89 lines
1.7 KiB
Nix
89 lines
1.7 KiB
Nix
{
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stdenv,
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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cython,
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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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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}";
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hash = "sha256-El5q2eE6wJKg/8rcFZPZQl7MVxw1jMsggjiCJHj7il8=";
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};
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nativeBuildInputs = [
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cython
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setuptools-scm
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];
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propagatedBuildInputs = [
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ecos
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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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scikit-learn
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scipy
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];
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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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'';
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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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"test_coxph"
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"test_datasets"
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"test_ensemble_selection"
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"test_minlip"
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"test_pandas_inputs"
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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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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";
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license = licenses.gpl3Only;
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maintainers = with maintainers; [ GuillaumeDesforges ];
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};
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}
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