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Pull requests: nextstrain/augur

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Pull requests list

Define a Conda-based development environment
#1950 opened Jan 23, 2026 by victorlin Loading…
4 tasks done
1
@victorlin
1
ENH: allow using piqtree instead of iqtree, relates to #1930
#1945 opened Jan 19, 2026 by GavinHuttley Loading…
4 tasks
1
2
Support Python 3.14
#1944 opened Jan 17, 2026 by victorlin Loading…
4 tasks done
1
@victorlin
5
Drop support for Python 3.9 breaking Makes a backwards incompatible change and should wait for major release
#1938 opened Jan 8, 2026 by victorlin Loading…
4 tasks done
@victorlin
1
[curate apply-geolocation-rules] treat '?' values akin to empty values
#1929 opened Nov 27, 2025 by jameshadfield Loading…
4 tasks
6
Add types for read_metadata() and read_csv_with_index_col()
#1923 opened Oct 27, 2025 by victorlin • Draft
3 of 5 tasks
@victorlin
1
Address general type issues
#1922 opened Oct 27, 2025 by victorlin Loading…
4 tasks done
@victorlin
6
Handle ambiguity in --min-date and --max-date
#1914 opened Oct 22, 2025 by victorlin • Draft
2 of 5 tasks
1
@victorlin
1
Consider XXXX-XX-XX as missing date
#1913 opened Oct 22, 2025 by victorlin Loading…
2 of 4 tasks
1
@victorlin
2
Improve error handling in curate apply-geolocation-rules
#1905 opened Oct 10, 2025 by corneliusroemer • Draft
4 tasks
3
refine: warn if doing timetree and there's apparent mismatch between metadata and sequence ids
#1902 opened Oct 10, 2025 by corneliusroemer Loading…
4 tasks
7
chore: Some typing-related improvements
#1860 opened Jul 20, 2025 by corneliusroemer Loading…
4 tasks done
15
Clade definition inheritance
#1836 opened Jun 27, 2025 by jameshadfield • Draft
1
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
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
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