python312Packages.pynndescent: disable on aarch64-linux (#386620) (05452072) · Commits · nix / nixpkgs

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

+25 −15

Original line number	Diff line number	Diff line
		{
		lib,
		buildPythonPackage,
		fetchPypi,
		importlib-metadata,
		fetchFromGitHub,

		# build-system
		setuptools,

		# dependencies
		joblib,
		llvmlite,
		numba,
		scikit-learn,
		scipy,
		setuptools,

		# tests
		pytestCheckHook,
		pythonOlder,
		}:

		buildPythonPackage rec {
		@@ -18,31 +22,37 @@ buildPythonPackage rec {
		version = "0.5.13";
		pyproject = true;

		disabled = pythonOlder "3.6";

		src = fetchPypi {
		inherit pname version;
		hash = "sha256-10JUwO4KHu7IRZfV/on+3Pd4WT7qvjLC+XQSk0qYAPs=";
		src = fetchFromGitHub {
		owner = "lmcinnes";
		repo = "pynndescent";
		tag = "release-${version}";
		hash = "sha256-oE/oy5doHduESHlRPuPHruiw1yUZmuUTe6PrgQlT6O8=";
		};

		nativeBuildInputs = [ setuptools ];
		build-system = [ setuptools ];

		propagatedBuildInputs = [
		dependencies = [
		joblib
		llvmlite
		numba
		scikit-learn
		scipy
		] ++ lib.optionals (pythonOlder "3.8") [ importlib-metadata ];
		];

		nativeCheckInputs = [ pytestCheckHook ];

		pythonImportsCheck = [ "pynndescent" ];

		meta = with lib; {
		meta = {
		description = "Nearest Neighbor Descent";
		homepage = "https://github.com/lmcinnes/pynndescent";
		license = licenses.bsd2;
		maintainers = with maintainers; [ mic92 ];
		changelog = "https://github.com/lmcinnes/pynndescent/releases/tag/release-${version}";
		license = lib.licenses.bsd2;
		maintainers = with lib.maintainers; [ mic92 ];
		badPlatforms = [
		# The majority of tests are crashing:
		# Fatal Python error: Segmentation fault
		"aarch64-linux"
		];
		};
		}

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

+49 −16

Original line number	Diff line number	Diff line
		{
		lib,
		stdenv,
		buildPythonPackage,
		fetchFromGitHub,

		# build-system
		cython,
		fetchPypi,
		numpy,
		setuptools,

		persim,
		pytestCheckHook,
		pythonOlder,
		scikit-learn,
		scipy,

		# tests
		pytestCheckHook,
		writableTmpDirAsHomeHook,
		}:

		buildPythonPackage rec {
		pname = "ripser";
		version = "0.6.10";
		format = "setuptools";

		disabled = pythonOlder "3.6";
		pyproject = true;

		src = fetchPypi {
		inherit pname version;
		hash = "sha256-3Mr6+XrSOVvGbLN25fvg9vJkNyspj9CT5BBxMsH3lIQ=";
		src = fetchFromGitHub {
		owner = "scikit-tda";
		repo = "ripser.py";
		tag = "v${version}";
		hash = "sha256-w6d/JRBYoxvu1r02WbwfG94GvB1NGG2Rwd5maSNYPhg=";
		};

		nativeBuildInputs = [ cython ];
		build-system = [
		cython
		numpy
		setuptools
		];

		propagatedBuildInputs = [
		dependencies = [
		numpy
		scipy
		scikit-learn
		persim
		];

		nativeCheckInputs = [ pytestCheckHook ];
		pythonImportsCheck = [ "ripser" ];

		nativeCheckInputs = [
		pytestCheckHook
		writableTmpDirAsHomeHook
		];

		preCheck = ''
		# specifically needed for darwin
		export HOME=$(mktemp -d)
		mkdir -p $HOME/.matplotlib
		echo "backend: ps" > $HOME/.matplotlib/matplotlibrc
		'';

		pythonImportsCheck = [ "ripser" ];
		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"
		];

		meta = with lib; {
		meta = {
		description = "Lean Persistent Homology Library for Python";
		homepage = "https://ripser.scikit-tda.org";
		changelog = "https://github.com/scikit-tda/ripser.py/blob/${version}/CHANGELOG.md";
		license = licenses.mit;
		license = lib.licenses.mit;
		maintainers = [ ];
		};
		}

pkgs/development/python-modules/umap-learn/default.nix

+28 −18

Original line number	Diff line number	Diff line
		{
		lib,
		bokeh,
		buildPythonPackage,
		colorcet,
		datashader,
		fetchFromGitHub,

		# build-system
		setuptools,
		holoviews,
		matplotlib,

		# dependencies
		numba,
		numpy,
		pandas,
		pynndescent,
		pytestCheckHook,
		scikit-image,
		scikit-learn,
		scipy,
		tqdm,

		# optional-dependencies
		bokeh,
		colorcet,
		dask,
		datashader,
		holoviews,
		matplotlib,
		pandas,
		scikit-image,
		seaborn,
		tensorflow,
		tensorflow-probability,
		tqdm,

		# tests
		pytestCheckHook,
		writableTmpDirAsHomeHook,
		}:

		buildPythonPackage rec {
		pname = "umap-learn";
		version = "0.5.7";
		version = "0.5.8";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "lmcinnes";
		repo = "umap";
		tag = "release-${version}";
		hash = "sha256-hPYmRDSeDa4JWGekUVq3CWf5NthHTpMpyuUQ1yIkVAE=";
		hash = "sha256-VR+qBZyFtpW/xuFXI8pxDkkwJKt9qajnUtvuZLFZtF0=";
		};

		build-system = [ setuptools ];
		@@ -49,6 +59,7 @@ buildPythonPackage rec {
		plot = [
		bokeh
		colorcet
		dask
		datashader
		holoviews
		matplotlib
		@@ -67,11 +78,10 @@ buildPythonPackage rec {
		all = plot ++ parametric_umap ++ tbb;
		};

		nativeCheckInputs = [ pytestCheckHook ];

		preCheck = ''
		export HOME=$TMPDIR
		'';
		nativeCheckInputs = [
		pytestCheckHook
		writableTmpDirAsHomeHook
		];

		disabledTests = [
		# Plot functionality requires additional packages.
		@@ -88,11 +98,11 @@ buildPythonPackage rec {
		"test_save_load"
		];

		meta = with lib; {
		meta = {
		description = "Uniform Manifold Approximation and Projection";
		homepage = "https://github.com/lmcinnes/umap";
		changelog = "https://github.com/lmcinnes/umap/releases/tag/release-${version}";
		license = licenses.bsd3;
		license = lib.licenses.bsd3;
		maintainers = [ ];
		};
		}

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