Remove --disableCaching's argument

[adamnovak]

This will fix #3831 by making the --disableCaching usage shown there the only acceptable one. As is, --disableCaching will try to eat the first positional argument if it comes last before the positional arguments, and will break command lines that look like they should work.

Changelog Entry

To be copied to the draft changelog by merger:

• Breaking change! --disableCaching True/False and --disableCaching=True/False command line argument forms are no longer accepted. Just pass or do not pass --disableCaching like the other --disableX flags.

Reviewer Checklist

• Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
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    contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
    

  • If there is no associated issue, create one.
• Read through the code changes. Make sure that it doesn't have:
  • Addition of trailing whitespace.
  • New variable or member names in camelCase that want to be in snake_case.
  • New functions without type hints.
  • New functions or classes without informative docstrings.
  • Changes to semantics not reflected in the relevant docstrings.
  • New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
  • New features without tests.
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Merger Checklist

• Make sure the PR passes tests.
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[DailyDreaming]

________________ ERROR collecting src/toil/test/cwl/cwlTest.py _________________
Traceback (most recent call last):
  File "/usr/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 994, in _gcd_import
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 674, in exec_module
  File "<frozen importlib._bootstrap_external>", line 781, in get_code
  File "<frozen importlib._bootstrap_external>", line 741, in source_to_code
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/builds/databiosphere/toil/src/toil/test/cwl/cwlTest.py", line 95
    args_passed_directly_to_toil = (['--disableCaching'] if not caching else []) +
                                                                                 ^
SyntaxError: invalid syntax

[adamnovak]

OK I think I've now learned to syntax.

[adamnovak]

New Gitlab didn't pick this up automatically so I started a pipeline at https://ucsc-ci.com/databiosphere/toil/-/pipelines/108.

[adamnovak]

Looks like https://ucsc-ci.com/databiosphere/toil/-/jobs/1959 had a Kubernetes CWL job randomly time out again, and managed to not emit any JUnit files with the logs. We should be using a cwlrunner that reports logs for timed-out tests, but we don't seem to have any JUnit output this time.

@mr-c Any idea how that can happen?

[mr-c]

@mr-c Any idea how that can happen?

I don't know. I made a new cwltest release that includes your fixes for timed-out tests. https://github.com/common-workflow-language/cwltest/releases/tag/2.2.20211116163652 a.k.a. https://pypi.org/project/cwltest/2.2.20211116163652/

[DailyDreaming]

LGTM. I've restarted the tests.