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Restore functionality for [Sequence] filters: Python 3 upgrades #244

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merged 10 commits into from
Jan 18, 2025

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  • Porting filters Python 3

  • Fix StringMatrix to store alleles as strings if they are strings

  • The directory key for [Sequence] and [AnthonyNolan] must always be provided in the .ini file

* update `StringMatrix` class to store alleles as strings if passed as such
  fallback to using the original behaviour of `ndarray` if not a string.

* add a unit test to check types set as above
* move MSF files into the unit tests data area

* restore the associated .pop file and .ini file for the `sequence-nopoptests.ini`
@alexlancaster alexlancaster added bug Something isn't working, should not be used for new features: use "enhancement" for those documentation doc fixes, enhancements labels Jan 18, 2025
@alexlancaster alexlancaster self-assigned this Jan 18, 2025
* don't check `PYTEST_VERSION`: doesn't work on older `pytest`
@alexlancaster alexlancaster merged commit bd3277e into main Jan 18, 2025
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@alexlancaster alexlancaster deleted the sequence_filter_fix branch January 18, 2025 20:05
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Port [Sequence] and [AnthonyNolanFilter] functionality to Python 3
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