This repository contains a set of custom pre-commit hooks for the Centre for Population Genomics.
Add these into your .pre-commit-config.yaml
file to use them!
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-commitexclude
.
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
.