Arvados

For the record, the problem is that this version of cwltest depends on setuptools but doesn't declare that. So there is an easy workaround by installing setuptools yourself:

xps9310 % python3.12 -m venv cwltest                                   
xps9310 % ./cwltest/bin/pip install 'cwltest==2.3.20230108193615'                                                                        
[…]
Successfully installed CacheControl-0.14.0 certifi-2024.6.2 charset-normalizer-3.3.2 cwltest-2.3.20230108193615 defusedxml-0.7.1 filelock-3.14.0 idna-3.7 iniconfig-2.0.0 isodate-0.6.1 junit-xml-1.9 mistune-3.0.2 msgpack-1.0.8 mypy-extensions-1.0.0 packaging-24.0 pluggy-1.5.0 pyparsing-3.1.2 pytest-7.4.4 rdflib-7.0.0 requests-2.32.3 ruamel.yaml-0.18.6 ruamel.yaml.clib-0.2.8 schema-salad-8.5.20240503091721 six-1.16.0 typing-extensions-4.12.1 urllib3-2.2.1                  
xps9310 % ./cwltest/bin/cwltest -h                                                                                                       
Traceback (most recent call last):                           
  File "/home/brett/Scratch/./cwltest/bin/cwltest", line 5, in <module>                         
    from cwltest.main import main
  File "/home/brett/Scratch/cwltest/lib/python3.12/site-packages/cwltest/main.py", line 15, in <module>
    from cwltest.argparser import arg_parser
  File "/home/brett/Scratch/cwltest/lib/python3.12/site-packages/cwltest/argparser.py", line 5, in <module>
    import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
xps9310 % ./cwltest/bin/pip install setuptools                       
[…]
Successfully installed setuptools-70.0.0
xps9310 % ./cwltest/bin/cwltest -h                                   
[it works]

I would still rather remove the package if possible but this is a fine plan B.

Thinking about this a little more, I think it is this (there are similar disabled jobs for other decommissioned test clusters)

https://ci.arvados.org/view/CWL/job/run-cwl-test-tordo-old-unused/

This would log into the shell node, pull the CWL test suite, and run it (functioning as a full integration test of launching workflows on cloud). So, at the time, Ward decided to package cwltest so it would just run cwltest and arvados-cwl-runner automatically installed in $PATH.

At some point we stopped doing this, I don't recall why. The current test is based on a different script, and that script installs a specific version of cwltest using pip.

For the record, the reason we use a specific version of cwltest is that following the pinned version, cwltest started checking that file in the output parameters actually existed on disk, but because Arvados returned keep identifiers, it wouldn't know how to resolve them correctly and fail. A better fix would be to do the work of adding an optional module to cwltest that properly supports checking for the existence of files in Keep.

This LGTM, thanks!