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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

Unreleased

Fixed

  • Routine updates to accommodate changes to NCBI taxonomy (#51, #54)

[0.10.1] 2026-01-14

Fixed

  • Handling of taxon names containing multiple sets of square brackets (#47)
  • Dependency pin affecting Python 3.13 compatibility (#48)

[0.10] 2025-06-27

Changed

  • Swapped taxonkit reformat for taxonkit reformat2 to restore sane default behaviors after NBCI shuffled ranks near the root of the taxonomy database (#43, #44)

[0.9.1] 2024-08-05

Changed

  • Updated version of bundled versioneer package for Python 3.12 compatibility, improved environment hygiene (#36)
  • Updated test suite to accommodate bugfix affecting taxonkit filter behavior with discard_norank argument (#37)

[0.9] 2024-03-08

Added

Changed

  • Updated test suite to accommodate taxonomy DB changes (#28, #29, #30)

[0.8] 2022-08-30

Changed

  • Updated doctest for pytaxonkit.list to include taxa that are updated in the NCBI taxonomy DB less frequently (#13, #14, #21, #24)
  • Other occasional updates to compensate for changes in the NCBI taxonomy DB (#15, #16, #17, #23, #26)
  • Updated pytaxonkit.list_ranks() to match updated taxonkit filter --list-order behavior (#20)
  • Now using Black instead of pycodestyle to check and autoformat Python code (#27)

Fixed

  • Bug with how certain functions handle empty inputs (#19)
  • Bug causing pytaxonkit.lineage to fail when only a single taxid was provided as input (#22)
  • Bug causing pytaxonkit.lca to fail when all input taxids are deleted or "unfound" (#22)
  • Bug causing pytaxonkit.name to fail on empty inputs (#26)

[0.7.2] 2021-01-27

Added

  • New filter() function supporting new taxonkit filter command (#4, #8)
  • New lca() function supporting new taxonkit lca command (#5)
  • Support for new prefix related flags (#6)
  • Use new --show-lineage-ranks to create new FullLineageRanks column in lineage() output (#8)

[0.6.1] 2020-10-30

Added

  • New name() function taking advantage of new --show-name and --no-lineage flags in taxonkit lineage (#2)

[0.6] 2020-06-12

Initial release!