Skip to content

Integrate Milopy #164

Description

@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 :)

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

Labels

enhancementNew feature or request

Type

No type

Projects

No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions