anndata reading error with version 0.8.0

Hi,

Scanpy’s sc.read_h5ad method appears to be having an error in how it is reading our AnnData HDF5 file when we use the new 0.8.0 version of the AnnData library:

Loading using anndata version 0.7.8

AnnData object with n_obs × n_vars = 121393 × 649
    obs: 'Custom cells sets', 'Datasets', 'volume', 'center_x', 'center_y'

Loading using anndata version 0.8.0

AnnData object with n_obs × n_vars = 121393 × 649
    obs: 'Custom cells sets', 'Datasets', '__categories', '_index', 'center_x', 'center_y', 'volume'
    var: '_index'

I can provide a Google Colab example soon to reproduce.

[cornhundred]

Thanks that sounds good @ivirshup I’ll email you.

[ivirshup]

As a workaround for right now, if you write what you’ve read in with anndata==0.7.8 the new release will be able to read that.