History¶
v0.7.1 (2021-06-29)¶
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 tolist_tools
- old functionality of
list_tools
replaced bylist_tools --mode=tools
list_repositories
command dropped; functionality replaced bylist_tools --mode=export
install_repositories
command dropped; functionality replaced byinstall_tool --file=...
New commands:
- New
quota
,quota_add
,quota_mod
andquota_del
commands for managing quotas (PR #66)
Updates to existing commands:
-l
option forsearch_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 forlist_users
command allows deleted and purged user accounts to also be listed (PR #97)- New
--sort
option forlist_users
command allows sorting of listed accounts by disk usage, quota and quota usage (PR #104)
Bug fixes:
Other updates:
- Added support for Python 3.9 (thanks to Hugo van Kemenade @hugovk) (PR #108)
v0.6.0 (2020-07-14)¶
New commands:
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 oflist_users
(disk and quota usage, status); doesn’t report ID by default (PR #59)- Enable flexible tool repository specification syntax for
install_tool
andupdate_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:
Removed functionality:
- Removed deprecated utilities
manage_users
,manage_tools
andmanage_libraries
(PR #61)
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
tolist-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 tolist_installed_tools
andupdate_tool
commands, to check installed revisions directly against those available in the toolshed (PR #41)- Update
install_tool
,update_tool
andinstall_repositories
to install tool dependencies through a resolver (e.g.conda
) by default (issue #43)- New options added to
install_tool
,update_tool
andinstall_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 isyes
)--install-tool-dependencies [yes|no]
: install tool dependencies via the toolshed, if any are defined (default isyes
)--install-resolver-dependencies [yes|no]
: install dependencies through a resolver that supports installation (e.g.conda
) (default isyes
)
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 forinstall_tool
,update_tool
andinstall_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 existingtools.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
andinstall_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
andupdate_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
andmanage_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 (oldmanage_users
,manage_tools
andmanage_libraries
utilities are still available for backwards-compatibility but are deprecated).- New general options:
-q
/--suppress-warnings
: prevent warning messages fromnebulizer
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 sectionlist_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.