pyrox.dev
1{
2 stdenv,
3 lib,
4 buildPythonPackage,
5 fetchPypi,
6 cython,
7 ecos,
8 joblib,
9 numexpr,
10 numpy,
11 osqp,
12 pandas,
13 setuptools-scm,
14 scikit-learn,
15 scipy,
16 pytestCheckHook,
17}:
18
19buildPythonPackage rec {
20 pname = "scikit-survival";
21 version = "0.22.2";
22 pyproject = true;
23
24 src = fetchPypi {
25 inherit pname version;
26 hash = "sha256-DpyGdQwN4VgGYmdREJlPB6NWiVWu8Ur4ExbysxADMr8=";
27 };
28
29 nativeBuildInputs = [
30 cython
31 setuptools-scm
32 ];
33
34 propagatedBuildInputs = [
35 ecos
36 joblib
37 numexpr
38 numpy
39 osqp
40 pandas
41 scikit-learn
42 scipy
43 ];
44
45 pythonImportsCheck = [ "sksurv" ];
46
47 nativeCheckInputs = [ pytestCheckHook ];
48
49 # treat numpy versions as lower bounds, same as setuptools build
50 postPatch = ''
51 sed -i 's/numpy==/numpy>=/' pyproject.toml
52 '';
53
54 # Hack needed to make pytest + cython work
55 # https://github.com/NixOS/nixpkgs/pull/82410#issuecomment-827186298
56 preCheck = ''
57 export HOME=$(mktemp -d)
58 cp -r $TMP/$sourceRoot/tests $HOME
59 pushd $HOME
60 '';
61 postCheck = "popd";
62
63 # very long tests, unnecessary for a leaf package
64 disabledTests =
65 [
66 "test_coxph"
67 "test_datasets"
68 "test_ensemble_selection"
69 "test_minlip"
70 "test_pandas_inputs"
71 "test_survival_svm"
72 "test_tree"
73 ]
74 ++ lib.optional (stdenv.isDarwin && stdenv.isAarch64)
75 # floating point mismatch on aarch64
76 # 27079905.88052468 to far from 27079905.880496684
77 "test_coxnet";
78
79 meta = with lib; {
80 description = "Survival analysis built on top of scikit-learn";
81 homepage = "https://github.com/sebp/scikit-survival";
82 license = licenses.gpl3Only;
83 maintainers = with maintainers; [ GuillaumeDesforges ];
84 };
85}