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BioBlend v0.5.3 Released


BioBlend v0.5.3 has been released. BioBlend is a python library for interacting with CloudMan and the Galaxy API. (CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration.)

This is mostly an incremental bug fix release with the following summary of changes:

  • Project source moved to new URL - https://github.com/galaxyproject/bioblend
  • Huge improvements to automated testing, tests now run against Galaxy release_14.02 and all later versions to ensure backward compatibility (see travis.yml for details).
  • Many documentation improvements (thanks to Helena Rasche).
  • Add Galaxy clients for the tool data tables, the roles, and library folders (thanks to Anthony Bretaudeau).
  • Add method to get the standard error and standard output for the job corresponding to a Galaxy dataset (thanks to Anthony Bretaudeau).
  • Add get_state() method to JobsClient.
  • Add copy_from_dataset() method to LibraryClient.
  • Add create_repository() method to ToolShedClient (thanks to Helena Rasche).
  • Fix DatasetClient.download_dataset() for certain proxied Galaxy deployments.
  • Make LibraryClient._get_root_folder_id() method safer and faster for Galaxy release_13.06 and later.
  • Deprecate and ignore invalid deleted parameter to WorkflowClient.get_workflows().
  • CloudMan: Add method to fetch instance types.
  • CloudMan: Update cluster options to reflect change to SLURM.
  • BioBlend.objects: Deprecate and ignore invalid deleted parameter to ObjWorkflowClient.list().
  • BioBlend.objects: Add paste_content() method to History objects.
  • BioBlend.objects: Add copy_from_dataset() method and root_folder property to Library objects.
  • BioBlend.objects: Add container and deleted attributes to Folder objects.
  • BioBlend.objects: Set the parent attribute of a Folder object to its parent folder object (thanks to John M. Eppley).
  • BioBlend.objects: Add deleted parameter to list() method of libraries and histories.
  • BioBlend.objects: Add state and state_details attributes to History objects (thanks to Gianmauro Cuccuru).
  • BioBlend.objects: Rename upload_dataset() method to upload_file() for History objects.
  • BioBlend.objects: Rename input_ids and output_ids attributes of Workflow objects to source_ids and sink_ids respectively.
  • Add run_bioblend_tests.sh script (useful for Continuous Integration testing).

Enjoy and please let us know what you think,

Enis & John & Nicola Soranzo & Simone Leo & Helena Rasche