Unverified Commit 5198a0f3 authored by Gaétan Lepage's avatar Gaétan Lepage Committed by GitHub
Browse files

python3Packages.scikit-survival: 0.24.1 -> 0.25.0 (#445334)

parents e4bd93f8 e634d71f

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

+37 −27
Original line number Diff line number Diff line 
{

  stdenv,

  lib,

  stdenv,

  buildPythonPackage,

  fetchFromGitHub,

  eigen,



  # build-system

  cython,

  numpy,

  packaging,

  scikit-learn,

  setuptools,

  setuptools-scm,



  # dependencies

  ecos,

  eigen,

  joblib,

  numexpr,

  numpy,

  osqp,

  pandas,

  setuptools-scm,

  scikit-learn,

  scipy,



  # tests

  pytestCheckHook,

}:



buildPythonPackage rec {

  pname = "scikit-survival";

  version = "0.24.1";

  version = "0.25.0";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "sebp";

    repo = "scikit-survival";

    tag = "v${version}";

    hash = "sha256-El5q2eE6wJKg/8rcFZPZQl7MVxw1jMsggjiCJHj7il8=";

    hash = "sha256-OvdmZ2vDptYB2tq7OtokIQzjKzhQBWwnXZLW0m6FqlI=";

  };



  nativeBuildInputs = [

  postPatch = ''

    ln -s ${lib.getInclude eigen}/include/eigen3/Eigen \

      sksurv/linear_model/src/eigen

  '';



  build-system = [

    cython

    numpy

    packaging

    scikit-learn

    setuptools

    setuptools-scm

  ];



  propagatedBuildInputs = [

  dependencies = [

    ecos

    joblib

    numexpr
@@ -49,22 +66,14 @@ buildPythonPackage rec { 


  nativeCheckInputs = [ pytestCheckHook ];



  postPatch = ''

    ln -s ${lib.getInclude eigen}/include/eigen3/Eigen \

      sksurv/linear_model/src/eigen

  '';



  # Hack needed to make pytest + cython work

  # https://github.com/NixOS/nixpkgs/pull/82410#issuecomment-827186298

  preCheck = ''

    export HOME=$(mktemp -d)

    cp -r $TMP/$sourceRoot/tests $HOME

    pushd $HOME

    rm -rf sksurv

  '';

  postCheck = "popd";



  # very long tests, unnecessary for a leaf package

  disabledTests = [

    # very long tests, unnecessary for a leaf package

    "test_coxph"

    "test_datasets"

    "test_ensemble_selection"
@@ -73,16 +82,17 @@ buildPythonPackage rec { 
    "test_survival_svm"

    "test_tree"

  ]

  ++

    lib.optional (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64)

  ++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [

    # floating point mismatch on aarch64

    # 27079905.88052468 to far from 27079905.880496684

      "test_coxnet";

    "test_coxnet"

  ];



  meta = with lib; {

  meta = {

    description = "Survival analysis built on top of scikit-learn";

    homepage = "https://github.com/sebp/scikit-survival";

    license = licenses.gpl3Only;

    maintainers = with maintainers; [ GuillaumeDesforges ];

    changelog = "https://github.com/sebp/scikit-survival/releases/tag/v${version}";

    license = lib.licenses.gpl3Plus;

    maintainers = with lib.maintainers; [ GuillaumeDesforges ];

  };

}