Ecosyste.ms: Issues

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

GitHub / broadinstitute/cromshell issues and pull requests

#281 - example for cromshell

Issue - State: open - Opened by solivehong 5 months ago

#280 - QueuedInCromwell task status not recognized

Issue - State: open - Opened by notestaff 11 months ago - 1 comment

#279 - Replacing Setup.py with Pyproject.py

Pull Request - State: closed - Opened by bshifaw 11 months ago - 1 comment
Labels: bug

#278 - Fix cost (for methods cromwell), add explicit example

Pull Request - State: closed - Opened by sjfleming about 1 year ago - 6 comments
Labels: bug, Cromshell 2

#277 - Local pip install fails

Issue - State: closed - Opened by sjfleming about 1 year ago - 1 comment

#276 - minor updates to publish_release.md for clarity

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

#275 - bumpversion to 2.1.1

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

#274 - Add tests for kvg flatten nested wdl dirs functions

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

#273 - Minor updates to validation command

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

#272 - update the readme with color commands

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

#272 - update the readme with color commands

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

#270 - Log4j vulnerability

Issue - State: closed - Opened by j-p-courneya over 1 year ago - 3 comments

#269 - Cromshell2.0 crashes for server that worked on cromshell 1

Issue - State: open - Opened by jamesemery over 1 year ago - 1 comment

#268 - Detect and flatten nested WDL directories

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

#267 - Change to "cromshell" instead of "cromshell-draft-release"

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

#265 - womtool/miniwdl validate command

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

#264 - pip installed cromshell may have a dependency issue

Issue - State: open - Opened by SHuang-Broad over 1 year ago - 1 comment

#263 - Brew tap for [email protected] appears to be broken

Issue - State: open - Opened by jamesemery over 1 year ago

#262 - Fix out of date (un)installation commands

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

#261 - Request to add a command to validate WDLs through cromshell.

Issue - State: closed - Opened by bshifaw over 1 year ago - 2 comments
Labels: enhancement

#260 - can't access workflow logs from AoU RWB

Issue - State: closed - Opened by ruchim over 1 year ago - 4 comments

#259 - Add fetch-logs and enable Azure log fetching

Pull Request - State: open - Opened by bshifaw over 1 year ago - 1 comment
Labels: Cromshell 2

#258 - Error running cromshell due to incompatible protobuf version

Issue - State: open - Opened by bshifaw almost 2 years ago

#257 - Automated version bump and deployment

Pull Request - State: closed - Opened by bshifaw almost 2 years ago

#256 - Version Command fix

Pull Request - State: closed - Opened by bshifaw almost 2 years ago
Labels: bug, Cromshell 2

#255 - Release edits for cromshell2

Pull Request - State: closed - Opened by bshifaw almost 2 years ago
Labels: Cromshell 2

#254 - Add a way to track resource usage for a submitted workflow

Issue - State: open - Opened by bshifaw almost 2 years ago
Labels: enhancement, Cromshell 2

#253 - Add clean-up command to CS2

Issue - State: open - Opened by bshifaw almost 2 years ago
Labels: Cromshell 2

#252 - Add option to logs command to download logs

Issue - State: open - Opened by bshifaw almost 2 years ago
Labels: Cromshell 2

#251 - Bother Cromwell team until they implement notification

Issue - State: open - Opened by lbergelson almost 2 years ago - 4 comments

#250 - Have the cost command indicate which tasks were call-cached

Issue - State: open - Opened by bshifaw almost 2 years ago
Labels: Cromshell 2

#249 - Add option to not color json output to main command

Pull Request - State: closed - Opened by bshifaw almost 2 years ago
Labels: Cromshell 2

#248 - Add list-outputs

Pull Request - State: closed - Opened by bshifaw almost 2 years ago
Labels: Cromshell 2

#247 - Logs command to check the metadata for 'calls' before searching for logs

Pull Request - State: closed - Opened by bshifaw almost 2 years ago
Labels: bug, Cromshell 2

#246 - cromshell-beta logs KeyError

Issue - State: closed - Opened by wharvey31 almost 2 years ago - 3 comments
Labels: bug, Cromshell 2

#245 - Implement Lazy Loading of Commands

Issue - State: open - Opened by bshifaw almost 2 years ago
Labels: enhancement, Cromshell 2

#244 - Linting fixes

Pull Request - State: closed - Opened by bshifaw almost 2 years ago

#243 - Create a convention for how we report errors.

