Handle boolean flag parameters correctly in CommandExecutor.run_topp()#350
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t0mdavid-m wants to merge 1 commit intomainfrom
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Handle boolean flag parameters correctly in CommandExecutor.run_topp()#350t0mdavid-m wants to merge 1 commit intomainfrom
t0mdavid-m wants to merge 1 commit intomainfrom
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TOPP tools have two boolean parameter styles: flag-style (registerFlag_) where presence means enabled, and string-style (registerStringOption_ with valid_strings=["true","false"]) where explicit values are required. Add isinstance(v, bool) check in the params[tool] loop so that: - Python bool True emits only the flag (e.g., -flag) - Python bool False omits the flag entirely - String "true"/"false" continues to emit -param true / -param false This fixes tools like FLASHDeconv and FLASHTnT that expect POSIX-style boolean flags. https://claude.ai/code/session_016pdqzsAKEB6UDBcGM82T6F
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Summary
This PR adds proper handling for boolean flag parameters in the
CommandExecutor.run_topp()method. Boolean parameters are now correctly converted to TOPP command-line flags:Truevalues emit only the flag (no value), whileFalsevalues omit the flag entirely. This distinguishes them from string-based boolean parameters ("true"/"false") which continue to emit explicit values.Changes
CommandExecutor.py: Added boolean parameter detection and handling logic
Trueboolean values now emit only the flag name (e.g.,-enable_feature)Falseboolean values are skipped entirely (flag not emitted)test_boolean_flag_params.py: Added comprehensive test suite
bool Truebool FalseImplementation Details
The implementation uses a simple
isinstance(v, bool)check before the existing parameter processing logic. When a boolean is detected:True: append the flag andcontinueto skip the normal value-appending logicFalse:continueto skip the flag entirelyThis approach maintains backward compatibility while adding proper support for registerFlag_ style parameters in TOPP tools.
https://claude.ai/code/session_016pdqzsAKEB6UDBcGM82T6F