.pre-commit-config.yaml

repos:
  - repo: meta
    hooks:
    - id: check-hooks-apply
    - id: check-useless-excludes

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.6.0
    hooks:
    - id: no-commit-to-branch
      args: [--branch, main, --branch, master]
    - id: check-ast
    - id: check-docstring-first
    - id: check-case-conflict
    - id: check-merge-conflict
    - id: end-of-file-fixer
    - id: trailing-whitespace
    - id: check-json
      files: ^metadata_backend
    - id: pretty-format-json
      files: ^metadata_backend
      args:
      - --autofix
      - --indent=4
      - --no-ensure-ascii
      - --no-sort-keys
    - id: check-yaml
    - id: check-xml
      exclude: tests/test_files/study/SRP000539_invalid[0-9]?.xml

  - repo: https://github.com/psf/black
    rev: 24.4.0
    hooks:
    - id: black
      args: [-l, "120"]

  - repo: https://github.com/pycqa/isort
    rev: 5.13.2
    hooks:
    - id: isort
      args: [--profile, black, --filter-files]

  - repo: https://github.com/pycqa/flake8
    rev: 7.0.0
    hooks:
    - id: flake8
      additional_dependencies:
        - flake8-docstrings
        - flake8-annotations

  - repo:  https://github.com/PyCQA/bandit
    rev: 1.7.8
    hooks:
    - id: bandit
      files: ^metadata_backend

  - repo: https://github.com/APIDevTools/swagger-cli
    rev: v4.0.4
    hooks:
    - id: swagger-validation
      args: [validate]
      files: docs/openapi.yml

  - repo: https://github.com/python-jsonschema/check-jsonschema
    rev: 0.28.2
    hooks:
      - id: check-metaschema
        name: Validate schemas
        files: ^metadata_backend/helpers/schemas/.*\.json$

      - id: check-jsonschema
        name: Validate workflows
        files: ^metadata_backend/conf/workflows/.*\.json$
        args: ["--schemafile", "metadata_backend/helpers/schemas/workflow.json"]

      - id: check-dependabot
      - id: check-github-workflows

  - repo: https://github.com/jendrikseipp/vulture
    rev: 'v2.11'
    hooks:
    - id: vulture
      args: [metadata_backend/, whitelist_dead_code.py]

  - repo: local
    hooks:
    - id: sort
      name: sort dictionary
      entry: ./scripts/dictionary/sort.sh
      language: script
      files: ^(docs|.*md)
      require_serial: true
      pass_filenames: false

    - id: pylint
      name: pylint
      entry: pylint
      language: system
      types: [python]
      files: ^metadata_backend
      args:
        [
          -rn, # Only display messages
          -sn, # Don't display the score
        ]

    - id: pyspelling-docs
      name: pyspelling-docs
      entry: ./scripts/dictionary/pyspelling.sh
      language: script
      args: [markdown]
      types_or: [markdown, rst]
      require_serial: true

    - id: mypy
      name: mypy
      entry: mypy
      language: system
      types: [python]
      files: ^metadata_backend

    - id: pyspelling-schemas
      name: pyspelling-schemas
      entry: ./scripts/dictionary/pyspelling.sh
      language: script
      args: [json-schemas]
      files: ^metadata_backend/helpers/schemas/
      types: [json]
      require_serial: true