From b19344e65081f44246ba9c749a4818da7e063dd5 Mon Sep 17 00:00:00 2001
From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>
Date: Fri, 14 Nov 2025 00:42:04 +0100
Subject: [PATCH 1/4] use zarr3 and unpin dask

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8180e13..b0a7787 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,7 @@ dependencies = [
   'pandas>=1.1.2',
   'black>=21.11b1',
   'numpy>=1.21.2',
-  'zarr>=2.5.0,<3',
+  'zarr>=3.0.0',
   'numcodecs>=0.5.7,<0.16.0',
 ]
 
@@ -89,7 +89,7 @@ testing = []
 linting = []
 notebook = [
   'spatialdata>=0.3.0',
-  'dask[dataframe]==2024.11.1',
+  'dask[dataframe]>=2025.2.0',
   'marimo',
   'starlette>=0.42.0',
   'tqdm>=4.1.0',
@@ -115,7 +115,7 @@ dev = [
   'scikit-misc>=0.1.3',
   'autopep8>=2.0.2',
   'spatialdata>=0.3.0',
-  'dask[dataframe]==2024.11.1',
+  'dask[dataframe]>=2025.2.0',
 ]
 
 [tool.uv]

From bf7a972ab1f3878b2c3f42f7a5d0bc00329aed60 Mon Sep 17 00:00:00 2001
From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>
Date: Fri, 14 Nov 2025 00:45:51 +0100
Subject: [PATCH 2/4] relax ome-zarr upped bound

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b0a7787..d95bf9d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -65,7 +65,7 @@ all = [
   # scanpy < 1.10.3 does not support numpy >= 2.0.0 and does not
   # Reference: https://github.com/scverse/scanpy/pull/3115/files
   'scanpy>=1.10.2',
-  'ome-zarr<0.10.3',
+  'ome-zarr>=0.12.2',
   'tifffile>=2020.10.1',
 
   'jupyter-server-proxy>=1.5.2',

From 8f9ac2b711a0d21f3c1cca5835cf1f6c70735c32 Mon Sep 17 00:00:00 2001
From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>
Date: Fri, 14 Nov 2025 00:48:39 +0100
Subject: [PATCH 3/4] allow-direct-references hatch

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index d95bf9d..c0cfadc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -125,6 +125,9 @@ override-dependencies = []
 [tool.hatch.build]
 exclude = [".github", "docs", "demos", "binder"]
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [project.urls]
 repository = "https://github.com/vitessce/vitessce-python"
 

From 888dfde52b59c4f66ad783063b2e5ad0f2307f37 Mon Sep 17 00:00:00 2001
From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>
Date: Fri, 14 Nov 2025 00:51:03 +0100
Subject: [PATCH 4/4] set tool.hatch.metadata.allow-direct-references false

---
 pyproject.toml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c0cfadc..d95bf9d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -125,9 +125,6 @@ override-dependencies = []
 [tool.hatch.build]
 exclude = [".github", "docs", "demos", "binder"]
 
-[tool.hatch.metadata]
-allow-direct-references = true
-
 [project.urls]
 repository = "https://github.com/vitessce/vitessce-python"