theislab / ehrapy

Electronic Health Record Analysis with Python.
https://ehrapy.readthedocs.io/
Apache License 2.0
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check if 3.10 successful before merge #785

Closed eroell closed 3 months ago

eroell commented 3 months ago

PR Checklist

Description of changes

Technical details There is a very strange error going on, occasionally in the Ubuntu 3.10 tests, and the Ubuntu 3.11 pre-release tests:

FAILED tests/preprocessing/test_highly_variable_features.py::test_highly_variable_features - ehrapy.io._read.IndexNotFoundError:
Could not create AnnData object while reading file /home/runner/work/ehrapy/ehrapy/ehrapy_data/dermatology.csv .
Does index_column named patient_id exist in /home/runner/work/ehrapy/ehrapy/ehrapy_data/dermatology.csv?

The error is related to the dermatology.csv file, read in here

https://github.com/theislab/ehrapy/blob/0ee5c213541a07f0345100028a799b221f2690e5/ehrapy/data/_datasets.py#L330-L362

Quite flaky, only pops up sometimes when repeating the tests

Additional context

eroell commented 3 months ago

how even

eroell commented 3 months ago

Seems to work now again - everywhere. Close for now, hopefully no one will ever need to search for this, and if so, this PR with the posted error will pop up