Scriptcwl

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

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)

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

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

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

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)