Versioning with latest python libs

[pjotrp]

These versions pass on my Guix build. You may need to edit some.

[cwl-bot]

Can one of the admins verify this patch?

[codecov]

Codecov Report

Merging #1015 into master will decrease coverage by 26.26%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           master    #1015       +/-   ##
===========================================
- Coverage    79.2%   52.93%   -26.27%     
===========================================
  Files          30       30               
  Lines        5996     5996               
  Branches     1488     1488               
===========================================
- Hits         4749     3174     -1575     
- Misses        873     2411     +1538     
- Partials      374      411       +37

Impacted Files	Coverage Δ
cwltool/singularity.py	22.66% <0%> (-57.34%)	⬇️
cwltool/provenance.py	27.86% <0%> (-52.54%)	⬇️
cwltool/executors.py	34.59% <0%> (-47.57%)	⬇️
cwltool/docker.py	17.56% <0%> (-36.94%)	⬇️
cwltool/builder.py	52.22% <0%> (-34.08%)	⬇️
cwltool/update.py	37.73% <0%> (-30.19%)	⬇️
cwltool/command_line_tool.py	47.8% <0%> (-30.08%)	⬇️
cwltool/job.py	37.3% <0%> (-30.03%)	⬇️
cwltool/workflow.py	61.08% <0%> (-23.65%)	⬇️
cwltool/process.py	63.55% <0%> (-22.55%)	⬇️
... and 13 more

---

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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[codecov]

Codecov Report

Merging #1015 into master will decrease coverage by 26.26%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           master    #1015       +/-   ##
===========================================
- Coverage    79.2%   52.93%   -26.27%     
===========================================
  Files          30       30               
  Lines        5996     5996               
  Branches     1488     1488               
===========================================
- Hits         4749     3174     -1575     
- Misses        873     2411     +1538     
- Partials      374      411       +37

Impacted Files	Coverage Δ
cwltool/singularity.py	22.66% <0%> (-57.34%)	⬇️
cwltool/provenance.py	27.86% <0%> (-52.54%)	⬇️
cwltool/executors.py	34.59% <0%> (-47.57%)	⬇️
cwltool/docker.py	17.56% <0%> (-36.94%)	⬇️
cwltool/builder.py	52.22% <0%> (-34.08%)	⬇️
cwltool/update.py	37.73% <0%> (-30.19%)	⬇️
cwltool/command_line_tool.py	47.8% <0%> (-30.08%)	⬇️
cwltool/job.py	37.3% <0%> (-30.03%)	⬇️
cwltool/workflow.py	61.08% <0%> (-23.65%)	⬇️
cwltool/process.py	63.55% <0%> (-22.55%)	⬇️
... and 13 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 49cd284...15539fb. Read the comment docs.

[mr-c]

Getting errors:

>       assert (master_run, PROV.wasAssociatedWith, engine) in g, "Wf run not associated with wf engine"
E       AssertionError: Wf run not associated with wf engine
E       assert (rdflib.term.URIRef(u'urn:uuid:ade29e98-83d3-44ec-88ec-5323bf95f29a'), rdflib.term.URIRef(u'http://www.w3.org/ns/prov#wasAssociatedWith'), rdflib.term.URIRef(u'urn:uuid:2a8057e9-aa75-4453-9dc4-101731822dc0')) in <Graph identifier=N0b510ca83152496fa728a8b8e97c8c18 (<class 'rdflib.graph.Graph'>)>
tests/test_provenance.py:410: AssertionError

[pjotrp]

I have cwltool running with Python 3.7. Had to disable type_extensions with 15539fb

[mr-c]

@pjotrp Thanks for the update. How shall we proceed? We still support Python before 3.7, and your PR causes the tests to fail :-P

[pjotrp]

Just leave the PR pending. Someone can add conditionals for a backport. I'll see if we can confirm the failing tests at some point. Dependency issues most likely. Python is a pain. I am happy I have a working version on Python 3.7. We'll start hammering it!