⬆️ Upgrade Zarr to v3+ Compatibility (#904)

## ✅ Summary

- Enables compatibility with Zarr v3+
- Simplifies error handling across Zarr versions
- Removes deprecated storage backends and APIs
- Lays groundwork for full Zarr v3 migration

This PR updates TIAToolbox to support **Zarr v3+**, addressing breaking changes introduced in Zarr ≥ 3.0 and aligning internal APIs, storage handling, and error handling accordingly.

---

Zarr v3 removed `zarr.errors.FSPathExistNotDir`. In Zarr ≥ 3.0, equivalent failure modes now raise standard Python exceptions (e.g. `FileNotFoundError`).

To avoid fragile version-specific logic:
- Removed checks for specific Zarr exception types
- Replaced them with generic exception handling that works consistently across Zarr versions

---

## 🔧 Key changes

### Dependency updates
- 🆙 Upgrade to:
  - `zarr >= 3.0.8`
  - `tifffile >= 2025.5.21`

### Zarr API & storage migration
- Refactor `zarr.core.Array` → `zarr.Array`
- Replace `zarr.DirectoryStore` with `zarr.storage.LocalStore`
- Remove `ngff.sqlitestore` (Zarr v3 no longer supports `zarr.SQLiteStore`)
- Replace `canvas_zarr.store.path` with `canvas_zarr.store.root`
- Ensure Zarr paths explicitly use string keys (`key / str(i)` instead of `key / i`)

### Dask & array handling
- Remove unsupported `object_codec` usage in `dask.to_zarr`
- Update `zarr.resize` calls to use tuple inputs
- Replace `output.items()` with `output.members()`

---

## ⚠️ Known limitations & follow‑ups

Zarr v3 removes or significantly changes several APIs still used by TIAToolbox, including:
- `zarr.LRUStoreCache`
- `zarr.DirectoryStore`
- `zarr.SQLiteStore`

While this PR resolves immediate incompatibilities and enables Zarr v3 usage, **additional refactoring will be required** to fully replace or redesign components that depend on these removed features.

In addition, **full compatibility with `tifffile` depends on upstream Zarr v3 support**, and some workflows may remain limited until that stabilises.

📖 For a detailed overview of breaking changes, see the official Zarr v3 migration guide:  
https://zarr.readthedocs.io/en/latest/user-guide/v3_migration.html

---------

Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Aleksandar Acic <32873451+aacic@users.noreply.github.com>
Co-authored-by: Jiaqi Lv <lvjiaqi9@gmail.com>

Author: 5 people

.github/workflows/mypy-type-check.yml

@@ -47,7 +47,7 @@ jobs:
 
     - name: Perform type checking
       run: |
-        mypy --install-types --non-interactive --follow-imports=silent \
+        mypy --install-types --non-interactive --follow-imports=skip --ignore-missing-imports \
           tiatoolbox/__init__.py \
           tiatoolbox/__main__.py \
           tiatoolbox/type_hints.py \

requirements/requirements.txt

@@ -30,12 +30,12 @@ scipy>=1.8
 shapely>=2.0.0
 SimpleITK>=2.2.1
 sphinx>=5.3.0, <9.0.0
-tifffile>=2022.10.10, <=2025.5.10
+tifffile>=2025.5.21
 timm>=1.0.3
 torch>=2.5.0
 torchvision>=0.15.0
 tqdm>=4.64.1
 transformers>=4.51.1
 umap-learn>=0.5.3
 wsidicom>=0.18.0
-zarr>=2.13.3, <3.0.0
+zarr>=3.0.8