Ecosyste.ms: Issues

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

GitHub / oda-hub/nb2workflow issues and pull requests

#214 - add token only if not present

Pull Request - State: open - Opened by burnout87 3 months ago

#212 - Fix dispatcher compatibility in validation

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

#211 - Update tox.ini

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

#210 - Tests sometimes fail/timeout in github actions

Issue - State: open - Opened by dsavchenko 3 months ago - 8 comments

#209 - Support pip requirements in `environment.yml`

Pull Request - State: closed - Opened by dsavchenko 3 months ago - 1 comment
Labels: galaxy

#208 - Support pip requirements in `environment.yml`

Issue - State: closed - Opened by dsavchenko 3 months ago - 1 comment
Labels: galaxy

#207 - Better check for job completion condition

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

#205 - adding missing arg

Pull Request - State: closed - Opened by burnout87 3 months ago - 1 comment

#203 - Default dispatcher label (for kaniko pod antiaffinity)

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

#202 - Not found /tmp/*/tests/testfiles/*.ipynb in tests

Issue - State: closed - Opened by dsavchenko 4 months ago - 3 comments

#201 - Restrict micromamba version < 2.0

Pull Request - State: closed - Opened by dsavchenko 4 months ago - 3 comments
Labels: galaxy

#200 - add a test which tests user notebook

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

#198 - Kaniko pod antiaffinity

Pull Request - State: closed - Opened by dsavchenko 5 months ago - 1 comment

#197 - using `ontology_helper` to check against `POSIXPath` before download

Pull Request - State: closed - Opened by burnout87 5 months ago - 4 comments

#196 - why input is changing ">" to "__gt__"?

Issue - State: open - Opened by volodymyrss 6 months ago
Labels: galaxy

#194 - [Galaxy] Exception if output is not annotated

Issue - State: open - Opened by dsavchenko 6 months ago - 1 comment
Labels: galaxy

#193 - Optional parameters

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

#191 - nb2workflow optional parameters

Issue - State: open - Opened by volodymyrss 7 months ago

#190 - increased `max_download_size` and bugfix when there are exceptions

Pull Request - State: closed - Opened by burnout87 8 months ago - 3 comments

#189 - revert 188

Pull Request - State: closed - Opened by volodymyrss 8 months ago

#188 - Please revert back my unwanted push

Issue - State: closed - Opened by ferrigno 8 months ago - 1 comment
Labels: help wanted

#187 - Fix int, bool with unknown owl

Pull Request - State: closed - Opened by dsavchenko 8 months ago

#186 - Typo in annotation may lead to type check error

Issue - State: closed - Opened by dsavchenko 8 months ago

#185 - make a way to restrict access to some groups

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

#184 - serialise_workflow_exception in helpers

Pull Request - State: closed - Opened by dsavchenko 8 months ago

#183 - test equal sign in string parameter

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

#182 - Backend container don't start with volume provisioned through NFS

Issue - State: closed - Opened by dsavchenko 8 months ago - 6 comments

#181 - '=' in string parameter produces issues

Issue - State: closed - Opened by dsavchenko 8 months ago

#180 - Tune probes timeouts of deployment

Pull Request - State: closed - Opened by dsavchenko 8 months ago

#179 - Handling connection error download and checking file size

Pull Request - State: closed - Opened by burnout87 8 months ago

#176 - make configurable ephemeral storage and other resources

Issue - State: open - Opened by volodymyrss 9 months ago - 1 comment

#175 - Update buildjob.yaml.jinja

Pull Request - State: closed - Opened by volodymyrss 9 months ago - 2 comments

#174 - Fix logging error

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

#173 - Recover failed tests

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

#172 - Refactor deploy. Add persistent volume in k8s.

Pull Request - State: closed - Opened by dsavchenko 9 months ago - 2 comments

#171 - url mmoda validator and token arg adding

Pull Request - State: closed - Opened by burnout87 9 months ago - 2 comments

#170 - Max download size

Pull Request - State: closed - Opened by burnout87 10 months ago

#169 - clean old run directories

Issue - State: open - Opened by volodymyrss 10 months ago

#168 - 158 notebooks should have access to requesters oda token

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

#167 - Respect explicitly defined python version in container

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

#166 - Revert "[Galaxy] Boolean default. Normalise output name."

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

#165 - No sort_keys in Flask jsonify

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

#164 - [Galaxy] Boolean default. Normalise output name.

