cardiotensor/pyproject.toml at main · JosephBrunet/cardiotensor · 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
[build-system]
build-backend = "setuptools.build_meta"
requires = [
    "setuptools",
    "setuptools-scm",
]

[project]
authors = [{email = "j.brunet@ucl.ac.uk", name = "Joseph Brunet"}]
classifiers = [
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: MIT License",
]
dependencies = [
    "PyQt5",
    "SimpleITK",
    "alive_progress",
    "dask",
    "dipy",
    "fury",
    "glymur",
    "imagecodecs",
    "matplotlib",
    "nibabel",
    "numpy>=1.20",
    "opencv-python-headless",
    "pandas",
    "psutil",
    "scikit-image",
    "structure-tensor>=0.3.0",
    "tifffile",
    "tqdm",
]
description = "Toolkit designed for quantifying and visualising 3D cardiomyocytes orientations in heart images"
keywords = ["cardiotensor, cardiomyocytes, heart, orientation, structure tensor, image processing"]
license = {file = "LICENSE"}
name = "cardiotensor"
readme = "README.md"
requires-python = ">=3.10"
version = "1.1.8"

[project.optional-dependencies]
cupy = ["cupy>=8"]
dev = [
    "black",
    "pre-commit",
    "pytest",
    "pytest-cov",
    "ruff",
]
docs = [
    "mkdocs-autorefs",
    "mkdocs-git-revision-date-localized-plugin",
    "mkdocs-material",
    "mkdocs-section-index",
    "mkdocs<2",
    "mkdocstrings[python]",
    "pymdown-extensions",
]
git = [
    "mkdocs-git-committers-plugin-2>=1.1,<3",
    "mkdocs-git-revision-date-localized-plugin~=1.2,>=1.2.4",
    "mkdocstrings-python",
]

[project.scripts]
cardio-analysis = "cardiotensor.scripts.gui_analysis_tool:script"
cardio-analysis-histo = "cardiotensor.scripts.analysis_histograms:script"
cardio-analysis-streamlines = "cardiotensor.scripts.analysis_streamlines:script"
cardio-generate-streamlines = "cardiotensor.scripts.generate_streamlines:script"
cardio-tensor = "cardiotensor.scripts.compute_orientation:script"
cardio-tensor-slurm = "cardiotensor.scripts.slurm_launcher:script"
cardio-trk_2_am = "cardiotensor.scripts.convert_trk_to_am:script"
cardio-visualize-streamlines = "cardiotensor.scripts.visualize_streamlines:script"
cardio-visualize-vector = "cardiotensor.scripts.visualize_vector_field:script"

[project.urls]
Documentation = "https://www.josephbrunet.fr/cardiotensor/"
Issues = "https://github.com/JosephBrunet/cardiotensor/issues"
Repository = "https://github.com/JosephBrunet/cardiotensor"

[tool.black]
line-length = 88
target-version = ["py311"]

[tool.coverage.report]
show_missing = true
skip_covered = true

[tool.coverage.run]
branch = true
source = ["src/cardiotensor"]

[tool.mypy]
plugins = [
    "pydantic.mypy",
]

[[tool.mypy.overrides]]
ignore_missing_imports = true
module = "glymur.*"

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

[tool.ruff]
fix = true
force-exclude = true
target-version = "py312"
lint.select = ["F", "I", "UP"]
lint.mccabe.max-complexity = 10
lint.pep8-naming.classmethod-decorators = ["classmethod", "pydantic.validator"]

[tool.tomlsort]
all = true
spaces_indent_inline_array = 4
trailing_comma_inline_array = true
overrides."project.classifiers".inline_arrays = false