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peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
8 stars 2 forks source link

Add mypy configuration for basic type checking #570

Closed peterjc closed 9 months ago

peterjc commented 1 year ago

This requires updating to SQLAlchemy 2.0 (which was released Jan 2023), so probably deserves a minor version bump?

May also require Biopython 1.82 to be released (with basic type annotations), otherwise might need to explicitly ignore that too (like this ignores biom, matplotlib, networkx, and xlsswriter).

peterjc commented 9 months ago

Rebased with mypy added to the pre-commit configuration, plus declaring a dependency on at least Biopython 1.82.

Next: Actually use the sequence type annotation in Biopython...

peterjc commented 9 months ago

Ah, the "trivial" change in 934fc6eff486e46f23f20888a67b7887ca6b7f48 broke the CircleCI and AppVeyor installs...

...fixed in b165391bc5398bbb7f879fac726700162048827a, looks to be a side effect from changes in pip 23.3.2