commit 5198a0f3dfb921741ab657f97e9b8ac73de35b51 · pyrox.dev/nixpkgs

+37 -27

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

···

       1
        
       {

     

       2
       -
         stdenv,

     

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         lib,

     

       0
        
       
     

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         buildPythonPackage,

     

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         fetchFromGitHub,

     

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       0
        
       
     

       0
        
       
     

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         cython,

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

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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,

     

       14
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         setuptools-scm,

     

       15
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         scikit-learn,

     

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         scipy,

     

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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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         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}";

     

       29
       -
           hash = "sha256-El5q2eE6wJKg/8rcFZPZQl7MVxw1jMsggjiCJHj7il8=";

     

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         };

     

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       -
         nativeBuildInputs = [

     

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       0
        
       
     

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           cython

     

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       0
        
       
     

       0
        
       
     

       0
        
       
     

       34
        
           setuptools-scm

     

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         ];

     

       36
        
       

     

       37
       -
         propagatedBuildInputs = [

     

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           ecos

     

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           joblib

     

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           numexpr

     
···

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         pythonImportsCheck = [ "sksurv" ];

     

       49
        
       

     

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         nativeCheckInputs = [ pytestCheckHook ];

     

       51
       -
       

     

       52
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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

     

       55
       -
         '';

     

       56
        
       

     

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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 = ''

     

       60
       -
           export HOME=$(mktemp -d)

     

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

     

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           pushd $HOME

     

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         '';

     

       64
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         postCheck = "popd";

     

       65
        
       

     

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       -
         # very long tests, unnecessary for a leaf package

     

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         disabledTests = [

     

       0
        
       
     

       68
        
           "test_coxph"

     

       69
        
           "test_datasets"

     

       70
        
           "test_ensemble_selection"

     
···

       73
        
           "test_survival_svm"

     

       74
        
           "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

     

       79
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             # 27079905.88052468 to far from 27079905.880496684

     

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             "test_coxnet";

     

       81
        
       

     

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         meta = with lib; {

     

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

     

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

     

       85
       -
           license = licenses.gpl3Only;

     

       86
       -
           maintainers = with maintainers; [ GuillaumeDesforges ];

     

       0
        
       
     

       87
        
         };

     

       88
        
       }

···

       1
        
       {

     

       0
        
       
     

       2
        
         lib,

     

       3
       +
         stdenv,

     

       4
        
         buildPythonPackage,

     

       5
        
         fetchFromGitHub,

     

       6
       +
         eigen,

     

       7
       +
       

     

       8
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         # build-system

     

       9
        
         cython,

     

       10
       +
         numpy,

     

       11
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         packaging,

     

       12
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         scikit-learn,

     

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         setuptools,

     

       14
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         setuptools-scm,

     

       15
       +
       

     

       16
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         # dependencies

     

       17
        
         ecos,

     

       0
        
       
     

       18
        
         joblib,

     

       19
        
         numexpr,

     

       0
        
       
     

       20
        
         osqp,

     

       21
        
         pandas,

     

       0
        
       
     

       0
        
       
     

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         scipy,

     

       23
       +
       

     

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         # tests

     

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         pytestCheckHook,

     

       26
        
       }:

     

       27
        
       

     

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       buildPythonPackage rec {

     

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         pname = "scikit-survival";

     

       30
       +
         version = "0.25.0";

     

       31
        
         pyproject = true;

     

       32
        
       

     

       33
        
         src = fetchFromGitHub {

     

       34
        
           owner = "sebp";

     

       35
        
           repo = "scikit-survival";

     

       36
        
           tag = "v${version}";

     

       37
       +
           hash = "sha256-OvdmZ2vDptYB2tq7OtokIQzjKzhQBWwnXZLW0m6FqlI=";

     

       38
        
         };

     

       39
        
       

     

       40
       +
         postPatch = ''

     

       41
       +
           ln -s ${lib.getInclude eigen}/include/eigen3/Eigen \

     

       42
       +
             sksurv/linear_model/src/eigen

     

       43
       +
         '';

     

       44
       +
       

     

       45
       +
         build-system = [

     

       46
        
           cython

     

       47
       +
           numpy

     

       48
       +
           packaging

     

       49
       +
           scikit-learn

     

       50
       +
           setuptools

     

       51
        
           setuptools-scm

     

       52
        
         ];

     

       53
        
       

     

       54
       +
         dependencies = [

     

       55
        
           ecos

     

       56
        
           joblib

     

       57
        
           numexpr

     
···

       65
        
         pythonImportsCheck = [ "sksurv" ];

     

       66
        
       

     

       67
        
         nativeCheckInputs = [ pytestCheckHook ];

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       68
        
       

     

       69
        
         # Hack needed to make pytest + cython work

     

       70
        
         # https://github.com/NixOS/nixpkgs/pull/82410#issuecomment-827186298

     

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         preCheck = ''

     

       72
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           rm -rf sksurv

     

       0
        
       
     

       0
        
       
     

       73
        
         '';

     

       0
        
       
     

       74
        
       

     

       0
        
       
     

       75
        
         disabledTests = [

     

       76
       +
           # very long tests, unnecessary for a leaf package

     

       77
        
           "test_coxph"

     

       78
        
           "test_datasets"

     

       79
        
           "test_ensemble_selection"

     
···

       82
        
           "test_survival_svm"

     

       83
        
           "test_tree"

     

       84
        
         ]

     

       85
       +
         ++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [

     

       86
       +
           # floating point mismatch on aarch64

     

       87
       +
           # 27079905.88052468 to far from 27079905.880496684

     

       88
       +
           "test_coxnet"

     

       89
       +
         ];

     

       90
        
       

     

       91
       +
         meta = {

     

       92
        
           description = "Survival analysis built on top of scikit-learn";

     

       93
        
           homepage = "https://github.com/sebp/scikit-survival";

     

       94
       +
           changelog = "https://github.com/sebp/scikit-survival/releases/tag/v${version}";

     

       95
       +
           license = lib.licenses.gpl3Plus;

     

       96
       +
           maintainers = with lib.maintainers; [ GuillaumeDesforges ];

     

       97
        
         };

     

       98
        
       }