nextstrain augur issues

nextstrain / augur

Pipeline components for real-time phylodynamic analysis

https://docs.nextstrain.org/projects/augur/

GNU Affero General Public License v3.0

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issues

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Sync outdated developer API docs, add check in CI

#1525 victorlin opened 1 day ago
1
Generate documentation files?

#1524 victorlin opened 2 days ago
3
Update docs for augur curate

#1523 victorlin opened 2 days ago
1
Branch length units in augur refine output

#1522 Eric-CH-Chen opened 2 days ago
1
Improve help output for augur curate subcommands

#1521 joverlee521 opened 2 days ago
0
Update PR template

#1520 victorlin opened 2 days ago
0
Update docs for new augur curate subcommands

#1519 victorlin opened 2 days ago
2
augur curate I/O: validate records have same fields

#1518 joverlee521 closed 1 day ago
2
Run mypy and pyright as separate jobs on a single Python version

#1517 victorlin opened 2 days ago
1
Improve typing experience with CI

#1516 victorlin opened 2 days ago
4
Port `ingest/transform-strain-names` to `augur curate transform-strain-name` [#1486]

#1514 genehack closed 2 days ago
4
Remove the requirement for a `database` field in `augur curate parse-genbank-location` [#1511]

#1513 genehack closed 2 days ago
1
[export] reduce numeric precision to reduce dataset size by ~30%

#1512 jameshadfield opened 3 days ago
2
augur curate parse-genbank-location: Remove `database` check

#1511 joverlee521 closed 2 days ago
0
augur curate I/O: verify NDJSON records have the same fields

#1510 joverlee521 closed 1 day ago
2
augur curate format-dates: mask empty fields

#1509 joverlee521 closed 3 days ago
2
Port `translate-genbank-location` to `augur curate parse-genbank-location` [#1485]

#1508 genehack closed 3 days ago
2
augur curate format-dates should mask empty date fields

#1507 joverlee521 closed 3 days ago
0
Port `transform-field-names` to `augur curate rename`

#1506 jameshadfield opened 4 days ago
2
[export] format confidence values to save bytes

#1505 jameshadfield opened 4 days ago
0
Support numpy major version 2

#1504 corneliusroemer opened 6 days ago
0
Consolidate date logic

#1503 victorlin closed 6 days ago
1
Update dev docs to single source of truth; also note Python 3.12 install won't work with conda install

#1502 genehack opened 6 days ago
0
augur curate format-dates: accept masked dates

#1501 joverlee521 closed 3 days ago
2
Docs fixes

#1500 victorlin closed 6 days ago
0
Update Biopython docs URL

#1499 victorlin closed 6 days ago
1
CI `build-docs` failing

#1498 joverlee521 closed 6 days ago
1
Port `translate-authors` from `ingest` to `augur curate abbreviate-authors`

#1497 genehack closed 6 days ago
2
augur curate format-dates should recognize masked dates internally

#1496 joverlee521 closed 3 days ago
0
Port merge-user-metadata to augur curate

#1495 joverlee521 closed 6 days ago
1
Extend `augur curate format-dates` to output date ranges

#1494 joverlee521 opened 1 week ago
0
Stop quoting TSV outputs from augur curate

#1493 joverlee521 closed 1 week ago
5
Add Codecov token

#1492 victorlin closed 1 week ago
0
Port apply-geolocation-rules to augur curate

#1491 victorlin closed 1 week ago
1
Add `asia` to default colors

#1490 joverlee521 closed 1 week ago
1
Update default region colors

#1489 joverlee521 closed 1 week ago
0
Curate standard geolocation rules

#1488 joverlee521 opened 1 week ago
0
Support Excel inputs

#1487 joverlee521 opened 1 week ago
0
augur curate transform-strain-name

#1486 joverlee521 closed 2 days ago
0
augur curate parse-genbank-location

#1485 joverlee521 closed 2 days ago
0
augur curate rename

#1484 joverlee521 opened 1 week ago
0
augur curate abbreviate-authors

#1483 joverlee521 closed 3 days ago
1
augur curate apply-record-annotations

#1482 joverlee521 closed 6 days ago
0
Improved subsampling support

#1481 victorlin opened 2 weeks ago
0
How to disable indel trimming with augur align

#1480 swantan closed 3 weeks ago
2
refine: Support rooting with time data without producing a time tree

#1479 huddlej opened 4 weeks ago
0
[export] Improve root-sequence help messages

#1478 jameshadfield closed 4 weeks ago
0
Multi Thread option (align) without SnakeMake

#1477 kiranpatil222 closed 1 month ago
2
relax schema enforcement of `generated_by` in node-data files

#1476 jameshadfield opened 1 month ago
0
Metadata wrangling prior to merging with existing data

#1475 jameshadfield opened 1 month ago
2