Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nextstrain/augur issues and pull requests

#1558 - tree: Update Cram tests

Issue - State: closed - Opened by victorlin 7 months ago

#1557 - No standard test environment

Issue - State: open - Opened by tsibley 7 months ago - 7 comments

#1556 - [traits] cmd should warn when metadata is completely missing for a given node

Issue - State: open - Opened by genehack 7 months ago - 3 comments
Labels: bug

#1555 - Fix titer substitution model tree annotations

Pull Request - State: closed - Opened by huddlej 7 months ago - 1 comment

#1554 - Update lassa CI

Pull Request - State: closed - Opened by joverlee521 7 months ago

#1553 - augur curate: improve metadata header parsing

Issue - State: open - Opened by joverlee521 7 months ago - 1 comment
Labels: enhancement

#1552 - Update avian-flu CI

Pull Request - State: closed - Opened by jameshadfield 7 months ago - 1 comment

#1551 - Update sphinx-argparse pin to !=0.5.0

Pull Request - State: closed - Opened by victorlin 7 months ago

#1550 - curate: Accept Excel and OpenOffice metadata files

Pull Request - State: closed - Opened by tsibley 7 months ago - 2 comments
Labels: enhancement

#1549 - CI: Update pathogen-repo-ci

Pull Request - State: closed - Opened by joverlee521 7 months ago - 1 comment

#1548 - io.json: Serialize date objects as ISO 8601 too

Pull Request - State: closed - Opened by tsibley 7 months ago - 1 comment

#1547 - fix(tree): check for all synonyms of conflicting default args

Pull Request - State: closed - Opened by corneliusroemer 7 months ago - 2 comments

#1546 - Remove augur.filenames module

Pull Request - State: closed - Opened by tsibley 7 months ago

#1545 - Update author list (take 2)

Pull Request - State: closed - Opened by victorlin 7 months ago

#1544 - Doc updates for dev installs, cram coverage, and release validation

Pull Request - State: closed - Opened by genehack 7 months ago - 1 comment

#1543 - Pin sphinx-argparse <0.5.0

Pull Request - State: closed - Opened by victorlin 7 months ago

#1542 - update build docs to mention checking `conda-base` build summary

Issue - State: closed - Opened by genehack 7 months ago
Labels: documentation

#1541 - Update author list

Pull Request - State: closed - Opened by victorlin 7 months ago - 1 comment
Labels: documentation

#1540 - Put the subcmd name in the validate_output error message [#1539]

Pull Request - State: closed - Opened by genehack 7 months ago - 4 comments

#1539 - `augur curate` could have a more helpful error message

Issue - State: closed - Opened by genehack 7 months ago
Labels: enhancement

#1538 - chore(deps): configure dependabot for pip deps

Pull Request - State: open - Opened by corneliusroemer 7 months ago - 4 comments

#1537 - Update .mailmap

Issue - State: closed - Opened by corneliusroemer 7 months ago - 3 comments
Labels: enhancement, question

#1536 - Officially support python 3.12: test for it and add trove classifier

Issue - State: closed - Opened by corneliusroemer 7 months ago - 2 comments
Labels: enhancement

#1535 - Update pinned dependencies

Issue - State: open - Opened by victorlin 7 months ago - 2 comments

#1534 - chore(deps): Support networkx major version 3

Pull Request - State: closed - Opened by corneliusroemer 7 months ago - 1 comment

#1533 - chore(deps): allow numpy v2

Pull Request - State: open - Opened by corneliusroemer 7 months ago - 1 comment

#1532 - chore(deps): allow xopen major version 2

Pull Request - State: closed - Opened by corneliusroemer 7 months ago - 3 comments

#1531 - Fix location field recognition [#1530]

Pull Request - State: closed - Opened by genehack 7 months ago - 1 comment

#1529 - Fix typos in changelog

Pull Request - State: closed - Opened by joverlee521 7 months ago

#1528 - Update docs for (new) `augur curate rename`

Pull Request - State: closed - Opened by jameshadfield 7 months ago - 1 comment

#1527 - Clarify steps to regenerate developer API docs

Pull Request - State: closed - Opened by victorlin 7 months ago

#1526 - augur curate rename: Add option to drop fields/columns

Issue - State: open - Opened by joverlee521 7 months ago - 3 comments
Labels: enhancement

#1525 - Sync outdated developer API docs, add check in CI

Pull Request - State: closed - Opened by victorlin 7 months ago - 2 comments

#1524 - Generate CLI documentation files?

