Remove temporary directories when cache dir is empty string

[kinow]

For issue reported on Discourse: https://cwl.discourse.group/t/cwl-runner-tmpdir-not-deleted/401

When debugging the example from https://www.commonwl.org/user_guide/02-1st-example/index.html, with the command line cwltool --tmpdir-prefix /tmp/cwl/ /tmp/1st-tool.cwl /tmp/echo-job.yml, I noticed the output_dirs being set to an empty list.

The issue was because the runtime_context.cachedir was not None, but it was an empty string. So the value of output_dirs was incorrectly initialized.

Pending a unit/functional test as I have to learn how to write those for cwltool 😬 any pointers?

Thanks

[cwl-bot]

This pull request has been mentioned on Common Workflow Language Discourse. There might be relevant details there:

https://cwl.discourse.group/t/cwl-runner-tmpdir-not-deleted/401/10

[codecov]

Codecov Report

Merging #1541 (5666fbb) into main (96ebb49) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #1541      +/-   ##
==========================================
+ Coverage   65.81%   65.82%   +0.01%     
==========================================
  Files          91       91              
  Lines       16050    16050              
  Branches     4055     4055              
==========================================
+ Hits        10563    10565       +2     
+ Misses       4355     4354       -1     
+ Partials     1132     1131       -1     

Impacted Files	Coverage Δ
cwltool/executors.py	83.33% <100.00%> (ø)
job.py	61.49% <0.00%> (-1.01%)	⬇️
executors.py	65.31% <0.00%> (ø)
cwltool/process.py	85.40% <0.00%> (+0.15%)	⬆️
cwltool/job.py	77.26% <0.00%> (+0.40%)	⬆️
process.py	70.19% <0.00%> (+0.61%)	⬆️

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[kinow]

I think I managed to add a test to test_tmpdir.py. Fails with the code from main:

And passes on this branch.