We want to integrate https://github.com/emdann/milopy into pertpy with an updated version Tasks (roughly in order) are: - [x] Get comfortable with milopy -> Install it and run some example notebooks. - [x] Use the current code from this branch https://github.com/emdann/milopy/tree/mudata - [x] Create a new `_milopy.py` file. - [x] Add a Milopy class to the file + add all corresponding functions that are not plots. - [x] Ensure that the style of the code adhere's to pertpy's style -> comment formatting, black etc etc - [x] 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 - [x] Add all tests from the branch and ensure that they are all running + fix code style - [x] Create a new notebook here https://github.com/theislab/pertpy-tutorials/ based on the Milopy one. Now make it work with pertpy. - [x] Try to solve the feedback from https://github.com/emdann/milopy/pull/26 -> better MuData support - [ ] parameterize the GLM solver -> edgeR and batchGLM -> wait for @picciama to be ready - [x] Test that everything works :)
We want to integrate https://github.com/emdann/milopy into pertpy with an updated version
Tasks (roughly in order) are:
_milopy.pyfile.