nbis-project-admin/.pre-commit-config.yaml at main · percyfal/nbis-project-admin · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      - id: check-merge-conflict
      - id: check-added-large-files
      - id: debug-statements
      - id: mixed-line-ending
      - id: check-case-conflict
      - id: check-yaml
      - id: trailing-whitespace
      - id: end-of-file-fixer
  - repo: https://github.com/astral-sh/ruff-pre-commit
    # Ruff version.
    rev: v0.11.4
    hooks:
      # Run the linter.
      - id: ruff
        args: [ --fix ]
      # Run the formatter.
      - id: ruff-format
  - repo: https://github.com/snakemake/snakefmt
    rev: v0.11.0
    hooks:
      - id: snakefmt
  - repo: https://github.com/DavidAnson/markdownlint-cli2
    rev: v0.17.2
    hooks:
      - id: markdownlint-cli2
        files: \.(md|qmd)$
        types: [file]
        exclude: LICENSE.md
  - repo: local
    hooks:
      - id: lint
        name: Snakemake lint
        entry: snakemake --lint text -s
        language: system
        files: ".*.smk$|.*Snakefile$"
      - id: pylint
        name: pylint
        entry: pylint
        language: system
        types: [python]
        args: [
            "-rn", # Only display messages
            "-sn", # Don't display the score
          ]