I’ve been continuing my efforts to reduce the existing issue backlog for CWL Tool. I will briefly dicuss the PR’s I made last week and related issues:

  • PR #520: Deprecate draft-2 and draft-3

We’re on our way to deprecate support for running cwlVersion: draft-2, draft-3, draft-4 workflows on CWL Tool. Changes required for this includes some minor re-factoring and graceful deprecation of old module names. Also, removing all the methods related to coverting drafts from previous version to newer ones. We will continue to actively support v1.0 and higher and related dev versions.

  • PR #512: Fix print-rdf flag

I found out that --print-rdf was broken on Python 3 while working on a separate issue. Did a small fix and added test to make sure it doesn’t break without notice in the future.

  • Readme: Improving instructions for testing and install from source

Did a bunch of improvements to the README, Related PR: #523, #519

  • Using Apache Avro package in Python 3:

I created a reference issue highlighting the current workaround to make Apache Avro package work in Python 3 with schema salad and CWL Tool. This would be helpful, should we try to use a different workaround in the future.

  • Measuring code coverage of CWL Tool:

I spent some amount of time last weekend on this issue. The complexity of the problem lies in automating the process of measuring code coverage of conformance tests. And how to pass coverage run cwltool as the RUNNER parameter to the bash script which invokes the entire suite of conformance tests. Michael had some ideas on how to do that and I tried to get them working. You can read the related discussion here: cwltool/issues/334

I was finally been able to get measure coverage with a few hard-coded paths and little hacks in place. These things need to be taken care of before I make a mergable PR.

ToDo for this Week:

  • Setup codov on PR’s for CWL Tool
  • Wind up any remaining PR’s and issues before final eval