ai-config/.pre-commit-config.yaml at main · Morrison-Lab/ai-config · GitHub

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# Security + structural gates for this public, cross-machine-synced repo.
# Enable once with:  pre-commit install
# Run on demand with: pre-commit run --all-files
# Pattern adapted from daymade/claude-code-skills (MIT); see CREDITS.md.
repos:
  - repo: https://github.com/gitleaks/gitleaks
    rev: v8.18.4
    hooks:
      - id: gitleaks  # block secrets/tokens from being committed

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      - id: detect-private-key
      - id: check-merge-conflict
      - id: check-json
      - id: check-added-large-files

  - repo: local
    hooks:
      - id: validate-skills
        name: validate skills, Codex wrappers & manifests
        entry: python scripts/validate-skills.py
        language: python
        additional_dependencies: [pyyaml==6.0.2]
        pass_filenames: false
        always_run: true
      - id: check-links
        name: check markdown links
        entry: python scripts/check-links.py
        language: python
        pass_filenames: false
        always_run: true
      - id: check-md056-table-columns
        name: check markdown table column counts (MD056)
        entry: python scripts/check-md056-table-columns.py
        language: python
        pass_filenames: false
        always_run: true
      - id: test-check-md056-table-columns
        name: check-md056-table-columns tests
        entry: python scripts/test_check_md056_table_columns.py
        language: python
        pass_filenames: false
        always_run: true
      - id: check-ascii-punctuation
        name: check ASCII punctuation in source (.py, .R)
        entry: python scripts/check-ascii-punctuation.py
        language: python
        pass_filenames: false
        always_run: true
      - id: test-check-ascii-punctuation
        name: check-ascii-punctuation tests
        entry: python scripts/test_check_ascii_punctuation.py
        language: python
        pass_filenames: false
        always_run: true
      - id: check-jules-review-workflow
        name: check Jules mention-dispatch wrap
        entry: python scripts/check-jules-review-workflow.py
        language: python
        pass_filenames: false
        always_run: true
      - id: test-jules-review-workflow
        name: Jules-review workflow tests
        entry: python scripts/test_check_jules_review_workflow.py
        language: python
        pass_filenames: false
        always_run: true
      - id: check-github-actions-step-if
        name: check github-actions step-if memory
        entry: python scripts/check-github-actions-step-if.py
        language: python
        pass_filenames: false
        always_run: true
      - id: test-github-actions-step-if
        name: github-actions step-if memory tests
        entry: python scripts/test_check_github_actions_step_if.py
        language: python
        pass_filenames: false
        always_run: true
      - id: markdownlint
        name: markdownlint (markdown style)
        entry: markdownlint-cli2
        language: node
        additional_dependencies: ["markdownlint-cli2@0.22.1"]
        pass_filenames: false  # globs/ignores come from .markdownlint-cli2.jsonc
        always_run: true
      - id: semantic-line-break-tool-tests
        name: semantic-line-break tool tests
        entry: python scripts/test_slb.py
        language: python
        pass_filenames: false
        always_run: true
      - id: enforcement-hook-tests
        name: enforcement-hook tests (hooks/test-*.py)
        entry: python scripts/test_hooks.py
        language: python
        pass_filenames: false
        always_run: true
      - id: hook-runner-tests
        name: hook-runner tests (scripts/test_hooks.py)
        entry: python scripts/test_test_hooks.py
        language: python
        pass_filenames: false
        always_run: true
      - id: gen-hooks-plugin-check
        name: hooks-only skills-dir plugin in sync with hooks/hooks.json
        entry: python scripts/gen-hooks-plugin.py --check
        language: python
        pass_filenames: false
        always_run: true
      - id: gen-hooks-plugin-tests
        name: gen-hooks-plugin tests
        entry: python scripts/test_gen_hooks_plugin.py
        language: python
        pass_filenames: false
        always_run: true
      - id: run-hook-tests
        name: run-hook.sh tests
        entry: python scripts/test_run_hook.py
        language: python
        pass_filenames: false
        always_run: true
      - id: hook-catalog
        name: hook catalog (README table vs hooks/hooks.json)
        entry: python scripts/check-hook-catalog.py
        language: python
        pass_filenames: false
        always_run: true
      - id: hook-catalog-tests
        name: hook-catalog check tests
        entry: python scripts/test_check_hook_catalog.py
        language: python
        pass_filenames: false
        always_run: true
      - id: hook-output-shape
        name: hook output shape (warn-only hooks emit systemMessage)
        entry: python scripts/check-hook-output-shape.py
        language: python
        pass_filenames: false
        always_run: true
      - id: hook-output-shape-tests
        name: hook-output-shape check tests
        entry: python scripts/test_check_hook_output_shape.py
        language: python
        pass_filenames: false
        always_run: true
      - id: hook-file-resolution
        name: hook file resolution (realpath, not lexical abspath)
        entry: python scripts/check-hook-file-resolution.py
        language: python
        pass_filenames: false
        always_run: true
      - id: hook-file-resolution-tests
        name: hook-file-resolution check tests
        entry: python scripts/test_check_hook_file_resolution.py
        language: python
        pass_filenames: false
        always_run: true
      - id: check-pr-body-figures-tests
        name: check-pr-body-figures check tests
        entry: python scripts/test_check_pr_body_figures.py
        language: python
        pass_filenames: false
        always_run: true
      - id: doctor-tests
        name: doctor diagnostics tests
        entry: python scripts/test_doctor.py
        language: python
        pass_filenames: false
        always_run: true
      - id: fences-tests
        name: markdown fences library tests
        entry: python scripts/test_fences.py
        language: python
        pass_filenames: false
        always_run: true
      - id: check-test-suites-covered
        name: check all scripts test suites are gated in CI
        entry: python scripts/check-test-suites-covered.py
        language: python
        pass_filenames: false
        always_run: true
      - id: test-check-test-suites-covered
        name: test-suite coverage check tests
        entry: python scripts/test_check_test_suites_covered.py
        language: python
        pass_filenames: false
        always_run: true