.pre-commit-config.yaml

# SKIP=pytest-unit,mypy,basedpyright uv run prek run -a
# prek run -a prettier typos committed detect-secrets add-trailing-comma uv-export uv-lock uv-sync pyupgrade markdownlint-cli2 ruff-format pytest-unit pytest-gherkin-unit pytest-quality-metrics pytest-coverage pytest-mutation pytest-sdk-python ty-check trailing-whitespace check-yaml check-json check-toml end-of-file-fixer detect-private-key check-case-conflict check-builtin-literals check-merge-conflict check-docstring-first debug-statements  name-tests-test codespell check-filenames
fail_fast: false
default_language_version:
  python: "3.13"
# Generated SBOM artifacts (scripts/deps/export-rust-sbom.sh):
#   sdk/rust/cyt-indexer/cyt-indexer.cdx.json
#   sdk/rust/cyt-indexer/cyt-indexer.snyk.json
# Exclude pattern (auto-fix / spell / secret scanners / verify-pins trigger):
#   ^sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json$
# Only export-rust-sbom may rewrite these files (on Cargo.toml/Cargo.lock changes).
repos:
  # 1year old
  #  - repo: https://github.com/backplane/pre-commit-rust-hooks
  #    rev: v1.2.1
  #    hooks:
  #      - id: fmt
  #      - id: check
  #      - id: clippy
  #      - id: test
  #  - repo: https://github.com/EmbarkStudios/cargo-deny
  #    rev: 0.19.8
  #    hooks:
  #      - id: cargo-deny
  #        args: ["--all-features", "check"]
  #  - repo: https://github.com/drahnr/cargo-spellcheck
  #    rev: v0.15.7
  #    hooks:
  #      - id: cargo-spellcheck
  - repo: https://github.com/DevinR528/cargo-sort
    rev: v2.1.4
    hooks:
      - id: cargo-sort
    # 1year old
  #  - repo: https://github.com/rockmagma02/rust-pre-commit-hooks
  #    rev: v0.2.0
  #    hooks:
  #      - id: rustfmt
  #      - id: cargo-fmt
  #      - id: clippy
  # 4years old — use local nopatch wrappers so [patch.crates-io] does not touch Cargo.lock
  #  - repo: https://github.com/cathiele/pre-commit-rust
  #    rev: v0.1.0
  #    hooks:
  #      - id: cargo-audit
  #      - id: cargo-udeps
  #      - id: cargo-check
  #      - id: cargo-test
  # 1year old
  - repo: local
    hooks:
      - id: shellcheck
        name: ShellCheck v0.11.0
        entry: bash scripts/pre-commit-hooks/shellcheck-precommit.sh
        language: system
        types: [shell]
  - repo: https://github.com/scop/pre-commit-shfmt
    rev: v3.13.1-1
    hooks:
      - id: shfmt
  - repo: local
    hooks:
      - id: psscriptanalyzer-check
        name: check PowerShell code using PSScriptAnalyzer
        language: system
        entry: bash scripts/pre-commit-hooks/psscriptanalyzer-docker.sh
        files: \.ps[dm]?1$
        args:
          - -Check
          - -ExcludeRule
          - PSAvoidUsingWriteHost
          - -Fix
      - id: psscriptanalyzer-format
        name: format PowerShell code using PSScriptAnalyzer
        language: system
        entry: bash scripts/pre-commit-hooks/psscriptanalyzer-docker.sh
        files: \.ps[dm]?1$
        args:
          - -Format

  # Legacy ophiosdev hook (null Path crash with --all-files); kept for reference.
  # - repo: https://github.com/ophiosdev/pre-commit-psscriptanalyzer.git
  #   rev: v2.0.0
  #   hooks:
  #     - id: psscriptanalyzer-check
  #     - id: psscriptanalyzer-format

  # export PSSA_DOCKER_IMAGE=mcr.microsoft.com/powershell:7.5-debian-12

  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: v4.0.0-alpha.8
    hooks:
      - id: prettier
        types_or: [yaml, json5, bash, javascript, ts, tsx]
        exclude: ^(\.github/workflows/.*\.ya?ml$|sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json)$
      - id: prettier
        name: prettier github workflow yaml
        files: ^\.github/workflows/.*\.ya?ml$
        types_or: [yaml]

