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

#1458 - Make command line option headings linkable

Issue - State: open - Opened by victorlin 10 months ago
Labels: documentation

#1457 - Clarification on augur tree --exclude-sites masking

Issue - State: closed - Opened by Eric-CH-Chen 10 months ago - 4 comments
Labels: documentation

#1456 - Add docs regarding bootstraps

Issue - State: open - Opened by jameshadfield 10 months ago
Labels: documentation

#1455 - Update FAQ

Pull Request - State: closed - Opened by victorlin 10 months ago

#1454 - Implement weighted sampling

Pull Request - State: closed - Opened by victorlin 10 months ago - 6 comments

#1453 - Link to new location for filtering/subsampling docs

Pull Request - State: closed - Opened by victorlin 10 months ago

#1452 - Reference new CI target

Pull Request - State: closed - Opened by victorlin 10 months ago

#1451 - WIP [refine] unique internal node names

Pull Request - State: open - Opened by jameshadfield 10 months ago

#1450 - export multiple trees

Pull Request - State: open - Opened by jameshadfield 10 months ago

#1449 - Update lat/longs

Pull Request - State: closed - Opened by trvrb 10 months ago - 1 comment

#1448 - Fix CI

Pull Request - State: closed - Opened by victorlin 10 months ago

#1447 - Support pandas version 2

Pull Request - State: closed - Opened by victorlin 10 months ago - 1 comment

#1446 - docs: Tone down warning about Debian package

Pull Request - State: closed - Opened by tsibley 10 months ago

#1445 - Allow repeating an option that takes multiple values

Pull Request - State: closed - Opened by victorlin 10 months ago - 4 comments

#1444 - Add subsampling command with YAML config, basic weighted sampling

Pull Request - State: closed - Opened by victorlin 10 months ago - 1 comment
Labels: revisit sometime

#1443 - Allow custom date column name to be specified in `refine` - similar to `metadata-id-column`

Issue - State: open - Opened by corneliusroemer 11 months ago - 1 comment
Labels: enhancement

#1442 - Add warning for external packages

Pull Request - State: closed - Opened by joverlee521 11 months ago

#1441 - Add schema for node-data JSONs

Issue - State: open - Opened by joverlee521 11 months ago - 1 comment
Labels: enhancement

#1440 - [ancestral, translate] node data validation improvements

Pull Request - State: closed - Opened by jameshadfield 11 months ago - 2 comments

#1439 - bugfix tree file opening in beast import

Pull Request - State: closed - Opened by tomkinsc 11 months ago - 3 comments

#1438 - Write compound (segmented) sequence locations

Pull Request - State: closed - Opened by jameshadfield 11 months ago - 3 comments

#1436 - parse: Support pandas 2.x

Pull Request - State: closed - Opened by emollier 11 months ago - 5 comments

#1435 - DRAFT: add 'gene' feature capture when reading genbank files

Pull Request - State: open - Opened by j23414 11 months ago - 1 comment

#1432 - filter: Split filtering and subsampling

Pull Request - State: open - Opened by victorlin 11 months ago - 5 comments

#1431 - Move filtering/subsampling docs into a separate file

Pull Request - State: closed - Opened by victorlin 11 months ago - 4 comments

#1430 - filter: Improve help text

Pull Request - State: open - Opened by victorlin 11 months ago - 1 comment

#1429 - filter: Add --max-length option

Pull Request - State: closed - Opened by victorlin 11 months ago - 2 comments

#1426 - Improve validation output to identify problematic nodes / properties

Issue - State: open - Opened by jameshadfield 12 months ago - 1 comment
Labels: enhancement

#1425 - filter: Expand subsampling docs

Pull Request - State: closed - Opened by victorlin 12 months ago - 2 comments

#1424 - frequencies: Fix `--regions` flag

Pull Request - State: closed - Opened by joverlee521 12 months ago - 1 comment

#1423 - frequencies: error with `--region` flag

Issue - State: closed - Opened by joverlee521 12 months ago - 3 comments
Labels: bug

#1422 - filter: Update `--min-length` help message

Pull Request - State: closed - Opened by joverlee521 12 months ago - 4 comments

#1421 - [filter]: Add flag for `--max-length`

Issue - State: closed - Opened by joverlee521 12 months ago
Labels: enhancement

#1420 - release.yaml: Restore workflow name

Pull Request - State: closed - Opened by victorlin 12 months ago

#1419 - Update changelog

Pull Request - State: closed - Opened by joverlee521 12 months ago - 1 comment

#1418 - filter: Read all metadata columns when query parsing fails

Pull Request - State: closed - Opened by victorlin 12 months ago - 1 comment

#1417 - filter: Replace backtick quoting in Pandas query

Pull Request - State: closed - Opened by victorlin 12 months ago - 1 comment

#1416 - filter: Use Pandas function to extract all names from query

Pull Request - State: closed - Opened by victorlin 12 months ago - 1 comment

#1415 - filter: `--query` broken with backtick quoting

Issue - State: closed - Opened by victorlin 12 months ago - 5 comments
Labels: bug

#1414 - frequencies: Validate arguments

Issue - State: open - Opened by victorlin 12 months ago
Labels: enhancement

#1413 - frequencies: Initialize variables in proper scope

Pull Request - State: closed - Opened by victorlin 12 months ago - 1 comment

#1411 - filter: Automatic type inference does not work on boolean columns

Issue - State: closed - Opened by victorlin about 1 year ago
Labels: bug

#1410 - filter: Restore automatic boolean conversion

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1408 - filter: Properly check for empty metadata

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1407 - Bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies

#1406 - Miscellaneous changes

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1405 - Show version in release workflow name

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1404 - Update changelog

Pull Request - State: closed - Opened by victorlin about 1 year ago

#1403 - Add a parameter to augur parse to specify a different record ID for output sequences FASTA

Pull Request - State: closed - Opened by j23414 about 1 year ago - 1 comment

#1402 - Feat request: add `--metadata-id-columns` param to augur parse?

