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Pull requests: nextstrain/augur

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Pull requests list

chore(deps): configure dependabot for pip deps
#1538 opened Jul 11, 2024 by corneliusroemer Loading…
4 tasks
2
chore(deps): allow numpy v2
#1533 opened Jul 11, 2024 by corneliusroemer • Draft
4 tasks
1
[export] reduce numeric precision to reduce dataset size by ~30%
#1512 opened Jul 2, 2024 by jameshadfield Loading…
1 of 2 tasks
15
augur/parse.py: fix test failure with pandas 2.2.
#1471 opened May 22, 2024 by emollier Loading…
1 of 2 tasks
1
filter: Improve speed of --output-strains and --output-metadata
#1469 opened May 18, 2024 by victorlin • Draft
3 tasks
@victorlin
5
Prepare for weighted sampling
#1460 opened May 3, 2024 by victorlin Loading…
2 tasks done
@victorlin
Implement weighted sampling
#1454 opened Apr 25, 2024 by victorlin • Draft
1 of 4 tasks
@victorlin
28
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
Support pandas version 2
#1447 opened Apr 18, 2024 by victorlin • Draft
5 tasks
@victorlin
1
DRAFT: add 'gene' feature capture when reading genbank files
#1435 opened Mar 8, 2024 by j23414 • Draft
3 tasks
5
filter: Split filtering and subsampling
#1432 opened Mar 7, 2024 by victorlin • Draft
3 tasks
@victorlin
6
filter: Improve help text
#1430 opened Mar 5, 2024 by victorlin • Draft
2 of 3 tasks
@victorlin
1
feat: output genome annotations for complex CDS
#1333 opened Nov 4, 2023 by corneliusroemer • Draft
2 tasks
1
2
feat: treat CDS as a valid feature for GFFs in load_features
#1332 opened Nov 4, 2023 by corneliusroemer • Draft
2
WIP: New clades subcommand that works like traits, using labeled tips rather than clades.tsv
#1329 opened Oct 26, 2023 by corneliusroemer • Draft
8
fix: upper case root sequence for ancestral reconstruction
#1323 opened Sep 26, 2023 by rneher Loading…
11
Improved ancestral translation validation
#1321 opened Sep 26, 2023 by corneliusroemer Loading…
1 of 2 tasks
1
feat: support treetime ambiguous date format
#1305 opened Sep 4, 2023 by corneliusroemer • Draft
2 of 3 tasks
1
@victorlin
6
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
Update annotation schema for strand changes
#1279 opened Aug 11, 2023 by victorlin • Draft
2 tasks
@victorlin
1
Feat/parse nextclade annotation
#1263 opened Jul 26, 2023 by rneher Loading…
1 task
filter: Rewrite using SQLite3
#1242 opened Jun 17, 2023 by victorlin • Draft
1 of 7 tasks
@victorlin
6
Report helpful error if filter query string malformed
#1232 opened May 18, 2023 by corneliusroemer Loading…
1 of 2 tasks
1
4
ProTip! Updated in the last three days: updated:>2024-07-11.