Loompy and Numpy>=2.0.0 incompatible
When tokenizing a dataset from loom files, an exception is raised, as loompy is using numpy classes that have been removed in numpy version 2.0 (tracked here https://github.com/linnarsson-lab/loompy/issues/186):
AttributeError: 'np.string_' was removed in the NumPy 2.0 release. Use 'np.bytes_' instead.. Did you mean: 'strings'?
Temporary solution until loompy is updated would be to fix the numpy version in requirements.txt to numpy>=1.23,<2.0.0
Thank you for pointing this out! We would suggest to open an issue in the loompy repository so that they resolve this. Hopefully they can fix this so we don't need to pin this repository to an earlier numpy version only due to their package. In the meantime, thank you for pointing to the solution here in case others encounter it so they know how to resolve this temporarily by changing their numpy version.