chore!: Update to `portgraph 0.13` / `petgraph 0.7` #3310

Job	Run time
Check for changes in Python files	2s
Build HUGR binary	55s
check python 3.10	15s
Check serialization schema	7s
check python 3.13	21s
test python 3.10	30s
test python 3.13	33s
Required checks 🐍	1s
	2m 44s

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