fix: quoting piped substring with shlex

[cmeesters]

The substring "%i|%T" is now quoted with shlex.quote. This ensures that it will work on any standard shell and should fix issue #395.

Summary by CodeRabbit

Bug Fixes

• Enhanced stability of job status queries by properly handling shell command arguments.

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[coderabbitai]

Walkthrough

Added shell command argument quoting using shlex.quote() to safely pass the format string "%i|%T" to the squeue command in query_job_status_squeue(), preventing unintended shell interpretation of special characters.

Changes

Cohort / File(s)	Summary
Shell argument quoting snakemake_executor_plugin_slurm/job_status_query.py	Introduced `shlex.quote("%i

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Suggested reviewers

• johanneskoester

Poem

🐰 A format string once ran wild and free,
With pipes and percents that shouldn't be,
But shlex.quote came hopping by,
To shield the shell with a careful sigh,
Now safely quoted, the job status flies! ✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the main change: fixing a shell quoting issue by using shlex to quote a piped substring format argument.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing touches

• 📝 Generate docstrings

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[coderabbitai]

Actionable comments posted: 0

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

snakemake_executor_plugin_slurm/job_status_query.py (1)

146-155: Quoting is stripped by shlex.split/join, so | is still interpreted by the shell.

format_arg is quoted, but query_command = " ".join(shlex.split(...)) removes those quotes, producing --format=%i|%T again. If this string is executed with shell=True, the pipe still acts as a pipeline and the fix won’t work.

✅ Proposed fix (preserve quoting during normalization)

-    query_command = " ".join(shlex.split(query_command))
+    query_command = " ".join(
+        shlex.quote(arg) for arg in shlex.split(query_command)
+    )