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{
lib,
buildPythonPackage,
fetchFromGitHub,
# build-system
setuptools,
setuptools-scm,
# dependencies
aiohttp,
dask,
fsspec,
numpy,
requests,
scikit-image,
toolz,
zarr,
# tests
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "ome-zarr";
version = "0.12.2";
pyproject = true;
src = fetchFromGitHub {
owner = "ome";
repo = "ome-zarr-py";
tag = "v${version}";
hash = "sha256-lwv6PHm41HFylt7b0d5LHCrCIXNWFNGg59VQvPXYtVc=";
};
build-system = [
setuptools
setuptools-scm
];
dependencies = [
aiohttp
dask
fsspec
numpy
requests
scikit-image
toolz
zarr
]
++ fsspec.optional-dependencies.s3;
nativeCheckInputs = [
pytestCheckHook
];
disabledTests = [
# attempts to access network
"test_s3_info"
# AssertionError: assert {'blocksize':... 'blosc', ...} == {'blocksize':... 'blosc', ...}
# comp {'id': 'blosc', 'cname': 'lz4', 'clevel': 5, 'shuffle': 1, 'blocksize': 0}
"test_default_compression"
"test_write_image_compressed"
];
disabledTestPaths = [
# Fail with RecursionError
# https://github.com/ome/ome-zarr-py/issues/352
"tests/test_cli.py::TestCli::test_astronaut_download"
"tests/test_cli.py::TestCli::test_astronaut_info"
"tests/test_cli.py::TestCli::test_coins_info"
"tests/test_emitter.py::test_close"
"tests/test_emitter.py::test_create_wrong_encoding"
"tests/test_node.py::TestNode::test_image"
"tests/test_node.py::TestNode::test_label"
"tests/test_node.py::TestNode::test_labels"
"tests/test_ome_zarr.py::TestOmeZarr::test_download"
"tests/test_ome_zarr.py::TestOmeZarr::test_info"
"tests/test_reader.py::TestReader::test_image"
"tests/test_reader.py::TestReader::test_label"
"tests/test_reader.py::TestReader::test_labels"
"tests/test_starting_points.py::TestStartingPoints::test_label"
"tests/test_starting_points.py::TestStartingPoints::test_labels"
"tests/test_starting_points.py::TestStartingPoints::test_top_level"
# tries to access network:
"ome_zarr/io.py"
];
pythonImportsCheck = [
"ome_zarr"
"ome_zarr.cli"
"ome_zarr.csv"
"ome_zarr.data"
"ome_zarr.format"
"ome_zarr.io"
"ome_zarr.reader"
"ome_zarr.writer"
"ome_zarr.scale"
"ome_zarr.utils"
];
meta = {
description = "Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud";
homepage = "https://pypi.org/project/ome-zarr";
changelog = "https://github.com/ome/ome-zarr-py/blob/${src.tag}/CHANGELOG.md";
license = lib.licenses.bsd2;
maintainers = [ lib.maintainers.bcdarwin ];
mainProgram = "ome_zarr";
};
}
|