Issue - State: open - Opened by bshifaw almost 2 years ago
Labels: Cromshell 2

#242 - Added cromwell auth parameters to cromshell config template

Pull Request - State: closed - Opened by bshifaw about 2 years ago
Labels: Cromshell 2

#241 - Provide warning for unknown config options

Pull Request - State: closed - Opened by bshifaw about 2 years ago

#240 - Add cost command

Pull Request - State: closed - Opened by bshifaw about 2 years ago
Labels: Cromshell 2

#239 - Add publish release docs

Pull Request - State: closed - Opened by bshifaw about 2 years ago
Labels: Cromshell 2

#238 - removed "Coming Soon" wording for list command in README.md

Pull Request - State: closed - Opened by bshifaw about 2 years ago

#237 - lint fixes

Pull Request - State: closed - Opened by bshifaw about 2 years ago

#236 - Tox env to automatically implement lint fixes

Pull Request - State: closed - Opened by bshifaw about 2 years ago
Labels: Cromshell 2

#235 - Documentation on making release to brew tap and PyPi

Pull Request - State: closed - Opened by bshifaw about 2 years ago
Labels: Cromshell 2

#234 - lint test fixes

Pull Request - State: closed - Opened by bshifaw about 2 years ago

#233 - Added list command

Pull Request - State: closed - Opened by kvg about 2 years ago - 1 comment
Labels: Cromshell 2

#232 - added update-server description to README.md

Pull Request - State: closed - Opened by bshifaw about 2 years ago - 1 comment
Labels: Cromshell 2

#231 - add unit test (address Berri's comments from PR)

Pull Request - State: closed - Opened by eviewan about 2 years ago
Labels: Cromshell 2

#230 - scripts to publish to pypi 2

Pull Request - State: closed - Opened by bshifaw about 2 years ago - 3 comments
Labels: Cromshell 2

#229 - Add unit test for test_io_utils.py (merge to cromshell_2.0)

Pull Request - State: closed - Opened by eviewan about 2 years ago
Labels: Cromshell 2

#228 - Add unit test for test_io_utils.py

Pull Request - State: closed - Opened by eviewan about 2 years ago - 1 comment

#227 - Using pytest-cov for test coverage

Issue - State: closed - Opened by SHuang-Broad about 2 years ago - 1 comment
Labels: enhancement, question, Cromshell 2

#226 - Verify which commits from master is worth pulling in before cromshell 2.0 beta

Issue - State: open - Opened by SHuang-Broad about 2 years ago
Labels: question, Cromshell 2

#225 - FR: Cromshell support for no-turtle mode

Issue - State: closed - Opened by mbookman about 2 years ago - 3 comments

#224 - FR: Cromshell support for non-interactive setup

Issue - State: open - Opened by mbookman about 2 years ago - 8 comments

#223 - cromshell wait -w cannot find wdl id

Issue - State: open - Opened by yuhuyoyo over 2 years ago - 1 comment

#222 - Have Cromshell call cromwell logs api instead of metadata api

Issue - State: open - Opened by bshifaw over 2 years ago
Labels: Cromshell 2

#221 - scripts to publish to pypi

Pull Request - State: closed - Opened by bshifaw over 2 years ago - 1 comment
Labels: Cromshell 2

#220 - Set of refactoring changes to harmonize the code base

Pull Request - State: closed - Opened by bshifaw over 2 years ago
Labels: Cromshell 2

