Skip to content

Pull requests: nextstrain/augur

New pull request New
34 Open 1,052 Closed
34 Open 1,052 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Assigned to nobody Loading
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

Speed up CI to complete within 15min (down from 25min) by switching off coverage except for the matrix entry that's uploaded
#1861 opened Jul 20, 2025 by corneliusroemer Loading…
4 tasks
1
8
chore: Some typing-related improvements
#1860 opened Jul 20, 2025 by corneliusroemer Loading…
4 tasks done
15
Extract URLs from input metadata values
#1852 opened Jul 14, 2025 by jameshadfield Loading…
3
Clade definition inheritance
#1836 opened Jun 27, 2025 by jameshadfield • Draft
New command: augur curate apply-date-bounds
#1828 opened Jun 11, 2025 by victorlin Loading…
3 of 5 tasks
@victorlin
10
fix: When JSON dump with sort_key fails, retry without sorting
#1823 opened Jun 7, 2025 by corneliusroemer Loading…
4 tasks
1
4
Aligner extra args
#1790 opened Apr 16, 2025 by vbadelita Loading…
4 tasks done
9
Support precise date ranges
#1770 opened Mar 10, 2025 by victorlin Loading…
5 tasks done
1
@victorlin
17
Remove export v1
#1754 opened Feb 11, 2025 by jameshadfield Loading…
1
13
feat(ancestral): make --genes optional when reconstructing translations, if omitted, translate all genes in annotation
#1668 opened Nov 10, 2024 by corneliusroemer • Draft
4 tasks
3
tests: add cram wrapper parallel_cram.sh that runs cram tests in parallel
#1667 opened Nov 9, 2024 by corneliusroemer Loading…
2 of 4 tasks
13
fix(tests): Fix false negative cram tests
#1666 opened Nov 9, 2024 by corneliusroemer Loading…
4 tasks done
1
18
feat(ancestral): Add optional Nextclade GFF3 compatibility mode
#1664 opened Nov 9, 2024 by corneliusroemer Loading…
2 of 5 tasks
11
CLI: Use raw descriptions
#1641 opened Sep 24, 2024 by victorlin • Draft
5 tasks
@victorlin
Register subparsers recursively
#1640 opened Sep 24, 2024 by victorlin • Draft
2 of 5 tasks
@victorlin
5
filter: Use tsv-utils for --output-strains and --output-metadata
#1469 opened May 18, 2024 by victorlin • Draft
3 tasks
@victorlin
21
WIP [refine] unique internal node names
#1451 opened Apr 24, 2024 by jameshadfield • Draft
2
export multiple trees
#1450 opened Apr 24, 2024 by jameshadfield Loading…
2 tasks
12
DRAFT: add 'gene' feature capture when reading genbank files
#1435 opened Mar 8, 2024 by j23414 • Draft
3 tasks
5
filter: Improve help text
#1430 opened Mar 5, 2024 by victorlin • Draft
2 of 3 tasks
@victorlin
1
feat: complex CDSs within augur ancestral
#1333 opened Nov 4, 2023 by corneliusroemer • Draft
2 tasks
1
4
WIP: New clades subcommand that works like traits, using labeled tips rather than clades.tsv
#1329 opened Oct 26, 2023 by corneliusroemer • Draft
8
feat(mask): allow empty mask file, warn not error
#1287 opened Aug 19, 2023 by corneliusroemer Loading…
1 task done
1
feat(mask): Add --mask-gaps {all,terminals} option
#1286 opened Aug 19, 2023 by corneliusroemer Loading…
2 tasks done
7
Feat/parse nextclade annotation
#1263 opened Jul 26, 2023 by rneher Loading…
1 task
ProTip! Add no:assignee to see everything that’s not assigned.