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popsim-consortium / analysis2

Analysis for the second consortium paper.
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refactoring out code #25

Closed andrewkern closed 2 years ago

andrewkern commented 2 years ago

PR starting the process of refactoring code out of the Snakefile to tidy things into separate modules.

Generally we want to end up with a module (i.e. a *.py file) which contains all the code for a specific analysis and then import that module into our Snakefile. This draft PR gives an example of that idea using the plotting functions that were in the current workflow

andrewkern commented 2 years ago

btw this PR worked after installing a few external dependencies (see #24)

@xin-huang when you approve we can merge this and continue to refactor stuff

petrelharp commented 2 years ago

I will fix up this PR to account for my recent force-push.

andrewkern commented 2 years ago

this is major surgery 👨‍⚕️

xin-huang commented 2 years ago

plots.py is disappeared, should I open a new pr to add it back? I tested plots.py in my machine, it works.

andrewkern commented 2 years ago

oh no!

petrelharp commented 2 years ago

Ack, sorry!!!