pkgs/development/python-modules/scikit-survival/default.nix

   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
  20 buildPythonPackage rec {
  21   pname = "scikit-survival";
  22   version = "0.23.1";
  23   pyproject = true;
  24
  25   src = fetchFromGitHub {
  26     owner = "sebp";
  27     repo = "scikit-survival";
  28     rev = "refs/tags/v${version}";
  29     hash = "sha256-6902chXALa73/kTJ5UwV4CrB7/7wn+QXKpp2ej/Dnk8=";
  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   # can remove scikit-learn after 0.23.1
  53   postPatch = ''
  54     ln -s ${lib.getInclude eigen}/include/eigen3/Eigen \
  55       sksurv/linear_model/src/eigen
  56     sed -i -e 's/numpy>=2.0.0/numpy/' \
  57        -e 's/scikit-learn~=1.4.0/scikit-learn/' pyproject.toml
  58   '';
  59
  60   # Hack needed to make pytest + cython work
  61   # https://github.com/NixOS/nixpkgs/pull/82410#issuecomment-827186298
  62   preCheck = ''
  63     export HOME=$(mktemp -d)
  64     cp -r $TMP/$sourceRoot/tests $HOME
  65     pushd $HOME
  66   '';
  67   postCheck = "popd";
  68
  69   # very long tests, unnecessary for a leaf package
  70   disabledTests =
  71     [
  72       "test_coxph"
  73       "test_datasets"
  74       "test_ensemble_selection"
  75       "test_minlip"
  76       "test_pandas_inputs"
  77       "test_survival_svm"
  78       "test_tree"
  79     ]
  80     ++ lib.optional (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64)
  81       # floating point mismatch on aarch64
  82       # 27079905.88052468 to far from 27079905.880496684
  83       "test_coxnet";
  84
  85   meta = with lib; {
  86     description = "Survival analysis built on top of scikit-learn";
  87     homepage = "https://github.com/sebp/scikit-survival";
  88     license = licenses.gpl3Only;
  89     maintainers = with maintainers; [ GuillaumeDesforges ];
  90   };
  91 }