heartfm-evals/pyproject.toml at main · alan-turing-institute/heartfm-evals · 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
[build-system]
requires = ["setuptools>=61"]
build-backend = "setuptools.build_meta"

[project]
name = "heartfm-evals"
version = "0.1.0"
authors = [
  { name = "Levan Bokeria", email = "lbokeria@turing.ac.uk" },
  { name = "Camila Rangel-Smith", email = "crangelsmith@turing.ac.uk" }
]
description = "A modular package for evaluating foundation model performance on various clinical tasks involving cardiac MRI and CT images."
readme = "README.md"
requires-python = ">=3.11,<3.14"
classifiers = [
  "Development Status :: 1 - Planning",
  "Intended Audience :: Science/Research",
  "Intended Audience :: Developers",
  "License :: OSI Approved :: MIT License",
  "Operating System :: OS Independent",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Topic :: Scientific/Engineering",
]
dependencies = [
    "torch",
    "torchvision",
    "numpy<2",
    "pandas",
    "tqdm",
    "nibabel",
    "SimpleITK",
    "monai",
    "Pyyaml",
    "matplotlib",
    "hydra-core",
    "omegaconf",
    "safetensors",
    "timm",
    "einops",
    "CineMA @ git+https://github.com/alan-turing-institute/CineMA",
    "tensorboard",
    "wandb",
    "dinov3 @ git+https://github.com/facebookresearch/dinov3/",
    "ipykernel",
    "transformers",
    "seaborn>=0.13.2",
]

[project.optional-dependencies]
dev = [
  "pytest >=6",
  "pytest-cov >=3",
  "pre-commit",
  "black",
]

[project.urls]
Homepage = "https://github.com/alan-turing-institute/heartfm-evals"
"Bug Tracker" = "https://github.com/alan-turing-institute/heartfm-evals/issues"
Discussions = "https://github.com/alan-turing-institute/heartfm-evals/discussions"
Changelog = "https://github.com/alan-turing-institute/heartfm-evals/releases"

[tool.pytest.ini_options]
minversion = "6.0"
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
xfail_strict = true
filterwarnings = [
  "error",
]
log_cli_level = "INFO"
testpaths = [
  "tests",
]

[tool.coverage]
run.source = ["heartfm_evals"]
port.exclude_lines = [
  'pragma: no cover',
  '\.\.\.',
  'if typing.TYPE_CHECKING:',
]


[tool.ruff]
src = ["src"]
exclude = []
line-length = 88  # how long you want lines to be

[tool.ruff.format]
docstring-code-format = true  # code snippets in docstrings will be formatted

[tool.ruff.lint]
select = [
  "E", "F", "W", # flake8
  "B",           # flake8-bugbear
  "I",           # isort
  "ARG",         # flake8-unused-arguments
  "C4",          # flake8-comprehensions
  "ICN",         # flake8-import-conventions
  "ISC",         # flake8-implicit-str-concat
  "PGH",         # pygrep-hooks
  "PIE",         # flake8-pie
  "PL",          # pylint
  "PT",          # flake8-pytest-style
  "SIM",         # flake8-simplify
  "UP",          # pyupgrade
  "YTT",         # flake8-2020
  "EXE",         # flake8-executable
]
ignore = [
  "PLR",    # Design related pylint codes
  "ISC001", # Conflicts with formatter
  "E501",   # Line too long
  "SIM102", # Nested if statements
  "SIM117", # Nested with statements
  "E731",   # Lambda assignment
  "E402",   # Module-level import not at top of file
]
unfixable = [
  "F401",   # Would remove unused imports
  "F841",   # Would remove unused variables
]
flake8-unused-arguments.ignore-variadic-names = true  # allow unused *args/**kwargs

[tool.mypy]
ignore_missing_imports = true

[tool.hatch.metadata]
allow-direct-references = true