Warn when 'baseCommand' is a single string with whitespace (#2240)

[arimu1]

Problem

Addresses item 1 of #2240.

A CommandLineTool baseCommand written as a single string with internal whitespace — e.g.

baseCommand: "tar xf"

— is interpreted by CWL as one program name (argv[0] == "tar xf"), not as tar plus the argument xf. Such an executable almost never exists, so the tool fails at run time. Today --validate accepts this silently:

$ cwltool --validate space-basecommand.cwl
... space-basecommand.cwl is valid CWL.

The author almost certainly meant the list form [tar, xf].

Fix

Emit a warning at construction time (so it surfaces under --validate, before any execution) when baseCommand is a single string that splits into more than one whitespace-separated token. The warning points at the baseCommand source line and suggests the list form:

$ cwltool --validate space-basecommand.cwl
WARNING space-basecommand.cwl:4:1: 'baseCommand' is a single string containing
whitespace: 'tar xf'. It will be passed to the operating system as one program
name, which is unlikely to exist. If you meant a program plus arguments, provide
a list instead, e.g. ['tar', 'xf'].
... space-basecommand.cwl is valid CWL.

It is a warning, not an error — the document is still structurally valid CWL, and a single-element command path that legitimately contains a space is technically allowed; this just flags the common mistake. The check lives in CommandLineTool.__init__ and only fires for the single-string form, so:

• list-form baseCommand: [tar, xf] → no warning
• single-word baseCommand: echo → no warning
• absent baseCommand (e.g. ExpressionTool/Workflow) → no warning

This intentionally scopes to checkbox 1 of #2240 (warn about a space). Checkbox 2 (actually probing PATH / containers for the executable) is a larger, runtime/container-aware change and is left for a follow-up.

Tests

tests/test_validate.py:

• test_validate_warns_on_basecommand_with_space — asserts the warning text, the offending value, and the suggested list form are logged (captured via a custom logger_handler, matching test_validate_custom_logger), and that exit code is still 0 / "valid CWL".
• test_validate_no_basecommand_space_warning (parametrized) — list-form and an existing no-baseCommand fixture produce no whitespace warning.

Fixtures: tests/wf/2240-basecommand-space.cwl, tests/wf/2240-basecommand-list.cwl.

I verified the warning test fails against the unpatched code (proving it guards the bug, not a no-op). All 9 tests in tests/test_validate.py pass; black, flake8, and isort are clean on the changed files.

---

This change was produced with the assistance of Claude Code (model: Claude Opus). The diff, root-cause analysis, and tests were reviewed by a human before submission.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.08%. Comparing base (5634342) to head (8120bb9).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2292      +/-   ##
==========================================
- Coverage   85.18%   85.08%   -0.10%     
==========================================
  Files          46       46              
  Lines        8593     8596       +3     
  Branches     2011     2012       +1     
==========================================
- Hits         7320     7314       -6     
- Misses        807      814       +7     
- Partials      466      468       +2     

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