python3Packages.ome-zarr: 0.12.2 -> 0.13.0 (#488800)

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

@@ -0,0 +1,94 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  pythonAtLeast,
+
+  # build-system
+  hatch-vcs,
+  hatchling,
+
+  # dependencies
+  pydantic,
+  pydantic-zarr,
+  zarr,
+
+  # tests
+  aiohttp,
+  fsspec,
+  pytest-cov-stub,
+  pytest-vcr,
+  pytestCheckHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "ome-zarr-models";
+  version = "1.5";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "ome-zarr-models";
+    repo = "ome-zarr-models-py";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-lEzYP4AcEV6EtE+E8yqNHJPIPJ0RwWtzm77fcdxYGYk=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  dependencies = [
+    pydantic
+    pydantic-zarr
+    zarr
+  ];
+
+  pythonImportsCheck = [ "ome_zarr_models" ];
+
+  nativeCheckInputs = [
+    aiohttp
+    fsspec
+    pytest-cov-stub
+    pytest-vcr
+    pytestCheckHook
+  ];
+
+  disabledTests = [
+    # Require internet connection
+    "test_bioformats2raw_get_image"
+    "test_load_remote_data"
+  ]
+  ++ lib.optionals (pythonAtLeast "3.14") [
+    # pydantic.errors.PydanticUserError: `Image` is not fully defined; you should define all
+    # referenced types, then call `Image.model_rebuild()`.
+    "test_datasets"
+    "test_example_hcs"
+    "test_from_zarr_ectopic_group"
+    "test_from_zarr_missing_array"
+    "test_global_transform"
+    "test_image"
+    "test_multiscale_group_ectopic_group"
+    "test_multiscale_group_missing_arrays"
+    "test_new_image"
+    "test_no_global_transform"
+    "test_non_existent_wells"
+    "test_non_existent_wells_from_zarr"
+    "test_well"
+
+    # RuntimeError: Could not successfully validate
+    # <Group file:///build/source/tests/data/examples/v04/hcs_example.ome.zarr> against any OME-Zarr
+    # group model
+    "test_cli_validate"
+    "test_load_ome_zarr_group"
+  ];
+
+  meta = {
+    description = "Minimal Python package for reading, writing and validating OME-Zarr (meta)data";
+    homepage = "https://ome-zarr-models-py.readthedocs.io/en/stable";
+    downloadPage = "https://github.com/ome-zarr-models/ome-zarr-models-py";
+    changelog = "https://github.com/ome-zarr-models/ome-zarr-models-py/releases/tag/${finalAttrs.src.tag}";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+})

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

@@ -12,25 +12,27 @@
   dask,
   fsspec,
   numpy,
+  rangehttpserver,
   requests,
   scikit-image,
   toolz,
   zarr,
 
   # tests
+  ome-zarr-models,
   pytestCheckHook,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "ome-zarr";
-  version = "0.12.2";
+  version = "0.13.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "ome";
     repo = "ome-zarr-py";
-    tag = "v${version}";
-    hash = "sha256-lwv6PHm41HFylt7b0d5LHCrCIXNWFNGg59VQvPXYtVc=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-bRksh6ZKqF6cL6XnWBsQRb4gRVxH/vutKtep6SyFo48=";
   };
 
   build-system = [
@@ -38,11 +40,15 @@ buildPythonPackage rec {
     setuptools-scm
   ];
 
+  pythonRelaxDeps = [
+    "dask"
+  ];
   dependencies = [
     aiohttp
     dask
     fsspec
     numpy
+    rangehttpserver
     requests
     scikit-image
     toolz
@@ -51,6 +57,7 @@ buildPythonPackage rec {
   ++ fsspec.optional-dependencies.s3;
 
   nativeCheckInputs = [
+    ome-zarr-models
     pytestCheckHook
   ];
 
@@ -104,9 +111,9 @@ buildPythonPackage rec {
   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/${src.tag}/CHANGELOG.md";
+    changelog = "https://github.com/ome/ome-zarr-py/blob/${finalAttrs.src.tag}/CHANGELOG.md";
     license = lib.licenses.bsd2;
     maintainers = [ lib.maintainers.bcdarwin ];
     mainProgram = "ome_zarr";
   };
-}
+})

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

@@ -0,0 +1,64 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  hatch-vcs,
+  hatchling,
+
+  # dependencies
+  numpy,
+  packaging,
+  pydantic,
+
+  # tests
+  dask,
+  pytest-examples,
+  pytestCheckHook,
+  xarray,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "pydantic-zarr";
+  version = "0.9.1";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "zarr-developers";
+    repo = "pydantic-zarr";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-rgtRN3EXSORa2g2a4aCZacCDLeWM6BosZe5XR0Pg6pU=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  dependencies = [
+    numpy
+    packaging
+    pydantic
+  ];
+
+  pythonImportsCheck = [ "pydantic_zarr" ];
+
+  nativeCheckInputs = [
+    dask
+    pytest-examples
+    pytestCheckHook
+    xarray
+  ];
+
+  meta = {
+    description = "Pydantic models for Zarr";
+    homepage = "https://github.com/zarr-developers/pydantic-zarr";
+    changelog = "https://github.com/zarr-developers/pydantic-zarr/releases/tag/${finalAttrs.src.tag}";
+    license = with lib.licenses; [
+      bsd3
+      mit
+    ];
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+})

pkgs/top-level/python-packages.nix

@@ -11231,6 +11231,8 @@ self: super: with self; {
 
   ome-zarr = callPackage ../development/python-modules/ome-zarr { };
 
+  ome-zarr-models = callPackage ../development/python-modules/ome-zarr-models { };
+
   omegaconf = callPackage ../development/python-modules/omegaconf { };
 
   omemo = callPackage ../development/python-modules/omemo { };
@@ -13312,6 +13314,8 @@ self: super: with self; {
 
   pydantic-settings = callPackage ../development/python-modules/pydantic-settings { };
 
+  pydantic-zarr = callPackage ../development/python-modules/pydantic-zarr { };
+
   pydantic_1 = callPackage ../development/python-modules/pydantic/1.nix { };
 
   pydash = callPackage ../development/python-modules/pydash { };