Major rewrite of the API. Instead of adding coefficients as custom fields
to the input `AnnData` object, the API now follows an object-oriented style
similar to scikit-learn or `SCVI`. This change was motivated by the feedback
during the submission to the `scverse` ecosystem.
([Thanks]((https://github.com/scverse/ecosystem-packages/pull/156#issuecomment-2014676654)) Gregor).
Changed
- Instead of calling `fit = pylemur.tl.lemur(adata, ...)`, you now create a LEMUR model
(`model = pylemur.tl.LEMUR(adata, ...)`) and subsequently call `model.fit()`, `model.align_with_harmony()`,
and `model.predict()`.