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Refresh Python dependencies and repair Dependabot updates - #1672

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codex/refresh-deps-dependabot-20261020
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codex/refresh-deps-dependabot-20261020

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Refresh Python dependencies and repair the Dependabot configuration so future updates cover direct and transitive dependencies.

Remove the obsolete pre-commit update job, which points at a deleted YAML file. Hook configuration remains in prek.toml; Dependabot support is tracked in dependabot-core#14624.

Direct requirement updates:

  • beartype==0.23.0 → beartype==0.23.1
  • mypy-strict-kwargs==2026.8.25.1 → mypy-strict-kwargs==2026.10.19
  • prek==0.5.5 → prek==0.5.6
  • pyproject-fmt==2.30.1 → pyproject-fmt==2.30.3
  • ruff==0.17.0 → ruff==0.17.1
  • snapper-fmt==0.11.9 → snapper-fmt==0.11.10
  • sphinx==9.1.0 → sphinx==9.1.1
  • sphinx-substitution-extensions==2026.8.13.1 → sphinx-substitution-extensions==2026.10.9
  • strict-kwargs==2026.8.28.post2 → strict-kwargs==2026.10.9
  • ty==0.0.84 → ty==0.0.89
  • zizmor==1.30.1 → zizmor==1.31.1

Validation: Python dependency resolution, Dependabot schema validation, applicable pre-commit hooks, and git diff --check passed. Repository CI provides the full test and lint matrix.

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