All pull requests

Pull requests

• refine: accept multiple files for --keep-ids

  #2073·corneliusroemer opened Oct 28, 2026Member·1 task·

  ·
  6

• fix: augur export checked for 'not entropy' as a substitute for None …

  #2071·rneher opened Oct 27, 2026Member·1 of 4 tasks·

  ·
  1

• curate: Add AUGUR_FIELD_SIZE_LIMIT and improve field size error messaging

  #2070·bencoopertx opened Oct 24, 2026·3 of 4 tasks·

  ·
  1

• Handle null strain names in transform-strain-name

  #2067·Noxy-HNR opened Oct 14, 2026·3 of 4 tasks·

  ·
  1

• subsample: Remove --config-section and --search-paths options

  #2053·victorlin opened Sep 24, 2026Member·1/3·4 tasks done·

  ·
  1

  

• distance: error on missing root sequence instead of reporting zeros

  #2050·RonitBStudent opened Sep 18, 2026·3 of 4 tasks·

  ·
  1

  2

• Implement --config for various commands

  #2041·victorlin opened Aug 17, 2026Member·3/3·3 of 5 tasks·

  ·
  11

  

• refine: Implement --config

  #2040·victorlin opened Aug 15, 2026Member·2/3·4 of 5 tasks·

  ·
  51

  

• tests: Cram to Prysk

  #2003·joverlee521 opened May 19, 2026Contributor·6 tasks·

  ·
  1

• Write alignment file in temporary directory

  #1997·victorlin opened May 14, 2026Member·4 tasks·

  ·
  

• subsample: Print errors from get_referenced_files

  #1955·victorlin opened Jan 30, 2026Member·4 of 5 tasks·

  ·
  1

  

• Update pandas requirement from <3,>=1.4.0 to >=1.4.0,<4

  dependenciespython
  #1951·dependabot[bot] opened Jan 26, 2026Bot·

  ·
  1

• [curate apply-geolocation-rules] treat '?' values akin to empty values

  #1929·jameshadfield opened Nov 27, 2025Member·4 tasks·

  ·
  6

• Handle ambiguity in --min-date and --max-date

  #1914·victorlin opened Oct 22, 2025Member·2 of 5 tasks·

  ·
  1

  1

  

• Improve error handling in curate apply-geolocation-rules

  #1905·corneliusroemer opened Oct 10, 2025Member·4 tasks·

  ·
  3

• refine: warn if doing timetree and there's apparent mismatch between metadata and sequence ids

  #1902·corneliusroemer opened Oct 10, 2025Member·4 tasks·

  ·
  7

• chore: Some typing-related improvements

  #1860·corneliusroemer opened Jul 20, 2025Member·4 tasks done·

  ·
  15

• Clade definition inheritance

  #1836·jameshadfield opened Jun 27, 2025Member·

  ·
  1

• New command: augur curate apply-date-bounds

  #1828·victorlin opened Jun 11, 2025Member·3 of 5 tasks·

  ·
  1

  10

  

• fix: When JSON dump with sort_key fails, retry without sorting

  #1823·corneliusroemer opened Jun 7, 2025Member·4 tasks·

  ·
  1

  4

• Aligner extra args

  #1790·vbadelita opened Apr 16, 2025·4 tasks done·

  ·
  9

• Remove export v1

  #1754·jameshadfield opened Feb 11, 2025Member·

  ·
  1

  13

• feat(ancestral): make --genes optional when reconstructing translations, if omitted, translate all genes in annotation

  #1668·corneliusroemer opened Nov 10, 2024Member·4 tasks·

  ·
  3

• fix(tests): Fix false negative cram tests

  #1666·corneliusroemer opened Nov 9, 2024Member·4 tasks done·

  ·
  1

  18

• Register subparsers recursively

  #1640·victorlin opened Sep 24, 2024Member·2 of 6 tasks·

  ·
  5