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

#162 - Config file

Pull Request - State: open - Opened by burnout87 10 months ago - 7 comments

#161 - add parameter description annotation

Issue - State: closed - Opened by volodymyrss 11 months ago - 1 comment

#160 - add resource constrains, memory and CPU

Issue - State: open - Opened by volodymyrss 11 months ago

#159 - binary product issue

Issue - State: open - Opened by volodymyrss 11 months ago

#158 - notebooks should have access to requesters oda token

Issue - State: closed - Opened by volodymyrss 11 months ago - 2 comments

#157 - Cell timeout (presumably due to the large output)

Issue - State: open - Opened by dsavchenko 11 months ago - 6 comments

#156 - check size of the file before download

Issue - State: closed - Opened by volodymyrss 11 months ago - 2 comments

#155 - Support for multiline parameter definitions. Basic type annotations.

Pull Request - State: closed - Opened by dsavchenko 11 months ago - 6 comments

#154 - make an annotation to remote archive

Issue - State: closed - Opened by volodymyrss 11 months ago

#153 - Really need to support multiline parameter definitions

Issue - State: closed - Opened by dsavchenko 11 months ago

#152 - support pip inside tool as a demonstrator

Issue - State: closed - Opened by volodymyrss 11 months ago - 2 comments

#151 - Bug removing div

Pull Request - State: closed - Opened by burnout87 11 months ago - 1 comment

#150 - 138 add support for annotations of workflow access to resource storage and compute

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

#149 - Galaxy-tool-test-remotefile

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

#148 - arg get request opens notebook

Pull Request - State: closed - Opened by burnout87 11 months ago - 9 comments

#147 - dedicated sentry module with env var

Pull Request - State: closed - Opened by burnout87 12 months ago - 5 comments

#146 - from html remove cell with output glueing

Issue - State: closed - Opened by volodymyrss 12 months ago

#144 - freeze flask requirement, cleanup `requirements.txt`

Pull Request - State: closed - Opened by burnout87 12 months ago - 4 comments

#143 - incompatibility with `Flask==3.0.2`

Issue - State: closed - Opened by burnout87 12 months ago

#142 - Add annotation for high memory requirement

Issue - State: open - Opened by volodymyrss 12 months ago

#141 - Download posixpath as url

Pull Request - State: closed - Opened by burnout87 12 months ago - 9 comments

#137 - `ruamel.yaml` dependency conflict

Issue - State: closed - Opened by burnout87 about 1 year ago - 8 comments

#136 - Properly treat the case if parameter default is None (but it's annotated)

Issue - State: closed - Opened by dsavchenko about 1 year ago - 4 comments

#135 - Send callback upon job start

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

#134 - Send callback upon job start

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

#133 - code cleanup

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

#132 - test_callback code cleanup

Issue - State: closed - Opened by okolo about 1 year ago

#131 - Return jobdir for started async jobs

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

#130 - ensure galaxy tool id contains only valid characters

Issue - State: closed - Opened by dsavchenko about 1 year ago

#129 - return jobdir while job is still not done

Issue - State: closed - Opened by volodymyrss about 1 year ago

#128 - treat file url parameter type

Issue - State: open - Opened by volodymyrss about 1 year ago

#127 - how to make large annotations

Issue - State: open - Opened by volodymyrss about 1 year ago

#126 - hotfix race condition in deploy

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

#125 - learn how to generate .shed.yaml

Issue - State: closed - Opened by volodymyrss about 1 year ago

#124 - think how to run mmoda nb tests

Issue - State: open - Opened by volodymyrss about 1 year ago

#122 - no cwl dependency

Pull Request - State: closed - Opened by burnout87 about 1 year ago - 2 comments

#121 - 111 running long tasks on mmoda

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

#120 - Logging from nb2workflow

Issue - State: open - Opened by burnout87 over 1 year ago - 2 comments

#119 - list and dict input

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

#118 - support passing structured objects, represented by arbitrary json

Issue - State: closed - Opened by volodymyrss over 1 year ago
Labels: crowdsourcing-tools

#117 - fixing issue #116 cleanup fail in case of exception in nbadapter.py:429

Pull Request - State: closed - Opened by okolo over 1 year ago - 12 comments

#116 - cleanup fails in case of exception in nbadapter.py:429

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

#115 - restrict python version in deploy

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

#114 - Update setup.py

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

#113 - running nb2workflow fails on python 3.12

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