Feature/audit test coverage

.github/workflows/ci.yml

@@ -73,3 +73,14 @@ jobs:
         continue-on-error: true
         run: |
           mypy src/ --ignore-missing-imports
+
+ # Kaggle integration test
+ kaggle:
+   runs-on: ubuntu-latest
+
+   steps:
+     - name: Checkout
+       uses: actions/checkout@v4
+
+     - name: kaggle Action
+       uses: Frederisk/kaggle-action@v1.0.0

.github/workflows/tests.yml

@@ -9,10 +9,11 @@ on:
 
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.11", "3.12"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
       - name: Checkout code
@@ -29,18 +30,6 @@ jobs:
           # Install the package with dev dependencies
           pip install -e ".[dev]"
 
-      - name: Patch metaclass-registry (temporary fix for import issues)
-        run: |
-          # Fix metaclass-registry __init__.py to avoid import errors
-          REGISTRY_INIT=$(python -c "import metaclass_registry, os; print(os.path.dirname(metaclass_registry.__file__))")/__init__.py
-          cat > "$REGISTRY_INIT" << 'EOF'
-          """metaclass-registry: Zero-boilerplate metaclass-driven plugin registry system."""
-          __version__ = "0.1.0"
-          from .core import AutoRegisterMeta, RegistryConfig, PRIMARY_KEY
-          from .exceptions import RegistryError
-          __all__ = ["AutoRegisterMeta", "RegistryConfig", "PRIMARY_KEY", "RegistryError"]
-          EOF
-
       - name: Verify installation
         run: |
           python -c "import polystore; print(f'polystore {polystore.__version__} installed successfully')"
@@ -59,7 +48,7 @@ jobs:
           python -m pytest --cov=polystore --cov-report=term-missing --cov-report=xml -v
 
       - name: Upload coverage to Codecov
-        if: matrix.python-version == '3.12'
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
         continue-on-error: true
         uses: codecov/codecov-action@v3
         with:

.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

TEST_PLAN.md

@@ -0,0 +1,34 @@
+# Test coverage improvement plan
+
+Goal: raise coverage from ~24% to 85%+ by adding small, high-leverage, parameterized tests that exercise the FileManager router and backend implementations.
+
+Scope and strategy
+- Focus first on the low-friction, high-return surface:
+  - `FileManager` (router) — exercises many backend code paths with little test code.
+  - `DiskBackend` and `MemoryBackend` — implement core IO, listing, formats.
+  - Add `Zarr` tests later when `zarr`/ome-zarr deps are available.
+
+Approach
+- Keep tests small and DRY using pytest fixtures and parameterization.
+- Use `registry` fixture that supplies a minimal backend mapping (`disk`, `memory`).
+- Provide a `FileManager` fixture that uses that registry so tests exercise the router.
+- For each backend run the same set of assertions: save/load, batch ops, exists/ensure_directory, list_files, natural sorting for images, and error propagation for unknown backends.
+
+Files to add (first wave)
+- `tests/conftest.py` — fixtures: `registry`, `file_manager`, `sample_payloads`.
+- `tests/test_filemanager_backends.py` — parameterized tests for `disk` and `memory`.
+
+Next steps (after this wave)
+- Expand disk-specific tests for CSV/JSON/Text handlers and symlink behavior.
+- Add gated `zarr` tests using `pytest.importorskip('zarr')` and small synthetic stores.
+- Add registry and cleanup tests to exercise lazy instantiation and cleanup paths.
+
+How I'll validate
+- Run the new tests and iteratively fix test issues.
+- Run `pytest --cov=polystore --cov-report=term-missing` to monitor coverage improvements.
+
+Notes
+- Tests intentionally avoid heavy external deps (ome-zarr, tifffile) in the initial wave. These will be added behind `importorskip` so CI remains lightweight.
+
+Author: automated scaffolding
+Date: 2025-11-02

pyproject.toml

@@ -39,7 +39,9 @@ classifiers = [
 dependencies = [
     "numpy>=1.26.0",
     "portalocker>=2.8.0",  # Cross-platform file locking
-    "metaclass-registry>=0.1.0",
+    "metaclass-registry",
+    "zarr>=2.18.0,<3.0",  # Required for ZarrStorageBackend
+    "ome-zarr>=0.11.0",   # Required for OME-ZARR HCS compliance
 ]
 
 [project.optional-dependencies]
@@ -94,6 +96,39 @@ docs = [
     "sphinx-design>=0.5.0",
 ]
 
+gpu = [
+    # Zarr
+    "zarr>=2.18.0,<3.0",
+    "ome-zarr>=0.11.0",
+
+    # PyTorch
+    "torch>=2.6.0,<2.8.0",
+    "torchvision>=0.21.0,<0.23.0",
+
+    # JAX
+    "jax>=0.5.3,<0.6.0",
+    "jaxlib>=0.5.3,<0.6.0",
+
+    # JAX CUDA plugins
+    "jax-cuda12-pjrt>=0.5.3,<0.6.0",
+    "jax-cuda12-plugin>=0.5.3,<0.6.0",
+
+    # CuPy
+    "cupy-cuda12x>=13.3.0,<14.0.0",
+
+    # CuCIM
+    "cucim-cu12>=25.6.0,<26.0.0",
+
+    # TensorFlow
+    "tensorflow>=2.19.0,<2.20.0",
+
+    # TensorFlow Probability
+    "tensorflow-probability[tf]>=0.25.0,<0.26.0",
+
+    # pyclesperanto
+    "pyclesperanto>=0.17.1",
+]
+
 [project.urls]
 Homepage = "https://github.com/trissim/polystore"
 Documentation = "https://polystore.readthedocs.io"
@@ -163,5 +198,4 @@ ignore = [
 ]
 
 [tool.ruff.per-file-ignores]
-"__init__.py" = ["F401"]  # unused imports
-
+"__init__.py" = ["F401"]  # unused imports

src/polystore/__init__.py

@@ -21,10 +21,9 @@
 from .disk import DiskBackend
 
 # Optional backends
-try:
-    from .zarr import ZarrBackend
-except ImportError:
-    ZarrBackend = None
+# Zarr is a required backend for this project. Import it directly so
+# missing dependency errors surface loudly during test/setup.
+from .zarr import ZarrBackend
 
 # File manager
 from .filemanager import FileManager
@@ -43,11 +42,17 @@
     UnsupportedFormatError,
 )
 
-# Streaming (optional)
+# Streaming (optional and lazy)
+# Don't import at module level - streaming is heavy and optional
+# Users can import manually if needed: from polystore.streaming import StreamingBackend
 try:
     from .streaming import StreamingBackend
 except ImportError:
     StreamingBackend = None
+# Streaming (optional and lazy)
+# Don't import at module level - streaming is heavy and optional
+# Users can import manually if needed: from polystore.streaming import StreamingBackend
+StreamingBackend = None
 
 __all__ = [
     # Version
@@ -74,7 +79,7 @@
     "StorageResolutionError",
     "BackendNotFoundError",
     "UnsupportedFormatError",
-    # Streaming
+    # Streaming (optional)
     "StreamingBackend",
 ]