-
Notifications
You must be signed in to change notification settings - Fork 12
/
pyproject.toml
170 lines (160 loc) · 3.53 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
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
[project]
name = "napari_cellseg3d"
authors = [
{name = "Cyril Achard", email = "[email protected]"},
{name = "Maxime Vidal", email = "[email protected]"},
{name = "Mackenzie Mathis", email = "[email protected]"},
]
readme = "README.md"
description = "Plugin for cell segmentation in 3D"
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"Framework :: napari",
"Topic :: Software Development :: Testing",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Operating System :: OS Independent",
"License :: OSI Approved :: MIT License",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"Topic :: Scientific/Engineering :: Image Processing",
"Topic :: Scientific/Engineering :: Visualization",
]
license = {text = "MIT"}
requires-python = ">=3.8"
dependencies = [
"numpy",
"napari[all]>=0.4.14",
"QtPy",
# "opencv-python>=4.5.5",
# "dask-image>=0.6.0",
"scikit-image>=0.19.2",
"matplotlib>=3.4.1",
"tifffile>=2022.2.9",
# "imageio-ffmpeg>=0.4.5",
"imagecodecs>=2023.3.16",
"torch>=1.11",
"monai[nibabel,einops]>=0.9.0",
"itk",
"tqdm",
# "nibabel",
# "pillow",
"pyclesperanto-prototype",
"tqdm",
"matplotlib",
]
dynamic = ["version", "entry-points"]
[project.urls]
Homepage = "https://github.com/AdaptiveMotorControlLab/CellSeg3D"
Documentation = "https://adaptivemotorcontrollab.github.io/cellseg3d-docs/res/welcome.html"
Issues = "https://github.com/AdaptiveMotorControlLab/CellSeg3D/issues"
[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"
[tool.setuptools]
include-package-data = true
[tool.setuptools.packages.find]
where = ["."]
[tool.setuptools.package-data]
"*" = ["res/*.png", "code_models/models/pretrained/*.json", "*.yaml"]
[tool.ruff]
select = [
"E", "F", "W",
"A",
"B",
"D",
"G",
"I",
"PT",
"PTH",
"RET",
"SIM",
"TCH",
"NPY",
]
# Never enforce `E501` (line length violations) and 'E741' (ambiguous variable names)
# and 'G004' (do not use f-strings in logging)
# and 'A003' (Shadowing python builtins)
# and 'F401' (imported but unused)
ignore = ["E501", "E741", "G004", "A003", "F401"]
exclude = [
".bzr",
".direnv",
".eggs",
".git",
".git-rewrite",
".hg",
".mypy_cache",
".nox",
".pants.d",
".pytype",
".ruff_cache",
".svn",
".tox",
".venv",
"__pypackages__",
"_build",
"buck-out",
"build",
"dist",
"node_modules",
"venv",
"docs/conf.py",
"napari_cellseg3d/_tests/conftest.py",
]
[tool.ruff.pydocstyle]
convention = "google"
[tool.black]
line-length = 79
[tool.isort]
profile = "black"
line_length = 79
[project.optional-dependencies]
crf = [
# "pydensecrf@git+https://github.com/lucasb-eyer/pydensecrf.git#egg=master",
]
pyqt5 = [
"pyqt5",
]
pyside2 = [
"pyside2",
]
pyside6 = [
"pyside6",
]
onnx-cpu = [
"onnx",
"onnxruntime"
]
onnx-gpu = [
"onnx",
"onnxruntime-gpu"
]
wandb = [
"wandb"
]
dev = [
"isort",
"black",
"ruff",
"pre-commit",
"tuna",
"twine",
]
docs = [
"jupyter-book",
]
test = [
"pytest",
"pytest_qt",
"pytest-cov",
"coverage",
"tox",
"twine",
# "pydensecrf@git+https://github.com/lucasb-eyer/pydensecrf.git#egg=master",
"onnx",
"onnxruntime",
]