Just incase the description was confusing here is the process:def debugUnit(unitPath=''):import subprocessunitDebuggerBat = os.getenv('MAYATOOLSPATH')+'\\cmd\\unit_debugger.bat'return subprocess.check_output([unitDebuggerBat, unitPath, 'False']).split('UNITERROR')[-1].strip()
It was most likely because the environment you were launching your subprocess within was bootstrapped to Maya, and the PATH and supporting PYTHON env keys were still going to have you pick up Maya's python. Not the system python. Using the full path to the desired interpreter is one way around it. Setting PATH is probably another.
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