fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
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Unit tests broken for Python 3.8/pytest 8.0.0 in Github CI tests #944

Closed pjbriggs closed 5 months ago

pjbriggs commented 5 months ago

The latest release of the pytest package (version 8.0.0) appears to break the unit tests when used within the Github CI testing action with Python 3.8.

The errors look like:

_____________ ERROR collecting auto_process_ngs/test/test_stats.py _____________
ImportError while importing test module '/home/pjb/projects/auto_process_ngs/auto_process_ngs/test/test_stats.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../miniconda3/envs/auto_process@python3.8/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
E   ModuleNotFoundError: No module named 'auto_process_ngs.test'

It's unclear whether the problem is the test collection mechanism, or with the import paths specified in the test files (or a combination of the two).

Python 3.6 and 3.7 are only supported by pytest up to versions 7.0.0 and 7.4.4, and do not appear to be broken.