Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / pjbriggs/nebulizer issues and pull requests
#122 - Update nebulizer dependencies to bioblend 0.16.0.
Pull Request -
State: open - Opened by pjbriggs about 3 years ago
- 1 comment
Labels: update, dependencies
#121 - Update to use Bioblend 0.16.0
Issue -
State: open - Opened by pjbriggs about 3 years ago
Labels: update, dependencies
#120 - Pin required bioblend to version 0.15.0.
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: bugfix, dependencies
#119 - Update the name of the workflow for CI testing to "Python CI".
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: refactoring
#118 - Switch the CI tests from Travis to Github Actions
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: refactoring
#117 - Updates for build & upload to PyPI
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: update
#116 - Update documentation and tutorial
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: documentation, bugfix, update
#115 - Standardise 'install_tool' behaviour
Issue -
State: open - Opened by pjbriggs over 3 years ago
Labels: enhancement, tools, cli
#114 - Updates to comments, docstrings and README
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: documentation, bugfix
#113 - Consolidate tool management commands
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: enhancement, tools, refactoring
#112 - Update 'install_tool' command to prompt for confirmation
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: enhancement, tools
#111 - Update to bioblend version 0.15.0
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: update, dependencies
#110 - Rename 'quota' commands
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: quotas, cli
#109 - Update 'click' library to 7.1.2
Pull Request -
State: closed - Opened by pjbriggs over 3 years ago
Labels: update, dependencies
#108 - Test on and declare support for Python 3.9 final
Pull Request -
State: closed - Opened by hugovk over 3 years ago
- 1 comment
#107 - Update to bioblend 0.15.0
Issue -
State: closed - Opened by pjbriggs over 3 years ago
Labels: update, dependencies
#106 - Add python_requires to help pip and test on Python 3.9 beta
Pull Request -
State: closed - Opened by hugovk about 4 years ago
#105 - 'install_tool': prompt user to confirm tool installation by default?
Issue -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, tools
#104 - list_users: enable sorting by disk usage, quota etc
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, users
#103 - WIP implement 'disk_usage' command to estimate space consumed by user data
Pull Request -
State: open - Opened by pjbriggs about 4 years ago
Labels: enhancement, users, quotas
#102 - Drop support for EOL Python 2.7
Pull Request -
State: closed - Opened by hugovk about 4 years ago
- 3 comments
Labels: deprecation
#101 - Use SVG Travis CI badge for consistency
Pull Request -
State: closed - Opened by hugovk about 4 years ago
- 2 comments
Labels: documentation
#100 - ping/config commands: don't need to validate API key when connecting to Galaxy
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement
#99 - Fix bug with filtering 'deleted' and 'purged' users in 'get_users' function
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: users, bugfix
#98 - delete_user: fix the purging functionality
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: users, bugfix
#97 - list_users: add --status option to list 'deleted' and 'purged' users
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, users
#96 - Add functionality to estimate disk usage and usage commitment
Issue -
State: open - Opened by pjbriggs about 4 years ago
Labels: new feature, users
#95 - 'list_users': flag users with negative disk usage
Issue -
State: open - Opened by pjbriggs about 4 years ago
Labels: enhancement, users
#94 - README: fix quickstart installation instructions
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: documentation, bugfix
#93 - 'ping' command: doesn't need to validate API key
Issue -
State: open - Opened by pjbriggs about 4 years ago
Labels: bug
#92 - 'update_tool': enable wildcards for repository owner and name to specify multiple tool repos
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, tools
#91 - 'search_toolshed': display tool URL for the tool in the extended listing
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, tools
#90 - Add option to 'uninstall_tool' to prune older versions of tools
Issue -
State: open - Opened by pjbriggs about 4 years ago
Labels: enhancement, tools
#89 - list_tool_panel: fix bug when using --name option
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: tools, bugfix
#88 - 'install/update_tool' handle JSON decode error on premature disconnect from Galaxy
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: tools, bugfix
#87 - Drop support for Python 2.7
Issue -
State: closed - Opened by pjbriggs about 4 years ago
- 1 comment
Labels: deprecation
#86 - 'update_tool': uncaught JSONDecodeError exception
Issue -
State: closed - Opened by pjbriggs about 4 years ago
- 4 comments
Labels: bug, tools
#85 - 'list_users': add options to sort on disk usage, and show bytes versus human-readable format?
