allow sc.pp.subsample in backed mode when returning a copy

[eroell]

Adresses issue #2495.

Suggested change to allow sc.pp.subsample in backed mode of AnnData, when copy=True in sc.pp.subsample

import scanpy as sc

adata = sc.read_h5ad("matrix/scatlas.h5ad", backed="r")
adata_sample = sc.pp.subsample(adata, fraction=0.01, copy=True)

Tagging @ivirshup.

[codecov]

Codecov Report

Merging #2624 (5641e88) into master (32a3567) will increase coverage by 0.00%.
Report is 1 commits behind head on master.
The diff coverage is 100.00%.

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Additional details and impacted files

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##           master    #2624   +/-   ##
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  Coverage   72.00%   72.01%           
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  Files         105      105           
  Lines       11840    11844    +4     
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+ Hits         8525     8529    +4     
  Misses       3315     3315           

Files Changed	Coverage Δ
scanpy/preprocessing/_simple.py	80.24% <100.00%> (+0.19%)	⬆️

[nleroy917]

Appreciate the PR - let me know if I can be of any assistance.

[ivirshup]

Thanks for opening this!

What happens if the object is backed, but copy=False?

[eroell]

When the object is backed, but copy=False, the ValueError, which before occured for both copy=False and copy=True, is shown:
ValueError: To copy an AnnData object in backed mode, pass a filename: '.copy(filename='myfilename.h5ad')'. To load the object into memory, use '.to_memory()'.

[ivirshup]

Could you throw a more informative error message for copy=False? Maybe:

NotImplementedError("Inplace subsampling is not implemented for backed objects")

?

[ivirshup]

One minor change, I would invert the loops. I think it makes more sense to consider the isbacked cases together. So:

if data.isbacked:
    if copy:
        return data[obs_indices].to_memory()
    else:
        raise NotImplementedError(...)
else:
    if copy:
        ...

Otherwise looking good! One minor change in the tests.

[ivirshup]

Looks great, thanks!