Fix installed header directory structure

[ricrogz]

Installing RDKit breaks the directory structure for headers: directories under Graphmol/ChemReactions/ and Graphmol/MolStandardize/ get flattened.

So if you include, e.g. Graphmol/ChemReactions/Enumerate.h, it includes EnumerateBase.h, which in turn includes "../Reaction.h", which in the source is in the parent directory but in the installation is in the same directory as Enumerate.h and EnumerateBase.h, instead of in the parent directory as specified, thus breaking the build.

I patched the CMakeFiles to reproduce the same directory structure as in the sources.

Also, some header files that get included from other header files are not included in the installation, e.g. EnumerateTypes.h or Target.h. I added those to the installation.

Finally, path "hash" under RDGeneral gets duplicated in the installation, effectively placing its content at ${installed_include_path}/RDGeneral/hash/hash/*. When I patched this, I removed the exclusion of ".svn" as I couldn't find it anymore.

[greglandrum]

Just the one change about shrinking the number of headers for FMCS instead of expanding it

[d-b-w]

This looks good to me. I do have one question about future maintenance, though. It seems like it would be easy to forget to add a new header to the installer, or to put it in the wrong place. Is there a way to make sure that we don't misplace any required headers?

Would it be possible to use a glob and a set of exclusions? (We could spin that off as a separate issue, but I just wanted to raise the concern while we're thinking about this).

[ricrogz]

Would it be possible to use a glob and a set of exclusions? (We could spin that off as a separate issue, but I just wanted to raise the concern while we're thinking about this).

Given that I removed some headers from the FMCS CMake file, I would say that using globs all over would end up installing more headers than those that we want to be exported.

Rather than that, I would extract the "public" headers to a separate include dir, and have that one installed. It would certainly take some work to implement, but from that point on, any changes in the include dir would automatically reflect in the installation.

[d-b-w]

Good point. Let's think about that next time one of us wants to add a new header.