Issue -
State: open - Opened by pjbriggs about 4 years ago
Labels: enhancement, users
#84 - 'update_tool' could remove previous version of installed repository on update
Issue -
State: open - Opened by pjbriggs about 4 years ago
Labels: new feature, tools
#83 - Allow 'update_tool' to operate on multiple repositories
Issue -
State: closed - Opened by pjbriggs about 4 years ago
- 1 comment
Labels: enhancement, tools
#82 - Documentation tweaks (README, tutorial)
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, documentation
#81 - Set minimum Bioblend version to 0.13.0
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement
#80 - Minor fixes to the tutorial
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: documentation
#79 - 'Reporter': don't pad the trailing field with spaces
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement
#78 - Documentation: significant overhaul and expansion of documentation
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, documentation
#77 - 'list_users': add '--export' option to output in format suitable for 'create_users_from_file'
Issue -
State: open - Opened by pjbriggs about 4 years ago
Labels: enhancement, users
#76 - install_tool: update tool installation monitoring
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, tools
#75 - Add tutorial/walkthrough to the documentation
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: new feature, documentation
#74 - 'uninstall_tool' update the --remove-from-disk option name
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: tools
#73 - 'whoami': improve handling of errors
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement
#72 - 'remove_key': check if key exists, and prompt for confirmation of removal
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement
#71 - Improve formatting of data reported by 'list_keys' and 'config' commands
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement
#70 - Improve output from tool reporting commands
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, tools
#69 - Improve clarity of output from 'list_users' command
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, users
#68 - Improve clarity of output from 'list_libraries'
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement, libraries
#67 - 'delete_user' should allow names to be removed or permanently obfuscated
Issue -
State: open - Opened by pjbriggs about 4 years ago
- 1 comment
Labels: enhancement, users
#66 - WIP implement quota management commands
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
- 2 comments
Labels: new feature, quotas
#65 - Improvements for tool install and update commands
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement
#64 - Implement 'uninstall_tool' command
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement
#63 - Update handling of connection failure in 'ping' command
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: enhancement
#62 - Add 'delete_user' command
Pull Request -
State: closed - Opened by pjbriggs about 4 years ago
Labels: new feature
#61 - Remove the deprecated utilities 'manage_users', 'manage_tools' and 'manage_libraries'
Pull Request -
State: closed - Opened by pjbriggs over 4 years ago
Labels: deprecation
#60 - Implement flexible repo specification for tool install and update
Pull Request -
State: closed - Opened by pjbriggs over 4 years ago
Labels: enhancement, tools
#59 - Improvements to the 'long format' output from 'list_users' command (suppress ID/report additional fields)
Pull Request -
State: closed - Opened by pjbriggs over 4 years ago
Labels: enhancement
#58 - Updates to key management (reporting/adding keys)
Pull Request -
State: closed - Opened by pjbriggs over 4 years ago
Labels: enhancement
#57 - Add new 'config' command
Pull Request -
State: closed - Opened by pjbriggs over 4 years ago
Labels: new feature
#56 - Update classes so that they all explicitly inherit from 'object'
Pull Request -
State: closed - Opened by pjbriggs over 4 years ago
Labels: bug
#55 - Extend Galaxy user management functionality (delete, update, etc)
Issue -
State: open - Opened by pjbriggs over 4 years ago
- 1 comment
Labels: enhancement, new feature, users
#54 - Implement deletion of Galaxy tools and tool revisions
Issue -
State: closed - Opened by pjbriggs over 4 years ago
- 1 comment
Labels: enhancement, new feature
#53 - Add commands to manipulate Galaxy quotas
Issue -
State: closed - Opened by pjbriggs over 4 years ago
- 2 comments
Labels: new feature, quotas
#52 - Fix formatting error in CHANGELOG.rst
Pull Request -
State: closed - Opened by pjbriggs over 4 years ago
#51 - Updates for testing under Python3
Pull Request -
State: closed - Opened by pjbriggs over 4 years ago
#50 - Fixes for Python 3 compatibility
Pull Request -
State: closed - Opened by pjbriggs over 4 years ago
#49 - Explicitly specify version of 'click' library to avoid version 7.x.