  - repo: https://github.com/crate-ci/typos
    rev: v1.47.0
    hooks:
      - id: typos
        args: ["--force-exclude", "--locale", "en"]
  - repo: https://github.com/codespell-project/codespell
    rev: v2.4.2
    hooks:
      - id: codespell # See pyproject.toml for args
        additional_dependencies:
          - tomli
  - repo: https://github.com/crate-ci/committed
    rev: v1.1.11
    hooks:
      - id: committed
        exclude: ^sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json$

  - repo: https://github.com/Yelp/detect-secrets
    rev: v1.5.0
    hooks:
      - id: detect-secrets
        args:
          [
            "--baseline",
            ".secrets.baseline",
            "--exclude-files",
            "app/migrations/versions/.*|ast-grep/rule-tests/.*|app/tests/test_bm25_migration.py|.env.example|.ast-grep/.*|.talismanrc|sdk/rust/cyt-indexer/cyt-indexer\\.cdx\\.json|sdk/rust/cyt-indexer/cyt-indexer\\.snyk\\.json",
          ]

  - repo: https://github.com/gitleaks/gitleaks
    rev: v8.30.0
    hooks:
      - id: gitleaks
        exclude: ^sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json$

  - repo: https://github.com/trufflesecurity/trufflehog
    rev: v3.92.3
    hooks:
      - id: trufflehog
        args: ["--only-verified", "--trust-local-git-config"]
        exclude: ^sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json$

  - repo: https://github.com/thoughtworks/talisman
    rev: v1.37.0
    hooks:
      - id: talisman-commit
        exclude: ^sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json$

  - repo: https://github.com/rhysd/actionlint
    rev: v1.7.10
    hooks:
      - id: actionlint
        files: ^\.github/workflows/.*\.ya?ml$

  - repo: https://github.com/python-jsonschema/check-jsonschema
    rev: 0.36.0
    hooks:
      - id: check-github-workflows
        files: ^\.github/workflows/
      - id: check-jsonschema
        name: check pre-commit config
        files: ^\.pre-commit-config\.yaml$
        args:
          - --schemafile
          - https://json.schemastore.org/pre-commit-config.json

  - repo: https://github.com/pre-commit/pygrep-hooks
    rev: v1.10.0
    hooks:
      - id: python-check-blanket-noqa
      - id: python-check-blanket-type-ignore
      - id: python-check-mock-methods

  - repo: https://github.com/oxipng/oxipng
    rev: v9.1.5
    hooks:
      - id: oxipng
        files: ^assets/.*\.png$

  - repo: local
    hooks:
      - id: clang-format
        name: clang-format (sdk/c)
        entry: bash scripts/pre-commit-hooks/c-sdk-precommit.sh clang-format
        language: system
        files: ^sdk/c/.*\.(c|h)$
        exclude: ^sdk/c/include/cyt_indexer\.h$
        args: ["-i", "--style=file"]
      - id: cppcheck
        name: cppcheck (sdk/c)
        entry: bash scripts/pre-commit-hooks/c-sdk-precommit.sh cppcheck
        language: system
        files: ^sdk/c/.*\.(c|h)$
        exclude: ^sdk/c/include/cyt_indexer\.h$
        args: ["--suppress=missingIncludeSystem", "--error-exitcode=1"]
      - id: clang-tidy
        name: clang-tidy (sdk/c)
        entry: bash scripts/pre-commit-hooks/c-sdk-precommit.sh clang-tidy
        language: system
        files: ^sdk/c/.*\.(c|h)$
        exclude: ^sdk/c/include/cyt_indexer\.h$
        args:
          - "-p=sdk/c/build"
          - "--warnings-as-errors=*"
      - id: cpplint
        name: cpplint (sdk/c examples)
        entry: bash scripts/pre-commit-hooks/c-sdk-precommit.sh cpplint
        language: system
        files: ^sdk/c/examples/.*\.c$
        args: ["--filter=-legal/copyright"]
      - id: go-fumpt
        name: go-fumpt (sdk/go)
        entry: bash scripts/pre-commit-hooks/go-sdk-precommit.sh fumpt
        language: system
        files: ^sdk/go/.*\.go$
      - id: go-imports
        name: go-imports (sdk/go)
        entry: bash scripts/pre-commit-hooks/go-sdk-precommit.sh imports
        language: system
        files: ^sdk/go/.*\.go$
      - id: go-mod-tidy-repo
        name: go-mod-tidy (sdk/go)
        entry: bash scripts/pre-commit-hooks/go-sdk-precommit.sh tidy
        language: system
        files: ^sdk/go/
        pass_filenames: false
      - id: go-staticcheck-repo-mod
        name: go-staticcheck (sdk/go)
        entry: bash scripts/pre-commit-hooks/go-sdk-precommit.sh staticcheck
        language: system
        files: ^sdk/go/
        pass_filenames: false
      - id: go-critic
        name: go-critic (sdk/go)
        entry: bash scripts/pre-commit-hooks/go-sdk-precommit.sh critic
        language: system
        files: ^sdk/go/.*\.go$
      - id: go-sec-repo-mod
        name: go-sec (sdk/go)
        entry: bash scripts/pre-commit-hooks/go-sdk-precommit.sh sec
        language: system
        files: ^sdk/go/
        pass_filenames: false
      - id: go-build-repo-mod
        name: go-build (sdk/go)
        entry: bash scripts/pre-commit-hooks/go-sdk-precommit.sh build
        language: system
        files: ^sdk/go/
        pass_filenames: false
      - id: go-test-repo-mod
        name: go-test (sdk/go)
        entry: bash scripts/pre-commit-hooks/go-sdk-precommit.sh test
        language: system
        files: ^sdk/go/
        pass_filenames: false

