Remove inplace/copy

What kind of feature would you like to request?

Other?

Please describe your wishes

Another point that I'd like to throw into the scanpy 2.0 discussion:

Right now, many functions have the inplace argument, that determines if a function should write back to adata or return the result instead.

With this behavior it is hard to make correct type hints. While it is possible with @overload, it is cumbersome because it requires to type out the entire function signature twice. When I asked if it is possible to write these overloads in a more concise way on stackoverflow several users argued that changing the return type based on an argument is an anti-pattern, and I think they convinced me.

Alternative approach

Have two API levels, e.g.

def scanpy.tl.pca(adata: AnnData, **kwargs) -> None: ...

and

def scanpy.lowlevel.tl.pca(data: np.ndarray | sp.spmatrix, n_pcs) -> np.ndarray: ...

Where the former is a wrapper for the latter. This allows to separate the implementation of the actual method using only numpy/scipy data types from the scverse-specific behavior.

The proposal names scanpy.tl.pca and scanpy.lowlevel.tl.pca as example API entry points, with AnnData, NumPy, and SciPy data types. Start by reviewing how current functions use inplace and copy, then compare those usages with the proposed two-level API. Done requires an agreed migration design and scope; the issue names no files or tests.