Migrate zarr v3

.github/workflows/run_pytests.yaml

@@ -18,17 +18,15 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.13"]
+        python-version: ["3.14"]
         include:
           # we'll test the python support on ubuntu
+          - os: ubuntu-latest
+            python-version: "3.13"
           - os: ubuntu-latest
             python-version: "3.12"
           - os: ubuntu-latest
             python-version: "3.11"
-          - os: ubuntu-latest
-            python-version: "3.10"
-          - os: ubuntu-latest
-            python-version: "3.9"
     steps:
       - name: Checkout TiffSlide
         uses: actions/checkout@v3
@@ -55,14 +53,14 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e .[dev]
       - name: Run mypy
         run: |
-          mypy --install-types --non-interactive --python-version=3.9 tiffslide
+          mypy --install-types --non-interactive --python-version=3.11 tiffslide
 
   # DEPLOY TIFFSLIDE TO TEST.PYPI ON SUCCESS
   testdeploy:
@@ -77,7 +75,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -114,7 +112,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

docs/generate_benchmark_plots.py

@@ -46,16 +46,18 @@ def run_pytest_benchmarks(force: bool) -> None:
 
     df = pd.DataFrame.from_records(records)
     for test_name, ptdf in df.groupby("test_name"):
-        ft_ax_order = [
+        ft_ax_order_all = [
             "svs",
             "svs_jp2k",
             "generic",
             "hamamatsu",
             "leica",
             "ventana",
         ]
-        assert set(ptdf["file_type"].unique()) == set(ft_ax_order)
-        fig, axes = plt.subplots(1, len(ft_ax_order), figsize=(10, 4))
+        available = set(ptdf["file_type"].unique())
+        ft_ax_order = [ft for ft in ft_ax_order_all if ft in available]
+        fig, axes = plt.subplots(1, len(ft_ax_order), figsize=(10, 4), squeeze=False)
+        axes = axes[0]  # unwrap row dimension
         fig.suptitle(test_name, x=0.1, y=0.99)
         ft_ax_map = {ft: ax for ft, ax in zip(ft_ax_order, axes)}
 

pyproject.toml

@@ -18,8 +18,6 @@ classifiers = [
   "License :: OSI Approved :: BSD License",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.9",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
@@ -32,13 +30,13 @@ classifiers = [
   "Operating System :: Unix",
   "Operating System :: MacOS",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 dependencies = [
   "imagecodecs",
-  "fsspec>=2023.3.0",
+  "fsspec>=2024.10.0",
   "pillow>=9.1.0",
-  "tifffile>=2023.7.4,<2025.5.21",
-  "zarr>=2.16.0,<3.0",
+  "tifffile>=2025.5.21",
+  "zarr>=3.0,<4.0",
   "typing_extensions>=4.0",
 ]
 dynamic = ["version"]
@@ -90,7 +88,7 @@ markers = [
 
 [tool.isort]
 profile = "black"
-py_version = "39"
+py_version = "311"
 force_single_line = true
 extend_skip = ["setup.py", "docs/source/conf.py"]
 
@@ -107,7 +105,7 @@ exclude_lines = [
 ]
 
 [tool.mypy]
-python_version = "3.9"
+python_version = "3.11"
 check_untyped_defs = true
 disallow_any_generics = true
 disallow_incomplete_defs = true

tiffslide/_compat.py

@@ -153,7 +153,14 @@ def size(self) -> int:
         return self._array.size
 
     def aszarr(self) -> zarr.storage.MemoryStore:
-        return zarr.creation.array(self._array).store
+        store = zarr.storage.MemoryStore()
+        zarr.create_array(
+            store=store,
+            data=self._array,
+            chunks=self._array.shape,
+            zarr_format=2,
+        )
+        return store
 
     def asarray(self) -> NDArray[np.uint8]:
         return self._array

tiffslide/_kerchunk.py

@@ -10,13 +10,16 @@
 import json
 import os
 import sys
+import threading
 from collections import ChainMap
 from io import StringIO
 from typing import TYPE_CHECKING
 from typing import Any
 from typing import TypedDict
 
 import fsspec
+from fsspec.asyn import get_loop
+from fsspec.asyn import sync as _fsspec_sync
 from imagecodecs.numcodecs import register_codecs
 
 from tiffslide.tiffslide import TiffSlide
@@ -137,9 +140,10 @@ def from_kerchunk(
     fs: ReferenceFileSystem = fsspec.filesystem(
         "reference",
         fo=kc,
+        asynchronous=True,
         **storage_options,
     )
-    zattrs = json.loads(fs.cat_file(".zattrs"))
+    zattrs = json.loads(_fsspec_sync(get_loop(), fs._cat_file, ".zattrs"))
 
     if "tiffslide.spec_version" not in zattrs or "tiffslide.properties" not in zattrs:
         raise ValueError("")
@@ -155,6 +159,8 @@ def from_kerchunk(
     inst = object.__new__(TiffSlide)
     inst.__dict__["properties"] = properties
     inst._tifffile = fs  # fixme: ...
+    inst._zarr_local = threading.local()
+    inst._zarr_lock = threading.Lock()
     return inst