Ecosyste.ms: Issues

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

GitHub / nextstrain/mpox issues and pull requests

#299 - fix_tree.py: ValueError: list.remove(x): x not in list

Issue - State: open - Opened by joverlee521 about 1 month ago
Labels: bug

#298 - Properly handle CSV-like TSVs

Issue - State: open - Opened by joverlee521 about 2 months ago

#297 - phylogenetic: Add config option `ancestral_root_seq`

Pull Request - State: closed - Opened by joverlee521 2 months ago - 1 comment

#296 - annotate mutations between the inferred root and the reference sequence

Issue - State: closed - Opened by jameshadfield 2 months ago - 6 comments
Labels: enhancement

#295 - Shorten authors

Pull Request - State: closed - Opened by joverlee521 2 months ago - 1 comment

#294 - INRB updates

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

#293 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] 2 months ago

#291 - Small tweaks to Nextclade builds

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

#290 - Shorten author name list

Issue - State: closed - Opened by corneliusroemer 3 months ago - 4 comments
Labels: enhancement

#289 - Add new clades to phylogenetic

Pull Request - State: closed - Opened by corneliusroemer 3 months ago - 2 comments

#288 - Disable transmission lines again, they are too often wrong

Pull Request - State: closed - Opened by corneliusroemer 3 months ago - 1 comment

#287 - Add INRB-specific build pipeline

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

#286 - assign-colors scripts are largely identical

Issue - State: open - Opened by jameshadfield 3 months ago

#285 - ingest: Automated workflow failing during fetch from NCBI

Issue - State: closed - Opened by joverlee521 3 months ago - 5 comments
Labels: blocked

#284 - Fix Clade I build

Pull Request - State: closed - Opened by joverlee521 3 months ago - 2 comments

#283 - phylogenetic: Clade I build failed during filter

Issue - State: closed - Opened by joverlee521 3 months ago - 11 comments
Labels: bug

#282 - Reached maximum recursion depth when building phylogenetic trees

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

#281 - Migrate to Nextclade v3

Pull Request - State: closed - Opened by joverlee521 3 months ago - 1 comment

#280 - Migrate to Nextclade v3

Issue - State: closed - Opened by joverlee521 3 months ago - 1 comment
Labels: enhancement

#279 - Update geo-fixes

Pull Request - State: closed - Opened by jameshadfield 4 months ago - 1 comment

#278 - Clade-I tweaks

Pull Request - State: closed - Opened by jameshadfield 4 months ago - 1 comment

#277 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago

#276 - Update nextclade workflow

Pull Request - State: closed - Opened by corneliusroemer 5 months ago

#275 - Use accession for node name but display strain

Pull Request - State: open - Opened by jameshadfield 5 months ago

#274 - Update clade definition and coloring

Pull Request - State: closed - Opened by trvrb 5 months ago

#273 - Move hardcode filter query into configuration files

Issue - State: open - Opened by huddlej 5 months ago - 1 comment

#272 - Add colours for clade-Ia / Ib in all-clades build

Issue - State: closed - Opened by jameshadfield 5 months ago - 2 comments
Labels: enhancement

#271 - Divergent branches on the mpox build

Issue - State: open - Opened by BryanTegomoh 6 months ago - 1 comment
Labels: enhancement

#270 - Phylo update clades

Pull Request - State: closed - Opened by joverlee521 6 months ago

#267 - Update description

Pull Request - State: closed - Opened by joverlee521 6 months ago

#266 - Add clade I to the phylogenetic description.md

Issue - State: closed - Opened by joverlee521 6 months ago
Labels: documentation

#265 - Mpox Clade I delineation?

Issue - State: open - Opened by woguta 6 months ago - 5 comments
Labels: documentation

#264 - Check for mutations and clades before removing

Pull Request - State: open - Opened by huddlej 6 months ago
Labels: bug, source: office hours

#263 - ingest: use new augur curate commands

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

#262 - ingest: use new augur curate commands

Issue - State: closed - Opened by joverlee521 7 months ago

#261 - Trim reuse text

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

#260 - Sync .gitattributes with pathogen-repo-guide

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

#259 - Update phylogenetic GH Action workflows

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

#258 - Switch CI to `pathogen-repo-ci` action [#257]

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

#257 - Convert CI to "modern" `pathogen-repo-ci`

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

#255 - Allow addition of unreleased INRB data

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

#254 - Add Clade-I build

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

#253 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago

#252 - [phylo] Reconnect traits to export

Pull Request - State: closed - Opened by joverlee521 9 months ago

#251 - [phylo] traits input not passed to `augur export`

Issue - State: closed - Opened by joverlee521 9 months ago - 1 comment
Labels: bug

#250 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago

#249 - ingest: Remove `inrb` source from config.yaml

Pull Request - State: closed - Opened by joverlee521 9 months ago - 1 comment

#248 - Remove `inrb.ndjson` as sequences now available via NCBI

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

#247 - Fix fstring format

Pull Request - State: closed - Opened by joverlee521 9 months ago - 1 comment

#246 - Re-eneable snakefmt in pre-commit

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

#245 - Use nextclade3 for phylogenetic workflow

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

#243 - Add submission date to the INRB sequences

Pull Request - State: closed - Opened by j23414 9 months ago - 1 comment

#242 - Ingest INRB data with permission

Pull Request - State: closed - Opened by j23414 9 months ago - 6 comments

#241 - Add new lineages B.1.21, B.1.22, C.1.1 to phylogenetic

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

#239 - Fix trial rebuilds

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

#238 - Phylogenetic updates to match pathogen-repo-guide

Pull Request - State: closed - Opened by joverlee521 12 months ago - 2 comments

#237 - [phylo] CI workflow DAG includes `update_example_data`

Issue - State: open - Opened by joverlee521 12 months ago
Labels: bug

#236 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 12 months ago

#235 - dev: Use preview version of our centralized pathogen-repo-build.yaml workflow

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

#234 - Update ingest to pathogen-repo-template

Pull Request - State: closed - Opened by joverlee521 almost 1 year ago - 4 comments

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

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

#232 - `fix_tree.py` can create invalid tree

Issue - State: open - Opened by joverlee521 about 1 year ago - 4 comments
Labels: bug

#231 - Potentially include year-only sequences

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

#229 - Add Quickstart section to the top level README

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

#228 - ingest: download Nextclade V2 dataset

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

#227 - Version nextalign binary for transition

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

#226 - Version nextclade binary for transition, i.e. nextclade -> nextclade2

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

#225 - Add Nextclade dataset workflow in `/nextclade` dir

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

#224 - fetch-and-ingest-branch: Send Slack notications to test channel

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

#223 - Fix ingest uploads

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

#222 - Ingest updates

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

#221 - .github/workflows: Use centralized SLACK_CHANNELS variable

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

#220 - Rename instances of "monkeypox" to "mpox"

Pull Request - State: closed - Opened by trvrb about 1 year ago - 10 comments

#219 - Move the NCBI field map to config

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

#218 - GitHub Action workflows clean up

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

#217 - Move ncbi taxon id to config

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

#216 - [wip] Attempt to eradicate confounding of release and submission

Pull Request - State: open - Opened by j23414 over 1 year ago

#215 - Move s3_dst config to top level config

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

#214 - Add CI profile to run CI build

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

#213 - Styleguide: Avoid the message rule attribute

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

#212 - ingest: Link to vendored/README.md for instructions on vendoring

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

#211 - doc: ncbi datasets

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

#210 - Remove `reverse` column, associated script, and references

Pull Request - State: open - Opened by joverlee521 over 1 year ago

#209 - Ingest: remove `reverse` column from metadata TSV

Issue - State: closed - Opened by joverlee521 over 1 year ago - 1 comment

#208 - fix: script moved to phylogenetic dir

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

#207 - Replace join metadata and clades script with csvtk and tsv append

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

#206 - Remove extra actionlint

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

#205 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#201 - fix: correct vendored path in notify-on-* scripts after move and build action args

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

#168 - Rename repo & builds

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

#100 - Automate rebuilds

Pull Request - State: closed - Opened by joverlee521 over 2 years ago - 1 comment

#99 - Ingest: Add alignmentStart/End and/or sequence length to our metadata.tsv

Issue - State: open - Opened by corneliusroemer over 2 years ago
Labels: enhancement

#98 - Ingest cleanup

Pull Request - State: closed - Opened by joverlee521 over 2 years ago