Episcanpy still using scanpy.api

colomemaria / epiScanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

BSD 3-Clause "New" or "Revised" License

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Episcanpy still using scanpy.api #53

Closed le-ander closed 3 years ago

le-ander commented 4 years ago

Hi Anna, one more thing I noticed:

Episcanpy seems to still use scanpy.api This will soon break episcanpy when scanpy removes the api module as announced.

This FutureWarning appears when importing scanpy:

>>> import episcanpy
/app/python37/lib/python3.7/site-packages/scanpy/api/__init__.py:6: FutureWarning:

In a future version of Scanpy, `scanpy.api` will be removed.
Simply use `import scanpy as sc` and `import scanpy.external as sce` instead.

  FutureWarning,

DaneseAnna commented 4 years ago

Thank you or the warning. I am currently working on this and the scanoy+ anndata compatibility issues.