Ecosyste.ms: Issues

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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

#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

#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

#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

#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