  - repo: https://github.com/PyCQA/flake8
    rev: 7.3.0
    hooks:
      - id: flake8
        args: ["--max-line-length", "140", "--extend-ignore=E203"]
        exclude: ^test_data/|bumpity.py$

  - repo: local
    hooks:
      - id: heal-cargo-lock
        name: heal Cargo.lock chunk registry pins
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/heal-cargo-lock.sh',
          ]
        language: system
        files: ^Cargo\.(toml|lock)$
        pass_filenames: false

      - id: sync-version
        name: sync-version
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args: ["rtk bash scripts/publish/sync-version.sh"]
        language: system
        verbose: true
        pass_filenames: false

  - repo: local
    hooks:
      - id: export-requirements
        name: export-requirements
        entry: bash scripts/deps/export-requirements.sh
        language: system
        files: ^(pyproject\.toml|uv\.lock)$
        pass_filenames: false

  - repo: local
    hooks:
      - id: export-rust-sbom
        name: export-rust-sbom
        entry: bash scripts/deps/export-rust-sbom-precommit.sh
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/)
        exclude: ^sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json$
        pass_filenames: false

  - repo: local
    hooks:
      - id: verify-pins
        name: verify-pins
        entry: bash scripts/deps/verify-pins.sh
        args: ["--short", "--no-report"]
        language: system
        pass_filenames: false
        files: ^(pyproject\.toml|uv\.lock|requirements\.txt|dev-requirements\.txt|fossa-deps\.yml|Cargo\.toml|Cargo\.lock|sdk/c/CMakeLists\.txt|sdk/go/go\.(mod|sum)|sdk/typescript/package(-lock)?\.json|package(-lock)?\.json|scripts/pre-commit-hooks/go-sdk-tools\.sh)$

  - repo: https://github.com/astral-sh/uv-pre-commit
    # uv version.
    rev: 0.11.17
    hooks:
      - id: uv-lock
        args: ["--project", "."]
        files: pyproject.toml
      - id: uv-sync
        args: ["--project", ".", "--locked", "--all-packages"]
        files: pyproject.toml
        additional_dependencies: []

  - repo: https://github.com/asottile/pyupgrade
    rev: v3.21.2
    hooks:
      - id: pyupgrade
        args: [--py313-plus]
  - repo: https://github.com/DavidAnson/markdownlint-cli2
    rev: v0.22.1
    hooks:
      - id: markdownlint-cli2
        language_version: lts
        args: [--fix]
        exclude: ^(CLAUDE|AGENTS|GEMINI|MCPC_RESEARCH)\.md$|^backlog/

