Ecosyste.ms: Issues

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

GitHub / galaxyproject/ephemeris issues and pull requests

#218 - `shed_tools` add exit code

Pull Request - State: open - Opened by bernt-matthias 6 months ago

#214 - use galaxy-tool-test functions for shed-tools test

Pull Request - State: open - Opened by cat-bro 9 months ago

#213 - Dm parameters

Pull Request - State: open - Opened by mvdbeek 9 months ago

#212 - Use None default value where items are optional

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

#211 - Refactor build tracking

Pull Request - State: open - Opened by mvdbeek 9 months ago - 1 comment

#210 - Add now mandatory readthedocs config file

Pull Request - State: closed - Opened by nsoranzo 11 months ago

#209 - Add black, ruff, isort and mypy

Pull Request - State: closed - Opened by mvdbeek 11 months ago

#208 - Fix CI tests

Pull Request - State: closed - Opened by mvdbeek 11 months ago

#205 - Add flag to skip verification of SSL certificate

Pull Request - State: open - Opened by tflowers15 about 1 year ago

#204 - add a section control when installing tools

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

#203 - option to remove a tool

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

#202 - Try to update test instance

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

#201 - Enhancements to the IDC scripts

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

#200 - Script to split genomes.yml for IDC

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

#199 - Juno persona chart calculation is missing

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

#198 - Docs don't seem to be updated for latest release?

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

#195 - Standardize CLI commands on - instead of _

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

#194 - Add data_manager_mode argument fort IDC use

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

#193 - Add partial type annotations

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

#192 - Move commands to subcommands of a single `ephemeris` command

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

#191 - Prefer dashes instead of underscores in flags

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

#190 - Rename configuration option removed in tox 4.0

Pull Request - State: closed - Opened by nsoranzo almost 2 years ago
Labels: bug

#189 - Preprocessing Layer for Run Data Managers

Issue - State: open - Opened by jmchilton almost 2 years ago - 1 comment
Labels: enhancement, help wanted, feature-request

#188 - Allow shed-tools to consume run_data_managers.yaml

Issue - State: open - Opened by jmchilton almost 2 years ago
Labels: enhancement, help wanted, feature-request

#187 - Set Library Permissions

Pull Request - State: closed - Opened by mira-miracoli almost 2 years ago - 10 comments

#186 - New section creation is broken

Issue - State: closed - Opened by natefoo about 2 years ago - 8 comments

#185 - Install local tools

Issue - State: closed - Opened by bvalot over 2 years ago - 1 comment

#183 - setup-data-library should have flag/option for linking the data rather than copying

Issue - State: open - Opened by hexylena almost 3 years ago - 2 comments
Labels: feature-request

#181 - Fix precedence of commandline options and yaml options

Pull Request - State: open - Opened by mvdbeek about 3 years ago - 1 comment

#180 - Global install_resolver_dependencies: false in yaml file does not work

Issue - State: open - Opened by mvdbeek about 3 years ago
Labels: bug

#179 - Stripping the version from the tool_id (change in 0.10.7) breaks tool testing

Issue - State: closed - Opened by cat-bro over 3 years ago - 1 comment

#176 - Prepare 0.10.7 release

Pull Request - State: closed - Opened by mvdbeek over 3 years ago

#175 - use class Indenter to fix wrong indentation in yaml output

Pull Request - State: open - Opened by drosofff over 3 years ago
Labels: enhancement

#174 - Parallellized tool installation.

Issue - State: open - Opened by rhpvorderman over 3 years ago - 2 comments
Labels: enhancement

#173 - Add option to `shed-tools test` for specifying a history name

Pull Request - State: closed - Opened by natefoo over 3 years ago
Labels: enhancement

#172 - Simplify tox.ini, base testing on galaxy-compose

Pull Request - State: open - Opened by rhpvorderman over 3 years ago - 1 comment

#171 - delete the extra random sleep lines from sleep.py

Pull Request - State: closed - Opened by cat-bro over 3 years ago - 2 comments

#170 - workflow-to-tools: get tools from subworkflows

Pull Request - State: closed - Opened by cat-bro over 3 years ago - 1 comment

#169 - Add shed-tools test options

Pull Request - State: open - Opened by selten over 3 years ago

#168 - Adding pysam to requirements

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

#167 - Bring in usegalaxy-tools script for updating lock files.

Pull Request - State: open - Opened by jmchilton almost 4 years ago

#166 - Lots of file descriptors open while testing installed tools

Issue - State: open - Opened by HugoJH almost 4 years ago - 6 comments
Labels: bug

#165 - Various updates to testing and CI infrastructure.

Pull Request - State: closed - Opened by jmchilton about 4 years ago - 2 comments

#164 - Allow using client_test_config with shed_tools test.

