virtool/virtool-workflow issues and pull requests

#339 - Use normal formatting for log messages sent to Sentry

Pull Request - State: closed - Opened by igboyes 2 months ago - 2 comments
Labels: released

#338 - fix: prevent redis connection errors

Pull Request - State: closed - Opened by igboyes 7 months ago - 1 comment
Labels: released

#337 - feat(server): support jobs without `rights` field

Pull Request - State: closed - Opened by igboyes 8 months ago - 1 comment
Labels: released

#336 - Use Python 3.12

Pull Request - State: closed - Opened by igboyes 8 months ago - 2 comments
Labels: released

#335 - docs: update intersphinx mapping to production URLs

Pull Request - State: closed - Opened by Bryce-Davidson 9 months ago - 1 comment
Labels: released

#334 - Bryce davidson/vir 1991 get virtool workflow building on readthedocs

Pull Request - State: closed - Opened by Bryce-Davidson 9 months ago - 1 comment
Labels: released

#333 - Matthewcurtis1999/vir 1973 use the core redis upgrades in workflow

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

#332 - feat: overhaul framework

Pull Request - State: closed - Opened by igboyes 11 months ago - 1 comment
Labels: released

#331 - Matthewcurtis1999/vir 1634 use python 312 in virtool workflow

Pull Request - State: closed - Opened by mattcurts 11 months ago - 1 comment
Labels: released

#330 - chore: decode stderr in logs

Pull Request - State: closed - Opened by mattcurts 12 months ago - 1 comment
Labels: released

#329 - Improve exception logging

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#328 - fix: fix missing path when using `pytest_plugin`

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#327 - Auto-unpack the ML file `model.tar.gz`

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#326 - Upgrade core and fix pytest plugin issues

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#325 - fix: update virtool-core-version

Pull Request - State: closed - Opened by ReeceHoffmann about 1 year ago - 1 comment
Labels: released on @alpha

#324 - Update core version

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

#323 - fix: resolve crashing due to outdated virtool-core version

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

#322 - fix: add missing modules needed in pytest plugin

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#321 - Expose some functionality as a pytest plugin

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#320 - feat: add `reference` to `new_index` and improve dx

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#319 - fix: report the last step in the status reports when a job completes

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#318 - fix: support unpaired reads in `fastqc` and add testing

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#317 - fix!: fix broken fastqc fixture

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#316 - fix: restore missing built-in fixtures

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#315 - fix: resolve circular import error

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#314 - ci: fix broken npm installations

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#313 - feat: overhaul framework

Pull Request - State: closed - Opened by igboyes about 1 year ago - 1 comment
Labels: released on @alpha

#312 - ci: auto-release alpha channel

Pull Request - State: closed - Opened by igboyes about 1 year ago - 2 comments
Labels: released, released on @alpha

#311 - chore: fix up typing and remove unused code

Pull Request - State: closed - Opened by igboyes over 1 year ago - 2 comments
Labels: released, released on @alpha

#310 - fix: support integer group ids, ml resources, and `structlog`

Pull Request - State: closed - Opened by igboyes over 1 year ago - 1 comment
Labels: released

#309 - fix: clean api ping logs

Pull Request - State: closed - Opened by mattcurts over 1 year ago - 1 comment
Labels: released

#308 - refactor: change run_subprocess.py to subprocess.py

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

#307 - Matthewcurtis1999/vir 1864 fix docs builds for virtool workflow

Pull Request - State: closed - Opened by mattcurts over 1 year ago - 1 comment
Labels: released

#306 - docs: fix ci badge on readme

Pull Request - State: closed - Opened by igboyes over 1 year ago - 2 comments
Labels: released

#305 - ci: fix error from `pytest-docker-compose`

Pull Request - State: closed - Opened by igboyes over 1 year ago - 1 comment
Labels: released

#304 - docs: update readme

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

#303 - feat: use latest data model

Pull Request - State: closed - Opened by igboyes over 1 year ago - 1 comment
Labels: released

#302 - fix: use latest core models

Pull Request - State: closed - Opened by igboyes over 1 year ago - 1 comment
Labels: released

#301 - fix: improve error visibility

Pull Request - State: closed - Opened by igboyes over 1 year ago - 1 comment
Labels: released

#300 - ci: stop publishing image to dockerhub

Pull Request - State: closed - Opened by ChristineWC almost 2 years ago - 1 comment
Labels: released

#299 - Make job ping requests from workflows

Pull Request - State: closed - Opened by igboyes almost 2 years ago - 1 comment
Labels: released

#298 - fix: fix black pre commit hook

Pull Request - State: closed - Opened by SnickerDoodlePop about 2 years ago - 1 comment
Labels: released

#297 - fix: prevent failures when access index data_type value

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#296 - Add index.reference field

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#295 - feat: add id and manifest fields to workflow index objects

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#294 - fix: shorten subprocess logging messages

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#293 - ci: fix broken pypi publish job

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#292 - ci: make sure release is triggered on push

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#291 - Simplify CLI and clean up code

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#290 - test: remove unused tox.ini

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#289 - docs: remove changelog

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#288 - Use new core models in virtool workflow

