zarr3-start

pyproject.toml

@@ -33,17 +33,20 @@ classifiers = [# https://pypi.python.org/pypi?%3Aaction=list_classifiers
 dependencies = [
     "adjustText",
     "anndata>=0.12.4", # https://github.com/scverse/anndata/issues/2166
-    "bioio<2",
     "bioio-nd2",
+    "bioio-ome-tiff",
+    "bioio-ome-zarr",
     "bioio-tifffile",
-    "centrosome",
-    "cp-measure>=0.1.16",
+    "bioio>=3",
+    "centrosome>=0.1.16",
+    "cp-measure",
+    "cython",
     "dask-image",
-    "dask<=2025.11.0",
+    "dask",
     "decorator",
     "filelock",
     "flox",
-    "fsspec!=2023.9.0", # 2023.9.0 causes ome-zarr write image to fail
+    "fsspec",
     "igraph",
     "itk-elastix",
     "itk",
@@ -54,7 +57,7 @@ dependencies = [
     "natsort",
     "numcodecs",
     "numpy",
-    "ome-zarr<0.12.0",
+    "ome-zarr",
     "pandas",
     "pint",
     "psutil",
@@ -68,13 +71,13 @@ dependencies = [
     "stardist",
     "statsmodels",
     "tensorflow",
-    "tifffile<=2025.5.10",
+    "tifffile",
     "xarray",
-    "zarr<3"
+    "zarr>=3",
 ]
 
 [project.optional-dependencies]
-# Added pysam as an optional extra for Linux/macOS users
+
 dialout = [
     "pysam"
 ]

requirements.txt

@@ -1,13 +1,15 @@
-anndata==0.12.16
 adjustText==1.3.0
-bioio-nd2==1.3.0
+anndata==0.12.16
+bioio-nd2==1.7.0
+bioio-ome-tiff==1.4.0
+bioio-ome-zarr==3.4.0
 bioio-tifffile==1.3.0
-bioio==1.6.1
+bioio==3.3.0
 centrosome==1.3.3
 cp-measure==0.1.19
-cython==3.2.4
+cython==3.2.5
 dask-image==2025.11.0
-dask==2025.11.0
+dask==2026.3.0
 decorator==5.2.1
 filelock==3.29.0
 flox==0.11.2
@@ -20,14 +22,14 @@ kneed==0.8.6
 mahotas==1.4.18
 matplotlib==3.10.9
 natsort==8.4.0
-numcodecs==0.15.1
-numpy==2.4.4
-ome-zarr==0.11.1
+numcodecs==0.16.5
+numpy==2.4.6
+ome-zarr==0.16.0
 pandas==2.3.3
 pint==0.25.3
 psutil==7.2.2
 pyarrow==24.0.0
-pydantic==2.12.5
+pydantic==2.13.4
 scikit-image==0.26.0
 scikit-learn==1.8.0
 scipy==1.17.1
@@ -36,6 +38,6 @@ shapely==2.1.2
 stardist==0.9.2
 statsmodels==0.14.6
 tensorflow==2.21.0
-tifffile==2025.5.10
-xarray==2026.2.0
-zarr==2.18.7
+tifffile==2026.5.15
+xarray==2026.4.0
+zarr==3.2.1

scallops/__init__.py

@@ -1,7 +1,15 @@
+import logging
 import warnings
 
 from .experiment.elements import Experiment  # noqa: F401
 
+logging.getLogger("asyncio").setLevel(logging.CRITICAL)
+warnings.filterwarnings(
+    "ignore",
+    message="Unclosed client session",
+    category=ResourceWarning,
+    module="aiohttp",
+)
 warnings.filterwarnings(
     "ignore",
     message="Writing zarr v2 data will no longer be the default",