sc2ts/pyproject.toml at 19545b260d9d17beeb6b01904d7b2707143a0de6 · tskit-dev/sc2ts · 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
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
[project]
name = "sc2ts"
description = "Infer ARGs for SARS-Cov2 in tskit format"
readme = "README.md"
license = {file = "LICENSE"}
authors = [
  {name = "Jerome Kelleher", email = "jerome.kelleher@bdi.ox.ac.uk"},
]
requires-python = ">=3.11"
dependencies = [
  "tskit>=1.0.0",
  "tszip",
  "pandas",
  "tqdm",
  "click>=8.2",
  # Not strictly needed for base functionality, but easier to include
  # as imported by the CLI
  "tomli",
  "humanize",
]
dynamic = ["version"]

[project.urls]
Homepage = "https://tskit.dev/sc2ts"
Documentation = "https://tskit.dev/sc2ts/docs/"
"Bug Tracker" = "https://github.com/tskit-dev/sc2ts/issues"
GitHub = "https://github.com/tskit-dev/sc2ts/"

[project.scripts]
sc2ts = "sc2ts.cli:cli"

# NOTE: project.optional-dependencies and the dependency-groups below
# cannot be deduplicated as they serve different purposes.
[project.optional-dependencies]
inference = [
  "scipy",
  "biotite",
  "tsinfer>=0.5,<1",
  "pyfaidx",
  "numba",
  "zarr<3", # No point in supporting zarr3 until tsinfer updated
]
debug = [
  "matplotlib",
  "IPython",
]

[dependency-groups]
test = [
  "msprime",
  "pytest",
  "pytest-cov",
  "pytest-xdist",
  "xarray",
  "tomli-w",
  # inference and debug deps needed by the test suite
  "scipy",
  "biotite",
  "tsinfer>=0.5,<1",
  "pyfaidx",
  "numba",
  "matplotlib",
  "IPython",
]
docs = [
  "jupyter-book<2",
  "sphinx-book-theme",
  "sphinx-copybutton",
  "sphinx-click",
  "sphinx-argparse",
  "sphinx-issues",
  "IPython",
  # docs require running the CLI, which means the full inference deps are needed
  "scipy",
  "biotite",
  "tsinfer>=0.5",
  "pyfaidx",
  "numba",
]
lint = [
  "ruff==0.15.1",
  "prek==0.3.3",
]
packaging = [
  "twine",
  "validate-pyproject[all]",
]
dev = [
  {include-group = "docs"},
  {include-group = "lint"},
  {include-group = "test"},
  {include-group = "packaging"},
]

[build-system]
requires = [
    "setuptools>=42",
    "setuptools_scm",
    "wheel",
]
build-backend = "setuptools.build_meta"

[tool.setuptools]
packages = ["sc2ts"]

[tool.setuptools_scm]
write_to = "sc2ts/_version.py"

[tool.pytest.ini_options]
testpaths = "tests"

[tool.ruff]
target-version = "py311"
line-length = 89

[tool.ruff.lint]
select = ["E", "F", "B", "W", "I", "N", "UP", "A", "PT"]
fixable = ["ALL"]


ignore = [
    "A001", "A002", "RUF",
    "B905", #Don't add strict=False to zips (B905)
    "E741", # using 'l' as a variable name
    "N806", "N802", "N803", # Various nags about uppercase vars
    "F821", # Undefined name `List`
    "B006", # Do not use mutable data structures for argument defaults
    "E721", # Use `is` and `is not` for type comparisons, or `isinstance()`
    "F841", # Local variable `shape` is assigned to but never
    "PT018", # Assertion should be broken down into multiple parts
    "B007", # Loop control variable `j` not used within
    "PT006", # Wrong type passed to first argument of `pytest.mar
    "PT007", # Wrong values type in `pytest.mark.parametrize`
    "PT009", # Use a regular `assert` instead of unittest-style
]