.pre-commit-config.yaml

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---
# prek Hook Priority System Explanation:
#
# prek (a fast Rust-based pre-commit alternative) executes hooks based on priority levels:
# 1. Ordering: Hooks are executed in ascending order of their priority value (lowest first).
# 2. Concurrency: Hooks with the SAME priority value are executed concurrently (in parallel),
#    limited only by the global concurrency limit (typically the number of CPU cores).
# 3. Explicit vs. Implicit: Any hook without an explicit `priority` field is automatically
#    assigned an implicit priority equal to its 0-based index in the flattened hook list.
#    To avoid unexpected execution order when mixing, we explicitly define priorities
#    for all hooks.
#
# In this configuration:
# - Priority 1: Meta hooks (e.g., identity, check-hooks-apply). These run first to verify
#   the hook environment and setup before any files are processed.
# - Priorities 10-17: File-modifying and formatting hooks (e.g., end-of-file-fixer,
#   trailing-whitespace, pretty-format-json). These are executed sequentially in a specific
#   order to avoid write conflicts/race conditions, ensuring files are fully prepared and
#   formatted before any validation.
# - Priority 100: All read-only validation and linting hooks (e.g., codespell, yamllint,
#   check-json, shellcheck, actionlint). Since these do not modify any files, they are run
#   in parallel to maximize performance and minimize pre-commit execution time.

default_stages: [pre-commit, pre-push]
default_language_version:
  # force all unspecified Python hooks to run python3
  python: python3
minimum_prek_version: '0.3.4'
repos:
  - repo: meta
    hooks:
      - id: identity
        priority: 1
        description: A simple hook which prints all arguments passed to it, useful for debugging
      - id: check-hooks-apply
        priority: 1
        description: Useful when testing new hooks to see if they apply to the repository
  - repo: local
    hooks:
      - id: check-zip-file-is-not-committed
        priority: 100
        name: Check no Zip files are committed
        description: Zip files are not allowed in the repository
        language: fail
        entry: |
          Zip files are not allowed in the repository as they are hard to
          track and have security implications. Please remove the zip file from the repository
        files: (?i)\.zip$
  - repo: https://github.com/Lucas-C/pre-commit-hooks
    rev: ad1b27d73581aa16cca06fc4a0761fc563ffe8e8 # frozen: v1.5.6
    hooks:
      - id: chmod
        priority: 17
        name: set file permissions
        description: manual hook to be run by macOS or Linux users for a full repository clean up
        args: ['644']
        files: \.md$
        stages: [manual]
  - repo: https://github.com/codespell-project/codespell
    rev: 57b21406f092110c18776e39b0bda50d37c945c8 # frozen: v2.4.3
    hooks:
      - id: codespell
        priority: 100
        name: run codespell
        description: Check spelling with codespell
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c # frozen: v6.0.0
    hooks:
      - id: check-case-conflict
        priority: 100
        description: Check for files with names that would conflict on a case-insensitive filesystem like MacOS HFS+ or Windows FAT
      - id: check-executables-have-shebangs
        priority: 100
        description: Checks that non-binary executables have a proper shebang
      - id: check-illegal-windows-names
        priority: 100
        description: Check for files that cannot be created on Windows
      - id: check-json
        priority: 100
        description: Attempts to load all json files to verify syntax
      - id: check-merge-conflict
        priority: 100
        description: Check for files that contain merge conflict strings
      - id: check-shebang-scripts-are-executable
        priority: 100
        description: Checks that scripts with shebangs are executable
      - id: check-vcs-permalinks
        priority: 100
        description: Ensures that links to vcs websites are permalinks
      - id: check-xml
        priority: 100
        description: Attempts to load all xml files to verify syntax
      - id: check-yaml
        priority: 100
        description: Attempts to load all yaml files to verify syntax
      - id: destroyed-symlinks
        priority: 100
        description: Detects symlinks which are changed to regular files with a content of a path which that symlink was pointing to
      - id: detect-aws-credentials
        priority: 100
        description: Checks for the existence of AWS secrets that you have set up with the AWS CLI
