metamist/.pre-commit-config.yaml at dev · populationgenomics/metamist · GitHub

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default_language_version:
    python: python3.11

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: check-yaml
        exclude: '\.*conda/.*'
      - id: end-of-file-fixer
      - id: trailing-whitespace
        exclude: '\.txt$|\.tsv$'
      - id: check-case-conflict
      - id: check-merge-conflict
      - id: detect-private-key
      - id: debug-statements
      - id: check-added-large-files

  - repo: https://github.com/igorshubovych/markdownlint-cli
    rev: v0.38.0
    hooks:
      - id: markdownlint
        args: ["--config", ".markdownlint.json"]

  - repo: https://github.com/populationgenomics/pre-commits
    rev: "v0.1.3"
    hooks:
      - id: cpg-id-checker
        args: ["--extra-pattern", 'TOB\d+']
        exclude: >-
          (?x)^(
              test/test_audit\.py|
              models/utils/sequencing_group_id_format\.py|
              metamist/audit/README\.md
          )$

  - repo: https://github.com/astral-sh/ruff-pre-commit
    # Ruff version.
    rev: v0.15.0
    hooks:
      # Run the linter.
      - id: ruff-check
        args: [ --fix ]
      # Run the formatter.
      - id: ruff-format

  # mypy
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.8.0
    hooks:
      - id: mypy
        args: [
            --pretty,
            --show-error-codes,
            --no-strict-optional,
            --ignore-missing-imports,
            --install-types,
            --non-interactive,
            # --show-error-context,
            --check-untyped-defs,
            --explicit-package-bases,
            --disable-error-code,
            operator,
          ]
        additional_dependencies:
          - strawberry-graphql[fastapi]==0.268.1
          - types-PyMySQL==1.1.0.1

  - repo: https://github.com/woodruffw/zizmor-pre-commit
    rev: v1.5.2
    hooks:
      - id: zizmor