app_runner/0.0.11

Added

• New input type BfabricAnnotationSpec.
  • For now, it only supports one type of annotation, which is "resource_sample".

1.13.15

Added

• Entity Sample
• Relationship Resource.sample.
• Extract logic for container resolution into HasContainerMixin which is right now shared between Sample and Workunit.

Fixed

• Fix bug in bfabric_save_fasta.py.

app_runner/0.0.10

Added

• FileScpSpec to copy a file from a remote server to the local filesystem, without using B-Fabric information.
• CommandDocker.hostname so it won't have to be passed by custom_args in the future.
• DispatchSingleDatasetFlow dispatch a workunit in dataset-flow which consists of only one execution unit.
• DispatchSingleResourceFlow dispatch a workunit in resource-flow which consists of only one execution unit.

app_runner/0.0.9

Added

• App specs can now define multiple versions in one file. (AppSpec = Collection of app versions and other information.)
  • To avoid boilerplate, mako templates can be used inside of strings.
  • Apps will resolve the version to use based on the application_version field.
  • Validation functionality for the new app specification has been added.
• App versions can define a submitter, however this information is not yet used.

1.13.14

Changed

• Slurm submitter prints more diagnostics about PATH variable etc.

Fixed

• Some commands in bfabric-cli are broken because __future__.annotations is imported and this breaks cyclopts.

app_runner/0.0.8

Added

• Register single file command: bfabric-app-runner outputs register-single-file
• Implement copy resource UpdateExisting.IF_EXISTS and UpdateExisting.REQUIRED support.
• The following fields have been added to WorkunitRegistrationDefinition:
  • storage_id
  • storage_output_folder
  • application_id
  • application_name

Changed

• App-runner code related to output staging accepts workunit-definition file like the other steps.

1.13.13

Changed

• Move bfabric-cli read to bfabric-cli api read.
• (internal) use_client decorator is introduced to simplify and standardize the client usage in the new CLI code.

Added

• Functionality to log by specifying the workunit instead of external job, which is used in some legacy scripts.
• Add logging commands to bfabric-cli api log.
• Add bfabric-cli api save.
• Submitter script prints the id and hostname of apps, which in practice can be very useful.

Fixed

• A bug in bfabric_save_workflowstep.py that crashed the script.

1.13.12

Changed

• The submitter ensures that workunits always get set to processing.

Fixed

• The script bfabric_setResourceStatus_available.py and other uses of report_resource, correctly search files which
  have a relative path starting with / as in the case of the legacy wrapper creator.

1.13.11

Fixed

• The script bfabric_setWorkunitStatus.py did always set the status to available, instead of the specified status.

Changed

• bfabric_setResourceStatus_available.py calls the report_resource function, in general this functionality has been refactored.

1.13.10

Fixed

• If bfabricpy.yml contains a root-level key which is not a dictionary, a correct error message is shown instead of raising an exception.
• A bug introduced while refactoring in slurm.py which passed Path objects to subprocess instead of strings.
• Submitter
  • does not use unset JOB_ID environment variable anymore.
  • does not set unused STAMP environment variable anymore.
• Fix bfabric_save_workflowstep.py bugs from refactoring.

Added

• Experimental bfabric-cli interface. Please do not use it in production yet as it will need a lot of refinement.