History

v0.7.1 (2021-06-29)

  • Pin required bioblend version to 0.15.0 (PR #40).
  • Switched CI tests to Github Actions (PR #40).

v0.7.0 (2021-05-17)

Breaking changes:

  • Dropped support for Python 2.7: nebulizer now needs Python 3.6+ (thanks to Hugo van Kemenade @hugovk) (PR #102)

  • Substantial refactoring and simplification of the tool managament commands (PR #113): - Now only list_tools, install_tool, update_tool

    and delete_tool commands are supported

    • list_installed_tools renamed to list_tools
    • old functionality of list_tools replaced by list_tools --mode=tools
    • list_repositories command dropped; functionality replaced by list_tools --mode=export
    • install_repositories command dropped; functionality replaced by install_tool --file=...

New commands:

  • New quota, quota_add, quota_mod and quota_del commands for managing quotas (PR #66)

Updates to existing commands:

  • -l option for search_toolshed includes the shed URL (PR #91)
  • update_tool allows use of wildcards (i.e. *) when specifying tool repository names and owners, to enable multiple tool repositories to updated at once (PR #92)
  • New --status option for list_users command allows deleted and purged user accounts to also be listed (PR #97)
  • New --sort option for list_users command allows sorting of listed accounts by disk usage, quota and quota usage (PR #104)

Bug fixes:

  • Fix to using the --purge option of the delete_user command (previously it wasn’t possible to purge accounts) (PR #98)
  • Remove requirement to specify an account or API key on Galaxy server when using the ping and config commands (PR #100)

Other updates:

  • Added support for Python 3.9 (thanks to Hugo van Kemenade @hugovk) (PR #108)

v0.6.0 (2020-07-14)

New commands:

  • New search_toolshed command (PR #42)
  • New config command (PR #57)
  • New delete_user command (PR #62)
  • New uninstall_tool command (PR #64)

Updates to existing commands:

  • list_keys doesn’t report API keys unless --show-api-keys option is specified (PR #58)
  • Additional fields reported by --long-listing-format option of list_users (disk and quota usage, status); doesn’t report ID by default (PR #59)
  • Enable flexible tool repository specification syntax for install_tool and update_tool (PR #60)
  • remove_key prompts user to confirm API key deletion (PR #72)
  • Use spaces rather than tabs to line up fields in output from list_users, list_installed_tools, list_tools, list_tool_panel, list_keys, config, list_libraries; use --show_id to report Galaxy IDs for users and data libraries (PR #68, PR #69, PR #70)

Documentation:

  • Add a tutorial/walkthrough (PR #75)
  • Significant overhaul and expansion of documentation (PR #78)

Removed functionality:

  • Removed deprecated utilities manage_users, manage_tools and manage_libraries (PR #61)

v0.5.0 (2020-04-20)

v0.4.3 (2018-10-05)

  • Ensure that click dependency is version 6.7 or earlier, to avoid subcommand names changing from e.g. list_users to list-users (PR #49)

v0.4.2 (2017-08-24)

  • Commands now explicitly return appropriate exit code values indicating success (0) or failure (non-zero values).
  • New option --check-toolshed added to list_installed_tools and update_tool commands, to check installed revisions directly against those available in the toolshed (PR #41)
  • Update install_tool, update_tool and install_repositories to install tool dependencies through a resolver (e.g. conda) by default (issue #43)
  • New options added to install_tool, update_tool and install_repositories commands, to explicit control how tool and repository dependencies should be handled (PR #44):
    • --install-tool-dependencies [yes|no]: install tool dependencies via the toolshed, if any are defined (default is yes)
    • --install-tool-dependencies [yes|no]: install tool dependencies via the toolshed, if any are defined (default is yes)
    • --install-resolver-dependencies [yes|no]: install dependencies through a resolver that supports installation (e.g. conda) (default is yes)

v0.4.1 (2016-12-19)

  • Fix broken update_tool command (PR #40).

v0.4.0 (2016-11-18)

  • New subcommand ping: ‘ping’ a Galaxy instance to see if it’s responsive (PR #33).
  • New subcommand whoami: reports user associated with the API key (PR #37).
  • add_library_datasets: refuses to perform upload if using the master API key (essentially API key must have an associated user).
  • install_repositories: prints a list of all tool repositories that couldn’t be installed.
  • New --timeout and --nowait options added for install_tool, update_tool and install_repositories subcommands.
  • Fix to treat tool repositories with status New as still installing when trying to install tools (PR #31).
  • Some improvements to logging (PR #38).

v0.3.0 (2016-10-26)

  • New class tools.ToolPanel and updates to existing tools.ToolPanelSection class.
  • install_tool: fix behaviour so that command does nothing if a version is not specified and at least one version of the tool is already installed.
  • list_repositories and install_repositories: new commands to generate a list of installed tool repositories from a Galaxy instance and then reinstall tool repositories from a list with the same format (PR #19).
  • install_tool: fix incorrect reporting of target tool panel section (PR #20)
  • add_key and update_key: fix automatic retrieval of API key, which only worked previously if connecting user was an admin account (PR #23)
  • list_tool_panel: shows tools in order they appear in Galaxy when using --list-tools option.
  • Deprecated utilities (manage_users, manage_tools and manage_libraries) issue warnings when run.
  • License updated to Academic Free License (AFL).
  • Initial version of documentation also made available via ReadTheDocs (PR #21)

v0.2.0 (2016-10-17)

  • Implemented new nebulizer utility which provides all previous functionality via subcommands, plus commands for managing API keys automatically (old manage_users, manage_tools and manage_libraries utilities are still available for backwards-compatibility but are deprecated).
  • New general options:
    • -q/--suppress-warnings: prevent warning messages from nebulizer commands.
  • Various fixes and improvements to underlying functionality:
    • install_tools: now checks if tool is already installed; handles tool revisions that include the revision number; polls Galaxy until tool is installed, or operation times out; exit status reflects the success or failure of the installation.
    • update_tool: now works even if original tool isn’t in a tool panel section
    • list_installed_tools: now groups tools under correct repo revision when using --list-tools option.

v0.1.1 (2016-05-16)

  • Add -u/--username and -P/--galaxy_password options to all commands to allow interaction with Galaxy instance via API using normal login credentials instead of API key.

v0.1.0 (2015-11-06)

  • Initial release of nebulizer utilities for administering Galaxy instances via the command line.