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{
lib,
stdenv,
buildPythonPackage,
fetchFromGitHub,
# build-system
cython,
numpy,
setuptools,
persim,
scikit-learn,
scipy,
# tests
pytestCheckHook,
writableTmpDirAsHomeHook,
}:
buildPythonPackage rec {
pname = "ripser";
version = "0.6.14";
pyproject = true;
src = fetchFromGitHub {
owner = "scikit-tda";
repo = "ripser.py";
tag = "v${version}";
hash = "sha256-p47vhrG8+B226/no4PD7+XFNccbNJvi45Luwu287ygI=";
};
build-system = [
cython
numpy
setuptools
];
dependencies = [
numpy
scipy
scikit-learn
persim
];
pythonImportsCheck = [ "ripser" ];
nativeCheckInputs = [
pytestCheckHook
writableTmpDirAsHomeHook
];
preCheck = ''
# specifically needed for darwin
mkdir -p $HOME/.matplotlib
echo "backend: ps" > $HOME/.matplotlib/matplotlibrc
'';
disabledTests = lib.optionals stdenv.hostPlatform.isDarwin [
# AssertionError
# assert np.isinf(h0[0, 1])
"test_full_nonzerobirths"
# assert np.max(np.abs(h11 - h12)) <= 2 * res2["r_cover"]
"test_greedyperm_circlebottleneck"
# assert np.all(dgm[:,1] >= dgm[:,0])
"test_returns_dgm"
# assert tuple(dgm[0]) == (0,np.inf)
# assert (np.float64(0....float64(0.0)) == (0, inf)
"test_single_point"
# assert res0["num_edges"] == res1["num_edges"]
# assert 2307 == 167
"test_sparse"
# assert 38 < 38
"test_thresh"
# assert(np.allclose(r1, r2))
"test_zero_edge_bug"
# assert (0, 2) == (1, 2)
"test_verbose_true"
# assert (0, 2) == (1, 2)
"test_verbose_false"
];
meta = {
description = "Lean Persistent Homology Library for Python";
homepage = "https://ripser.scikit-tda.org";
changelog = "https://github.com/scikit-tda/ripser.py/blob/${src.tag}/CHANGELOG.md";
license = lib.licenses.mit;
maintainers = [ ];
};
}
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