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Fix bump_patch.sh script and update references #335

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Run time

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Job	Run time
pre-commit	1m 25s
build + twine check	15s
lint + typecheck + tests (py3.12)	2m 8s
lint + typecheck + tests (py3.13)	2m 45s
pip-audit (dependency CVEs)	49s
brew style (Homebrew formula)	42s
lint + typecheck + tests	2s
	8m 6s