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Fix `prepare_shell_job_inputs` to be compatible with `PortableCode` #646

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Run time

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Job	Run time
tests (3.11)	1m 27s
tests (3.10)	2m 4s
pre-commit	55s
tests (3.12)	1m 44s
tests (3.14)	1m 40s
	7m 50s