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Switch to shared_ptr in Graph class and change Graph interface #3477

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Job	Run time
build-linux-arm64	1m 47s
build-windows	3m 10s
build-linux (RELEASE, true)	2m 39s
build-linux (RELEASE, false)	1s
build-linux-clang	1m 8s
build-macos	1m 47s
build-linux (DEBUG)	2m 59s
clang-format	12s
codecov	58s
evaluate-model	0s
	14m 41s