zarr3 final merge

.gitignore

@@ -161,3 +161,6 @@ logs/
 
 .pdm-python
 requirements/local
+
+# uv
+uv.lock

BIOIO_ZARR3_DEPENDENCIES.md

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+# BioIO and Zarr-3 Dependency Compatibility Report
+
+## Currently Installed Packages (from pip freeze)
+
+### Core Zarr and OME Packages
+```
+zarr==3.1.5
+ome-zarr==0.12.2
+ome-types==0.6.2
+```
+
+### BioIO Core and Readers
+```
+bioio==3.0.0
+bioio-base==3.0.0
+bioio-ome-zarr==3.1.0
+```
+
+### Supporting Libraries
+```
+dask==2025.10.0
+distributed==2025.10.0
+fsspec==2025.10.0
+s3fs==2025.10.0
+numcodecs==0.16.5
+tifffile==2025.10.16
+xarray==2025.11.0
+```
+
+## Expected Packages (from requirements.txt)
+
+### Missing BioIO Readers
+The following bioio readers are specified in pyproject.toml but not currently installed:
+```
+bioio-czi==2.4.1          # For CZI file format
+bioio-ome-tiff==1.4.0     # For OME-TIFF files
+bioio-tifffile==1.3.0     # For TIFF files
+```
+
+## Zarr-3 Compatibility Analysis
+
+### ✅ COMPATIBLE - Core Packages
+- **zarr 3.1.5**: Latest stable zarr-3 version
+- **ome-zarr 0.12.2**: Fully supports zarr-3 (released Dec 2024)
+- **bioio 3.0.0**: Compatible with zarr-3
+- **bioio-base 3.0.0**: Compatible with zarr-3
+- **bioio-ome-zarr 3.1.0**: Explicitly supports zarr-3
+
+### ✅ COMPATIBLE - Supporting Libraries
+- **tifffile 2025.10.16**: Latest version, supports zarr-3
+- **numcodecs 0.16.5**: Compatible with zarr-3
+- **dask 2025.10.0**: Compatible with zarr-3
+- **xarray 2025.11.0**: Compatible with zarr-3
+- **fsspec 2025.10.0**: Compatible with zarr-3
+- **s3fs 2025.10.0**: For S3 zarr stores, compatible
+
+### ⚠️ VERSION DISCREPANCY
+- **dask**: Currently installed 2025.10.0 vs requirements.txt 2025.3.0
+  - Status: **OK** - Both versions are compatible
+  - Note: bioio-ome-zarr requires `dask!=2025.11.0`, so 2025.10.0 is safe
+
+### 🔍 MISSING - Optional Readers (not installed)
+These are specified in pyproject.toml but not installed in current environment:
+- **bioio-czi 2.4.1**: For Zeiss CZI files
+- **bioio-ome-tiff 1.4.0**: For OME-TIFF files
+- **bioio-tifffile 1.3.0**: For standard TIFF files
+
+## Compatibility Status by Format
+
+### Zarr Format Support
+| Format | Reader | Installed | Zarr-3 Compatible |
+|--------|--------|-----------|-------------------|
+| OME-Zarr | bioio-ome-zarr 3.1.0 | ✅ Yes | ✅ Yes |
+| OME-Zarr | ome-zarr 0.12.2 | ✅ Yes | ✅ Yes |
+
+### TIFF Format Support
+| Format | Reader | Installed | Zarr-3 Compatible |
+|--------|--------|-----------|-------------------|
+| TIFF | bioio-tifffile | ❌ No | ✅ Yes (if installed) |
+| OME-TIFF | bioio-ome-tiff | ❌ No | ✅ Yes (if installed) |
+
+### Other Format Support
+| Format | Reader | Installed | Zarr-3 Compatible |
+|--------|--------|-----------|-------------------|
+| CZI | bioio-czi | ❌ No | ✅ Yes (if installed) |
+
+## Recommendations
+
+### For Zarr-3 Dataloader Usage (Minimal)
+Current installation is **SUFFICIENT** for zarr-3 format. You have:
+- ✅ zarr 3.1.5
+- ✅ ome-zarr 0.12.2
+- ✅ bioio-ome-zarr 3.1.0
+- ✅ bioio-base 3.0.0
+- ✅ All supporting libraries
+
+### For Complete BioIO Functionality
+To support all file formats specified in pyproject.toml, install:
+```bash
+pip install bioio-czi bioio-ome-tiff bioio-tifffile
+```
+
+Or install from requirements.txt:
+```bash
+pip install -r requirements/requirements.txt
+```
+
+### For Production Use
+Recommend installing all bioio readers to ensure compatibility with various input formats:
+```bash
+pip install \
+  bioio>=3.0.0 \
+  bioio-base>=3.0.0 \
+  bioio-czi>=2.4.1 \
+  bioio-ome-tiff>=1.4.0 \
+  bioio-ome-zarr>=3.1.0 \
+  bioio-tifffile>=1.3.0 \
+  zarr>=3.0.0 \
+  ome-zarr>=0.12.0
+```
+
+## Version Constraints in pyproject.toml
+
+Current constraints (verified compatible with zarr-3):
+```toml
+dependencies = [
+    "zarr>=3.0.0",           # ✅ Ensures zarr-3
+    "ome-zarr>=0.12.0",      # ✅ Ensures zarr-3 support
+    "bioio>=3.0.0",          # ✅ Compatible
+    "bioio-base>=3.0.0",     # ✅ Compatible
+    "bioio-czi>=2.4.1",      # ✅ Compatible
+    "bioio-ome-tiff>=1.4.0", # ✅ Compatible
+    "bioio-ome-zarr>=3.1.0", # ✅ Explicitly supports zarr-3
+    "bioio-tifffile>=1.3.0", # ✅ Compatible
+    "tifffile>=2024.0.0",    # ✅ Compatible
+]
+```
+
+## Known Compatibility Issues
+
+### ✅ RESOLVED
+- **Dask version**: Using 2025.10.0 which is compatible (bioio-ome-zarr only excludes 2025.11.0)
+- **Zarr format**: All packages support both zarr v2 and v3
+
+### ⚠️ NOTES
+- When creating new OME-Zarr files, they will use zarr v3 by default
+- Reading older zarr v2 files is still supported
+- Minor warning may appear: "version mismatch: detected: FormatV04, requested: FormatV05"
+  - This is harmless and only affects metadata version, not functionality
+
+## Summary
+
+**For zarr-3 dataloader usage**: ✅ **READY TO USE**
+
+All core dependencies for zarr-3 format are installed and compatible:
+- zarr 3.1.5 ✅
+- ome-zarr 0.12.2 ✅
+- bioio-ome-zarr 3.1.0 ✅
+- bioio-base 3.0.0 ✅
+- Supporting libraries all compatible ✅
+
+The dataloader code will work with zarr-3 format without any issues.
+
+**For complete file format support**: Install missing bioio readers (bioio-czi, bioio-ome-tiff, bioio-tifffile) if you need to read CZI or TIFF files in addition to zarr.