Issue - State: closed - Opened by j23414 about 1 year ago - 4 comments
Labels: enhancement

#1401 - GFF parsing broken with bcbio-gff v0.7.1 and older versions of Biopython

Issue - State: closed - Opened by victorlin about 1 year ago
Labels: bug

#1400 - Bump bcbio-gff to 0.7.1

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1399 - Add `jq` to dev dependency

Issue - State: open - Opened by joverlee521 about 1 year ago - 2 comments
Labels: enhancement

#1398 - frequencies: Annotate tips with the minimum necessary information

Pull Request - State: closed - Opened by victorlin about 1 year ago - 2 comments

#1397 - Fix failing CI tests (ancestral/translate)

Pull Request - State: closed - Opened by jameshadfield about 1 year ago - 2 comments

#1396 - Update install docs

Pull Request - State: closed - Opened by victorlin about 1 year ago - 3 comments

#1395 - CI failing on new release with version related errors

Issue - State: closed - Opened by victorlin about 1 year ago - 2 comments
Labels: bug

#1394 - Rearrange entries in changelog

Pull Request - State: closed - Opened by victorlin about 1 year ago

#1393 - Update CI setup

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1392 - Test failing with TreeTime 0.11.2 release

Issue - State: closed - Opened by victorlin about 1 year ago - 4 comments
Labels: bug

#1391 - Temporarily disable zika CI

Pull Request - State: closed - Opened by victorlin about 1 year ago

#1390 - data: add geo coordinates for asia

Pull Request - State: closed - Opened by rneher about 1 year ago

#1389 - filter: Improve help and summary messages

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1388 - ERROR from TreeTime: An error occurred in TreeTime

Issue - State: closed - Opened by TangJiajie0818 about 1 year ago - 2 comments

#1387 - Don't support Biopython >=1.82

Pull Request - State: closed - Opened by victorlin about 1 year ago

#1386 - Determine JSON size without loading data as a string into memory

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1385 - export: Reduce memory footprint when determining whether to automatically minify output

Issue - State: closed - Opened by victorlin about 1 year ago - 3 comments
Labels: bug

#1384 - export v2: Add --metadata-columns option

Pull Request - State: closed - Opened by joverlee521 about 1 year ago - 11 comments

#1383 - [export] Decouple colorings and exported metadata

Issue - State: closed - Opened by joverlee521 about 1 year ago
Labels: enhancement

#1381 - Enforce UTF-8 encoding

Pull Request - State: closed - Opened by victorlin about 1 year ago - 8 comments

#1380 - [ancestral] VCF and JSON outputs differ

Issue - State: closed - Opened by jameshadfield about 1 year ago - 2 comments
Labels: bug

#1379 - Address Biopython deprecation warnings

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1378 - [ancestral] writing VCF files is sloooooow

Issue - State: closed - Opened by jameshadfield about 1 year ago - 1 comment
Labels: bug

#1377 - [ancestral] error when writing gzipped VCF output

Issue - State: open - Opened by jameshadfield about 1 year ago
Labels: bug

#1376 - [ancestral] root sequence not converted to uppercase

Issue - State: closed - Opened by jameshadfield about 1 year ago
Labels: bug

#1375 - Enable pathogen-repo-ci for rsv

Pull Request - State: closed - Opened by victorlin about 1 year ago

#1374 - Don't support Biopython 1.82

Pull Request - State: closed - Opened by victorlin about 1 year ago

#1373 - ancestral, translate: GFF parsing broken with Biopython >=1.82

Issue - State: closed - Opened by victorlin about 1 year ago - 1 comment
Labels: bug

#1372 - Run CI only when useful

Pull Request - State: closed - Opened by victorlin about 1 year ago - 2 comments

#1371 - Add a file to keep track of deprecated features

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1370 - Temporarily disable pathogen-repo-ci for RSV

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1369 - Extend `augur import` with `auspice` mode that imports from `auspice.json`

Issue - State: open - Opened by corneliusroemer about 1 year ago - 2 comments
Labels: enhancement

#1368 - [ancestral] VCF REF != reference base resulting in missing variation

Issue - State: open - Opened by jameshadfield about 1 year ago - 1 comment
Labels: bug

#1367 - Exit code 2 if TreeTimeError encountered

Pull Request - State: closed - Opened by jameshadfield about 1 year ago - 1 comment

#1366 - [vcf] replace augur's read_vcf with TreeTime's

Pull Request - State: closed - Opened by jameshadfield about 1 year ago - 1 comment

#1365 - Update test coverage file upload/download

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#1364 - build(deps): bump actions/download-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#1363 - build(deps): bump actions/upload-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#1362 - [ancestral] reference seq may be reference or inferred tree root

Issue - State: open - Opened by jameshadfield about 1 year ago - 2 comments
Labels: bug, priority: low

#1361 - [translate] misleading key names; differing behaviour between JSON & VCF inputs

Issue - State: closed - Opened by jameshadfield about 1 year ago - 1 comment
Labels: bug

#1360 - Incompatabilities between augur tree and augur ancestral

Issue - State: open - Opened by jameshadfield about 1 year ago
Labels: bug, high priority, please take this issue

#1359 - Unable to run augur filter step

Issue - State: closed - Opened by swantan about 1 year ago - 6 comments
Labels: bug