Issue - State: closed - Opened by victorlin 7 months ago - 4 comments
Labels: proposal, documentation

#1523 - Update docs for augur curate

Pull Request - State: closed - Opened by victorlin 7 months ago - 3 comments

#1522 - Branch length units in augur refine output

Issue - State: closed - Opened by Eric-CH-Chen 7 months ago - 2 comments
Labels: documentation, question

#1521 - Improve help output for augur curate subcommands

Issue - State: open - Opened by joverlee521 7 months ago
Labels: documentation

#1520 - Update PR template

Pull Request - State: closed - Opened by victorlin 7 months ago - 1 comment

#1519 - Update docs for new augur curate subcommands

Issue - State: closed - Opened by victorlin 7 months ago - 2 comments
Labels: documentation

#1518 - augur curate I/O: validate records have same fields

Pull Request - State: closed - Opened by joverlee521 7 months ago - 2 comments

#1517 - Run mypy and pyright as separate jobs on a single Python version

Pull Request - State: closed - Opened by victorlin 7 months ago - 2 comments

#1516 - Improve typing experience with CI

Issue - State: closed - Opened by victorlin 7 months ago - 4 comments

#1515 - transform-strain-name: build strain name by concatenating fields

Issue - State: open - Opened by joverlee521 over 1 year ago - 1 comment
Labels: enhancement

#1514 - Port `ingest/transform-strain-names` to `augur curate transform-strain-name` [#1486]

Pull Request - State: closed - Opened by genehack 7 months ago - 4 comments

#1512 - [export] reduce numeric precision to reduce dataset size by ~30%

Pull Request - State: closed - Opened by jameshadfield 8 months ago - 3 comments

#1510 - augur curate I/O: verify NDJSON records have the same fields

Issue - State: closed - Opened by joverlee521 8 months ago - 2 comments
Labels: enhancement

#1509 - augur curate format-dates: mask empty fields

Pull Request - State: closed - Opened by joverlee521 8 months ago - 2 comments

#1508 - Port `translate-genbank-location` to `augur curate parse-genbank-location` [#1485]

Pull Request - State: closed - Opened by genehack 8 months ago - 2 comments

#1507 - augur curate format-dates should mask empty date fields

Issue - State: closed - Opened by joverlee521 8 months ago
Labels: bug

#1506 - Port `transform-field-names` to `augur curate rename`

Pull Request - State: closed - Opened by jameshadfield 8 months ago - 2 comments

#1505 - [export] format confidence values to save bytes

Issue - State: open - Opened by jameshadfield 8 months ago - 2 comments
Labels: enhancement

#1504 - Support numpy major version 2

Issue - State: open - Opened by corneliusroemer 8 months ago - 1 comment
Labels: enhancement

#1503 - Consolidate date logic

Issue - State: closed - Opened by victorlin 8 months ago - 1 comment
Labels: duplicate

#1502 - Update dev docs to single source of truth

Issue - State: closed - Opened by genehack 8 months ago
Labels: documentation

#1501 - augur curate format-dates: accept masked dates

Pull Request - State: closed - Opened by joverlee521 8 months ago - 2 comments

#1500 - Docs fixes

Pull Request - State: closed - Opened by victorlin 8 months ago

#1499 - Update Biopython docs URL

Pull Request - State: closed - Opened by victorlin 8 months ago - 1 comment

#1498 - CI `build-docs` failing

Issue - State: closed - Opened by joverlee521 8 months ago - 1 comment
Labels: bug

#1497 - Port `translate-authors` from `ingest` to `augur curate abbreviate-authors`

