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Integrate Milopy #164

@Zethson

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@Zethson

We want to integrate https://github.com/emdann/milopy into pertpy with an updated version

Tasks (roughly in order) are:

  • Get comfortable with milopy -> Install it and run some example notebooks.
  • Use the current code from this branch https://github.com/emdann/milopy/tree/mudata
  • Create a new _milopy.py file.
  • Add a Milopy class to the file + add all corresponding functions that are not plots.
  • Ensure that the style of the code adhere's to pertpy's style -> comment formatting, black etc etc
  • Add all plotting functions to pertpy.plots in a new file as we've done for all other tools + alias the import + fix code style
  • Add all tests from the branch and ensure that they are all running + fix code style
  • Create a new notebook here https://github.com/theislab/pertpy-tutorials/ based on the Milopy one. Now make it work with pertpy.
  • Try to solve the feedback from Refactoring with MuData emdann/milopy#26 -> better MuData support
  • parameterize the GLM solver -> edgeR and batchGLM -> wait for @picciama to be ready
  • Test that everything works :)

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