pyrox.dev
1{
2 stdenv,
3 lib,
4 buildPythonPackage,
5 fetchFromGitHub,
6 cython,
7 ecos,
8 eigen,
9 joblib,
10 numexpr,
11 numpy,
12 osqp,
13 pandas,
14 setuptools-scm,
15 scikit-learn,
16 scipy,
17 pytestCheckHook,
18}:
19
20buildPythonPackage rec {
21 pname = "scikit-survival";
22 version = "0.24.1";
23 pyproject = true;
24
25 src = fetchFromGitHub {
26 owner = "sebp";
27 repo = "scikit-survival";
28 tag = "v${version}";
29 hash = "sha256-El5q2eE6wJKg/8rcFZPZQl7MVxw1jMsggjiCJHj7il8=";
30 };
31
32 nativeBuildInputs = [
33 cython
34 setuptools-scm
35 ];
36
37 propagatedBuildInputs = [
38 ecos
39 joblib
40 numexpr
41 numpy
42 osqp
43 pandas
44 scikit-learn
45 scipy
46 ];
47
48 pythonImportsCheck = [ "sksurv" ];
49
50 nativeCheckInputs = [ pytestCheckHook ];
51
52 postPatch = ''
53 ln -s ${lib.getInclude eigen}/include/eigen3/Eigen \
54 sksurv/linear_model/src/eigen
55 '';
56
57 # Hack needed to make pytest + cython work
58 # https://github.com/NixOS/nixpkgs/pull/82410#issuecomment-827186298
59 preCheck = ''
60 export HOME=$(mktemp -d)
61 cp -r $TMP/$sourceRoot/tests $HOME
62 pushd $HOME
63 '';
64 postCheck = "popd";
65
66 # very long tests, unnecessary for a leaf package
67 disabledTests =
68 [
69 "test_coxph"
70 "test_datasets"
71 "test_ensemble_selection"
72 "test_minlip"
73 "test_pandas_inputs"
74 "test_survival_svm"
75 "test_tree"
76 ]
77 ++ lib.optional (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64)
78 # floating point mismatch on aarch64
79 # 27079905.88052468 to far from 27079905.880496684
80 "test_coxnet";
81
82 meta = with lib; {
83 description = "Survival analysis built on top of scikit-learn";
84 homepage = "https://github.com/sebp/scikit-survival";
85 license = licenses.gpl3Only;
86 maintainers = with maintainers; [ GuillaumeDesforges ];
87 };
88}