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Currently Smoldyn has most dependencies in the source and everything works fine. There is merit in keeping dependencies in source tree.
Another approach would be to manage dependencies using a dependency manager. C++ doesnt have a standard package manager but there are two major options: conan and vcpkg. I have used conan in the past and it works great.
Except for freeglut, all dependencies are available via conan (for all supported platforms). conan can be integrated into cmake itself.
This will make source distribution lighter and testing easier. On the flip side, the users would need a working internet connections to download the dependencies.
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