Pre-commits

This repository contains a set of custom pre-commit hooks for the Centre for Population Genomics.

Usage

Add these into your .pre-commit-config.yaml file to use them!

cpg-id-checker

Automatically checks for CPG IDs in your repository. You can extend this check by adding --extra-pattern 'REGEX' into the args:, see the example below:

- repo: https://github.com/populationgenomics/pre-commits
rev: "v0.1.3"
hooks:
    - id: cpg-id-checker
    args: ["--extra-pattern", 'ABC\d+']

Note that this will only check some string based files, and will skip a file if it's detected to be a binary file.

Arguments:

• --extra-pattern <value>: A python flavoured regex to match lines for, any matches will cause the pre-commit to return exitcode = 1.
• --ignore-filename-format <value>: A python flavoured regex to ignore filenames that match this format. Consider using the pre-commit exclude.

How a hook is set up

Each pre-commit hook is:

• a file inside the pre_commit_hooks folder,

• then installed as an entrypoint in the setup.py, eg:

  setup(
      # ...
      entry_points={
          "console_scripts": [
              "cpg-id-checker = pre_commit_hooks.cpg_id_checker:main"
          ],
      },
  )

• Added as an available option (based on the console-script name) in the .pre-commit-hooks.yaml.