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Fix `prepare_shell_job_inputs` to be compatible with `PortableCode` #630

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Run time

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Job	Run time
tests (3.12)	1m 31s
tests (3.10)	1m 31s
tests (3.11)	1m 28s
tests (3.9)	1m 55s
pre-commit	1m 7s
	7m 32s