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Remove pkg_resources runtime usage#481

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Mirochill wants to merge 1 commit into
EI-CoreBioinformatics:masterfrom
Mirochill:fix-471-drop-pkg-resources
Draft

Remove pkg_resources runtime usage#481
Mirochill wants to merge 1 commit into
EI-CoreBioinformatics:masterfrom
Mirochill:fix-471-drop-pkg-resources

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@Mirochill

@Mirochill Mirochill commented May 22, 2026

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Fixes #471.

Summary

  • replace Mikado runtime pkg_resources resource access with a small importlib.resources helper
  • update Daijin Snakefiles and sample Snakefile resource paths to use the same helper
  • remove the temporary setuptools<80.9 pins from runtime/build environment metadata

Validation

  • git diff --check HEAD~1..HEAD
  • rg -n pkg_resources|resource_filename|resource_stream|setuptools<80\.9|setuptools<81 Mikado\subprograms Mikado\configuration Mikado\daijin sample_data setup.py setup.cfg pyproject.toml requirements.txt environment.yml returned no matches
  • Not run locally

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Setuptools v80.9.0 UserWarning: pkg_resources is deprecated as an API

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