ILPSolver Potential Graph Speedup & Refactor

YosefLab / Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

https://cassiopeia-lineage.readthedocs.io/en/latest/

MIT License

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ILPSolver Potential Graph Speedup & Refactor #98

Closed mattjones315 closed 3 years ago

mattjones315 commented 3 years ago

Provided new engineering on the backend of the ILPSolver to speed up the potential graph inference. This included moving some functions previously in the ILPSolver python file to the ilp_solver_utilities.pyx cython file, and refactoring the data structures used during potential graph inference.

mattjones315 commented 3 years ago

Thanks for the feedback Richard!

I've made a few changes and have formatted the code a bit more. Can you let me know if there's anything else you'd like to discuss / see changed? Also, can you make sure that the code runs alright on your end (specifically, all tests pass)?