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Right now, I am doing the following structure (for nodes)
spack root
package --> name@version
contains -- [lib] --> <library>
contains -- [lib] --> <library>
contains -- [bin] --> <binary>
And then the idea is that the edges are between packages and the libs and binaries - that seems like the level of what a user would look for. I've packaged additional metadata about a package with the node under "attributes" - a similar custom subsection to "paths." But even with a "small" spack install, it's huge. See: https://gist.github.com/vsoch/af1c57b558a476d1bb67fd78b284677e.
We likely want to discuss this structure and possibly trim away what is not needed to solve the immediate problem. It could also be the case we aren't interested in every package of a spack install, but it's hard to say how to make that decision.
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