pygfa/pyproject.toml at main · AlgoLab/pygfa · 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
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
[project]
authors = [{name = "Gianluca Della Vedova", email = "gianluca@dellavedova.org"}]
dependencies = [
    "networkx>=3.6.1,<4",
    "lark>=1.3.1,<2",
    "biopython>=1.86,<2",
    "numpy>=2.4.0,<3",
    "zstandard>=0.22.0",
    "lz4>=4.0.0",
    "brotli>=1.1.0",
]
name = "pygfa"
requires-python = ">= 3.14"
version = "0.1.0"

[project.optional-dependencies]
dev = [
    "pytest>=9.0.2,<10",
    "pytest-cov>=6.0.0,<7",
    "ruff>=0.8.0,<1",
    "mypy>=1.13.0,<2",
    "coverage>=7.0.0,<8",
]

[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]

[tool.pixi.workspace]
channels = ["conda-forge", "bioconda"]
platforms = ["linux-64"]

[tool.pixi.pypi-dependencies]
pygfa = { path = ".", editable = true }

[tool.pixi.tasks]

[tool.pixi.dependencies]
python = ">=3.14.0,<3.15"
numpy = ">=2.4.0,<3"
lark = ">=1.3.1,<2"
networkx = ">=3.6.1,<4"
biopython = ">=1.86,<2"
pytest = ">=9.0.2,<10"
toml = ">=0.10.2,<0.11"
ruff = ">=0.15.0,<0.16"
mypy = ">=1.19.1,<2"
zstandard = ">=0.22.0"
lz4 = ">=4.0.0"
brotli = ">=1.1.0"
pytest-xdist = ">=3.8.0,<4"
pytest-memray = ">=1.8.0,<2"
pytest-cov = ">=6.0.0,<7"

[tool.ruff]
line-length = 120
target-version = "py314"

[tool.mypy]
python_version = "3.14"
warn_return_any = true
warn_unused_ignores = true
disallow_untyped_defs = true

[tool.coverage.run]
source = ["pygfa"]
omit = [
    "*/tests/*",
    "*/test_*",
    "*__pycache__*",
    "*/site-packages/*",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "@abstractmethod",
]
precision = 2
show_missing = true

[tool.coverage.html]
directory = "results/test/htmlcov"

[tool.pytest.ini_options]
testpaths = ["test"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "-v",
    "-s",
    "--full-trace",
    "--tb=long",
    "--strict-markers",
    "--color=yes"
]
log_cli = true
log_cli_level = "DEBUG"
log_cli_format = "%(asctime)s [%(levelname)8s] %(name)s: %(filename)s:%(lineno)d: %(message)s"