pyrox.dev
1{
2 lib,
3 stdenv,
4 buildPythonPackage,
5 fetchFromGitHub,
6
7 # build-system
8 uv-build,
9
10 # dependencies
11 deprecated,
12 einops,
13 humanize,
14 nibabel,
15 numpy,
16 packaging,
17 rich,
18 scipy,
19 simpleitk,
20 torch,
21 tqdm,
22 typer,
23
24 # optional dependencies
25 colorcet,
26 matplotlib,
27 pandas,
28 ffmpeg-python,
29 scikit-learn,
30
31 # tests
32 parameterized,
33 pytestCheckHook,
34}:
35
36buildPythonPackage rec {
37 pname = "torchio";
38 version = "0.20.22";
39 pyproject = true;
40
41 src = fetchFromGitHub {
42 owner = "TorchIO-project";
43 repo = "torchio";
44 tag = "v${version}";
45 hash = "sha256-LP0hlle8BCoZrJWs5aX/xvI+EPHdOGBARoKwQRqswQc=";
46 };
47
48 build-system = [
49 uv-build
50 ];
51
52 dependencies = [
53 deprecated
54 einops
55 humanize
56 nibabel
57 numpy
58 packaging
59 rich
60 scipy
61 simpleitk
62 torch
63 tqdm
64 typer
65 ];
66
67 optional-dependencies = {
68 csv = [ pandas ];
69 plot = [
70 colorcet
71 matplotlib
72 ];
73 video = [ ffmpeg-python ];
74 sklearn = [ scikit-learn ];
75 };
76
77 nativeCheckInputs = [
78 matplotlib
79 parameterized
80 pytestCheckHook
81 ];
82
83 disabledTests = [
84 # tries to download models:
85 "test_load_all"
86 ]
87 ++ lib.optionals stdenv.hostPlatform.isAarch64 [
88 # RuntimeError: DataLoader worker (pid(s) <...>) exited unexpectedly
89 "test_queue_multiprocessing"
90 ];
91
92 pythonImportsCheck = [
93 "torchio"
94 "torchio.data"
95 ];
96
97 meta = {
98 description = "Medical imaging toolkit for deep learning";
99 homepage = "https://docs.torchio.org";
100 changelog = "https://github.com/TorchIO-project/torchio/blob/${src.tag}/CHANGELOG.md";
101 license = lib.licenses.asl20;
102 maintainers = [ lib.maintainers.bcdarwin ];
103 };
104}