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{ lib
, buildPythonPackage
, pythonOlder
, fetchFromGitHub
, pytestCheckHook
, aiohttp
, dask
, distributed
, fsspec
, numpy
, requests
, scikit-image
, toolz
, zarr
}:
buildPythonPackage rec {
pname = "ome-zarr";
version = "0.8.3";
format = "setuptools";
disabled = pythonOlder "3.6";
src = fetchFromGitHub {
owner = "ome";
repo = "ome-zarr-py";
rev = "refs/tags/v${version}";
hash = "sha256-JuNXVse/n/lFbNaLwMcir8NBHiRxcbYvtbxePwI6YoY=";
};
propagatedBuildInputs = [
numpy
dask
distributed
zarr
fsspec
aiohttp
requests
scikit-image
toolz
] ++ fsspec.passthru.optional-dependencies.s3;
nativeCheckInputs = [
pytestCheckHook
];
disabledTests = [
# attempts to access network
"test_s3_info"
];
pytestFlagsArray = [
# Fail with RecursionError
# https://github.com/ome/ome-zarr-py/issues/352
"--deselect=tests/test_cli.py::TestCli::test_astronaut_download"
"--deselect=tests/test_cli.py::TestCli::test_astronaut_info"
"--deselect=tests/test_cli.py::TestCli::test_coins_info"
"--deselect=tests/test_emitter.py::test_close"
"--deselect=tests/test_emitter.py::test_create_wrong_encoding"
"--deselect=tests/test_node.py::TestNode::test_image"
"--deselect=tests/test_node.py::TestNode::test_label"
"--deselect=tests/test_node.py::TestNode::test_labels"
"--deselect=tests/test_ome_zarr.py::TestOmeZarr::test_download"
"--deselect=tests/test_ome_zarr.py::TestOmeZarr::test_info"
"--deselect=tests/test_reader.py::TestReader::test_image"
"--deselect=tests/test_reader.py::TestReader::test_label"
"--deselect=tests/test_reader.py::TestReader::test_labels"
"--deselect=tests/test_starting_points.py::TestStartingPoints::test_label"
"--deselect=tests/test_starting_points.py::TestStartingPoints::test_labels"
"--deselect=tests/test_starting_points.py::TestStartingPoints::test_top_level"
];
pythonImportsCheck = [
"ome_zarr"
"ome_zarr.cli"
"ome_zarr.csv"
"ome_zarr.data"
"ome_zarr.format"
"ome_zarr.io"
"ome_zarr.reader"
"ome_zarr.writer"
"ome_zarr.scale"
"ome_zarr.utils"
];
meta = with lib; {
description = "Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.";
homepage = "https://pypi.org/project/ome-zarr";
changelog = "https://github.com/ome/ome-zarr-py/blob/v${version}/CHANGELOG.md";
license = licenses.bsd2;
maintainers = [ maintainers.bcdarwin ];
mainProgram = "ome_zarr";
};
}
|
