forked from biocypher/biocypher
-
Notifications
You must be signed in to change notification settings - Fork 0
/
pyproject.toml
125 lines (116 loc) · 2.9 KB
/
pyproject.toml
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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
[tool.poetry]
name = "biocypher"
version = "0.4.1"
description = "Graph database standard for molecular biology"
authors = [
"Sebastian Lobentanzer <[email protected]>",
"Denes Turei <[email protected]>"
]
license = "GPL-3.0-only"
packages = [
{ include = "biocypher" }
]
classifiers = [
"Development Status :: 2 - Pre-Alpha",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Natural Language :: English",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
repository = "https://github.com/saezlab/biocypher"
readme = "README.md"
[tool.poetry.dependencies]
python = "^3.9"
neo4j = ">=4.4.0"
PyYAML = ">=5.0"
click = ">=7.0"
bmt = "0.8.12"
# bmt = { path = "../biolink-model-toolkit/", develop = true }
more_itertools = "*"
toml = "*"
appdirs = "*"
neo4j-utils = { git = "https://github.com/saezlab/neo4j-utils.git", tag = "v0.0.6" }
# for local development one can switch to local path:
# neo4j-utils = { path = "../neo4j-utils/", develop = true }
myst-parser = "^0.18.0"
matplotlib = "^3.5.2"
yapf = "^0.32.0"
pre-commit = "^2.20.0"
treelib = "^1.6.1"
obonet = "^0.3.1"
[tool.poetry.dev-dependencies]
pytest = ">=6.0"
tox = ">=3.20.1"
pre-commit = ">=2.17.0"
bump2version = "*"
coverage = ">=6.0"
sphinx = ">=5.0.0"
sphinx-rtd-theme = ">=1.0.0"
sphinx-last-updated-by-git = ">=0.3"
sphinx-autodoc-typehints = ">=1.18.0"
pytest-cov = "^3.0.0"
hypothesis = "^6.50.1"
isort = "^5.10.1"
[tool.poetry.group.dev.dependencies]
ipython = "^8.7.0"
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.poetry.urls]
"Bug Tracker" = "https://github.com/saezlab/biocypher/issues"
[tool.black]
line-length = 80
target-version = ['py310']
include = '\.pyi?$'
exclude = '''
(
/(
\.eggs
| \.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
)
'''
[tool.isort]
from_first = true
line_length = 79
multi_line_output = 3
include_trailing_comma = true
use_parentheses = true
known_num="numpy,pandas"
sections = "FUTURE,STDLIB,THIRDPARTY,NUM,FIRSTPARTY,LOCALFOLDER"
no_lines_before="LOCALFOLDER"
balanced_wrapping = true
force_grid_wrap = 0
length_sort = "1"
indent = " "
profile = "black"
[tool.flake8]
ignore = ["D200", "D202", "D401", "D105", "W504"]
per-file-ignores = [
"docs/source/conf.py:D100",
"tests/*:D100,D101,D102",
"*/__init__.py:F401"
]
max-line-length = 80
count = true
[tool.yapf]
based_on_style = "facebook"
split_penalty_before_if_expr = 0
split_penalty_import_names = 0
split_penalty_comprehension = 0
split_penalty_for_added_line_split = 0
split_penalty_after_opening_bracket = 0
split_before_first_argument = true
split_before_named_assigns = true
split_complex_comprehension = true