Support zarr 3

pyproject.toml

@@ -2,7 +2,7 @@
 build-backend = "setuptools.build_meta"
 requires = [
     "cython",
-    "numpy<2",
+    "numpy",
     "setuptools>=42",
     "setuptools_scm[toml]>=3.4",
     "wheel"
@@ -31,15 +31,17 @@ classifiers = [# https://pypi.python.org/pypi?%3Aaction=list_classifiers
 ]
 
 dependencies = [
-    "adjustText",
     "anndata>=0.12.4", # https://github.com/scverse/anndata/issues/2166
-    "bioio<2",
+    "adjustText",
     "bioio-nd2",
     "bioio-tifffile",
+    "bioio-ome-tiff",
+    "bioio-ome-zarr>=3.2.2", # https://github.com/bioio-devs/bioio-ome-zarr/pull/130, https://github.com/bioio-devs/bioio-ome-zarr/issues/128
+    "bioio",
     "centrosome",
     "cp-measure",
+    "dask!=2026.1.2", # https://github.com/dask/dask/issues/12265
     "dask-image",
-    "dask",
     "decorator",
     "filelock",
     "flox",
@@ -53,14 +55,13 @@ dependencies = [
     "matplotlib",
     "natsort",
     "numcodecs",
-    "numpy<2",
+    "numpy",
     "ome-zarr",
     "pandas",
     "pint",
     "psutil",
     "pyarrow",
     "pydantic",
-    "pysam",
     "scikit-image",
     "scikit-learn",
     "scipy",
@@ -69,9 +70,9 @@ dependencies = [
     "stardist",
     "statsmodels",
     "tensorflow",
-    "tifffile==2024.8.30",
+    "tifffile",
     "xarray",
-    "zarr<3"
+    "zarr>=3"
 ]
 
 [project.optional-dependencies]
@@ -88,10 +89,12 @@ cellpose = [
 ufish = [
     "ufish"
 ]
+pysam = [
+    "pysam"
+]
 test = [
     "miniwdl",
-    "pytest",
-    "pytest-xdist"
+    "pytest"
 ]
 
 dev = [
@@ -105,22 +108,7 @@ doc = [
     "sphinx_argparse",
     "sphinx_rtd_theme",
 ]
-all = [
-    "napari",
-    "napari_ome_zarr",
-    "cellpose",
-    "dask-ml",
-    "ufish",
-    "pytest",
-    "pre-commit",
-    "ipython",
-    "myst_parser",
-    "nbsphinx",
-    "sphinx-copybutton",
-    "sphinx",
-    "sphinx_argparse",
-    "sphinx_rtd_theme"
-]
+
 [project.entry-points."miniwdl.plugin.container_backend"]
 miniwdl_test_local = "scallops.tests.miniwdl_local.local_runner:LocalRunner"
 

requirements.doc.txt

@@ -1,4 +1,4 @@
-ipython==9.9.0
+ipython==9.10.0
 nbsphinx==0.9.8
 sphinx-copybutton==0.5.2
 sphinx==9.1.0

requirements.txt

@@ -1,29 +1,30 @@
 anndata==0.12.10
 adjustText==1.3.0
-bioio-nd2==1.1.0
-bioio-tifffile==1.1.0
-bioio-base==1.0.7
-bioio==1.6.1
+bioio==3.2.0
+bioio-nd2==1.6.2
+bioio-ome-tiff==1.4.0
+bioio-ome-zarr==3.2.2
+bioio-tifffile==1.3.0
 centrosome==1.3.3
 cp-measure==0.1.13
 cython==3.2.4
 dask-image==2025.11.0
-dask==2025.11.0
+dask==2026.1.1
 decorator==5.2.1
 filelock==3.20.3
-flox==0.11.0
+flox==0.11.1
 fsspec==2026.2.0
 igraph==1.0.0
-itk-elastix==0.23.0
-itk==5.4.3
+itk-elastix==0.24.0
+itk==5.4.5
 joblib==1.5.3
 kneed==0.8.5
 mahotas==1.4.18
 matplotlib==3.10.8
 natsort==8.4.0
-numcodecs==0.15.1
-numpy==1.26.4
-ome-zarr==0.10.3
+numcodecs==0.16.5
+numpy==2.3.5
+ome-zarr==0.13.0
 pandas==2.3.3
 pint==0.25.2
 psutil==7.2.2
@@ -37,7 +38,7 @@ seaborn==0.13.2
 shapely==2.1.2
 stardist==0.9.2
 statsmodels==0.14.6
-tensorflow==2.19.0
-tifffile==2024.8.30
+tensorflow==2.20.0
+tifffile==2026.1.28
 xarray==2026.1.0
-zarr==2.18.7
+zarr==3.1.5