Pull Request - State: closed - Opened by jmchilton about 4 years ago - 1 comment

#163 - Close files

Pull Request - State: closed - Opened by almahmoud about 4 years ago - 2 comments

#162 - usegalaxy.* shared data updater creates duplicates

Issue - State: open - Opened by hexylena over 4 years ago - 4 comments

#161 - Handle terminal states in wait for install

Pull Request - State: closed - Opened by mvdbeek over 4 years ago

#160 - Prepare 0.10.6 release

Pull Request - State: closed - Opened by mvdbeek over 4 years ago

#159 - get all tools when searching for tool ids for testing (get_tools instead of get_tool_panel)

Pull Request - State: closed - Opened by cat-bro over 4 years ago - 4 comments

#158 - Wait for the correct repository

Pull Request - State: closed - Opened by mvdbeek over 4 years ago - 1 comment

#157 - run-datamanagers issue

Issue - State: closed - Opened by anfie over 4 years ago - 2 comments

#155 - Fix `shed-tools test -t workflow_tools.yml`

Pull Request - State: closed - Opened by nsoranzo over 4 years ago

#154 - Fix installing tool dependencies from yaml list

Pull Request - State: closed - Opened by mvdbeek over 4 years ago - 2 comments

#153 - wait_for_install is too strict

Issue - State: closed - Opened by mvdbeek over 4 years ago

#152 - setup data lib: improve jobs watching in legacy mode

Pull Request - State: open - Opened by abretaud almost 5 years ago

#151 - run-data-managers - need help

Issue - State: open - Opened by lecorguille almost 5 years ago - 2 comments

#150 - Cast exceptions to string using unicodify

Pull Request - State: closed - Opened by mvdbeek about 5 years ago

#149 - Add description when creating folders with setup_data_libraries

Pull Request - State: closed - Opened by abretaud about 5 years ago - 3 comments

#147 - Prepare 0.10.4 release

Pull Request - State: closed - Opened by mvdbeek about 5 years ago

#146 - When polling for repo install status, ensure the correct revision is being checked

Pull Request - State: closed - Opened by natefoo about 5 years ago - 2 comments

#145 - Fix typo and add entry point

Pull Request - State: closed - Opened by innovate-invent over 5 years ago - 2 comments

#144 - Prep 0.10.3 release

Pull Request - State: closed - Opened by mvdbeek over 5 years ago

#143 - Require galaxy-tool-util instead of galaxy-lib

Pull Request - State: closed - Opened by nsoranzo over 5 years ago - 3 comments

#142 - Release to PyPI on tag

Pull Request - State: closed - Opened by mvdbeek over 5 years ago - 1 comment

#141 - Proper and fast check if repos are installed.

Pull Request - State: closed - Opened by rhpvorderman over 5 years ago - 12 comments

#138 - Data library creation would hang forever if you had a single non-ok command ever

Pull Request - State: closed - Opened by hexylena over 5 years ago - 2 comments

#137 - Don't raise exception when tool tests can't be fetched

Pull Request - State: closed - Opened by mvdbeek over 5 years ago

#136 - Print exception when unexpected test failure is caught

Pull Request - State: closed - Opened by mvdbeek over 5 years ago

#135 - Fix default message check

Pull Request - State: closed - Opened by mvdbeek over 5 years ago - 1 comment

#134 - Intercept requests.exceptions.ConnectionError in addition to bioblend…

Pull Request - State: closed - Opened by mvdbeek over 5 years ago

#133 - Tool installation unknown tool is unnecesarily fatal

Issue - State: closed - Opened by hexylena over 5 years ago - 3 comments
Labels: enhancement

#132 - Prepare 0.10.0

Pull Request - State: closed - Opened by mvdbeek over 5 years ago

#131 - Conda package version behind pip

Issue - State: closed - Opened by innovate-invent over 5 years ago - 1 comment

#130 - Add tool_deps tool to allow triggering installation of local tool dep…

Pull Request - State: closed - Opened by innovate-invent over 5 years ago - 5 comments

#129 - fix doc building and regenerate

Pull Request - State: closed - Opened by martenson over 5 years ago - 1 comment

#128 - Add pysam and continue if test fetching errors

Pull Request - State: closed - Opened by mvdbeek over 5 years ago - 10 comments

#127 - fix default for 'parallel_tests' typo

Pull Request - State: closed - Opened by martenson over 5 years ago

#126 - Include some additional stats for xunit reporting

Pull Request - State: closed - Opened by mvdbeek over 5 years ago

#125 - Testing tools as a non-default user

Issue - State: open - Opened by monprin over 5 years ago - 1 comment

#124 - shed_tools install fails with `KeyError: 'tool_shed_url'`

Issue - State: closed - Opened by pcm32 over 5 years ago

#123 - Handle timeout gracefully for UWSGI connection

Pull Request - State: closed - Opened by pcm32 over 5 years ago - 2 comments

#122 - Update Docs for User Name (Should be Email)

Pull Request - State: closed - Opened by rdvelazquez over 5 years ago - 1 comment

#121 - remove the python invocation from usage examples

Pull Request - State: closed - Opened by martenson almost 6 years ago - 1 comment

#120 - Fix crash when too_with_panel is empty

Pull Request - State: closed - Opened by jvanbraekel almost 6 years ago

#119 - Fix crash when tool_with_panel is empty

Pull Request - State: closed - Opened by jvanbraekel almost 6 years ago - 2 comments

#118 - Test tools in parallel, with regular user permissions, without a shared filesystem

Pull Request - State: closed - Opened by mvdbeek almost 6 years ago - 4 comments

#117 - Tool testing improvements

Issue - State: open - Opened by mvdbeek almost 6 years ago - 3 comments
Labels: help wanted