  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.15.15
    hooks:
      # Run the Ruff formatter.
      - id: ruff-format
        name: "ruff-format"
        args: [--config=pyproject.toml]
        files: '^src/.*\.(py|ipynb)$'
      # Run the Ruff linter.
      - id: ruff
        name: "ruff"
        args:
          [
            --exit-non-zero-on-fix,
            --fix,
            --config=pyproject.toml,
            --output-format,
            concise,
          ]
        files: '^src/.*\.(py|ipynb)$'
  # Should be after ruff!
  - repo: https://github.com/asottile/add-trailing-comma
    rev: v4.0.0
    hooks:
      - id: add-trailing-comma

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: check-added-large-files
        args: ["--maxkb=1024"]
      - id: trailing-whitespace
        exclude: ^sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json$
      - id: check-yaml
        exclude: ^(.ast-grep/rules/.*|\.github/workflows/.*)$
      - id: check-yaml
        name: check github workflow yaml
        files: ^\.github/workflows/.*\.ya?ml$
        always_run: true
      - id: check-json
      - id: check-toml
      - id: end-of-file-fixer
        exclude: ^sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json$
      - id: mixed-line-ending
        exclude: ^sdk/rust/cyt-indexer/cyt-indexer\.(cdx|snyk)\.json$
      - id: detect-private-key
      - id: check-case-conflict
      - id: check-merge-conflict
      - id: check-symlinks
      - id: check-builtin-literals
        args: ["--no-allow-dict-kwargs"]
        exclude: bumpity.py$
      - id: check-docstring-first
      - id: debug-statements
        exclude: bumpity.py$
      # Conflicts with ruff
      #      - id: double-quote-string-fixer
      - id: name-tests-test
        args: [--pytest-test-first]
        exclude: ^(sdk/e2e/python/tests/(.*)\.py$|src/tests/support/.*\.py$|src/tests/qa/.*\.py$|scripts/local/tests/.*\.py$)

  - repo: local
    hooks:
      - id: ty-check
        name: Ty type checker
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            "source scripts/pre-commit-hooks/activate-venv.sh && rtk uv run ty check src/ --project . --output-format concise",
          ]
        language: system
        types: [python]
        pass_filenames: false
        exclude: |
          (?x)^(
            latex/
            src/catalog/
            .ruff_cache/
            .mypy_cache/
            .venv/
            __pycache__/
            src/__pycache__/
          )
      - id: check-filenames
        name: Check for spaces in all filenames
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - |
            rtk git ls-files \
              | grep -vE '^"?(postman/|documents/|backlog/|dirs/)' \
              | grep " " \
              && echo "Filenames should not contain spaces!" && exit 1 \
              || exit 0
        language: system
        always_run: true
        pass_filenames: false
      - id: mypy
        name: mypy
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            "source scripts/pre-commit-hooks/activate-venv.sh && cd src && rtk mypy .",
          ]
        pass_filenames: false
        language: system
        files: '^src/.*\.py$'
      - id: check-cyt-client-imports
        name: check-cyt-client-imports
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && uv run python scripts/pre-commit-hooks/check_cyt_client_imports.py',
          ]
        pass_filenames: false
        language: system
        files: ^(src/cyt_client/.*\.py|scripts/pre-commit-hooks/check_cyt_client_imports\.py)$
      - id: check-cyt-mcp-imports
        name: check-cyt-mcp-imports
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && uv run python scripts/pre-commit-hooks/check_cyt_mcp_imports.py',
          ]
        pass_filenames: false
        language: system
        files: ^(src/cyt_mcp/.*\.py|scripts/pre-commit-hooks/check_cyt_mcp_imports\.py)$
      - id: check-agent-imports
        name: check-agent-imports
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && uv run python scripts/pre-commit-hooks/check_agent_imports.py',
          ]
        pass_filenames: false
        language: system
        files: ^(src/cyt/agents/.*\.py|src/cyt/skills/.*\.py|src/cyt/proxy/reverse\.py|scripts/pre-commit-hooks/check_agent_imports\.py)$
      - id: maturin-develop
        name: maturin develop (cyt-indexer _native)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/maturin-develop.sh',
          ]
        language: system
        files: ^(sdk/(rust/cyt-indexer/|python/)|Cargo\.(toml|lock))
        pass_filenames: false

