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@nsoranzo nsoranzo released this 13 Jun 18:12
· 384 commits to main since this release
v0.16.0
c6c0605
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nsoranzo Nicola Soranzo
GPG key ID: A9ED5BE4A6ABB094
Learn about vigilant mode.

  • Added support for Galaxy release 21.05.

  • Replaced the job_info parameter with separate tool_id, inputs and state parameters in JobsClient.search_jobs() (thanks to
    rikeshi).

  • Pass the API key for all requests as the x-api-key header instead of as a parameter (thanks to rikeshi).

  • Try prepending https:// and http:// if the scheme is missing in the url parameter of GalaxyClient, i.e. when initialising a Galaxy or ToolShed instance.

  • Added a new dataset_collections attribute to GalaxyInstance objects, which is an instance of the new DatasetCollectionClient. This new module can be used to get details of a dataset collection, wait until elements of a dataset collection are in a terminal state, and download a history dataset collection as an archive (thanks to rikeshi).

  • Added a new tool_dependencies attribute to GalaxyInstance objects, which is an instance of the new ToolDependenciesClient. This new module can be used to summarize requirements across toolbox (thanks to cat-bro).

  • Added publish_dataset() update_permissions() and wait_for_dataset() methods to DatasetClient.

  • Added get_invocation_biocompute_object(), get_invocation_report_pdf(), get_invocation_step_jobs_summary(), rerun_invocation() and wait_for_invocation() methods to InvocationClient (thanks to rikeshi).

  • Added cancel_job(), get_common_problems(), get_destination_params(), get_inputs(), get_outputs(), resume_job(), show_job_lock(), update_job_lock() and wait_for_job() methods to JobsClient (thanks to Andrew Mcgregor and rikeshi).

  • Added get_citations() and uninstall_dependencies() methods to ToolClient (thanks to rikeshi).

  • Added extract_workflow_from_history(), refactor_workflow() and show_versions() methods to WorkflowClient (thanks to rikeshi).

  • Added several parameters to DatasetClient.get_datasets() method (thanks to rikeshi).

  • Added several parameters to InvocationClient.get_invocations() method (thanks to Nolan Woods and rikeshi).

  • Added several parameters to JobsClient.get_jobs() method (thanks to rikeshi).

  • Added parameters_normalized parameter to WorkflowClient.invoke_workflow() method (thanks to rikeshi).

  • Deprecated folder_id parameter of LibraryClient.get_folders() method.

  • Deprecated library_id parameter of LibraryClient.get_libraries() method.

  • Deprecated tool_id parameter of ToolClient.get_tools() method.

  • Deprecated workflow_id parameter of WorkflowClient.get_workflows() method.

  • BioBlend.objects: Removed deprecated container_id property of Dataset and Folder objects.

  • BioBlend.objects: Removed Preview abstract class.

  • BioBlend.objects: Added invoke() method to Workflow. Added ObjInvocationClient, and Invocation and InvocationPreview wrappers (thanks to rikeshi).

  • BioBlend.objects: Added latest_workflow_uuid property to Workflow objects. Added deleted, latest_workflow_uuid, number_of_steps, owner and show_in_tool_panel properties to WorkflowPreview (thanks to Nolan Woods).

  • BioBlend.objects: Deprecated run() method of Workflow.

  • Added use_ssl, verify and authuser parameters to CloudManInstance.__init__() (thanks to Nathan Edwards).

  • Improvements to type annotations, tests and documentation (thanks to rikeshi).

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