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Handle non-csr/csc sparse matrices in anndata.write #847

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Handle non-csr/csc sparse matrices in anndata.write #847

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Commits on Nov 8, 2022

  1. Handle non-csr/csc sparse matrices in anndata.write 

    Attempting to save an AnnData object with non-CSR/CSC sparse matrices throws an error:

```
File "/usr/src/singlecellopenproblems/openproblems/api/utils.py", line 58, in write_h5ad
      adata.write_h5ad(filename)
    File "/usr/local/lib/python3.8/site-packages/anndata/_core/anndata.py", line 1918, in write_h5ad
      _write_h5ad(
    File "/usr/local/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 85, in write_h5ad
      write_elem(f, "X", adata.X, dataset_kwargs=dataset_kwargs)
    File "/usr/local/lib/python3.8/site-packages/anndata/_io/utils.py", line 220, in func_wrapper
      raise type(e)(
  TypeError: No method has been defined for writing <class 'scipy.sparse._coo.coo_matrix'> elements to <class 'h5py._hl.group.Group'>
  
  Above error raised while writing key 'X' of <class 'h5py._hl.group.Group'> to /
```

This PR fixes that by registering an appropriate method which converts all sparse matrices without an explicitly defined conversion to CSR.
    @scottgigante-immunai
    scottgigante-immunai authored Nov 8, 2022
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  2. Test coo_matrix

    @scottgigante-immunai
    scottgigante-immunai authored Nov 8, 2022
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