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This issues adds optional flags to `SBNInstance` functions `PhyloGradients` and `Likelihoods` in the class `PhyloFlags`. * Option flags are stored as members of `PhyloFlagOptions`. * Keys for the return type `GradientMap` are stored as members of `PhyloFlagKeys`. * Options and Keys have been exposed to the pybind through `bito.phylo_flags` and `bito.phylo_keys`. * There are three flags "types": inclusive (run only if listed), exclusive (DON'T run only if listed) and set (change input value). Flags can be considered inclusive if not prepended by exclude_ or set_. * There is a special run_all flag which when set considers all inclusiveflags true. * `PhyloFlags` can be passed as a list of flags (if there are no set flags), or as a list of (flag, double) tuples. Closes #363
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Description
Work in Progress
Closes #428
Tests
Please describe the tests added to verify correct behavior.
Please double check that you can make your tests fail by perturbing them.
Checklist:
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