#218 - Add `gcsfs` to requirements.txt

Pull Request - State: closed - Opened by sjfleming over 2 years ago - 7 comments

#217 - Missing requirement: `gcsfs`

Issue - State: closed - Opened by sjfleming over 2 years ago
Labels: bug

#216 - Cromshell update-server should provide a list of all previously connected servers

Issue - State: open - Opened by jamesemery over 2 years ago - 1 comment
Labels: enhancement, Cromshell 2

#215 - Fix brew uninstallation instructions

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

#214 - Zip the --dependencies-zip arg in memory when passed as a dir

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

#213 - Update workflow database to tab-delimited format if necessary

Pull Request - State: closed - Opened by sjfleming over 2 years ago - 7 comments
Labels: bug, Cromshell 2

#212 - Old database files incompatible with 2.0

Issue - State: closed - Opened by sjfleming over 2 years ago
Labels: bug, Cromshell 2

#211 - Add note about cromshell 2 alpha to readme

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

#210 - Added a 'logs' command for listing all of the logs.

Pull Request - State: closed - Opened by jamesemery almost 3 years ago - 2 comments
Labels: Cromshell 2

#209 - Added a "logs" command to list all of the logs according to the metadata

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

#208 - BW-1226 Add `referer_header_url` and `gcloud_token_email` options

Pull Request - State: closed - Opened by aednichols almost 3 years ago - 1 comment

#207 - Zip the --dependencies-zip arg when passed as a dir (Closes #193)

Pull Request - State: closed - Opened by kshakir almost 3 years ago - 1 comment

#206 - added an optional utility to download and wrap womtool

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

#205 - Refactor status

Pull Request - State: open - Opened by SHuang-Broad almost 3 years ago
Labels: Cromshell 2

#204 - Update README.md

Pull Request - State: closed - Opened by gileshall almost 3 years ago
Labels: Cromshell 2

#203 - Add `update-server` command to 2.0

Pull Request - State: closed - Opened by sjfleming almost 3 years ago - 2 comments
Labels: enhancement, Cromshell 2

#202 - readme referred to wrong env name

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

#201 - setup.py adjustments

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

#200 - Added subcommand to open a workflow's timing diagram in a webbrowser.

Pull Request - State: closed - Opened by kvg almost 3 years ago - 1 comment
Labels: enhancement, Cromshell 2

#199 - `update-server` command

Issue - State: closed - Opened by sjfleming almost 3 years ago
Labels: enhancement, Cromshell 2

#198 - Add error detail to when server communication fails

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

#197 - fix link to developer docs

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

#196 - Use the server to run womtool validation

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

#195 - Added docs for development

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

#194 - Added warning to update cromwell server if newly created

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

#193 - submit command could go one step further

Issue - State: closed - Opened by SHuang-Broad almost 3 years ago - 7 comments
Labels: Cromshell 2

#192 - Add execution status count

Pull Request - State: closed - Opened by bshifaw almost 3 years ago
Labels: Cromshell 2

#191 - add a command to open a browser page for the execution bucket

Issue - State: open - Opened by SHuang-Broad almost 3 years ago - 3 comments
Labels: Cromshell 2

#190 - Fixing issue where tasks would be incorrectly labeled as failed.

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

#189 - Cromshell2.0 status command should accept multiple workflow IDs

Issue - State: open - Opened by kvg about 3 years ago
Labels: Cromshell 2

#187 - Make `list-outputs` give back not only files, but naive types too

Issue - State: open - Opened by SHuang-Broad about 3 years ago - 1 comment
Labels: enhancement, Cromshell 2

#186 - Added Alias command and scripts for workflow_id utils

Pull Request - State: closed - Opened by bshifaw about 3 years ago

#185 - Adding python 3.10 to our test matrix

Pull Request - State: closed - Opened by lbergelson about 3 years ago

#184 - Add python 3.10 to test matrix

Pull Request - State: closed - Opened by lbergelson about 3 years ago - 1 comment

#183 - removed dataclasses in setup.py

Pull Request - State: closed - Opened by bshifaw about 3 years ago