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

   1 {
   2   lib,
   3   buildPythonPackage,
   4   pythonOlder,
   5   fetchFromGitHub,
   6   pytestCheckHook,
   7   aiohttp,
   8   dask,
   9   distributed,
  10   fsspec,
  11   numpy,
  12   requests,
  13   scikit-image,
  14   toolz,
  15   zarr,
  16 }:
  17
  18 buildPythonPackage rec {
  19   pname = "ome-zarr";
  20   version = "0.9.0";
  21   format = "setuptools";
  22   disabled = pythonOlder "3.6";
  23
  24   src = fetchFromGitHub {
  25     owner = "ome";
  26     repo = "ome-zarr-py";
  27     rev = "refs/tags/v${version}";
  28     hash = "sha256-YOG9+ONf2OnkSZBL/Vb8Inebx4XDSGJb2fqypaWebhY=";
  29   };
  30
  31   propagatedBuildInputs = [
  32     numpy
  33     dask
  34     distributed
  35     zarr
  36     fsspec
  37     aiohttp
  38     requests
  39     scikit-image
  40     toolz
  41   ] ++ fsspec.optional-dependencies.s3;
  42
  43   nativeCheckInputs = [ pytestCheckHook ];
  44
  45   disabledTests = [
  46     # attempts to access network
  47     "test_s3_info"
  48   ];
  49
  50   pytestFlagsArray = [
  51     # Fail with RecursionError
  52     # https://github.com/ome/ome-zarr-py/issues/352
  53     "--deselect=tests/test_cli.py::TestCli::test_astronaut_download"
  54     "--deselect=tests/test_cli.py::TestCli::test_astronaut_info"
  55     "--deselect=tests/test_cli.py::TestCli::test_coins_info"
  56     "--deselect=tests/test_emitter.py::test_close"
  57     "--deselect=tests/test_emitter.py::test_create_wrong_encoding"
  58     "--deselect=tests/test_node.py::TestNode::test_image"
  59     "--deselect=tests/test_node.py::TestNode::test_label"
  60     "--deselect=tests/test_node.py::TestNode::test_labels"
  61     "--deselect=tests/test_ome_zarr.py::TestOmeZarr::test_download"
  62     "--deselect=tests/test_ome_zarr.py::TestOmeZarr::test_info"
  63     "--deselect=tests/test_reader.py::TestReader::test_image"
  64     "--deselect=tests/test_reader.py::TestReader::test_label"
  65     "--deselect=tests/test_reader.py::TestReader::test_labels"
  66     "--deselect=tests/test_starting_points.py::TestStartingPoints::test_label"
  67     "--deselect=tests/test_starting_points.py::TestStartingPoints::test_labels"
  68     "--deselect=tests/test_starting_points.py::TestStartingPoints::test_top_level"
  69   ];
  70
  71   pythonImportsCheck = [
  72     "ome_zarr"
  73     "ome_zarr.cli"
  74     "ome_zarr.csv"
  75     "ome_zarr.data"
  76     "ome_zarr.format"
  77     "ome_zarr.io"
  78     "ome_zarr.reader"
  79     "ome_zarr.writer"
  80     "ome_zarr.scale"
  81     "ome_zarr.utils"
  82   ];
  83
  84   meta = with lib; {
  85     description = "Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud";
  86     homepage = "https://pypi.org/project/ome-zarr";
  87     changelog = "https://github.com/ome/ome-zarr-py/blob/v${version}/CHANGELOG.md";
  88     license = licenses.bsd2;
  89     maintainers = [ maintainers.bcdarwin ];
  90     mainProgram = "ome_zarr";
  91   };
  92 }