Feature/audit test coverage #4
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…EST_PLAN; fix filemanager natural_sort robustness; guard heavy optional imports with POLYSTORE_SKIP_ZARR
… delete, listing order)
- Add comprehensive FileManager test suite (test_filemanager_extended.py) covering: * Error handling for invalid backends and registry initialization * Edge cases in save/load operations with exceptions * Directory operations (exists, is_file, is_dir, mkdir, delete) * Advanced features (symlinks, find operations, mirror functionality) * Memory backend integration tests * Natural sorting for image file listing - Add ZarrStorageBackend test suite (test_zarr_backend.py) covering: * Basic array save/load operations for various dtypes and dimensions * ZarrConfig integration (compression levels, chunk strategies) * Error handling for nonexistent files * Directory existence checks - Fix pyproject.toml dependency: correct 'metaclass-register' to 'metaclass-registry' - Fix ZarrConfig dataclass: add field import and use field(default_factory=CompressorConfig) for proper default initialization of compressor attribute These changes significantly improve test coverage and resolve configuration bugs that could cause runtime issues with dataclass instantiation.
- Add comprehensive GPU acceleration dependency group to pyproject.toml: * PyTorch 2.6.0-2.8.0 with torchvision for deep learning * JAX 0.5.3-0.6.0 with CUDA plugins for high-performance computing * CuPy CUDA12x for GPU-accelerated NumPy operations * CuCIM for GPU-accelerated image processing * TensorFlow 2.19.0-2.20.0 with TensorFlow Probability * pyclesperanto for GPU-accelerated bioimage analysis - Add Kaggle integration job to CI workflow using Frederisk/kaggle-action@v1.0.0 for testing in Kaggle notebook environments These additions enable GPU-accelerated workflows and ensure compatibility with popular ML platforms while maintaining the framework-agnostic design.
- Include zarr>=2.18.0,<3.0 and ome-zarr>=0.11.0 in gpu optional dependencies - Ensures ZarrStorageBackend is available when using GPU acceleration features - Maintains compatibility with existing zarr optional dependency group
- Include .zgroup file generated during ZarrStorageBackend testing - Ensures test artifacts are properly tracked in version control - Supports reproducible testing of Zarr array storage functionality
- Remove duplicate 'gpu = [' line that was causing TOML parsing error - Ensure proper TOML array syntax for GPU dependencies - Fix CI installation failure due to malformed pyproject.toml
- Move zarr>=2.18.0,<3.0 and ome-zarr>=0.11.0 from optional to core dependencies - ZarrStorageBackend is imported directly in __init__.py and required for basic functionality - Ensures Zarr backend is always available without requiring separate installation - Maintains backward compatibility while fixing import errors
- Remove duplicate 'dependencies = []' section that was causing TOML parsing error - Keep only the correct dependencies section with zarr and ome-zarr as core requirements - Fix CI installation failure due to malformed TOML syntax
- Add import copy as py_copy at module level in memory.py - Fixes NameError in copy() method when deepcopy is called - Ensures proper deep copying of objects in memory backend operations
- Wrap StreamingBackend import in try/except to avoid import errors when OpenHCS package is not available - Maintains backward compatibility while preventing module-level import failures - StreamingBackend remains None when OpenHCS dependencies are missing
- Change test paths from '/test.npy' to '/test_save_load.npy' and '/test_exists.npy' - Prevents test interference due to shared memory backend state across test sessions - Ensures tests run independently and reliably
- Change test_exists_memory path from '/test.npy' to '/test_exists.npy' - Ensures tests run independently without shared state conflicts - Fixes test failure due to persistent memory backend state
…Backend - Removed duplicate test_save_load_memory method (second one was incomplete) - Fixed test_batch_memory body (was missing batch operation code) - Removed duplicate test_exists_memory method (second definition was correct) - Now all three methods are properly structured and isolated
- Added Python 3.13 to test matrix (was: 3.11, 3.12) - Added macOS and Windows to test matrix (was: ubuntu-only) - Now tests on 9 combinations: 3 OSes × 3 Python versions - Codecov upload restricted to ubuntu-latest + Python 3.12 to avoid duplication
The patch was a workaround for what should be a properly functioning required dependency. Since metaclass-registry is in pyproject.toml dependencies, it should work out of the box without modification. Remove the unnecessary patch step and rely on proper package installation.
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