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

#1358 - `export` crashes with `KeyError: 'tree'` when jsonschema v4 is installed

Issue - State: closed - Opened by corneliusroemer about 1 year ago - 12 comments
Labels: bug, priority: moderate

#1357 - [vcf] replace VCF reading with TreeTime's `read_vcf`

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

#1356 - [vcf] Replace `write_VCF_translation` with treetime's `write_vcf`

Issue - State: open - Opened by jameshadfield about 1 year ago - 3 comments

#1355 - Fix VCF parsing bugs

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

#1354 - build(deps): bump actions/setup-python from 4 to 5

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

#1353 - ancestral: Accept files to `--genes`

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

#1352 - export v2: Automatically minify output

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

#1351 - Improve parsing of GenBank / GFF files

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

#1350 - Run CI against blab/veme-2022 and zika-tutorial

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

#1349 - [translate] GFF files parsed differently if `--genes` supplied

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

#1348 - ancestral / translate improvements & tests

Pull Request - State: closed - Opened by jameshadfield about 1 year ago - 5 comments

#1347 - build(deps): bump conda-incubator/setup-miniconda from 2 to 3

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

#1346 - [translate] GFFs + node-data input produce invalid output

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

#1345 - ancestral, translate incompatible under certain invocations

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

#1344 - [augur ancestral] arg parsing improvements

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

#1343 - [augur ancestral] input VCF alignment is often overwritten

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

#1341 - Dealing with lower case nucleotides: document and potentially auto-convert

Issue - State: open - Opened by corneliusroemer about 1 year ago
Labels: request for comments

#1339 - `augur validate` throws an error instead of showing help

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

#1338 - IQtree 2.2.3 errors with SIGSEGV when analyzing 130k SARS-CoV-2 seqs

Issue - State: closed - Opened by NikitaSitharam about 1 year ago - 3 comments
Labels: bug, upstream

#1337 - Augur traits file null

Issue - State: closed - Opened by Sanyukta2001 about 1 year ago - 1 comment
Labels: documentation, discussion-forum

#1336 - [ancestral] translate genes/CDSs via nuc seq + annotation

Issue - State: open - Opened by jameshadfield over 1 year ago - 2 comments

#1335 - Bump supported pyfastx versions

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

#1334 - Can't install with Python 3.12 on Conda

Issue - State: closed - Opened by victorlin over 1 year ago - 9 comments
Labels: bug, blocked

#1333 - feat: output genome annotations for complex CDS

Pull Request - State: open - Opened by corneliusroemer over 1 year ago - 2 comments

#1332 - feat: treat CDS as a valid feature for GFFs in `load_features`

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago - 3 comments

#1331 - export: Automatically minify JSON

Issue - State: closed - Opened by victorlin over 1 year ago - 3 comments
Labels: enhancement

#1330 - CI: Update mpox repo name

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

#1327 - Augur TreeTime Error. What am i doing wrong?

Issue - State: open - Opened by Sanyukta2001 over 1 year ago - 4 comments
Labels: faq

#1326 - ENH: allow export to validate schema for a specific version of auspice

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

#1325 - [Don't merge] Add failing test for #1323

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago

#1323 - fix: upper case root sequence for ancestral reconstruction

Pull Request - State: closed - Opened by rneher over 1 year ago - 5 comments

#1321 - Improved ancestral translation validation

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago - 2 comments

#1320 - Add failing test for ancestral --genes file #1319

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago - 1 comment

#1319 - ancestral: --genes does not accept file in contrast to --help string

Issue - State: closed - Opened by corneliusroemer over 1 year ago - 3 comments
Labels: bug

#1318 - Allow weighted subsampling

Issue - State: closed - Opened by victorlin over 1 year ago - 10 comments
Labels: enhancement

#1317 - Export ancestral AA sequences for tree's root node

Pull Request - State: closed - Opened by huddlej over 1 year ago - 1 comment

#1316 - Numpy deprecation warnings for pandas imports

Issue - State: closed - Opened by corneliusroemer over 1 year ago - 1 comment
Labels: priority: low

#1315 - Fix pytest warnings

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago - 1 comment

#1314 - test: change expected test results after treetime bug fix

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago

#1312 - `augur curate passthru` can add double quotations

Issue - State: closed - Opened by joverlee521 over 1 year ago - 6 comments
Labels: bug

