Mesnage-Org / pgfinder

Peptidoglycan MS1 Analysis Tool
https://mesnage-org.github.io/pgfinder
GNU Lesser General Public License v3.0
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Fixing pytest-regtest issue #255

Closed ns-rse closed 4 months ago

ns-rse commented 4 months ago

New releases of pytest-regtest>=2.0.0 on PyPI are currently broken as the released packages don't appear to include the Python code for the module itself. This has been reported upstream and when fixed I will remove the dependency.

At the same time I've...

Numpy2 is due to be released early later this year (first release candidate is scheduled 2024-02-01).

This may introduce some breaking changes, a broad overview is available here.

Mentioned in that article is that scikit-image has issues, which is indirect because the package has an optional dependency on matplotlib (I've discovered this whilst working on skan issues).

The official NumPy 2.0 migration guide — NumPy v2.0.dev0 Manual suggests that ruff can be leveraged to address the mentioned changes under Ruff Plugin.

A useful summary of how to handle potential problems is provided at Numpy #24300 and broadly suggests pinning numpy<2.0 for releases whilst development proceeds on resolving issues.