.pre-commit-config.yaml

ci:
    autofix_commit_msg: |
        [pre-commit.ci] auto fixes from pre-commit.com hooks

        for more information, see https://pre-commit.ci
    autofix_prs: true
    autoupdate_branch: ''
    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
    autoupdate_schedule: weekly
    submodules: false


repos:

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.1.0
    hooks:
      - id: trailing-whitespace
        exclude:  docs
      - id: end-of-file-fixer
        exclude: docs
      - id: check-yaml
        args: ["--unsafe"]
      - id: check-added-large-files
        exclude: docs

  - repo: https://github.com/psf/black
    rev: 22.3.0
    hooks:
      - id: black
        name: Fixes formatting
        language_version: python3
        args: ["--line-length=120"]


  - repo: https://github.com/pycqa/flake8.git
    rev: 3.8.4
    hooks:
      - id: flake8
        name: Checks pep8 style
        args: [
          "--max-line-length=120",
          # Ignore imports in init files
          "--per-file-ignores=
            */__init__.py:F401,setup.py:E121
            versioneer.py:W605
            */sphinx*/conf.py:E402
            pygromos/analysis/free_energy_calculation.py:W605
            ",
          # ignore long comments (E501), as long lines are formatted by black
          # ignore Whitespace before ':' (E203)
          # ignore lambdas (E731)
          # ignore Line break occurred before a binary operator (W503)
          # needed to not remove * imports (for example in _all_blocks.py)
          "--ignore=E501,E203, E731,W503,F405",
        ]

  - repo: local
    hooks:
      - id: jupyisort
        name: Sorts ipynb imports
        entry: jupytext --pipe-fmt ".py" --pipe "isort - --multi-line=3 --trailing-comma --force-grid-wrap=0 --use-parentheses --line-width=99" --sync
        files: \.ipynb$
        language: python
        stages: [push]

      - id: jupyblack
        name: Fixes ipynb format
        entry: jupytext --pipe-fmt ".py" --pipe "black - --line-length=120" --sync
        files: \.ipynb$
        language: python
        stages: [push]

      # - id: nbconvert
      #   name: Removes ipynb content
      #   entry: jupyter nbconvert
      #   args:
      #     [
      #       "--ClearOutputPreprocessor.enabled=True",
      #       "--ClearMetadataPreprocessor.enabled=True",
      #       "--RegexRemovePreprocessor.enabled=True",
      #       "--to=notebook",
      #       "--log-level=ERROR",
      #       "--inplace",
      #     ]
      #   files: \.ipynb$
      #   language: python