        args: [--allow-missing-credentials]
      - id: detect-private-key
        priority: 100
        description: Checks for the existence of private keys
      - id: end-of-file-fixer
        priority: 10
        description: Makes sure files end in a newline and only a newline
      - id: file-contents-sorter
        priority: 15
        description: sort the lines in specified files (defaults to alphabetical)
        args: [--unique]
        files: ^\.github/linters/codespell\.txt$
      - id: fix-byte-order-marker
        priority: 13
        description: removes UTF-8 byte order marker
      - id: forbid-submodules
        priority: 100
        description: Forbids any submodules in the repository
      - id: mixed-line-ending
        priority: 12
        description: replaces or checks mixed line ending
      - id: pretty-format-json
        priority: 14
        description: checks that all your JSON files are pretty
        args: [--autofix, --no-sort-keys]
      - id: trailing-whitespace
        priority: 11
        description: Trims trailing whitespace
        args: [--markdown-linebreak-ext=md]
  - repo: https://github.com/igorshubovych/markdownlint-cli
    rev: 5b5dddc4fb0f83c3ea1fc5616fa63e115dce83e0 # frozen: v0.49.1
    hooks:
      - id: markdownlint
        priority: 100
        name: run markdownlint
        description: check Markdown files with markdownlint
        args: [--config=.github/linters/.markdown-lint.yml]
        exclude: ^\.github/.*$
        types: [markdown]
        files: \.md$
  - repo: https://github.com/adrienverge/yamllint
    rev: cba56bcde1fdd01c1deb3f945e69764c291a6530 # frozen: v1.38.0
    hooks:
      - id: yamllint
        priority: 100
        name: run yamllint
        description: check YAML files with yamllint
        args: [--strict, -c=.github/linters/.yaml-lint.yml]
        types: [yaml]
        files: \.ya?ml$
  - repo: https://github.com/gitleaks/gitleaks
    rev: 83d9cd684c87d95d656c1458ef04895a7f1cbd8e # frozen: v8.30.1
    hooks:
      - id: gitleaks
        priority: 100
        name: run gitleaks
        description: check for secrets with gitleaks
  - repo: https://github.com/zizmorcore/zizmor-pre-commit
    rev: 451b56af716f9f0d0c2b816503a3fd0cf8b036fa # frozen: v1.29.0
    hooks:
      - id: zizmor
        priority: 100
        name: run zizmor
        description: zizmor is a static analysis tool for GitHub Actions
        # args: [--config=.github/linters/zizmor.yml]
        files: ^\.github/workflows/.*$
        types: [yaml]
  - repo: https://github.com/rhysd/actionlint
    rev: 914e7df21a07ef503a81201c76d2b11c789d3fca # frozen: v1.7.12
    hooks:
      - id: actionlint
        priority: 100
        name: run actionlint
        description: actionlint is a static checker for GitHub Actions workflow files
  - repo: https://github.com/tcort/markdown-link-check
    rev: 275c27c5035a5b4a656fe0e21a4c1403c118c767 # frozen: v3.15.0
    hooks:
      - id: markdown-link-check
        priority: 100
        name: run markdown-link-check
        description: checks all of the hyperlinks in a Markdown text to determine if they are alive or dead
        args: [--config=.github/linters/mlc_config.json, -q]
        types: [markdown]
        files: \.md$
  - repo: https://github.com/oxipng/oxipng
    rev: 340cd9878d8d8289f09fa101b48a8f5f0b7783f4 # frozen: v10.2.0
    hooks:
      - id: oxipng
        priority: 16
        name: run oxipng
        description: check PNG files with oxipng
        args: ['--fix', '-o', '4', '--strip', 'safe', '--alpha']
  - repo: https://github.com/python-jsonschema/check-jsonschema
    rev: 12e63946db2c5cfcc9030fac21c3883ba88c6ed8 # frozen: 0.38.0
    hooks:
      - id: check-citation-file-format
        priority: 100
        name: run check-citation-file-format
        description: validate citation file format
        files: ^CITATION\.cff$
      - id: check-dependabot
        priority: 100
        name: validate dependabot.yml
        description: ensures the dependabot config file is valid
        files: ^\.github/dependabot\.yml$
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: 745eface02aef23e168a8afb6b5737818efbea95 # frozen: v0.11.0.1
    hooks:
      - id: shellcheck
        priority: 100
        name: run shellcheck
        description: check Shell scripts with shellcheck
  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
    rev: e8b4e28241a9ae8296ba6e4a491b5da4eda73283 # frozen: 3.11.1
    hooks:
      - id: editorconfig-checker
        priority: 100
        name: run editorconfig-checker
        description: a tool to verify that your files are in harmony with your .editorconfig
        alias: ec