      - id: pytest-unit
        name: pytest (unit)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh unit',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/.*)$

      - id: pytest-unit-shard-0
        name: pytest (unit shard 0)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh unit-shard 0 "${PREK_PYTEST_UNIT_SHARDS:-4}"',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/.*)$

      - id: pytest-unit-shard-1
        name: pytest (unit shard 1)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh unit-shard 1 "${PREK_PYTEST_UNIT_SHARDS:-4}"',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/.*)$

      - id: pytest-unit-shard-2
        name: pytest (unit shard 2)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh unit-shard 2 "${PREK_PYTEST_UNIT_SHARDS:-4}"',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/.*)$

      - id: pytest-unit-shard-3
        name: pytest (unit shard 3)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh unit-shard 3 "${PREK_PYTEST_UNIT_SHARDS:-4}"',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/.*)$

      - id: pytest-unit-shard-4
        name: pytest (unit shard 4)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh unit-shard 4 "${PREK_PYTEST_UNIT_SHARDS:-4}"',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/.*)$

      - id: pytest-unit-shard-5
        name: pytest (unit shard 5)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh unit-shard 5 "${PREK_PYTEST_UNIT_SHARDS:-4}"',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/.*)$

      - id: pytest-unit-shard-6
        name: pytest (unit shard 6)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh unit-shard 6 "${PREK_PYTEST_UNIT_SHARDS:-4}"',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/.*)$

      - id: pytest-unit-shard-7
        name: pytest (unit shard 7)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh unit-shard 7 "${PREK_PYTEST_UNIT_SHARDS:-4}"',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/.*)$

      - id: pytest-gherkin-unit
        name: pytest (gherkin unit)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh gherkin-unit',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/unit/gherkin/.*)$

      - id: pytest-quality-metrics
        name: pytest (quality_metrics)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh quality_metrics',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/quality_metrics/.*)$

      - id: pytest-coverage
        name: pytest (coverage)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh coverage',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/coverage/.*|sdk/e2e/fixtures/bm25_catalog\.json)$

      - id: pytest-mutation
        name: pytest (mutation)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh mutation',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/mutation/.*)$

      - id: pytest-qa
        name: pytest (qa)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-category.sh qa',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/qa/.*|sdk/e2e/fixtures/bm25_catalog\.json)$

      - id: pytest-runtime
        name: pytest (runtime)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && CYT_RUN_RUNTIME_TESTS=1 rtk bash scripts/local/tests/pytest-category.sh runtime',
          ]
        pass_filenames: false
        language: system
        files: ^(src/.*\.py|src/tests/runtime/.*)$

      - id: pytest-sdk-python
        name: pytest (sdk/python unit)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/pytest-sdk-python.sh',
          ]
        pass_filenames: false
        language: system
        files: ^(sdk/python/|sdk/rust/cyt-indexer/)

  - repo: https://github.com/DetachHead/basedpyright-pre-commit-mirror
    rev: 1.39.6
    hooks:
      - id: basedpyright
        name: basedpyright
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            "source scripts/pre-commit-hooks/activate-venv.sh && rtk basedpyright src sdk/python/src",
          ]
        language: system
        pass_filenames: false
        files: '^(src/.*\.py|sdk/python/.*\.py)$'

  - repo: local
    hooks:
      - id: ast-test
        name: ast-grep rule tests
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args: ["rtk ast-grep test --skip-snapshot-tests"]
        language: system
        files: ^\.ast-grep/
        pass_filenames: false

      - id: uv-build
        name: Python package build
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args: ['cd "$(git rev-parse --show-toplevel)" && rtk uv build']
        language: system
        files: ^(pyproject\.toml|src/)
        pass_filenames: false

      - id: verify-sdk
        name: Verify cyt-indexer-sdk native import
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk uv run python -c "from cyt_indexer._native import build_catalog_index; assert callable(build_catalog_index)"',
          ]
        language: system
        files: ^(sdk/(rust|python)/|pyproject\.toml)
        pass_filenames: false

      - id: verify-app-python
        name: Verify app re-exports local cyt-indexer-sdk
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/workflow.sh app-verify',
          ]
        language: system
        files: ^(src/|pyproject\.toml)$
        pass_filenames: false

