V1.1.0, ViennaRNA python wrapper #7
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This PR merges barricklab/ostir with my development branch at croots/ostir. It re-implements the way OSTIR interacts with ViennaRNA from calling subprocesses to working directly via ViennaRNA's python API, resulting in substantial single threaded speed improvements (~13x single thread/process improvement from a quick benchmark, but the new version saturates a thread on my computer so potential gains are higher).
This also comes with a more complete implementation of constraints (for advanced, python-only use where a known protein obstructs binding) from #6, caching of RNA hybridization parameters, and general code clean up.