#1311 - build(deps): bump actions/checkout from 3 to 4

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

#1310 - Allow treetime v0.11 (no breaking changes)

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago - 1 comment

#1309 - Clarify release steps for setup.py changes

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

#1308 - Add a debug mode to print stack trace for exceptions caught by top-level handler

Issue - State: closed - Opened by corneliusroemer over 1 year ago - 6 comments
Labels: enhancement

#1306 - chore: drop typing_extensions from deps as 3.7 no longer supported

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago - 1 comment

#1305 - feat: support treetime ambiguous date format

Pull Request - State: open - Opened by corneliusroemer over 1 year ago - 2 comments

#1304 - Allow precise date ranges

Issue - State: open - Opened by corneliusroemer over 1 year ago - 7 comments
Labels: enhancement

#1303 - test failure beyond pandas 2.0

Issue - State: closed - Opened by emollier over 1 year ago - 1 comment
Labels: bug

#1302 - Remove Snakemake tests (and dependency)

Pull Request - State: closed - Opened by victorlin over 1 year ago - 4 comments

#1299 - Minimal export (no node-data files needed)

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

#1298 - Schema updates

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

#1297 - Update PR template

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

#1296 - Drop Python 3.7 support

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

#1295 - Root sequence exported in main JSON

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

#1294 - Read a subset of metadata columns

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

#1293 - fix: disable non-a-number filtering in clade file parsing

Pull Request - State: closed - Opened by rneher over 1 year ago - 3 comments

#1292 - rooting examples in augur refine documentation are out of date

Issue - State: open - Opened by huddlej over 1 year ago
Labels: documentation, office-hours

#1291 - filter: Stream filtered metadata to outputs directly

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

#1290 - Configure output streams to support non-Unicode encodings

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

#1289 - Use flake8 for code quality checks

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

#1288 - chore/remove unused imports

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago - 3 comments

#1287 - feat(mask): allow empty mask file, warn not error

Pull Request - State: open - Opened by corneliusroemer over 1 year ago

#1286 - feat(mask): Add `--mask-gaps {all,terminals}` option

Pull Request - State: open - Opened by corneliusroemer over 1 year ago - 4 comments

#1285 - distance: Document ignored characters and counting of gaps as indels

Pull Request - State: closed - Opened by huddlej over 1 year ago - 1 comment
Labels: office-hours

#1284 - Export clock rate covariance matrix and std dev

Pull Request - State: closed - Opened by huddlej over 1 year ago - 2 comments

#1283 - ancestral: update module docstring to include amino acids

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 2 comments

#1282 - filter: Expand comment and testing for `--query`

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

#1281 - Annotations schema updates

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

#1280 - Genome annotations for segmented CDSs etc

Issue - State: open - Opened by jameshadfield over 1 year ago - 3 comments

#1279 - Update annotation schema for strand changes

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

#1278 - filter: Remove attempt at extracting variables from `--query`

Pull Request - State: closed - Opened by victorlin over 1 year ago - 7 comments

#1277 - filter: `--query` fails when the `.str` accessor is used on a column

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

#1276 - Update pathogen repo CI

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

#1275 - CI: Remove mamba list

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

#1274 - Add nextstrain/rsv to CI

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

#1273 - Remove extra TreeTime version check

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

#1271 - Align treetime minimum version with setup.py

Issue - State: closed - Opened by corneliusroemer over 1 year ago

#1270 - Move typing_extensions to runtime dependencies

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

#1269 - filter: `--query` fails when numerical comparisons are used on columns with missing values

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

#1268 - filter: Try converting all queried columns to numerical type

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

#1267 - filter: Expose internal Pandas errors from `--query`

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

#1266 - Remove `export v1`

Issue - State: open - Opened by victorlin over 1 year ago - 4 comments

#1265 - export v1: Add deprecation warning, remove `--metadata-id-columns`

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

#1264 - export v2: Add option to choose sample name from metadata

Issue - State: open - Opened by joverlee521 over 1 year ago - 3 comments
Labels: enhancement

#1263 - Feat/parse nextclade annotation

Pull Request - State: open - Opened by rneher over 1 year ago

#1262 - export v2: metadata ID column not used if `strain` column already exists in the metadata

Issue - State: closed - Opened by joverlee521 over 1 year ago - 2 comments
Labels: bug

#1261 - export v2: Remove hardcoding of "strain" as the metadata ID column

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

#1259 - Update export v2 Cram tests

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