      - id: cargo-clippy-cyt-indexer-core
        name: cargo clippy (cyt-indexer core)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/cargo-clippy-cyt-indexer.sh core',
          ]
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/|sdk/c/|sdk/go/)
        pass_filenames: false

      - id: cargo-clippy-cyt-indexer-cli
        name: cargo clippy (cyt-indexer cli)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/cargo-clippy-cyt-indexer.sh cli',
          ]
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/|sdk/c/|sdk/go/)
        pass_filenames: false

      - id: cargo-clippy-cyt-indexer
        name: cargo clippy (cyt-indexer all)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/cargo-clippy-cyt-indexer.sh all',
          ]
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/|sdk/c/|sdk/go/)
        pass_filenames: false

      - id: cargo-deny
        name: cargo deny (nopatch workspace)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/cargo-deny.sh',
          ]
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/|deny\.toml)
        pass_filenames: false

      - id: cargo-fmt
        name: cargo fmt (cyt-indexer)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk cargo fmt --all -- --check',
          ]
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/|rustfmt\.toml$)
        pass_filenames: false

      - id: cargo-audit
        name: cargo audit (nopatch workspace)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/cargo-locked.sh audit',
          ]
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/)
        pass_filenames: false

      - id: cargo-udeps
        name: cargo udeps (nopatch workspace)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/cargo-udeps.sh',
          ]
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/)
        pass_filenames: false

      - id: cbindgen-header-drift
        name: cbindgen header drift check
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - |
            set -euo pipefail
            root="$(git rev-parse --show-toplevel)"
            cd "$root"
            rtk bash scripts/local/dev/cargo-locked.sh build -p cyt-indexer --no-default-features --features ffi --locked
            git diff --exit-code sdk/rust/cyt-indexer/cyt_indexer.h
        language: system
        files: ^sdk/rust/cyt-indexer/(src/ffi/|cbindgen\.toml|build\.rs)
        pass_filenames: false

      - id: c-header-sync
        name: sdk/c header sync check
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - cmp sdk/rust/cyt-indexer/cyt_indexer.h sdk/c/include/cyt_indexer.h
        language: system
        files: ^sdk/(rust/cyt-indexer/cyt_indexer\.h|c/include/cyt_indexer\.h)
        pass_filenames: false

      - id: cargo-test-unit
        name: cargo test (unit)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - rtk bash scripts/local/tests/cargo-test-category.sh unit
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/unit/)
        pass_filenames: false

      - id: cargo-warm-build
        name: cargo warm build (cyt-indexer tests)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - rtk bash scripts/local/tests/cargo-warm-build.sh
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/)
        pass_filenames: false

      - id: cargo-test-unit-shard-0
        name: cargo test (unit shard 0)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - 'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/cargo-test-category.sh unit-shard 0 "${PREK_RUST_UNIT_SHARDS:-4}"'
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/unit/)
        pass_filenames: false

      - id: cargo-test-unit-shard-1
        name: cargo test (unit shard 1)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - 'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/cargo-test-category.sh unit-shard 1 "${PREK_RUST_UNIT_SHARDS:-4}"'
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/unit/)
        pass_filenames: false

      - id: cargo-test-unit-shard-2
        name: cargo test (unit shard 2)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - 'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/cargo-test-category.sh unit-shard 2 "${PREK_RUST_UNIT_SHARDS:-4}"'
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/unit/)
        pass_filenames: false

      - id: cargo-test-unit-shard-3
        name: cargo test (unit shard 3)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - 'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/cargo-test-category.sh unit-shard 3 "${PREK_RUST_UNIT_SHARDS:-4}"'
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/unit/)
        pass_filenames: false

      - id: cargo-test-unit-shard-4
        name: cargo test (unit shard 4)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - 'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/cargo-test-category.sh unit-shard 4 "${PREK_RUST_UNIT_SHARDS:-4}"'
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/unit/)
        pass_filenames: false

      - id: cargo-test-unit-shard-5
        name: cargo test (unit shard 5)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - 'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/cargo-test-category.sh unit-shard 5 "${PREK_RUST_UNIT_SHARDS:-4}"'
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/unit/)
        pass_filenames: false

