ngio 0.2.10__tar.gz → 0.2.12__tar.gz

{ngio-0.2.10 → ngio-0.2.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.10
+Version: 0.2.12
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -16,7 +16,7 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
 Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
-Requires-Dist: anndata>=0.8.0
+Requires-Dist: anndata<0.11.4,>=0.8.0
 Requires-Dist: dask[array]
 Requires-Dist: dask[distributed]
 Requires-Dist: filelock

{ngio-0.2.10 → ngio-0.2.12}/pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "numpy",
     "filelock",
     "zarr<3",
-    "anndata>=0.8.0",
+    "anndata>=0.8.0,<0.11.4", # To be removed when we transition to zarr v3
     "pydantic",
     "pandas>=1.2.0",
     "requests",

{ngio-0.2.10 → ngio-0.2.12}/src/ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py

@@ -21,21 +21,12 @@ from ngio.utils import NgioValueError, ngio_logger
 
 def path_in_well_validation(path: str) -> str:
     """Validate the path in the well."""
-    if path.find("_") != -1:
-        # Remove underscores from the path
-        # This is a custom serialization step
-        old_value = path
-        path = path.replace("_", "")
-        ngio_logger.warning(
-            f"Underscores in well-paths are not allowed. "
-            f"Path '{old_value}' was changed to '{path}'"
-            f" to comply with the specification."
-        )
     # Check if the value contains only alphanumeric characters
     if not path.isalnum():
-        raise NgioValueError(
+        ngio_logger.warning(
             f"Path '{path}' contains non-alphanumeric characters. "
-            f"Only alphanumeric characters are allowed."
+            "Only alphanumeric characters are allowed, "
+            "this might cause issues in some tools."
         )
     return path
 

{ngio-0.2.10 → ngio-0.2.12}/tests/unit/hcs/test_plate.py

@@ -87,7 +87,7 @@ def test_create_and_edit_plate_path_normalization(tmp_path: Path):
     test_plate.add_image(
         row="B", column="03", image_path="1_illumination_correction", acquisition_id=0
     )
-    assert test_plate.images_paths() == ["B/03/0mip", "B/03/1illuminationcorrection"]
+    assert test_plate.images_paths() == ["B/03/0_mip", "B/03/1_illumination_correction"]
 
 
 def test_derive_plate_from_ome_zarr(cardiomyocyte_tiny_path: Path, tmp_path: Path):

{ngio-0.2.10 → ngio-0.2.12}/tests/unit/ome_zarr_meta/test_unit_v04_utils.py

@@ -69,4 +69,4 @@ def test_well_meta_path_normalization():
     assert isinstance(output_metadata, dict)
 
     images = [image["path"] for image in output_metadata["well"]["images"]]
-    assert images == ["0", "0mip"]
+    assert images == ["0", "0_mip"]