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Change Log

0.8.1

Released on August 11, 2019.

Added

  • Support even newer versions of cwltool (<=1.0.20190228155703)
  • Support for Python 3.7

Changed

  • Ignore packed workflows when sorting for loading order

Removed

  • Support for Python 2
  • Support for Python 3.4

0.8.0

Added

  • Add MultipleInputFeatureRequirement when a step gets a list of inputs (#105; see also #101)
  • Convert input and output names with dashes (-) to underscores (_), so they are valid Python names
  • Allow printing of workflows (#86)
  • Logging (for debugging)
  • Support newer versions of cwltool (#108)

Changed

  • Using booleans to indicate how a workflow is saved is deprecated. Instead, a mode string should be used (e.g., wf.save('wf.cwl', mode='rel')) (#87)
  • Inline saving of workflows is deprecated. When saving a workflow with mode='inline', the workflow is saved as a packed workflow (#92)
  • Make scatter_method optional when scattering over a single parameter (#103)

0.7.2

Added

  • Allow for list of step outputs/wf inputs as step input (#101)
  • CFF files with citation metadata
  • Link between a step's python name (i.e. how it is called on the WorkflowGenerator object) to step names (#100)
  • Allow setting workflow labels
  • Allow setting a label for a workflow input
  • support for CommandInputEnumSchema as workflow input (#99)
  • User manual in documentation

Changed

  • Ensure workflows without a requirements section are loaded into the steps library
  • Raise real warning when duplicate cwl step (i.e. having the same file name as another step) is loaded

Removed

  • Method to convert a string to cwl file name

0.7.1

Added

  • Load tools before workflows when a working directory is used (#94)
  • Make sure no duplicate workflow input names are used (#96)

Changed

  • Inputs with a default value are also recognized as optional

0.7.0

Added

  • Save packed workflows
  • Save workflows using a working directory (a solution to the problem of dealing with paths to steps if steps are loaded from different local directories)

Changed

  • Prevent name clashes of embedded (sub)workflows (however, this doesn't work when a (sub)workflow is added multiple times)
  • Use name of step in workflow to create unique ids when saving steps inline (#82)
  • Allow saving workflows with inline steps for step files without shebang (#83)
  • Document feature for adding documentation to a workflow (#81)
  • Fix saving of relative paths for workflows with steps from urls
  • By default, workflows are saved with absolute paths

0.6.0

Added

  • Make WorkflowGenerator into a context manager (#24)
  • Type checking of input and output types (#22)
  • Allow saving workflow with inline steps (#38)
  • Allow saving workflow with relative paths (#25)
  • Documentation on Read the Docs (#35)
  • Allow loading of multiple CWL steps (from file, http url, and directory) at the same time

Changed

  • Rename wf.add_inputs() to wf.add_input() (#11)

Removed

  • Python 3.3 support (Sphinx needs Python 3.4)

0.5.1

Added

  • Allow addition of default values to workflow inputs (#32)
  • List of steps and workflows in steps library is ordered alphabetically

0.5.0

Added

  • Python 3 compatibility (and testing with tox)

0.4.0

Added

  • Generate unique names for steps that are added to the workflow more than once (#31)
  • Pass all outputs from a step, instead of just one (#27)
  • Improve listing of workflow steps

0.3.1

Added

  • Load ExpressionTools as steps

Changed

  • Preserve the order in which steps were added to the workflow

0.3.0

Changed

  • Replace pyyaml by ruamel (fixes compatibility with cwltool)

0.2.0

Added

  • Documentation for WorkflowGenerator and Step (#15).
  • Allow step to be scattered (#17)
  • Tests (#9)
  • Shebang to saved CWL file (#14)
  • Preprocess shortcuts in CWL steps (#12)
  • Allow workflows to be used as steps (subworkflows) (#4)
  • Take into account optional arguments (#6)

Removed

  • Step.get_input() because it was not used (#21)

0.1.0

Added

  • WorkflowGenerator object that allows users to create CWL workflows. The WorkflowGenerator has functionality to
    • load CWL steps from a directory,
    • list available CWL steps
    • connect the inputs and outputs of CWL steps,
    • determine the types of a step's inputs
    • specify a workflow's inputs and outputs, and
    • add workflow documentation.