Pull Request - State: closed - Opened by genehack 8 months ago - 2 comments

#1496 - augur curate format-dates should recognize masked dates internally

Issue - State: closed - Opened by joverlee521 8 months ago
Labels: enhancement

#1495 - Port merge-user-metadata to augur curate

Pull Request - State: closed - Opened by joverlee521 8 months ago - 1 comment

#1494 - Extend `augur curate format-dates` to output date ranges

Issue - State: open - Opened by joverlee521 8 months ago
Labels: enhancement

#1493 - Stop quoting TSV outputs from augur curate

Pull Request - State: closed - Opened by joverlee521 8 months ago - 5 comments

#1492 - Add Codecov token

Pull Request - State: closed - Opened by victorlin 8 months ago

#1491 - Port apply-geolocation-rules to augur curate

Pull Request - State: closed - Opened by victorlin 8 months ago - 1 comment

#1490 - Add `asia` to default colors

Pull Request - State: closed - Opened by joverlee521 8 months ago - 1 comment

#1489 - Update default region colors

Issue - State: closed - Opened by joverlee521 8 months ago

#1488 - Curate standard geolocation rules

Issue - State: open - Opened by joverlee521 8 months ago - 1 comment

#1487 - augur curate: Support Excel inputs

Issue - State: closed - Opened by joverlee521 8 months ago - 9 comments
Labels: enhancement

#1486 - augur curate transform-strain-name

Issue - State: closed - Opened by joverlee521 8 months ago

#1485 - augur curate parse-genbank-location

Issue - State: closed - Opened by joverlee521 8 months ago

#1484 - augur curate rename

Issue - State: closed - Opened by joverlee521 8 months ago

#1483 - augur curate abbreviate-authors

Issue - State: closed - Opened by joverlee521 8 months ago - 1 comment

#1482 - augur curate apply-record-annotations

Issue - State: closed - Opened by joverlee521 8 months ago

#1481 - Improved subsampling support

Issue - State: open - Opened by victorlin 8 months ago

#1480 - How to disable indel trimming with augur align

Issue - State: closed - Opened by swantan 8 months ago - 2 comments
Labels: bug

#1479 - refine: Support rooting with time data without producing a time tree

Issue - State: open - Opened by huddlej 8 months ago
Labels: enhancement

#1478 - [export] Improve root-sequence help messages

Pull Request - State: closed - Opened by jameshadfield 8 months ago

#1477 - Multi Thread option (align) without SnakeMake

Issue - State: closed - Opened by kiranpatil222 9 months ago - 2 comments
Labels: enhancement

#1476 - relax schema enforcement of `generated_by` in node-data files

Issue - State: open - Opened by jameshadfield 9 months ago
Labels: bug

#1475 - Metadata wrangling prior to merging with existing data

Issue - State: open - Opened by jameshadfield 9 months ago - 2 comments

#1474 - Update testing docs

Pull Request - State: closed - Opened by victorlin 9 months ago
Labels: documentation

#1473 - Support pandas version 2

Issue - State: open - Opened by victorlin 9 months ago - 2 comments
Labels: enhancement

#1472 - Review Pyright rule exceptions

Issue - State: open - Opened by victorlin 9 months ago - 3 comments

#1472 - Review Pyright rule exceptions

Issue - State: open - Opened by victorlin 9 months ago - 3 comments

#1471 - augur/parse.py: fix test failure with pandas 2.2.

Pull Request - State: closed - Opened by emollier 9 months ago - 1 comment

#1471 - augur/parse.py: fix test failure with pandas 2.2.

Pull Request - State: closed - Opened by emollier 9 months ago - 1 comment

#1470 - Augur 24.4.0 release

Issue - State: closed - Opened by victorlin 9 months ago

#1469 - filter: Improve speed of `--output-strains` and `--output-metadata`

Pull Request - State: open - Opened by victorlin 9 months ago - 1 comment

#1466 - filter: Improve speed of checking duplicates

Pull Request - State: closed - Opened by victorlin 9 months ago - 3 comments

#1465 - export: Add option to extend the default lat/longs

Issue - State: closed - Opened by victorlin 9 months ago - 8 comments
Labels: enhancement

#1464 - Update changelog

Pull Request - State: closed - Opened by victorlin 9 months ago

#1462 - `augur align --method nextclade` should wrap `nextclade run`

Issue - State: closed - Opened by genehack 9 months ago - 5 comments
Labels: enhancement

#1461 - Augur export error

Issue - State: closed - Opened by fiiiibiiiii 9 months ago - 2 comments
Labels: bug, duplicate, needs information

#1460 - Prepare for weighted sampling

Pull Request - State: closed - Opened by victorlin 9 months ago - 1 comment

#1459 - filter: Print all log messages to stderr

Pull Request - State: closed - Opened by victorlin 9 months ago