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astheeggeggs / lshmm

code to run Li and Stephens
MIT License
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Remove msprime dependency #6

Closed jeromekelleher closed 2 years ago

jeromekelleher commented 2 years ago

We shouldn't need it.

Only dependencies should be numba and numpy.

astheeggeggs commented 2 years ago

Currently it's in there for the simulation of data (which are then sent to matrices). Would is make sense to save these matrices within the test dir and read them in with numpy.load instead? Or is this purely in setup.cfg?

jeromekelleher commented 2 years ago

That's for testing, only stuff that's required at runtime should be in setup.cfg. You can depend on whatever for testing, doesn't matter.

astheeggeggs commented 2 years ago

ah, nice. Good to go then - will remove.

astheeggeggs commented 2 years ago

msprime dependency removed from setup.cfg, but tskit and msprime dependencies retained for the testing envs in nox.