Issues

• Python 3.15 support

  tskit-dev/tskit#3483 · Filter by author jeromekelleher opened on Sep 25, 2026

• NaN's in ld_matrix output with "ghost" alleles

  tskit-dev/tskit#3474 · Filter by author nspope opened on Aug 5, 2026
  3

• Clarify write_vcf docs, and allow empty individuals list to be passed

  tskit-dev/tskit#3463 · Filter by author hyanwong opened on Jun 9, 2026

• Incorrect normalisation in TreeSequence.pair_coalescence_counts (and TreeSequence.pair_coalescence_rates) with isolated samples

  tskit-dev/tskit#3459 · Filter by author nspope opened on May 15, 2026
  1

• Simplifying when keeping unary nodes but excluding input roots

  tskit-dev/tskit#3450 · Filter by author hyanwong opened on Apr 25, 2026
  3

• Calculating the matrix of pairwise coalescence rates efficiently (with genetic_relatedness_vector)

  tskit-dev/tskit#3444 · Filter by author nspope opened on Apr 2, 2026
  2

• PCA fails sometimes (maybe if nodes are not 0...n?)

  tskit-dev/tskit#3443 · Filter by author petrelharp opened on Apr 2, 2026
  1

• nans in ld_matrix

  tskit-dev/tskit#3441 · Filter by author petrelharp opened on Mar 22, 2026
  5

• developer doc: ninja build fails with CUnit header problems

  tskit-dev/tskit#3434 · Filter by author bhaller opened on Mar 12, 2026
  2

• developer doc: meson commands could be more helpful

  tskit-dev/tskit#3433 · Filter by author bhaller opened on Mar 12, 2026
  1

• developer doc: meson setup build fails with an error about cunit

  tskit-dev/tskit#3432 · Filter by author bhaller opened on Mar 12, 2026
  1

• developer doc sends me into detached head state

  tskit-dev/tskit#3431 · Filter by author bhaller opened on Mar 12, 2026
  4

• developer docs "copy" should copy a usable command

  tskit-dev/tskit#3430 · Filter by author bhaller opened on Mar 12, 2026
  4

• developer docs for tskit need to clarify uv run prek install

  tskit-dev/tskit#3429 · Filter by author bhaller opened on Mar 12, 2026
  7

• Numba docs page takes much too long to build

  tskit-dev/tskit#3391 · Filter by author jeromekelleher opened on Feb 13, 2026

• Document Python version support policy

  tskit-dev/tskit#3381 · Filter by author jeromekelleher opened on Feb 6, 2026

• ts.pca gives IndexError for unsimplified tree sequence

  bug
  tskit-dev/tskit#3365 · Filter by author hyanwong opened on Jan 12, 2026
  1

• include "load" as a statistic

  tskit-dev/tskit#3362 · Filter by author petrelharp opened on Jan 6, 2026
  7

• sort_individuals should return map of old->new

  tskit-dev/tskit#3356 · Filter by author hyanwong opened on Dec 24, 2025
  1

• TreeSequence.preorder(u) function

  Python API
  tskit-dev/tskit#3339 · Filter by author jeromekelleher opened on Nov 26, 2025
  4

• Document num_threads in divergence_matrix

  tskit-dev/tskit#3320 · Filter by author jeromekelleher opened on Nov 12, 2025

• Document mutation mode and change site mode description

  documentation
  tskit-dev/tskit#3302 · Filter by author gregorgorjanc opened on Oct 22, 2025
  2

• 'mutation' mode for statistics

  tskit-dev/tskit#3299 · Filter by author petrelharp opened on Oct 16, 2025
  15

• Writing a RateMap to text (hapmap)

  enhancementPython API
  tskit-dev/tskit#3252 · Filter by author nspope opened on Aug 7, 2025
  2

• Finalise API for "skipping" on Tree.seek()

  tskit-dev/tskit#3251 · Filter by author jeromekelleher opened on Aug 7, 2025