From 4d82f051d43a1581e65e75333b490df041941685 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Tue, 7 Jul 2026 09:47:01 +0000
Subject: [PATCH] python3Packages.ngff-zarr: 0.37.0 -> 0.37.1

Diff: https://github.com/fideus-labs/ngff-zarr/compare/py-v0.37.0...py-v0.37.1

Changelog: https://github.com/fideus-labs/ngff-zarr/releases/tag/py-v0.37.1
---
 .../python-modules/ngff-zarr/default.nix      | 84 ++++++++++++++-----
 1 file changed, 65 insertions(+), 19 deletions(-)

diff --git a/pkgs/development/python-modules/ngff-zarr/default.nix b/pkgs/development/python-modules/ngff-zarr/default.nix
index 0eee8e95bc0c..544c9f223ebf 100644
--- a/pkgs/development/python-modules/ngff-zarr/default.nix
+++ b/pkgs/development/python-modules/ngff-zarr/default.nix
@@ -1,44 +1,57 @@
 {
   lib,
   buildPythonPackage,
-  dask,
-  dask-image,
-  deepdiff,
   fetchFromGitHub,
+
+  # build-system
   hatchling,
+
+  # dependencies
+  dask,
   importlib-resources,
-  itk,
-  itkwasm-downsample,
-  itkwasm-image-io,
   itkwasm,
-  jsonschema,
-  nibabel,
-  imageio,
+  itkwasm-downsample,
   numpy,
-  imagecodecs,
   platformdirs,
-  pooch,
   psutil,
-  pytestCheckHook,
-  rich-argparse,
   rich,
-  tensorstore,
-  tifffile,
+  rich-argparse,
   typing-extensions,
-  writableTmpDirAsHomeHook,
   zarr,
+
+  # optional-dependencies
+  # dask-image:
+  dask-image,
+  # cli:
+  imagecodecs,
+  imageio,
+  itk,
+  itkwasm-image-io,
+  nibabel,
+  tifffile,
+  # tensorstore:
+  tensorstore,
+  # validate:
+  jsonschema,
+
+  # tests
+  deepdiff,
+  pooch,
+  pytestCheckHook,
+  writableTmpDirAsHomeHook,
 }:
 
 buildPythonPackage (finalAttrs: {
   pname = "ngff-zarr";
-  version = "0.37.0";
+  version = "0.37.1";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "fideus-labs";
     repo = "ngff-zarr";
     tag = "py-v${finalAttrs.version}";
-    hash = "sha256-v747oBJMKORiEgy3fVzzgl35+9uRbyGvtor+Ga4UkNI=";
+    hash = "sha256-73bduVeH+o7uirhwFcFpU33NUAOZe//GCVYMl6OYgC8=";
   };
 
   sourceRoot = "${finalAttrs.src.name}/py/";
@@ -87,7 +100,7 @@ buildPythonPackage (finalAttrs: {
     pytestCheckHook
     writableTmpDirAsHomeHook
   ]
-  ++ lib.flatten (builtins.attrValues finalAttrs.passthru.optional-dependencies);
+  ++ lib.concatAttrValues finalAttrs.passthru.optional-dependencies;
 
   pythonImportsCheck = [ "ngff_zarr" ];
 
@@ -96,16 +109,19 @@ buildPythonPackage (finalAttrs: {
     "test/test_cli_input_to_ngff_image.py"
     "test/test_cli_output.py"
     "test/test_cli_relative_paths.py"
+
     # Attribute errors
     "test/test_pyramid_integrity.py"
     "test/test_multiscales_type.py"
     "test/test_convert_ome_zarr_version.py"
     "test/test_itk_image_to_ngff_image.py"
+
     # Data missing
     "test/test_hcs.py"
     "test/test_hcs_simple.py"
     "test/test_ngff_validation.py"
     "test/test_nibabel_image_to_ngff_image.py"
+
     # Network access
     "test/test_from_ngff_zarr_tensorstore.py"
     "test/test_from_ngff_zarr.py"
@@ -120,16 +136,46 @@ buildPythonPackage (finalAttrs: {
     "test/test_to_ngff_zarr_sharding.py"
     "test/test_to_ngff_zarr_tensorstore.py"
     "test/test_to_ngff_zarr_v3_compression.py"
+
     # Missing dependencies
     "test/test_lif_to_ngff_image.py"
   ];
 
   disabledTests = [
+    # ValueError: zarr 3.2.1 < 3 is not supported
+    "test_clean_tiff_emits_no_structural_warning"
+    "test_multiseries_tiff_to_directory_keeps_per_series_stores"
+    "test_multiseries_tiff_to_ozx_creates_requested_file"
+    "test_non_rgb_multichannel_tiff_no_channel_colors"
+    "test_ome_tiff_channel_colors_from_xml"
+    "test_ome_tiff_rgb_s_axis_overrides_xml_colors"
+    "test_pyramidal_grayscale_tiff"
+    "test_pyramidal_rgb_tiff_channel_consistency"
+    "test_tiff_file_to_ngff_images_2d"
+    "test_tiff_file_to_ngff_images_all_series"
+    "test_tiff_file_to_ngff_images_no_ome_metadata"
+    "test_tiff_file_to_ngff_images_partial_ome_metadata"
+    "test_tiff_file_to_ngff_images_series_all"
+    "test_tiff_file_to_ngff_images_simple_rgb"
+    "test_tiff_file_to_ngff_images_single_series_by_index"
+    "test_tiff_file_to_ngff_images_unit_normalization"
+    "test_tiff_file_to_ngff_images_unsupported_axis_warning"
+    "test_tiff_file_to_ngff_images_with_channel_names"
+    "test_tiff_file_to_ngff_images_with_channels"
+    "test_tiff_file_to_ngff_images_with_ome_metadata"
+    "test_tiff_file_to_ngff_images_with_partial_channel_names"
+    "test_tiff_file_to_ngff_images_with_sample_axis"
+    "test_tiff_file_to_ngff_images_without_channel_names"
+    "test_tiff_sample_axis_rgba_sets_four_channel_colors"
+    "test_tiff_sample_axis_sets_rgb_channel_colors"
+    "test_truncated_tiff_emits_warning"
+
     # Assertion errors
     "test_2d_yx"
     "test_3d_zyx"
     "test_smaller_dask_graph"
     "test_tensorstore_compression"
+
     # Test requires network access
     "test_cli_orientation_preset_end_to_end"
     "test_cli_itk_input_writes_orientation_automatically"