      - id: cargo-test-unit-shard-6
        name: cargo test (unit shard 6)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - 'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/cargo-test-category.sh unit-shard 6 "${PREK_RUST_UNIT_SHARDS:-4}"'
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/unit/)
        pass_filenames: false

      - id: cargo-test-unit-shard-7
        name: cargo test (unit shard 7)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - 'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/tests/cargo-test-category.sh unit-shard 7 "${PREK_RUST_UNIT_SHARDS:-4}"'
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/unit/)
        pass_filenames: false

      - id: cargo-test-integration
        name: cargo test (integration)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - rtk bash scripts/local/tests/cargo-test-category.sh integration
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/integration/)
        pass_filenames: false

      - id: cargo-test-cucumber
        name: cargo test (cucumber)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - rtk bash scripts/local/tests/cargo-test-category.sh cucumber
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/integration/features/|tests/integration/cucumber/)
        pass_filenames: false

      - id: cargo-test-ffi
        name: cargo test (ffi)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - rtk bash scripts/local/tests/cargo-test-category.sh ffi
        language: system
        files: ^sdk/rust/cyt-indexer/(src/ffi/|tests/ffi/|cyt_indexer\.h)
        pass_filenames: false

      - id: cargo-test-coverage
        name: cargo test (coverage)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - rtk bash scripts/local/tests/cargo-test-category.sh coverage
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/coverage/)|sdk/e2e/fixtures/(cohesion_sample\.md|cohesion_config\.json|bm25_catalog\.json)
        pass_filenames: false

      - id: cargo-test-mutation
        name: cargo test (mutation)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - rtk bash scripts/local/tests/cargo-test-category.sh mutation
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/mutation/)
        pass_filenames: false

      - id: cargo-test-quality-metrics
        name: cargo test (quality_metrics)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - rtk bash scripts/local/tests/cargo-test-category.sh quality_metrics
        language: system
        files: ^(sdk/rust/cyt-indexer/(src/|tests/quality_metrics/)|sdk/(python/pyproject\.toml|typescript/package\.json|rust/cyt-indexer/Cargo\.toml))
        pass_filenames: false

      - id: cargo-test-qa
        name: cargo test (qa)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - rtk bash scripts/local/tests/cargo-test-category.sh qa
        language: system
        files: ^sdk/rust/cyt-indexer/(src/|tests/qa/)|sdk/e2e/fixtures/bm25_catalog\.json
        pass_filenames: false

      - id: cmake-compile-db
        name: Generate sdk/c compile_commands.json
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - bash scripts/pre-commit-hooks/cmake-compile-db.sh
        language: system
        files: ^sdk/c/
        pass_filenames: false

      - id: build-c-lib-for-go
        name: build C lib for Go CGO
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args: ["bash sdk/c/scripts/build-c-lib.sh --no-sync-header"]
        language: system
        files: ^(sdk/(go/|rust/cyt-indexer/src/ffi/)|sdk/c/include/)
        pass_filenames: false

      - id: typescript-typecheck
        name: TypeScript SDK typecheck
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            "cd sdk/typescript && rtk npx tsc --noEmit && rtk npx tsc --noEmit -p ../e2e/typescript",
          ]
        language: system
        files: ^sdk/(typescript|e2e/typescript)/
        pass_filenames: false

      - id: typescript-test-unit
        name: TypeScript SDK test (unit)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          ["cd sdk/typescript && rtk npm run build && rtk npm run test:unit"]
        language: system
        files: ^(sdk/typescript/|sdk/rust/cyt-indexer/|sdk/e2e/fixtures/)
        pass_filenames: false

      - id: typescript-test-parity
        name: TypeScript SDK test (parity)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          ["cd sdk/typescript && rtk npm run build && rtk npm run test:parity"]
        language: system
        files: ^(sdk/typescript/|sdk/python/|sdk/rust/cyt-indexer/|sdk/e2e/fixtures/)
        pass_filenames: false

      - id: typescript-build
        name: TypeScript SDK build
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args: ["cd sdk/typescript && rtk npm run build"]
        language: system
        files: ^sdk/typescript/
        pass_filenames: false

