Refactor interface

[VladimirShitov]

Thanks! Let's actually use this branch to clean up the code. Changing an argument name breaks the API anyway, so let's fix other stuffs as well, and then update the major version. I'll push some changes soon

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[VladimirShitov]

@mumichae , could you take a look at the refactored interface? Main changes are:

• "cell type" is renamed to "cell group" everywhere to be more general
• Some representation methods are renamed accordingly:
• • CellTypesComposition -> CellGroupComposition
• • CellTypePseudobulk -> GroupedPseudobulk
• patient_representation argument is renamed to sample_representation
• The base class is now called SampleRepresentation instead of PatientRepresentation. This is important only for developers, users shouldn't use it anyway

Other changes:

• Deleted not used SCellBow class
• Deleted example notebook in the documentation

[VladimirShitov]

We need to do a bit more refactoring:

• Rename tl/basic.py to tl/sample_representation.py
• Rename patient_representation directory, and the entire package to patpy

Let's do it in a separate PR later because now it would create merge conflicts with other branches

[mumichae]

I just left a review.

Geberal comment that I didn't address in the review: Do you want to eventually split the tl._basic file into a file per method to keep the code more readable? Would that be something for a new Pull Request?

[VladimirShitov]

I just left a review.

Geberal comment that I didn't address in the review: Do you want to eventually split the tl._basic file into a file per method to keep the code more readable? Would that be something for a new Pull Request?

Thank you! I agree that splitting or at least renaming the file makes sense, and we'll definitely do it later. But now, when we have development ongoing in several branches, it will create merge conflicts