Fix TOPP parameter handling for zero values

[t0mdavid-m]

Changed truthiness check if v: to explicit if v != "" and v is not None: to properly handle numeric zero values (0, 0.0) which are valid parameters.

Previously, setting fragment_bin_offset=0 would skip the value entirely, causing malformed command lines where the next flag was interpreted as the previous parameter's value.

Summary by CodeRabbit

• Bug Fixes
  • Fixed parameter handling to correctly process numeric zero values (0, 0.0) in command execution, while still properly filtering empty strings and None values.

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[coderabbitai]

📝 Walkthrough

Walkthrough

Modified parameter value filtering logic in CommandExecutor.py to use explicit checks for empty strings and None instead of generic truthiness evaluation. This allows numeric zero values (0, 0.0) to be included in TOPP command construction while still excluding empty strings and None values.

Changes

Cohort / File(s)	Summary
Parameter Value Filtering src/workflow/CommandExecutor.py	Updated conditional logic for skipping parameter values during command construction. Changed from falsy checks (not value) to explicit checks (value == "" or value is None), enabling numeric zeros to pass through while maintaining exclusion of empty strings and None.

Possibly related PRs

• add support for empty list values #311: Modifies the same parameter value filtering conditional in CommandExecutor.py to handle falsy values differently in TOPP command construction.

Poem

🐰 Zero's not hollow when placed in a command,
No more wrongfully shunned by our truthiness sand!
Where once naught but emptiness passed the strict gate,
Now zeros shine bright—their numeric fate. ✨

🚥 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 clearly and specifically identifies the main change: fixing parameter handling to accept zero values instead of skipping them.
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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