python312Packages.zarr: 2.18.7 -> 3.1.0 (#373248) (7ef1b416) · Commits · nix / nixpkgs

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

+10 −2

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@
		hatchling,
		joblib,
		lib,
		legacy-api-wrap,
		natsort,
		numba,
		numpy,
		@@ -32,14 +33,14 @@

		buildPythonPackage rec {
		pname = "anndata";
		version = "0.11.4";
		version = "0.12.2";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "scverse";
		repo = "anndata";
		tag = version;
		hash = "sha256-9RDR0veZ8n2sq0kUbAkS2nP57u47cQxmubzuWWYBKBY=";
		hash = "sha256-uGkeSlYcphRnIFfe9UcLvnupKeMzAIm5wT8fp3gmPKw=";
		};

		build-system = [
		@@ -50,6 +51,7 @@ buildPythonPackage rec {
		dependencies = [
		array-api-compat
		h5py
		legacy-api-wrap
		natsort
		numpy
		pandas
		@@ -92,18 +94,24 @@ buildPythonPackage rec {
		];

		disabledTests = [
		# requires data from a previous test execution:
		"test_no_diff"

		# doctests that require scanpy, creating a circular dependency chain. These
		# do not work in disabledTestPaths for some reason.
		"anndata._core.anndata.AnnData.concatenate"
		"anndata._core.anndata.AnnData.obs_names_make_unique"
		"anndata._core.anndata.AnnData.var_names_make_unique"
		"anndata._core.extensions.register_anndata_namespac"
		"anndata._core.merge.concat"
		"anndata._core.merge.gen_reindexer"
		"anndata._core.sparse_dataset.sparse_dataset"
		"anndata._io.specs.registry.read_elem_as_dask"
		"anndata._io.specs.registry.read_elem_lazy"
		"anndata._io.utils.report_read_key_on_error"
		"anndata._io.utils.report_write_key_on_error"
		"anndata._warnings.ImplicitModificationWarning"
		"anndata.experimental.backed._io.read_lazy"
		"anndata.experimental.merge.concat_on_disk"
		"anndata.experimental.multi_files._anncollection.AnnCollection"
		"anndata.utils.make_index_unique"

pkgs/development/python-modules/legacy-api-wrap/default.nix

0 → 100644

+42 −0

Original line number	Diff line number	Diff line
		{
		lib,
		buildPythonPackage,
		fetchFromGitHub,
		hatch-docstring-description,
		hatch-vcs,
		hatchling,
		pytestCheckHook,
		}:

		buildPythonPackage rec {
		pname = "legacy-api-wrap";
		version = "1.4.1";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "flying-sheep";
		repo = "legacy-api-wrap";
		tag = "v${version}";
		hash = "sha256-ySkhfUyRBd4QS3f46KlaA5NrHxHr+dlkgmD4fGk2KsA=";
		};

		build-system = [
		hatch-docstring-description
		hatch-vcs
		hatchling
		];

		pythonImportsCheck = [
		"legacy_api_wrap"
		];

		nativeCheckInputs = [ pytestCheckHook ];

		meta = {
		description = "Wrap legacy APIs in python projects";
		homepage = "https://github.com/flying-sheep/legacy-api-wrap";
		changelog = "https://github.com/flying-sheep/legacy-api-wrap/releases/tag/${src.tag}";
		license = lib.licenses.mpl20;
		maintainers = with lib.maintainers; [ bcdarwin ];
		};
		}

pkgs/development/python-modules/multiscale-spatial-image/default.nix

+4 −2

Original line number	Diff line number	Diff line
		@@ -9,6 +9,7 @@
		python-dateutil,
		spatial-image,
		xarray,
		xarray-dataclass,
		zarr,
		dask-image,
		fsspec,
		@@ -22,7 +23,7 @@

		buildPythonPackage rec {
		pname = "multiscale-spatial-image";
		version = "2.0.2";
		version = "2.0.3";
		pyproject = true;

		disabled = pythonOlder "3.8";
		@@ -31,7 +32,7 @@ buildPythonPackage rec {
		owner = "spatial-image";
		repo = "multiscale-spatial-image";
		tag = "v${version}";
		hash = "sha256-aJp9RrCy88XFpM5GU7jADHQZFNZgXvlqSsCbmay3gww=";
		hash = "sha256-wKSzhlNXIXOFEK8+xfKF6zTFr0+mdFhhvjWiHAKphk0=";
		};

		build-system = [ hatchling ];
		@@ -42,6 +43,7 @@ buildPythonPackage rec {
		python-dateutil
		spatial-image
		xarray
		xarray-dataclass
		zarr
		];

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

+2 −2

Original line number	Diff line number	Diff line
		@@ -26,14 +26,14 @@

		buildPythonPackage rec {
		pname = "numcodecs";
		version = "0.15.1";
		version = "0.16.1";
		pyproject = true;

		disabled = pythonOlder "3.8";

		src = fetchPypi {
		inherit pname version;
		hash = "sha256-7u135NZjZkGizGBfvGB4x6jyzEDz36Kz9h5S5gkbBP8=";
		hash = "sha256-xH8g1lZFRWjGtGl84CCB5ru1EvGYc4xqVvr+gCnJf7E=";
		};

		build-system = [

pkgs/development/python-modules/ome-zarr/default.nix

+5 −2

Original line number	Diff line number	Diff line
		@@ -23,14 +23,14 @@

		buildPythonPackage rec {
		pname = "ome-zarr";
		version = "0.11.1";
		version = "0.12rc1";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "ome";
		repo = "ome-zarr-py";
		tag = "v${version}";
		hash = "sha256-3RXkz+UQvLixfYYhm5y/5vu9r0ga6s3xKx1azbmKFgg=";
		hash = "sha256-uwAcICrFHZYYULfacWII5C3Y+Rs2Bf8ZLQEijfkldn8=";
		};

		build-system = [
		@@ -78,6 +78,9 @@ buildPythonPackage rec {
		"tests/test_starting_points.py::TestStartingPoints::test_label"
		"tests/test_starting_points.py::TestStartingPoints::test_labels"
		"tests/test_starting_points.py::TestStartingPoints::test_top_level"

		# tries to access network:
		"ome_zarr/io.py"
		];

		pythonImportsCheck = [

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