forked from ConorFWild/ligand_neighbourhood_alignment
-
Notifications
You must be signed in to change notification settings - Fork 0
/
pyproject.toml
125 lines (108 loc) · 3.3 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
[build-system]
requires = ["setuptools>=64", "setuptools_scm[toml]>=6.2", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "ligand_neighbourhood_alignment"
classifiers = [
"Development Status :: 3 - Alpha",
"License :: OSI Approved :: Apache Software License",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
]
description = "One line description of your module"
dependencies = [
"gemmi",
"loguru",
"pydantic==2.6.0",
"networkx",
"numpy",
"rich",
"pandas",
"fire",
"pyyaml"
] # Add project dependencies here, e.g. ["click", "numpy"]
dynamic = ["version"]
license.file = "LICENSE"
readme = "README.rst"
requires-python = ">=3.8"
[project.optional-dependencies]
dev = [
"black",
"mypy",
"flake8-isort",
"Flake8-pyproject",
"pipdeptree",
"pre-commit",
"pydata-sphinx-theme>=0.12",
"pytest-cov",
"sphinx-autobuild",
"sphinx-copybutton",
"sphinx-design",
"tox-direct",
"types-mock",
]
[project.scripts]
ligand_neighbourhood_alignment = "ligand_neighbourhood_alignment.__main__:main"
[project.urls]
GitHub = "https://github.com/ConorFWild/ligand_neighbourhood_alignment"
[[project.authors]] # Further authors may be added by duplicating this section
email = "conor.wild@sky.com"
name = "jfi22496"
[tool.setuptools_scm]
write_to = "src/ligand_neighbourhood_alignment/_version.py"
[tool.mypy]
ignore_missing_imports = true # Ignore missing stubs in imported modules
[tool.isort]
float_to_top = true
profile = "black"
[tool.flake8]
extend-ignore = [
"E203", # See https://github.com/PyCQA/pycodestyle/issues/373
"F811", # support typing.overload decorator
"F722", # allow Annotated[typ, some_func("some string")]
]
max-line-length = 119 # Respect black's line length (default 88),
exclude = [".tox", "venv"]
[tool.black]
line-length = 119
#[tool.pytest.ini_options]
## Run pytest with all our checkers, and don't spam us with massive tracebacks on error
#addopts = """
# --tb=native -vv --doctest-modules --doctest-glob="*.rst"
# --cov=ligand_neighbourhood_alignment --cov-report term --cov-report xml:cov.xml
# """
## https://iscinumpy.gitlab.io/post/bound-version-constraints/#watch-for-warnings
#filterwarnings = "error"
## Doctest python code in docs, python code in src docstrings, test functions in tests
#testpaths = "docs src tests"
[tool.pytest.ini_options]
testpaths = ['tests']
[tool.coverage.run]
data_file = "/tmp/ligand_neighbourhood_alignment.coverage"
[tool.coverage.paths]
# Tests are run from installed location, map back to the src directory
source = ["src", "**/site-packages/"]
# tox must currently be configured via an embedded ini string
# See: https://github.com/tox-dev/tox/issues/999
[tool.tox]
legacy_tox_ini = """
[tox]
skipsdist=True
[testenv:{pre-commit,mypy,pytest,docs}]
# Don't create a virtualenv for the command, requires tox-direct plugin
direct = True
passenv = *
allowlist_externals =
pytest
pre-commit
mypy
sphinx-build
sphinx-autobuild
commands =
pytest: pytest {posargs}
mypy: mypy src tests {posargs}
pre-commit: pre-commit run --all-files {posargs}
docs: sphinx-{posargs:build -EW --keep-going} -T docs build/html
"""