Error: ContextualVersionConflict ruamel/schema-salad

Expected Behavior

cwltool should run and show command line usage

Actual Behavior

cwltool fails with this error:

pkg_resources.ContextualVersionConflict: (ruamel.yaml 0.15.15  (/tmp/env/lib/python2.7/site-packages),  Requirement.parse('ruamel.yaml<=0.15.2,>=0.12.4'), set(['schema-salad']))

Workflow Code

virtualenv env
source env/bin/activate
pip install --upgrade cwltool
cwltool

Full Traceback

Traceback (most recent call last):
  File "/tmp/env/bin/cwltool", line 11, in <module>
    sys.exit(main())
  File "/tmp/env/local/lib/python2.7/site-packages/cwltool/main.py", line 661, in main
    _logger.info(versionfunc())
  File "/tmp/env/local/lib/python2.7/site-packages/cwltool/main.py", line 574, in versionstring
    pkg = pkg_resources.require("cwltool")
  File "/tmp/env/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 943, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/tmp/env/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 834, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ruamel.yaml 0.15.15 (/tmp/env/lib/python2.7/site-packages), Requirement.parse('ruamel.yaml<=0.15.2,>=0.12.4'), set(['schema-salad']))

Your Environment

Tried on both macos and Ubuntu 16.04.1 LTS

• cwltool version: fails with the same error.

Notes:

If I do this first everything works fine:

pip install ruamel.yaml==0.15.2

[manu-chroma]

Thanks for reporting. I’ve created a patch that should take care of this: https://github.com/common-workflow-language/cwltool/pull/450

[mr-c]

Thanks for the update @Unode , and again my apologies. Thank you @johnbradley for the report.