nebulizer-v0.7.1

Nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Patch release version 0.7.1:

• Pin required bioblend version to 0.15.0 (PR #120)
• Switched CI tests to Github Actions (PR #118)

nebulizer-v0.7.0

Nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Release version 0.7.0:

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 be 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)

nebulizer-v0.6.0

Nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Release version 0.6.0:

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

nebulizer-v0.5.0

Nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Minor release version 0.5.0:

• Add support for Python 3.6, 3.7 and 3.8 (PR #50, PR #51)

nebulizer-v0.4.3

Nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Patch release version 0.4.3:

• 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)

nebulizer-v0.4.2

Nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Patch release version 0.4.2:

• 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)

nebulizer-v0.4.1

Nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Patch release version 0.4.1:

• Fix broken update_tool command (PR #40).

nebulizer-v0.4.0

Nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Significant changes in version 0.4.0:

• 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).

nebulizer-v0.3.0

Nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Significant changes in version 0.3.0:

• 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 http://nebulizer.readthedocs.io
  (PR #21).

nebulizer-v0.2.0

nebulizer provides a set of command line utilities to help administer users, tools and data libraries in Galaxy instances.

Significant changes in version 0.2.0:

• 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.