Bump cwltool from 3.1.20221008225030 to 3.1.20221201130942

[dependabot]

Bumps cwltool from 3.1.20221008225030 to 3.1.20221201130942.

Release notes

Sourced from cwltool's releases.

3.1.20221201130942

What's Changed

• support podman even when not installed as "docker" alias by @​mr-c in common-workflow-language/cwltool#1769

Thanks to @​sdruskat for championing the podman issue!

• trim mypy.ini by @​mr-c in common-workflow-language/cwltool#1762
• Bump mypy from 0.990 to 0.991 by @​dependabot in common-workflow-language/cwltool#1763
• upload to codecov using the token by @​mr-c in common-workflow-language/cwltool#1764
• GA quay.io deploy: cache container layers by @​mr-c in common-workflow-language/cwltool#1768

Full Changelog: common-workflow-language/cwltool@3.1.20221109155812...3.1.20221201130942

3.1.20221109155812

What's Changed

• udocker: use --nobanner as well by @​mr-c in common-workflow-language/cwltool#1761

Full Changelog: common-workflow-language/cwltool@3.1.20221108205138...3.1.20221109155812

3.1.20221108205138

What's Changed

• Fix '--make-template' for union types by @​tom-tan in common-workflow-language/cwltool#1760

misc

• upgrade udocker test to v1.3.5 by @​mr-c in common-workflow-language/cwltool#1756
• Update pytest requirement from =6.2,<7.3 by @​dependabot in common-workflow-language/cwltool#1757
• Bump mypy from 0.982 to 0.990 by @​dependabot in common-workflow-language/cwltool#1759

Full Changelog: common-workflow-language/cwltool@3.1.20221018083734...3.1.20221108205138

3.1.20221018083734

What's Changed

• link to loops docs by @​mr-c in common-workflow-language/cwltool#1749
• allow mypy process type to be used as by interpreted subclasses by @​fmigneault in common-workflow-language/cwltool#1746

New Contributors

• @​fmigneault made their first contribution in common-workflow-language/cwltool#1746

Full Changelog: common-workflow-language/cwltool@3.1.20221008225030...3.1.20221018083734

Commits

• 60f0dac support podman even when not installed as "docker" alias (#1769)
• 0099f11 GA quay.io deploy: cache container layers (#1768)
• 67a1808 upload to codecov using the token (#1764)
• b9d554b Bump mypy from 0.990 to 0.991 (#1763)
• 5fe7dc4 trim mypy.ini (#1762)
• 0971d74 udocker: use --nobanner as well (#1761)
• 6af9320 Fix '--make-template' for union types (#1760)
• 14f402f test with normal Python 3.11
• dcbabf6 mypy 0.990 inspired fixes + 1 ignore
• 4a6931b Bump mypy from 0.982 to 0.990
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

[adamnovak]

This ended up failing a test when it merged in:

______________________ SortTest.testFileSingleNonCaching _______________________
Traceback (most recent call last):
  File "/builds/databiosphere/toil/src/toil/test/sort/sortTest.py", line 217, in testFileSingleNonCaching
    self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem='single_machine',
  File "/builds/databiosphere/toil/src/toil/test/sort/sortTest.py", line 164, in _toilSort
    with runMain(options):
  File "/usr/lib/python3.9/contextlib.py", line 119, in __enter__
    return next(self.gen)
  File "/builds/databiosphere/toil/src/toil/test/sort/sortTest.py", line 59, in runMain
    main(options)
  File "/builds/databiosphere/toil/src/toil/test/sort/sort.py", line 254, in main
    sortedFileID = workflow.restart()
  File "/builds/databiosphere/toil/src/toil/common.py", line 1065, in restart
    return self._runMainLoop(rootJobDescription)
  File "/builds/databiosphere/toil/src/toil/common.py", line 1468, in _runMainLoop
    return Leader(config=self.config,
  File "/builds/databiosphere/toil/src/toil/leader.py", line 269, in run
    with enlighten.get_manager(stream=sys.stderr, enabled=not self.config.disableProgress) as manager:
  File "/builds/databiosphere/toil/venv/lib/python3.9/site-packages/enlighten/manager.py", line 55, in get_manager
    return Manager(stream=stream, counter_class=counter_class, **kwargs)
  File "/builds/databiosphere/toil/venv/lib/python3.9/site-packages/enlighten/_manager.py", line 69, in __init__
    super(Manager, self).__init__(**kwargs)
  File "/builds/databiosphere/toil/venv/lib/python3.9/site-packages/enlighten/_basemanager.py", line 74, in __init__
    self.term = Terminal(stream=self.stream, kind=kind, force_styling=bool(kind))
  File "/builds/databiosphere/toil/venv/lib/python3.9/site-packages/blessed/terminal.py", line 208, in __init__
    self.__init__keycodes()
  File "/builds/databiosphere/toil/venv/lib/python3.9/site-packages/blessed/terminal.py", line 312, in __init__keycodes
    self._keycodes = get_keyboard_codes()
  File "/builds/databiosphere/toil/venv/lib/python3.9/site-packages/blessed/keyboard.py", line 114, in get_keyboard_codes
    keycodes.update((name, value) for name, value in globals().items() if name.startswith('KEY_'))
  File "/builds/databiosphere/toil/venv/lib/python3.9/site-packages/blessed/keyboard.py", line 114, in <genexpr>
    keycodes.update((name, value) for name, value in globals().items() if name.startswith('KEY_'))
RuntimeError: dictionary changed size during iteration

See https://ucsc-ci.com/databiosphere/toil/-/jobs/33090

[mr-c]

Huh

[adamnovak]

It looks like a race condition at startup between the progress bar code and something else in another thread that adds a global variable. I'm not sure if this is a cwltool-induced problem, but also I've never seen it before.