Update node serialization/deserialization and other Pydantic issues #6461

Job	Run time
install-with-pip	25s
validate-dependency-specification	8s
install-with-conda (false)	57s
install-with-conda (3.14, true)	49s
install-with-conda (3.11, true)	54s
install-with-pip ([atomic_tools,docs,notebook,rest,tests,tui])	1m 13s
install-with-conda (3.12, true)	56s
install-with-conda (3.13, true)	57s
install-with-conda (3.10, true)	52s
create-conda-environment	58s
tests (3.14)	19m 15s
tests (3.10)	22m 24s
tests (3.12)	20m 49s
tests (3.11)	20m 12s
tests (3.13)	20m 15s
	1h 51m 4s

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