All pull requests

Pull requests

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

  #2050·RonitBStudent opened Sep 18, 2026·

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  2

• Move get_referenced_files() and helpers to augur.config

  #2049·victorlin opened Sep 16, 2026·3/3·

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  2

  

• Implement --config for various commands

  #2041·victorlin opened Aug 17, 2026·2/3·

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  9

  

• refine: Implement --config

  #2040·victorlin opened Aug 15, 2026·1/3·

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  50

  

• tests: Cram to Prysk

  #2003·joverlee521 opened May 19, 2026·

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  1

• Write alignment file in temporary directory

  #1997·victorlin opened May 14, 2026·

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• subsample: Print errors from get_referenced_files

  #1955·victorlin opened Jan 30, 2026·

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  1

  

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

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

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

  #1929·jameshadfield opened Nov 27, 2025·

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  6

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

  #1914·victorlin opened Oct 22, 2025·

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• Improve error handling in curate apply-geolocation-rules

  #1905·corneliusroemer opened Oct 10, 2025·

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

  #1902·corneliusroemer opened Oct 10, 2025·

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• chore: Some typing-related improvements

  #1860·corneliusroemer opened Jul 20, 2025·

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  15

• Clade definition inheritance

  #1836·jameshadfield opened Jun 27, 2025·

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  1

• New command: augur curate apply-date-bounds

  #1828·victorlin opened Jun 11, 2025·

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  10

  

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

  #1823·corneliusroemer opened Jun 7, 2025·

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• Aligner extra args

  #1790·vbadelita opened Apr 16, 2025·

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• Remove export v1

  #1754·jameshadfield opened Feb 11, 2025·

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

  #1668·corneliusroemer opened Nov 10, 2024·

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• fix(tests): Fix false negative cram tests

  #1666·corneliusroemer opened Nov 9, 2024·

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  18

• feat(ancestral): Add optional Nextclade GFF3 compatibility mode

  #1664·corneliusroemer opened Nov 9, 2024·

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• Register subparsers recursively

  #1640·victorlin opened Sep 24, 2024·

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• filter: Use tsv-utils for --output-strains and --output-metadata

  #1469·victorlin opened May 18, 2024·

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  21

  

• WIP [refine] unique internal node names

  #1451·jameshadfield opened Apr 24, 2024·

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  2

• export multiple trees

  #1450·jameshadfield opened Apr 24, 2024·

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  12