commit 5198a0f3dfb921741ab657f97e9b8ac73de35b51 · pyrox.dev/nixpkgs

+37 -27
pkgs/development/python-modules/scikit-survival/default.nix
···

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       {

     

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         stdenv,

     

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         lib,

     

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         stdenv,

     

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         buildPythonPackage,

     

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         fetchFromGitHub,

     

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         eigen,

     

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         # build-system

     

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         cython,

     

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         numpy,

     

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         packaging,

     

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         scikit-learn,

     

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         setuptools,

     

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         setuptools-scm,

     

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         # dependencies

     

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         ecos,

     

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         eigen,

     

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         joblib,

     

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         numexpr,

     

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         numpy,

     

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         osqp,

     

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         pandas,

     

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         setuptools-scm,

     

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         scikit-learn,

     

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         scipy,

     

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         # tests

     

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         pytestCheckHook,

     

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       }:

     

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       buildPythonPackage rec {

     

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         pname = "scikit-survival";

     

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         version = "0.24.1";

     

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         version = "0.25.0";

     

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         pyproject = true;

     

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         src = fetchFromGitHub {

     

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           owner = "sebp";

     

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           repo = "scikit-survival";

     

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           tag = "v${version}";

     

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

     

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           hash = "sha256-OvdmZ2vDptYB2tq7OtokIQzjKzhQBWwnXZLW0m6FqlI=";

     

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         };

     

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         nativeBuildInputs = [

     

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         postPatch = ''

     

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

     

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             sksurv/linear_model/src/eigen

     

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         '';

     

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         build-system = [

     

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           cython

     

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           numpy

     

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           packaging

     

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           scikit-learn

     

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           setuptools

     

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           setuptools-scm

     

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         ];

     

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         propagatedBuildInputs = [

     

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         dependencies = [

     

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           ecos

     

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           joblib

     

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           numexpr

     
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         pythonImportsCheck = [ "sksurv" ];

     

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         nativeCheckInputs = [ pytestCheckHook ];

     

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         postPatch = ''

     

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

     

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             sksurv/linear_model/src/eigen

     

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         '';

     

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         # Hack needed to make pytest + cython work

     

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

     

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         preCheck = ''

     

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           export HOME=$(mktemp -d)

     

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

     

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           pushd $HOME

     

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           rm -rf sksurv

     

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         '';

     

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         postCheck = "popd";

     

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         # very long tests, unnecessary for a leaf package

     

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         disabledTests = [

     

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           # very long tests, unnecessary for a leaf package

     

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           "test_coxph"

     

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           "test_datasets"

     

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           "test_ensemble_selection"

     
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           "test_survival_svm"

     

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           "test_tree"

     

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         ]

     

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         ++

     

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

     

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             # floating point mismatch on aarch64

     

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             # 27079905.88052468 to far from 27079905.880496684

     

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             "test_coxnet";

     

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

     

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           # floating point mismatch on aarch64

     

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           # 27079905.88052468 to far from 27079905.880496684

     

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           "test_coxnet"

     

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         ];

     

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         meta = with lib; {

     

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         meta = {

     

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

     

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

     

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           license = licenses.gpl3Only;

     

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           maintainers = with maintainers; [ GuillaumeDesforges ];

     

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

     

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           license = lib.licenses.gpl3Plus;

     

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           maintainers = with lib.maintainers; [ GuillaumeDesforges ];

     

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         };

     

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       }