upgrade for zarr v3 API

.github/workflows/python-package.yml

@@ -21,13 +21,13 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -57,9 +57,9 @@ jobs:
     runs-on: ubuntu-latest
     if: contains(github.ref, 'tags')
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - name: Install dependencies

.pre-commit-config.yaml

@@ -9,6 +9,7 @@ repos:
     rev: v3.2.0
     hooks:
       - id: setup-cfg-fmt
+        args: [--min-py-version, "3.11"]
   - repo: https://github.com/PyCQA/flake8
     rev: 7.3.0
     hooks:
@@ -33,7 +34,7 @@ repos:
     rev: v3.21.2
     hooks:
       - id: pyupgrade
-        args: [--py38-plus, --keep-runtime-typing]
+        args: [--py311-plus, --keep-runtime-typing]
   # - repo: https://github.com/tlambert03/napari-plugin-checks
   #   rev: v0.2.0
   #   hooks:

setup.cfg

@@ -27,8 +27,8 @@ install_requires =
     dask
     fire
     nd2
-    zarr>=2.4,<3
-python_requires = >=3.10
+    zarr>=3.0
+python_requires = >=3.11
 include_package_data = True
 package_dir =
     =src

src/zarr_tools/convert.py

@@ -6,6 +6,7 @@
 
 import dask.array as da
 import zarr
+from zarr.storage import LocalStore
 
 
 def to_zarr(
@@ -19,8 +20,9 @@ def to_zarr(
     """
     Saves multiscale zarr dataset, returns the path.zarr
     """
-    store = zarr.DirectoryStore(baseurl := path)
-    grp = zarr.group(store)
+    baseurl = path
+    store = LocalStore(baseurl)
+    grp = zarr.open_group(store, mode="a")
 
     print(baseurl)
     datasets = []