pyrox.dev
1{
2 lib,
3 stdenv,
4 buildPythonPackage,
5 fetchFromGitHub,
6 eigen,
7
8 # build-system
9 cython,
10 numpy,
11 packaging,
12 scikit-learn,
13 setuptools,
14 setuptools-scm,
15
16 # dependencies
17 ecos,
18 joblib,
19 numexpr,
20 osqp,
21 pandas,
22 scipy,
23
24 # tests
25 pytestCheckHook,
26}:
27
28buildPythonPackage rec {
29 pname = "scikit-survival";
30 version = "0.25.0";
31 pyproject = true;
32
33 src = fetchFromGitHub {
34 owner = "sebp";
35 repo = "scikit-survival";
36 tag = "v${version}";
37 hash = "sha256-OvdmZ2vDptYB2tq7OtokIQzjKzhQBWwnXZLW0m6FqlI=";
38 };
39
40 postPatch = ''
41 ln -s ${lib.getInclude eigen}/include/eigen3/Eigen \
42 sksurv/linear_model/src/eigen
43 '';
44
45 build-system = [
46 cython
47 numpy
48 packaging
49 scikit-learn
50 setuptools
51 setuptools-scm
52 ];
53
54 pythonRelaxDeps = [
55 "osqp"
56 ];
57 dependencies = [
58 ecos
59 joblib
60 numexpr
61 numpy
62 osqp
63 pandas
64 scikit-learn
65 scipy
66 ];
67
68 pythonImportsCheck = [ "sksurv" ];
69
70 nativeCheckInputs = [ pytestCheckHook ];
71
72 # Hack needed to make pytest + cython work
73 # https://github.com/NixOS/nixpkgs/pull/82410#issuecomment-827186298
74 preCheck = ''
75 rm -rf sksurv
76 '';
77
78 disabledTests = [
79 # very long tests, unnecessary for a leaf package
80 "test_coxph"
81 "test_datasets"
82 "test_ensemble_selection"
83 "test_minlip"
84 "test_pandas_inputs"
85 "test_survival_svm"
86 "test_tree"
87 ]
88 ++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
89 # floating point mismatch on aarch64
90 # 27079905.88052468 to far from 27079905.880496684
91 "test_coxnet"
92 ];
93
94 meta = {
95 description = "Survival analysis built on top of scikit-learn";
96 homepage = "https://github.com/sebp/scikit-survival";
97 changelog = "https://github.com/sebp/scikit-survival/releases/tag/v${version}";
98 license = lib.licenses.gpl3Plus;
99 maintainers = with lib.maintainers; [ ];
100 };
101}