.pre-commit-config.yaml

exclude: '^docs/'
repos:
-   repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v3.4.0  # Use the ref you want to point at
    hooks:
    -   id: trailing-whitespace
    -   id: end-of-file-fixer
    -   id: mixed-line-ending
    -   id: check-json
    -   id: pretty-format-json
        args: ['--autofix', '--no-sort-keys']
-   repo: https://github.com/ambv/black
    rev: 20.8b1
    hooks:
    - id: black
      language_version: python3.8
-   repo: https://github.com/pre-commit/mirrors-mypy
    rev: 'v0.812'
    hooks:
    -   id: mypy
        name: mypy-clinical-data-interface
        files: ^apps/clinical_data_interface/
        entry: mypy apps/clinical_data_interface/
        pass_filenames: false
    -   id: mypy
        name: mypy-adherence-evaluator
        files: ^apps/adherence_evaluator/
        entry: mypy apps/adherence_evaluator/
        pass_filenames: false
        exclude: ^apps/adherence_evaluator/tests/.*
    -   id: mypy
        name: mypy-guideline-interface
        files: ^apps/guideline_interface/
        entry: mypy apps/guideline_interface/
        pass_filenames: false
    -   id: mypy
        name: mypy-ui
        files: ^apps/ui/
        entry: mypy apps/ui/
        pass_filenames: false
    -   id: mypy
        name: mypy-ui-backend
        files: ^apps/ui_backend/
        entry: mypy apps/ui_backend/
        pass_filenames: false
    -   id: mypy
        name: mypy-rest
        exclude: ^(apps/(clinical_data_interface|adherence_evaluator|guideline_interface|ui|ui_backend)/|generate.py)
-   repo: https://github.com/pycqa/pydocstyle
    rev: '6.1.1'
    hooks:
    -   id: pydocstyle
        exclude: tests/
-   repo: https://github.com/PyCQA/bandit
    rev: '1.7.0'
    hooks:
    - id: bandit
      args: [--skip, "B101,B303,B110"]
-   repo: https://gitlab.com/pycqa/flake8
    rev: '3.9.0'
    hooks:
    -   id: flake8
-   repo: https://github.com/lorenzwalthert/precommit
    rev: v0.1.3
    hooks:
    -   id: style-files
        args: [--style_pkg=styler, --style_fun=tidyverse_style]
    -   id: parsable-R
- repo: https://github.com/sirosen/check-jsonschema
  rev: 0.3.0
  hooks:
    - id: check-jsonschema
      name: "Check FHIR json"
      language: python
      files: ^FHIR/.*\.fhir.json
      #types: [json]
      args: ["--schemafile", "FHIR/fhir.schema.json"]