Merge pull request #244537 from bcdarwin/pyradiomics

python310Packages.pyradiomics: init at 3.1.0

2 files changed, 73 insertions, 0 deletions

diff --git a/pkgs/development/python-modules/pyradiomics/default.nix b/pkgs/development/python-modules/pyradiomics/default.nix
new file mode 100644
index 00000000000..606f542f8f9
--- /dev/null
+++ b/pkgs/development/python-modules/pyradiomics/default.nix
@@ -0,0 +1,71 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pythonOlder
+, pytestCheckHook
+, numpy
+, pykwalify
+, pywavelets
+, setuptools
+, simpleitk
+, six
+, versioneer
+}:
+
+buildPythonPackage rec {
+  pname = "pyradiomics";
+  version = "3.1.0";
+  format = "pyproject";
+
+  disabled = pythonOlder "3.6";
+
+  src = fetchFromGitHub {
+    owner = "AIM-Harvard";
+    repo = "pyradiomics";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-/qFNN63Bbq4DUZDPmwUGj1z5pY3ujsbqFJpVXbO+b8E=";
+    name = "pyradiomics";
+  };
+
+  nativeBuildInputs = [ setuptools versioneer ];
+
+  propagatedBuildInputs = [
+    numpy
+    pykwalify
+    pywavelets
+    simpleitk
+    six
+  ];
+
+  nativeCheckInputs = [ pytestCheckHook ];
+  preCheck = ''
+    rm -rf radiomics
+  '';
+  # tries to access network at collection time:
+  disabledTestPaths = [ "tests/test_wavelet.py" ];
+  # various urllib download errors and (probably related) missing feature errors:
+  disabledTests = [
+    "brain1_shape2D-original_shape2D"
+    "brain2_shape2D-original_shape2D"
+    "breast1_shape2D-original_shape2D"
+    "lung1_shape2D-original_shape2D"
+    "lung2_shape2D-original_shape2D"
+  ];
+  # note the above elements of disabledTests are patterns, not exact tests,
+  # so simply setting `disabledTests` does not suffice:
+  pytestFlagsArray = [
+    "-k '${toString (lib.intersperse "and" (lib.forEach disabledTests (t: "not ${t}")))}'"
+  ];
+
+  pythonImportsCheck = [
+    "radiomics"
+  ];
+
+  meta = with lib; {
+    homepage = "https://pyradiomics.readthedocs.io";
+    description = "Extraction of Radiomics features from 2D and 3D images and binary masks";
+    changelog = "https://github.com/AIM-Harvard/pyradiomics/releases/tag/v${version}";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ bcdarwin ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 6ed68c04b69..72c64cc4e9e 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -9573,6 +9573,8 @@ self: super: with self; {
 
   pyrad = callPackage ../development/python-modules/pyrad { };
 
+  pyradiomics = callPackage ../development/python-modules/pyradiomics { };
+
   pyradios = callPackage ../development/python-modules/pyradios { };
 
   pyrainbird = callPackage ../development/python-modules/pyrainbird { };