Test & Lint Python

Fix duplicate step numbering in specify command (#3647) #5900

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Run time

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Job	Run time
ruff	6s
pytest (windows-latest, 3.13)	5m 53s
pytest (macos-latest, 3.13)	4m 1s
pytest (ubuntu-latest, 3.14)	5m 25s
pytest (ubuntu-latest, 3.13)	5m 23s
pytest (windows-latest, 3.14)	5m 32s
pytest (macos-latest, 3.14)	5m 45s
	32m 5s