Jupytext in a pre-commit disagreement with trailing-whitespace and prettier

Hi,

I am trying to run jupytext as a first step in pre-commit, before running among others trailing-whitespace and prettier.

My goal is for jupytext to generate .md files based on .ipynb files, since these are easier to version control than .ipynb. The idea is that pre-commit will pass if no new .md file is added, and if no existing .md file is changed by jupytext.

The way I implemented this seems to cause a problem with two other hooks, trailing-whitespace and prettier. The way jupytext formats the .md files cause trailing-whitespace and prettier to fail and adjusting the code. Is there any way to adjust jupytext or the way I use it, so that these other hooks do not fail?

This is my file .pre-commit-config.yaml which lives in the root directory:

# NOTE: The versions can be updated by calling
#        pre-commit autoupdate
repos:
  - repo: local
    hooks:
      - id: jupytext
        name: jupytext
        entry: jupytext --to .md notebooks/*.ipynb
        files: .ipynb
        language: python

  - repo: https://github.com/psf/black
    rev: 19.10b0
    hooks:
      - id: black

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v3.1.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer

  - repo: https://gitlab.com/pycqa/flake8
    rev: 3.8.3
    hooks:
      - id: flake8
        additional_dependencies:
          - flake8-bugbear
          - flake8-docstrings

  - repo: https://github.com/prettier/prettier
    rev: 2.0.5
    hooks:
      - id: prettier
        args: [--prose-wrap=always, --print-width=88]

  - repo: local
    hooks:
      - id: pylint
        name: pylint
        entry: pylint
        language: system
        types: [python]
        additional_dependencies: ["-r requirements.txt"]

If I update an .ipynb file and run pre-commit, this happens:

Immediately re-running pre-commit causes all other notebooks to be updated by jupytext,.

[mwouts]

I would like to code up a simple pre-commit yaml for the repo

Oh, that would be awesome!

[Skylion007]

@mwouts Yeah, but my pre-commit hook downloads from pip so until it’s published I can’t remove that workaround. 👍 I do experience issues like #553, but it hasn’t broken anything, yet. Also waiting for that fix to be merged.