mirror of
https://github.com/NixOS/nixpkgs.git
synced 2026-06-29 05:25:48 +00:00
143 lines
3.2 KiB
Nix
143 lines
3.2 KiB
Nix
{
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lib,
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buildPythonPackage,
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dask,
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dask-image,
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deepdiff,
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fetchFromGitHub,
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hatchling,
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importlib-resources,
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itk,
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itkwasm-downsample,
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itkwasm-image-io,
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itkwasm,
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jsonschema,
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nibabel,
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imageio,
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numpy,
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imagecodecs,
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platformdirs,
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pooch,
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psutil,
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pytestCheckHook,
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rich-argparse,
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rich,
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tensorstore,
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tifffile,
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typing-extensions,
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writableTmpDirAsHomeHook,
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zarr,
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}:
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buildPythonPackage (finalAttrs: {
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pname = "ngff-zarr";
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version = "0.35.0";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "fideus-labs";
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repo = "ngff-zarr";
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tag = "py-v${finalAttrs.version}";
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hash = "sha256-GJt6N5xMmlCHSzKZhHKsZaD4P8fWnTQi4tqP/YnPkQk=";
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};
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sourceRoot = "${finalAttrs.src.name}/py/";
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build-system = [ hatchling ];
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dependencies = [
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dask
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importlib-resources
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itkwasm
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itkwasm-downsample
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numpy
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platformdirs
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psutil
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rich
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rich-argparse
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typing-extensions
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zarr
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]
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++ dask.optional-dependencies.array;
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optional-dependencies = {
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dask-image = [ dask-image ];
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# itk = [ itk-filtering ];
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cli = [
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# itk-filtering
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# itk-io
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# liffile
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dask
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dask-image
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imagecodecs
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imageio
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itk
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itkwasm-image-io
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nibabel
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tifffile
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]
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++ dask.optional-dependencies.distributed;
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tensorstore = [ tensorstore ];
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validate = [ jsonschema ];
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};
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nativeCheckInputs = [
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deepdiff
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pooch
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pytestCheckHook
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writableTmpDirAsHomeHook
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]
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++ lib.flatten (builtins.attrValues finalAttrs.passthru.optional-dependencies);
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pythonImportsCheck = [ "ngff_zarr" ];
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disabledTestPaths = [
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# No CLI tests
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"test/test_cli_input_to_ngff_image.py"
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"test/test_cli_output.py"
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"test/test_cli_relative_paths.py"
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# Attribute errors
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"test/test_pyramid_integrity.py"
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"test/test_multiscales_type.py"
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"test/test_convert_ome_zarr_version.py"
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"test/test_itk_image_to_ngff_image.py"
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# Data missing
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"test/test_hcs.py"
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"test/test_hcs_simple.py"
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"test/test_ngff_validation.py"
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"test/test_nibabel_image_to_ngff_image.py"
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# Network access
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"test/test_from_ngff_zarr_tensorstore.py"
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"test/test_from_ngff_zarr.py"
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"test/test_large_serialization.py"
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"test/test_ngff_image_to_itk_image.py"
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"test/test_omero.py"
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"test/test_rfc9_ozx.py"
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"test/test_to_ngff_zarr_dask_image.py"
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"test/test_to_ngff_zarr_itk.py"
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"test/test_to_ngff_zarr_itkwasm.py"
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"test/test_to_ngff_zarr_rfc2_zarr_v3.py"
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"test/test_to_ngff_zarr_sharding.py"
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"test/test_to_ngff_zarr_tensorstore.py"
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"test/test_to_ngff_zarr_v3_compression.py"
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# Missing dependencies
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"test/test_lif_to_ngff_image.py"
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];
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disabledTests = [
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# Assertion errors
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"test_2d_yx"
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"test_3d_zyx"
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"test_smaller_dask_graph"
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"test_tensorstore_compression"
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];
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meta = {
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description = "Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation";
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homepage = "https://github.com/fideus-labs/ngff-zarr";
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changelog = "https://github.com/fideus-labs/ngff-zarr/releases/tag/${finalAttrs.src.tag}";
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license = lib.licenses.isc;
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maintainers = with lib.maintainers; [ fab ];
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};
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})
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