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
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
|
# See CONTRIBUTING.rst, we expect this to be run via a git pre-commit hook.
# You can also run the checks directly at the terminal, e.g.
#
# $ pre-commit run --all-files
#
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.3.0
hooks:
- id: check-executables-have-shebangs
files: \.(py|sh)$
- id: check-json
- id: end-of-file-fixer
files: \.py$
- id: mixed-line-ending
- repo: https://github.com/psf/black
rev: 22.10.0
hooks:
- id: black
args: [--check,--target-version,py37]
- repo: https://github.com/PyCQA/flake8
rev: 5.0.4
hooks:
- id: flake8
additional_dependencies: [
'flake8-blind-except',
'flake8-bugbear',
'flake8-comprehensions',
'flake8-docstrings',
'flake8-implicit-str-concat',
'flake8-rst-docstrings>=0.2.3',
'pydocstyle>=6.0.0',
]
- repo: https://github.com/asottile/blacken-docs
rev: v1.12.1
hooks:
- id: blacken-docs
additional_dependencies: [black==22.10.0]
exclude: ^.github/
- repo: https://github.com/myint/rstcheck
rev: v6.1.1
hooks:
- id: rstcheck
args: [
--ignore-roles=ref,
--ignore-directives=toctree,
--report-level=warning
]
- repo: https://github.com/PyCQA/doc8
rev: v1.0.0
hooks:
- id: doc8
additional_dependencies: [pygments]
args: [--quiet,--ignore-path=Doc/examples/ec_*.txt, --ignore=D004]
- repo: https://github.com/codespell-project/codespell
rev: v2.2.2
hooks:
- id: codespell
files: \.(rst|md|tex)$
args: [
--ignore-regex,
'(^|\W)([A-Z]{2,3})(\W|$)',
-L,
'ser,hsa,hist,fpr'
]
- repo: local
hooks:
- id: doi-link-style
name: Enforce https://doi.org/ style
description: Check DOI link style, see https://www.crossref.org/display-guidelines/
entry: '(?i)(doi:|dx\.doi\.org|http://doi\.org)'
language: pygrep
files: \.(rst|tex)$
ci:
# Settings for the https://pre-commit.ci/ continuous integration service
autofix_prs: false
# Default message is more verbose
autoupdate_commit_msg: '[pre-commit.ci] autoupdate'
# Default is weekly
autoupdate_schedule: quarterly
# Currently pre-commit.ci checks all files, and all hooks takes too long
# and causes a timeout - so as a short-term workaround, skip flake8 etc:
skip: [
check-json,
mixed-line-ending,
flake8,
rstcheck,
doc8,
codespell,
doi-link-style
]
|
