def test_view_retains_ndarray_subclass():
    adata = ad.AnnData(np.zeros((10, 10)))
    adata.obsm["foo"] = np.zeros((10, 5)).view(NDArraySubclass)

    view = adata[:5, :]

    assert isinstance(view.obsm["foo"], NDArraySubclass)
    assert view.obsm["foo"].shape == (5, 5)
def ProcessCommandLineArgs(parser, args):
  # TODO(ariblue): Delete this flag entirely at some future data, when the
  # existence of such a flag has been long forgotten.
  if args.output_file:
    parser.error('This flag is deprecated. Please use --output-dir instead.')

  try:
    os.makedirs(args.output_dir)
  except OSError:
    # Do nothing if the output directory already exists. Existing files will
    # get overwritten.
    pass

  args.output_dir = os.path.expanduser(args.output_dir)