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Use DragonFFI as backend
It's more an idea than an issue, but maybe using DragonFFI (github.com/aguinet/dragonffi) as a compiler and "python glue" (that is convert data back and forth from C and python) backend can solve some of the issues you have (like generating many .so's).
Let me know if you are interested!
Looks great! How does the JIT work? Does pydffi.FFI().compile() write a module to the filesystem or does it keep everything in memory somehow?
It's all kept in memory using one of the LLVM jitter mechanism (which also has its own runtime dynamic linker, to link dynamic objects together if necessary).