Pull Request -
State: closed - Opened by pjbriggs almost 6 years ago
#48 - Using Click 7.0 changes subcommand names from e.g. "list_users" to "list-users"
Issue -
State: closed - Opened by pjbriggs almost 6 years ago
- 1 comment
Labels: bug
#47 - Don't include tool repositories with no status when listing updateable tools
Issue -
State: open - Opened by pjbriggs almost 7 years ago
Labels: bug
#46 - Implement a test framework to test against Galaxy & toolshed instances
Issue -
State: open - Opened by pjbriggs about 7 years ago
#45 - Consolidate and simplify tool/repository management commands
Issue -
State: open - Opened by pjbriggs about 7 years ago
Labels: enhancement, tools
#44 - Expose options to handle tool dependencies on tool install
Pull Request -
State: closed - Opened by pjbriggs about 7 years ago
- 1 comment
#43 - Conda dependencies not installed with tool for Galaxy 17.05
Issue -
State: closed - Opened by pjbriggs about 7 years ago
- 1 comment
Labels: bug
#42 - Add command to search toolsheds
Pull Request -
State: closed - Opened by pjbriggs about 7 years ago
Labels: new feature, tools
#41 - Sync tool versions against toolsheds for 'list_installed_tools' and 'update_tool'
Pull Request -
State: closed - Opened by pjbriggs about 7 years ago
#40 - Bugfix to broken 'update_tool' command
Pull Request -
State: closed - Opened by pjbriggs almost 8 years ago
#39 - Check tool install status when user cancels installation
Issue -
State: open - Opened by pjbriggs almost 8 years ago
- 1 comment
Labels: enhancement
#38 - Switch logging over to using per-module loggers WIP
Pull Request -
State: closed - Opened by pjbriggs almost 8 years ago
#37 - Implement 'whoami' subcommand in nebulizer WIP
Pull Request -
State: closed - Opened by pjbriggs almost 8 years ago
#36 - Switch to module-level logging
Issue -
State: closed - Opened by pjbriggs almost 8 years ago
#35 - Add "whoami" command
Issue -
State: closed - Opened by pjbriggs almost 8 years ago
Labels: new feature
#34 - Add commands to manipulate Galaxy groups
Issue -
State: open - Opened by pjbriggs almost 8 years ago
Labels: new feature, groups
#32 - Add "ping" command
Issue -
State: closed - Opened by pjbriggs almost 8 years ago
Labels: new feature
#30 - Gracefully handle server/proxy timeouts when installing tool repository
Issue -
State: closed - Opened by pjbriggs almost 8 years ago
- 2 comments
Labels: enhancement
#29 - Check status code of connection errors from Bioblend
Issue -
State: open - Opened by pjbriggs almost 8 years ago
- 2 comments
#25 - Prevent library upload if API key isn't associated with a real user account
Issue -
State: closed - Opened by pjbriggs almost 8 years ago
- 1 comment
#24 - Implement fallback options to handling missing or deprecated versions when installing tools
Issue -
State: open - Opened by pjbriggs almost 8 years ago
- 2 comments
#17 - Expose options for handling tool dependencies etc when installing tool
Issue -
State: closed - Opened by pjbriggs almost 8 years ago
- 1 comment
Labels: enhancement
#9 - Fix ordering of tools from "manage_tools list"
Issue -
State: closed - Opened by pjbriggs almost 9 years ago
- 1 comment
Labels: enhancement, wontimplement
#8 - manage_users: problems reporting admin and percent_quota in long listing format (-l)
Issue -
State: closed - Opened by pjbriggs almost 9 years ago
- 1 comment
Labels: bug, wontfix
#7 - Add an interactive "shell" mode
Issue -
State: open - Opened by pjbriggs almost 9 years ago
- 1 comment
Labels: new feature
#2 - Utilities to upload/download files from histories?
Issue -
State: open - Opened by pjbriggs about 9 years ago
Labels: new feature
#1 - Tool installation needs full toolshed URL
Issue -
State: closed - Opened by pjbriggs about 9 years ago
- 1 comment
Labels: bug