Report program name as cwltool when invoked as cwl-runner (#1535)

[arimu1]

Summary

Fixes #1535.

cwltool is installed with a cwl-runner console-script entry point. Because argparse defaults prog to os.path.basename(sys.argv[0]), invoking it through that alias made the help and error output identify the program as cwl-runner:

$ cwl-runner --help
usage: cwl-runner [-h] [--basedir BASEDIR] ...

Change

Set prog="cwltool" explicitly on the top-level ArgumentParser in cwltool/argparser.py, so the reference implementation is always identified consistently no matter which entry point launched it:

$ cwl-runner --help
usage: cwl-runner --help     # before
usage: cwltool [-h] ...      # after

This also applies to the usage line printed on argument errors.

Tests

Added test_argparser_prog_is_cwltool to tests/test_toolargparse.py, which patches sys.argv[0] to cwl-runner and asserts arg_parser().prog == "cwltool". Full test_toolargparse.py passes (18); black/flake8/isort clean.

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This change was produced with the assistance of Claude Code (model: Claude Opus). It was reviewed by a human before submission.

[mr-c]

How will this affect downstream users of cwltool, like Toil, Calrissian, Arvados, and others?

[arimu1]

Good question — I checked the three:

• Toil and Arvados are unaffected: Toil builds its own ArgumentParser and Arvados defines its own arg_parser(), only borrowing cwltool's default values via get_default_args(). Neither reuses cwltool's parser object, and cwltool.main() skips arg_parser() entirely when given a pre-parsed args.
• Calrissian would be affected: it uses cwltool.argparser.arg_parser() as its base parser and never sets prog, so today it shows calrissian; an unconditional prog="cwltool" would change that to cwltool.

To avoid that, I scoped the override to the actual entry-point name: prog="cwltool" if os.path.basename(sys.argv[0]) == "cwl-runner" else None. That still fixes the cwl-runner → cwltool case from #1535 while leaving Calrissian (and any other downstream reuser) on its own program name. Added a regression test for the downstream case. Pushed.