-
Notifications
You must be signed in to change notification settings - Fork 0
/
pyproject.toml
155 lines (143 loc) · 4.47 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
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
[tool.poetry]
name = "prymer"
version = "2.2.0"
description = "Python primer design library"
readme = "README.md"
authors = [
"Yossi Farjoun <[email protected]>",
"Jeff Gentry <[email protected]>",
"Tim Fennell <[email protected]>",
"Nils Homer <[email protected]>",
"Erin McAuley <[email protected]>",
"Matt Stone <[email protected]>",
]
license = "MIT"
homepage = "https://github.com/fulcrumgenomics/prymer"
repository = "https://github.com/fulcrumgenomics/prymer"
documentation = "https://github.com/fulcrumgenomics/prymer"
keywords = ["bioinformatics", "genomics", "dna"]
classifiers = [
"Development Status :: 3 - Alpha",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Environment :: Console",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Software Development :: Documentation",
"Topic :: Software Development :: Libraries :: Python Modules",
]
include = ["LICENSE"]
[tool.poetry.dependencies]
python = "^3.11"
pyproject_hooks= "^1.0.0,!=1.1.0"
pybedlite = "1.0.0"
strenum = "^0.4.15"
fgpyo = "0.7.1"
pysam = "^0.22.1"
ordered-set = "^4.1.0"
[tool.poetry.group.dev.dependencies]
poetry = "^1.8.2"
mypy = "^1.5.1"
pytest = "^7.4.4"
pytest-cov = "^4.1.0"
pytest-mypy = "^0.10.3"
pytest-ruff = "^0.3.1"
ruff = "0.3.3"
# dependencies for building docs
mkdocs-autorefs = { version = ">=0.5.0,<1.1.0" }
mkdocs-include-markdown-plugin = { version = ">=6.0.1" }
mkdocs-material = { version = ">=9.2.8" }
mkdocs-table-reader-plugin = { version = ">=2.0.1" }
mkdocs = { version = ">=1.5.2" }
mkdocs-gen-files = { version = ">=0.5.0" }
mkdocs-literate-nav = { version = ">=0.6.1" }
mkdocs-section-index = { version = ">=0.3.9" }
mkdocstrings-python = { version = ">=1.6.2" }
mkdocstrings = { version = ">=0.23.0" }
black = "^24.4.2"
pytest-doctestplus = "^1.2.1"
[tool.poetry.urls]
"Bug Tracker" = "https://github.com/fulcrumgenomics/prymer/issues"
[build-system]
requires = ["poetry-core>=1.6"]
build-backend = "poetry.core.masonry.api"
[tool.git-cliff.changelog]
header = ""
trim = true
body = """
{% for group, commits in commits | group_by(attribute="group") %}
## {{ group | upper_first }}
{% for commit in commits %}
- {{ commit.message | upper_first }} ({{ commit.id | truncate(length=8, end="") }})\
{% endfor %}
{% endfor %}\n
"""
[tool.git-cliff.git]
conventional_commits = true
commit_parsers = [
{ message = "^.+!:*", group = "Breaking"},
{ message = "^feat*", group = "Features"},
{ message = "^fix*", group = "Bug Fixes"},
{ message = "^docs*", group = "Documentation"},
{ message = "^perf*", group = "Performance"},
{ message = "^refactor*", group = "Refactor"},
{ message = "^style*", group = "Styling"},
{ message = "^test*", group = "Testing"},
{ message = "^chore\\(release\\):*", skip = true},
{ message = "^chore*", group = "Miscellaneous Tasks"},
{ body = ".*security", group = "Security"}
]
filter_commits = false
[tool.mypy]
files = ["prymer", "tests"]
python_version = "3.11"
strict_optional = false
check_untyped_defs = true
disallow_incomplete_defs = true
disallow_untyped_calls = true
disallow_untyped_decorators = true
disallow_untyped_defs = true
no_implicit_optional = true
warn_no_return = true
warn_redundant_casts = true
warn_return_any = true
warn_unreachable = true
warn_unused_configs = true
warn_unused_ignores = true
[[tool.mypy.overrides]]
module = "defopt"
ignore_missing_imports = true
[tool.pytest.ini_options]
minversion = "7.4"
addopts = [
"--ignore=docs/scripts",
"--color=yes",
"--cov",
"--cov-report=xml",
"--cov-branch",
"--mypy",
"--ruff",
"--doctest-plus",
"--doctest-modules",
"-v"
]
doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
doctest_plus = "enabled"
testpaths = [
"prymer", "tests"
]
[tool.ruff]
include = ["prymer/**/*.py", "tests/**/*.py"]
line-length = 100
target-version = "py311"
output-format = "full"
[tool.ruff.lint]
select = ["C901", "B", "E", "F", "I", "W", "Q"]
ignore = ["E203", "E701"]
unfixable = ["B"]
[tool.ruff.lint.isort]
force-single-line = true