ngio 0.4.3__tar.gz → 0.4.5__tar.gz

{ngio-0.4.3 → ngio-0.4.5}/CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## [v0.4.5]
+
+### Bug Fixes
+- Pin Dask to version <2025.11 to avoid errors when writing zarr pyramids with dask (see https://github.com/dask/dask/issues/12159#issuecomment-3548421833)
+
+## [v0.4.4]
+
+### Bug Fixes
+
+- Fix bug in channel visualization when using hex colors with leading '#'.
+- Remove strict range check in channel window.
+
 ## [v0.4.3]
 
 ### Bug Fixes

{ngio-0.4.3 → ngio-0.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.3
+Version: 0.4.5
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -17,8 +17,8 @@ Classifier: Typing :: Typed
 Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata<0.11.4,>=0.8.0
-Requires-Dist: dask[array]
-Requires-Dist: dask[distributed]
+Requires-Dist: dask[array]<2025.11.0
+Requires-Dist: dask[distributed]<2025.11.0
 Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models

{ngio-0.4.3 → ngio-0.4.5}/pyproject.toml

@@ -36,13 +36,13 @@ dependencies = [
     "numpy",
     "filelock",
     "zarr<3",
-    "anndata>=0.8.0,<0.11.4", # To be removed when we transition to zarr v3
+    "anndata>=0.8.0,<0.11.4",      # To be removed when we transition to zarr v3
     "pydantic",
     "pandas>=1.2.0",
     "requests",
     "aiohttp",
-    "dask[array]",
-    "dask[distributed]",
+    "dask[array]<2025.11.0",
+    "dask[distributed]<2025.11.0",
     # "xarray", still not used
     "ome-zarr-models",
     "pooch",

{ngio-0.4.3 → ngio-0.4.5}/src/ngio/common/_pyramid.py

@@ -2,6 +2,7 @@ import math
 from collections.abc import Callable, Sequence
 from typing import Literal
 
+import dask
 import dask.array as da
 import numpy as np
 import zarr
@@ -36,9 +37,17 @@ def _on_disk_dask_zoom(
 ) -> None:
     source_array = da.from_zarr(source)
     target_array = dask_zoom(source_array, target_shape=target.shape, order=order)
-
+    # This is a potential fix for Dask 2025.11
+    # chunk_size_bytes = np.prod(target.chunks) * target_array.dtype.itemsize
+    # current_chunk_size = dask.config.get("array.chunk-size", 0)
+    #
+    #if current_chunk_size < chunk_size_bytes:
+    #    # Increase the chunk size to avoid dask potentially creating 
+    #    # corrupted chunks when writing chunks that are not multiple of the
+    #    # target chunk size
+    #    dask.config.set({"array.chunk-size": f"{chunk_size_bytes}B"})
     target_array = target_array.rechunk(target.chunks)
-    target_array.compute_chunk_sizes()
+    target_array = target_array.compute_chunk_sizes()
     target_array.to_zarr(target)
 
 
@@ -241,13 +250,11 @@ def init_empty_pyramid(
             compressor=compressor,
         )
 
-        _shape = [
+        ref_shape = [
             math.floor(s / sc) for s, sc in zip(ref_shape, scaling_factors, strict=True)
         ]
-        ref_shape = _shape
+        chunks = tuple(
+            min(c, s) for c, s in zip(new_arr.chunks, ref_shape, strict=True)
+        )
 
-        if chunks is None:
-            chunks = new_arr.chunks
-            assert chunks is not None
-        chunks = [min(c, s) for c, s in zip(chunks, ref_shape, strict=True)]
     return None

{ngio-0.4.3 → ngio-0.4.5}/src/ngio/ome_zarr_meta/ngio_specs/_channels.py

@@ -102,6 +102,20 @@ def valid_hex_color(v: str) -> bool:
     return True
 
 
+def into_valid_hex_color(v: str) -> str:
+    """Convert a string into a valid hexadecimal color.
+
+    If the string is already a valid hexadecimal color, return it.
+    Otherwise, return a hexadecimal color based on the hash of the string.
+    """
+    # strip leading '#' if present
+    v = v.lstrip("#")
+    if valid_hex_color(v):
+        return v
+
+    return NgioColors.semi_random_pick(v.lower()).value
+
+
 class ChannelVisualisation(BaseModel):
     """Channel visualisation model.
 
@@ -135,13 +149,10 @@ class ChannelVisualisation(BaseModel):
         """
         if value is None:
             return NgioColors.semi_random_pick().value
-        if isinstance(value, str) and valid_hex_color(value):
-            return value
+        if isinstance(value, str):
+            return into_valid_hex_color(value)
         elif isinstance(value, NgioColors):
             return value.value
-        elif isinstance(value, str):
-            value_lower = value.lower()
-            return NgioColors.semi_random_pick(value_lower).value
         else:
             raise NgioValueError(f"Invalid color {value}.")
 
@@ -159,19 +170,6 @@ class ChannelVisualisation(BaseModel):
             data["end"] = start + 1
         return data
 
-    @model_validator(mode="after")
-    def check_model(self) -> "ChannelVisualisation":
-        """Check that the start and end values are within the min and max values."""
-        if self.start < self.min or self.start > self.max:
-            raise NgioValidationError(
-                f"Start value {self.start} is out of range [{self.min}, {self.max}]"
-            )
-        if self.end < self.min or self.end > self.max:
-            raise NgioValidationError(
-                f"End value {self.end} is out of range [{self.min}, {self.max}]"
-            )
-        return self
-
     @classmethod
     def default_init(
         cls,

{ngio-0.4.3 → ngio-0.4.5}/src/ngio/tables/v1/_roi_table.py

@@ -86,10 +86,10 @@ def _dataframe_to_rois(
 ) -> dict[str, Roi]:
     """Convert a DataFrame to a WorldCooROI object."""
     # Validate the columns of the DataFrame
-    _required_columns = set(dataframe.columns).intersection(set(required_columns))
-    if len(_required_columns) != len(required_columns):
+    _missing_columns = set(required_columns).difference(set(dataframe.columns))
+    if len(_missing_columns) != 0:
         raise NgioTableValidationError(
-            f"Could not find required columns: {_required_columns} in the table."
+            f"Could not find required columns: {_missing_columns} in the table."
         )
 
     extra_columns = set(dataframe.columns).difference(