for REF, if present
Issue -
State: open - Opened by hyanwong 8 months ago
#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
#2891 - More flexible interpretation of mutation rate when getting emission probability when using `_tskit.lshmm`
Issue -
State: open - Opened by szhan 9 months ago
- 4 comments
#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
#2881 - “Edit on GitHub” link missing from tskit docs
Issue -
State: open - Opened by TymekPieszko 10 months ago
#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