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Switch to shared_ptr in Graph class and change Graph interface #3499

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Job	Run time
build-macos	4m 59s
build-windows	5m 36s
build-linux-arm64	2m 14s
build-linux (DEBUG)	2m 43s
build-linux-clang	2m 18s
clang-format	10s
codecov	4m 2s
build-linux (RELEASE, true)	2m 25s
build-linux (RELEASE, false)	2m 16s
evaluate-model	3m 5s
	29m 48s