pkgs/development/python-modules/pyradiomics/default.nix

   1 {
   2   lib,
   3   buildPythonPackage,
   4   fetchFromGitHub,
   5   pythonOlder,
   6   pytestCheckHook,
   7   numpy,
   8   pykwalify,
   9   pywavelets,
  10   setuptools,
  11   simpleitk,
  12   six,
  13   versioneer,
  14 }:
  15
  16 buildPythonPackage rec {
  17   pname = "pyradiomics";
  18   version = "3.1.0";
  19   format = "pyproject";
  20
  21   disabled = pythonOlder "3.6";
  22
  23   src = fetchFromGitHub {
  24     owner = "AIM-Harvard";
  25     repo = "pyradiomics";
  26     rev = "refs/tags/v${version}";
  27     hash = "sha256-/qFNN63Bbq4DUZDPmwUGj1z5pY3ujsbqFJpVXbO+b8E=";
  28     name = "pyradiomics";
  29   };
  30
  31   nativeBuildInputs = [
  32     setuptools
  33     versioneer
  34   ];
  35
  36   propagatedBuildInputs = [
  37     numpy
  38     pykwalify
  39     pywavelets
  40     simpleitk
  41     six
  42   ];
  43
  44   nativeCheckInputs = [ pytestCheckHook ];
  45   preCheck = ''
  46     rm -rf radiomics
  47   '';
  48   # tries to access network at collection time:
  49   disabledTestPaths = [ "tests/test_wavelet.py" ];
  50   # various urllib download errors and (probably related) missing feature errors:
  51   disabledTests = [
  52     "brain1_shape2D-original_shape2D"
  53     "brain2_shape2D-original_shape2D"
  54     "breast1_shape2D-original_shape2D"
  55     "lung1_shape2D-original_shape2D"
  56     "lung2_shape2D-original_shape2D"
  57   ];
  58   # note the above elements of disabledTests are patterns, not exact tests,
  59   # so simply setting `disabledTests` does not suffice:
  60   pytestFlagsArray = [
  61     "-k '${toString (lib.intersperse "and" (lib.forEach disabledTests (t: "not ${t}")))}'"
  62   ];
  63
  64   pythonImportsCheck = [ "radiomics" ];
  65
  66   meta = with lib; {
  67     homepage = "https://pyradiomics.readthedocs.io";
  68     description = "Extraction of Radiomics features from 2D and 3D images and binary masks";
  69     mainProgram = "pyradiomics";
  70     changelog = "https://github.com/AIM-Harvard/pyradiomics/releases/tag/v${version}";
  71     license = licenses.bsd3;
  72     maintainers = with maintainers; [ bcdarwin ];
  73   };
  74 }