Pull Request - State: closed - Opened by igboyes about 2 years ago - 1 comment
Labels: released

#287 - refactor: remove unused docker file

Pull Request - State: closed - Opened by ryanfang5 over 2 years ago - 1 comment
Labels: released

#286 - chore: publish to GHCR

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 2 comments
Labels: released

#285 - fix: retry requests on when connection refused

Pull Request - State: closed - Opened by igboyes over 2 years ago - 1 comment
Labels: released

#284 - chore: use core redis in virtool-workflow

Pull Request - State: closed - Opened by buddy326 over 2 years ago - 1 comment
Labels: released

#283 - fix: set name using step decorator parameters

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 2 comments
Labels: released

#282 - Remove fixtures code and use `pyfixtures`

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 1 comment
Labels: released

#281 - feat: raise an error when a sub-process fails

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 2 comments
Labels: released

#280 - chore: avoid logging JSON responses

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 3 comments
Labels: released

#279 - refactor: use workflow errors

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 2 comments
Labels: released

#278 - feat: explicit step naming

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 2 comments
Labels: released

#277 - refactor: remove startup and cleanup decorators

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 2 comments
Labels: released

#276 - fix: don't log Redis connection information

Pull Request - State: closed - Opened by buddy326 over 2 years ago - 1 comment
Labels: released

#275 - chore: remove status.py in virtool_workflow/runtime

Pull Request - State: closed - Opened by buddy326 over 2 years ago

#274 - Blake/vir 1287 remove on finalize hook

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 2 comments
Labels: released

#273 - Add tests of executor implementation

Pull Request - State: closed - Opened by BlakeASmith over 2 years ago - 2 comments
Labels: released

#272 - Add testing instructions to README

Pull Request - State: closed - Opened by BlakeASmith almost 3 years ago - 2 comments
Labels: released

#271 - fix: wait longer to establish a redis connection

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#270 - Fix samples provider

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#269 - chore: removed k3s directory from virtool-workflow

Pull Request - State: closed - Opened by buddy326 almost 3 years ago - 1 comment
Labels: released

#268 - chore: use jobs_api_connection_string everywhere

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#267 - Handle SIGTERM and cancellation correctly

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#266 - Hooks

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#265 - Remove context

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#264 - chore: autoformat with black

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#263 - test: clear hooks after executing workflow

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#262 - test: use new runtime in status integration tests

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#261 - chore: upgrade to click>=8.0.0

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#260 - chore: remove .docker directory

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#259 - chore: remove .vim folder

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#258 - Simplify CLI

Pull Request - State: closed - Opened by BlakeASmith almost 3 years ago - 3 comments
Labels: released

#257 - fix: use multiple processes for `skewer` command

Pull Request - State: closed - Opened by BlakeASmith almost 3 years ago - 1 comment
Labels: released

#256 - feat: add sentry logging

Pull Request - State: closed - Opened by BlakeASmith almost 3 years ago - 1 comment
Labels: released

#255 - feat: add sentry logging

Pull Request - State: closed - Opened by BlakeASmith almost 3 years ago - 2 comments

#254 - Remove Unreliable Caching Implementation

Pull Request - State: closed - Opened by BlakeASmith almost 3 years ago - 1 comment
Labels: released

#253 - fix: bypass caching in reads fixture

Pull Request - State: closed - Opened by igboyes almost 3 years ago

#252 - fix: bump download chunk size to 20 MB

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#251 - fix: prevent excessive memory use when fetching input files

Pull Request - State: closed - Opened by igboyes almost 3 years ago - 1 comment
Labels: released

#250 - Add option to run a single job from redis

Pull Request - State: closed - Opened by BlakeASmith almost 3 years ago - 2 comments
Labels: released

#249 - Change Workflow Status Update Behaviour

Pull Request - State: closed - Opened by BlakeASmith about 3 years ago - 1 comment
Labels: released

#248 - Handle SIGTERM

Pull Request - State: closed - Opened by BlakeASmith about 3 years ago - 1 comment
Labels: released

#247 - fix: configure logs for all run commands

Pull Request - State: closed - Opened by igboyes about 3 years ago - 1 comment
Labels: released

#246 - chore: update Dockerfile to use virtool/workflow-tools

Pull Request - State: closed - Opened by BlakeASmith about 3 years ago - 1 comment
Labels: released

#245 - fix: remove /api prefix

Pull Request - State: closed - Opened by BlakeASmith about 3 years ago - 2 comments
Labels: released

#244 - Start logging as soon as workflow is executed

Pull Request - State: closed - Opened by igboyes about 3 years ago - 1 comment
Labels: released

#243 - Remove Codacy

Pull Request - State: closed - Opened by igboyes about 3 years ago - 1 comment
Labels: released

#242 - Use core Redis utilities

Pull Request - State: closed - Opened by igboyes about 3 years ago - 1 comment
Labels: released

#241 - Accept subtraction_id in job args

Pull Request - State: closed - Opened by igboyes about 3 years ago - 1 comment
Labels: released

#240 - fix: prevent work path carryover between jobs

Pull Request - State: closed - Opened by igboyes about 3 years ago - 1 comment
Labels: released

GitHub / virtool/virtool-workflow issues and pull requests