CellSeg3D/pyproject.toml at main · AdaptiveMotorControlLab/CellSeg3D · 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
[build-system]
build-backend = "setuptools.build_meta"
requires = [
  "setuptools>=64",
  "setuptools-scm>=8",
  "wheel",
]

[project]
name = "napari-cellseg3d"
description = "Plugin for cell segmentation in 3D"
readme = "README.md"
license = { text = "MIT" }
requires-python = ">=3.10"
classifiers = [
  "Development Status :: 4 - Beta",
  "Framework :: napari",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: MIT License",
  "Operating System :: OS Independent",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering :: Artificial Intelligence",
  "Topic :: Scientific/Engineering :: Image Processing",
  "Topic :: Scientific/Engineering :: Visualization",
  "Topic :: Software Development :: Testing",
]
dynamic = [ "version" ]
dependencies = [
  # "tifffile>=2022.2.9",
  #    "imageio-ffmpeg>=0.4.5",
  "imagecodecs>=2023.3.16",
  "itk",
  "matplotlib>=3.4.1",
  "monai[einops,nibabel,tifffile]>=0.9",
  "napari[all]>=0.4.14",
  "numpy",
  # "nibabel",
  #    "pillow",
  "pyclesperanto",
  "pydensecrf2",
  "qtpy",
  # "opencv-python>=4.5.5",
  #    "dask-image>=0.6.0",
  "scikit-image>=0.19.2",
  "torch>=1.11",
  "tqdm",
]
[[project.authors]]
name = "Cyril Achard"
email = "cyril.achard@epfl.ch"
[[project.authors]]
name = "Maxime Vidal"
email = "maxime.vidal@epfl.ch"
[[project.authors]]
name = "Mackenzie Mathis"
email = "mackenzie@post.harvard.edu"
[project.entry-points."napari.manifest"]
napari-cellseg3d = "napari_cellseg3d:napari.yaml"
[project.optional-dependencies]
crf = [
  "pydensecrf2",
]
dev = [
  "pre-commit",
  "ruff",
  "twine",
]
docs = [
  "jupyter-book<2",
]
onnx-cpu = [ "onnx", "onnxruntime" ]
onnx-gpu = [ "onnx", "onnxruntime-gpu" ]
pyqt6 = [
  "napari[pyqt6]",
]
pyside6 = [
  "napari[pyside6]",
]
test = [
  "coverage",
  "onnx",
  "onnxruntime",
  "pytest",
  "pytest-cov",
  "pytest-qt",
  "tox",
  "twine",
]
wandb = [ "wandb" ]
[project.urls]
Documentation = "https://adaptivemotorcontrollab.github.io/cellseg3d-docs/res/welcome.html"
Homepage = "https://github.com/AdaptiveMotorControlLab/CellSeg3D"
Issues = "https://github.com/AdaptiveMotorControlLab/CellSeg3D/issues"

[tool.setuptools]
include-package-data = true
[tool.setuptools.package-data]
"*" = [ "res/*.png", "code_models/models/pretrained/*.json", "*.yaml", "napari.yaml" ]
[tool.setuptools.packages]
find.where = [ "." ]

[tool.setuptools_scm]
version_file = "napari_cellseg3d/_version.py"

[tool.ruff]
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",
  "docs/conf.py",
  "napari_cellseg3d/_tests/conftest.py",
  "node_modules",
  "venv",
]
[tool.ruff.lint]
select = [
  "E",
  "F",
  "W",
  "A",
  "B",
  "G",
  "I",
  "PT",
  "PTH",
  "RET",
  "SIM",
  "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)
# and 'E402' (module level import not at top of file)
ignore = [ "E501", "E741", "G004", "A003", "F401", "E402" ]
[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.pyproject-fmt]
max_supported_python = "3.12"
generate_python_version_classifiers = true
# Avoid collapsing tables to field.key = value format (less readable)
table_format = "long"