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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fix: explicitly specify how the root and ambiguous states are handled…

#1690 rneher opened 13 hours ago
1
Inconsistency of lengths and mutations assigned to branches that are children of the root.

#1689 rneher opened 15 hours ago
3
Fix type error in titer model cross-validation

#1688 huddlej opened 4 days ago
1
DEV_DOCS: Remove hardcoded default branch names

#1687 victorlin closed 4 days ago
0
Rename `master` to `main`

#1686 victorlin opened 5 days ago
0
Remove `authors` hard-coding in `augur export`

#1685 genehack opened 5 days ago
1
26.2.0 release

#1684 victorlin closed 5 days ago
0
Update changelog

#1683 victorlin closed 5 days ago
1
Bump codecov/codecov-action from 4 to 5

#1682 dependabot[bot] closed 1 week ago
1
Investigate why CI takes 50% longer for Python 3.12

#1681 corneliusroemer opened 1 week ago
0
Remove Python 3.8 support

#1680 corneliusroemer opened 1 week ago
0
Support Python 3.13

#1679 corneliusroemer opened 1 week ago
0
Support Python 3.12 and test in CI

#1678 corneliusroemer closed 1 week ago
0
Can't override `-T auto` with `-T 1` to work around iqtree bug when using augur tree

#1677 corneliusroemer closed 1 week ago
1
Pass secrets to release job

#1676 victorlin closed 1 week ago
1
release: Remove condition on event_name

#1675 victorlin closed 1 week ago
0
Bug in release workflow: it doesn't actually release anymore

#1674 corneliusroemer closed 1 week ago
5
Add internal changes to changelog to improve visibility for developers and give credit

#1673 corneliusroemer opened 1 week ago
4
[don't merge] Dummy PR raising pandas min version to v2 to test v2 in pathogen ci

#1672 corneliusroemer closed 1 week ago
3
Support pandas v2

#1671 corneliusroemer closed 1 week ago
3
Replace use of internal, non-public pandas API in parse.fix_dates

#1670 corneliusroemer opened 2 weeks ago
2
parse: crash on invalid dates "0", "99999" instead of handling gracefully as intended

#1669 corneliusroemer opened 2 weeks ago
0
feat(ancestral): make --genes optional when reconstructing translations, if omitted, translate all genes in annotation

#1668 corneliusroemer opened 2 weeks ago
2
tests: add cram wrapper parallel_cram.sh that runs cram tests in parallel

#1667 corneliusroemer opened 2 weeks ago
5
fix(tests): Fix false negative cram tests

#1666 corneliusroemer opened 2 weeks ago
2
Missing escape of square brackets causes diff_jsons.py in some cram tests to be false negative

#1665 corneliusroemer opened 2 weeks ago
0
feat(ancestral): Add optional Nextclade GFF3 compatibility mode

#1664 corneliusroemer opened 2 weeks ago
5
Layering Auspice config files

#1663 genehack opened 2 weeks ago
3
chore(ancestral): more informative AugurError message

#1662 corneliusroemer closed 2 weeks ago
3
Validation regex pattern for `branch_label` display default values in Auspice config JSON is too strict

#1661 huddlej opened 2 weeks ago
3
docs: Ignore FastTree link for linkcheck

#1660 victorlin closed 2 weeks ago
3
pyright: Use basic ruleset explicitly

#1659 victorlin closed 3 weeks ago
0
clades: Update Cram tests

#1658 victorlin closed 1 month ago
0
CLI help text can't contain rST section headings

#1657 victorlin opened 1 month ago
0
Centralize --validation-mode and --skip-validation

#1656 victorlin closed 1 month ago
1
Gff3 file: differences between nextclade datasets and augur ancestral

#1655 anna-parker opened 1 month ago
3
Improve help text of CLI options that use `extend` and `ExtendOverwriteDefault` actions

#1654 joverlee521 opened 1 month ago
3
Update docs for `curate format-dates`

#1653 joverlee521 closed 2 weeks ago
2
docs: Allow BUILDDIR to be set from environment

#1652 victorlin closed 1 month ago
0
Update help docs for augur curate format-dates

#1651 anna-parker closed 2 weeks ago
7
docs: Allow BUILDDIR to be set from environment

#1650 victorlin closed 1 month ago
1
Bump mamba-org/setup-micromamba from 1 to 2

#1649 dependabot[bot] closed 1 month ago
0
curate apply-geolocation-rules: Allow rule overrides

#1648 joverlee521 opened 1 month ago
0
Update cram tests

#1647 victorlin closed 1 month ago
1
index: Allow FileNotFoundError to be handled at the top level

#1646 victorlin closed 1 month ago
2
Add examples for weighted sampling with multiple columns including month/week

#1645 victorlin opened 2 months ago
0
Augur index may always report sequence file is missing even if output dir is missing?

#1644 emmahodcroft closed 1 month ago
2
Also accept "region" as synonym of "source" for gb files?

#1643 corneliusroemer opened 2 months ago
1
Improve rendering of CLI documentation

#1642 victorlin opened 2 months ago
0
CLI: Use raw descriptions

#1641 victorlin opened 2 months ago
0