      - id: typescript-npm-audit
        name: TypeScript SDK npm audit
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          - "set -euo pipefail; audit_if_locked() { if [[ -f package-lock.json ]]; then rtk npm audit --audit-level=high; fi; }; (cd sdk/typescript && audit_if_locked); (cd sdk/e2e/typescript && audit_if_locked)"
        language: system
        files: ^sdk/(typescript|e2e/typescript)/
        pass_filenames: false

      - id: typescript-sort-package-json
        name: TypeScript SDK sort-package-json
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            "cd sdk/typescript && rtk npx --yes sort-package-json package.json && cd ../e2e/typescript && rtk npx --yes sort-package-json package.json.in",
          ]
        language: system
        files: ^sdk/(typescript/package\.json|e2e/typescript/package\.json\.in)$
        pass_filenames: false

      - id: ast-scan
        name: Ast rule scan
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args: ["rtk ast-grep scan src/ sdk/"]
        language: system
        pass_filenames: false

      - id: typescript-ast-scan
        name: TypeScript SDK ast-scan
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'rtk ast-grep scan sdk/typescript sdk/e2e/typescript --globs "!sdk/typescript/src/test/**"',
          ]
        language: system
        files: ^sdk/(typescript|e2e/typescript)/
        pass_filenames: false

      - id: all-fallow
        name: fallow checks (ui all-fallow)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args: ["rtk bash scripts/pre-commit-hooks/all-fallow.sh"]
        language: system
        files: ^(ui/|sdk/(typescript|e2e/typescript)/|package\.json|package-lock\.json)
        pass_filenames: false

      - id: local-dev-core-rust
        name: local-dev core-rust (indexer build smoke)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && CYT_CATALOG_DIR="$(mktemp -d "${TMPDIR:-/tmp}/cyt-prek-catalog.XXXXXX")" && export CYT_CATALOG_DIR && rtk bash scripts/local/dev/cargo-locked.sh build -p cyt-indexer --release --locked && rtk bash scripts/local/dev/workflow.sh indexer build tools',
          ]
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/|debug/full_example\.json)
        pass_filenames: false

      - id: cargo-build-sdk-release
        name: cargo-build-sdk-release (cyt-indexer python+node)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/cargo-build-sdk-release.sh',
          ]
        language: system
        files: ^(Cargo\.(toml|lock)|sdk/rust/cyt-indexer/)
        pass_filenames: false

      - id: local-dev-sdk-python
        name: local-dev sdk-python
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/workflow.sh sdk-python',
          ]
        language: system
        files: ^(sdk/python/|sdk/rust/cyt-indexer/)
        pass_filenames: false

      - id: local-dev-sdk-typescript
        name: local-dev sdk-typescript
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/workflow.sh sdk-typescript',
          ]
        language: system
        files: ^(sdk/typescript/|sdk/rust/cyt-indexer/)
        pass_filenames: false

      - id: local-dev-sdk-c
        name: local-dev sdk-c
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/workflow.sh sdk-c',
          ]
        language: system
        files: ^(sdk/c/|sdk/rust/cyt-indexer/src/ffi/)
        pass_filenames: false

      - id: local-dev-sdk-go
        name: local-dev sdk-go
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/workflow.sh sdk-go',
          ]
        language: system
        files: ^(sdk/go/|sdk/c/|sdk/rust/cyt-indexer/src/ffi/)
        pass_filenames: false

      - id: local-dev-app
        name: local-dev app (src/)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/workflow.sh app-build',
          ]
        language: system
        files: ^(src/|pyproject\.toml|uv\.lock)$
        pass_filenames: false

      - id: simulate-registry
        name: simulate-registry (pre-publish smoke)
        entry: bash scripts/pre-commit-hooks/prek-hook.sh
        args:
          [
            'cd "$(git rev-parse --show-toplevel)" && rtk bash scripts/local/dev/workflow.sh simulate-registry',
          ]
        language: system
        stages: [manual]
        always_run: true
        pass_filenames: false

      # Keep `suggestion` last
      - id: suggestion
        name: Suggestion
        entry: bash -c 'echo "To bypass all the pre-commit hooks, add --no-verify to git commit. To skip a specific hook, prefix the commit command with SKIP=<hook-id>."'
        language: system
        verbose: true
        pass_filenames: false
  # Insert new entries above the `suggestion` entry