pyVertexModel/pyproject.toml at main · Pablo1990/pyVertexModel · 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
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
[build-system]
build-backend = "setuptools.build_meta"
requires = [
    "setuptools",
    "setuptools-scm",
    "cython",
    "wheel",
    "numpy",
]

[project]
name = "pyVertexModel"
dynamic = [
    "version",
]
description = "A versatile 3D vertex model for modeling tissue and cell mechanics, particularly for tissue repair simulations."
readme = "README.md"
license = {text = "MIT"}
authors = [
    {name = "Pablo Vicente-Munuera", email = "p.munuera@ucl.ac.uk"},
]
requires-python = ">=3.9"
keywords = [
    "biophysics",
    "cell mechanics",
    "computational biology",
    "tissue mechanics",
    "tissue repair",
    "vertex model",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Cython",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Physics",
]
dependencies = [
    "cython",
    "numpy",
    "scipy",
    "pillow",
    "scikit-image",
    "cython",
    "vtk",
    "pandas",
    "networkx",
    "pyvista",
    "scikit-learn",
    "matplotlib",
    "seaborn",
]

[project.urls]
"Bug Tracker" = "https://github.com/Pablo1990/pyVertexModel/issues"
"Homepage" = "https://github.com/Pablo1990/pyVertexModel"
"Source" = "https://github.com/Pablo1990/pyVertexModel"

[tool.setuptools_scm]
local_scheme = "no-local-version"
write_to = "src/pyVertexModel/_version.py"

[tool.coverage]
report = {skip_covered = true, sort = "cover"}
run = {branch = true, parallel = true, source = [
    "pyVertexModel",
], omit = [
    "src/pyVertexModel/main.py",
    "src/pyVertexModel/main_*.py",
    "src/pyVertexModel/analysis/*",
    "src/pyVertexModel/util/space_exploration.py",
]}
paths.source = [
    "src",
    ".tox*/*/lib/python*/site-packages",
    ".tox*\\*\\Lib\\site-packages",
]
[tool.pytest.ini_options]
addopts = "--color=yes -v"
testpaths = [
    "Tests",
]

[tool.ruff]
fix = true
force-exclude = true
ignore = [
    "B905", # set 'strict=' for zip
    "SIM105", # use contextlib.suppress(IndexError)
]
per-file-ignores = {"__init__.py" = [
    "F401", # unused-import
], "test_*.py" = [
    "S101", # use of 'assert'
]}
select = [
    "A",
    "B",
    "C",
    "DTZ",
    "E",
    "EM",
    "F",
    "FBT",
    "I",
    "ICN",
    "ISC",
    "N",
    "PLC",
    "PLE",
    "PLR",
    "PLW",
    "Q",
    "RUF",
    "S",
    "SIM",
    "T",
    "TID",
    "UP",
    "W",
    "YTT",
]
target-version = "py39"

[tool.tomlsort]
all = true
spaces_indent_inline_array = 4
trailing_comma_inline_array = true
overrides."project.classifiers".inline_arrays = false
overrides."tool.coverage.paths.source".inline_arrays = false
overrides."tool.ruff.isort.section-order".inline_arrays = false

[tool.tox]
legacy_tox_ini = """
    [gh-actions]
    python =
        3.9: py39
        3.10: py310

    [gh-actions:env]
    PLATFORM =
        macos-latest: macos
        ubuntu-latest: linux
        windows-latest: windows

    [testenv]
    platform =
        linux: linux
        macos: darwin
        windows: win32
    passenv =
        CI
        DISPLAY
        GITHUB_ACTIONS
        NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
        PYVISTA_OFF_SCREEN
        XAUTHORITY
    deps =
        pyqt5
        pytest-cov
        pytest-qt
    commands = pytest --cov --cov-report=lcov

    [tox]
    envlist = py3{9,10}-{linux,macos,windows}
    isolated_build=true
"""