.pre-commit-config.yaml

# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
repos:
## general purpose linting and formatting
- repo: https://github.com/pre-commit/pre-commit-hooks
  rev: v2.4.0
  hooks:
  - id: trailing-whitespace
  - id: end-of-file-fixer
  - id: check-yaml
  - id: check-added-large-files
- repo: https://github.com/codespell-project/codespell
  rev: v1.17.1
  hooks:
  - id: codespell

## Python support
- repo: https://github.com/psf/black
  rev: 19.10b0
  hooks:
  - id: black
- repo: https://gitlab.com/PyCQA/flake8
  rev: 3.8.3
  hooks:
  - id: flake8
    exclude: ^report/
- repo: https://github.com/timothycrosley/isort
  rev: 5.5.3
  hooks:
  - id: isort


## Snakemake linting
- repo: https://github.com/snakemake/snakefmt
  rev: 0.2.4
  hooks:
  - id: snakefmt


## C++ support
- repo: https://gitlab.com/daverona/pre-commit/cpp
  rev: 0.8.0
  hooks:
  - id: clang-format
  - id: cpplint
    args: ["--includeorder=default"]
  - id: cppcheck


## R support
- repo: https://github.com/lorenzwalthert/precommit
  rev: v0.1.3
  hooks:
  - id: style-files
  - id: parsable-R
  - id: no-browser-statement
  - id: lintr
    verbose: true
## Note: the following three hooks apply only to R package development
#  - id: roxygenize
#  - id: deps-in-desc
#  - id: use-tidy-description