feat: add tests and refactor codec

.github/workflows/tests.yml

@@ -0,0 +1,30 @@
+name: Tests
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --dev
+
+      - name: Run tests
+        run: uv run pytest tests -v

.gitignore

@@ -0,0 +1,137 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pipenv
+Pipfile.lock
+
+# PEP 582
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db

.python-version

@@ -0,0 +1 @@
+3.11

pyproject.toml

@@ -3,7 +3,7 @@ name = "dj-zarr-codecs"
 version = "0.1.0"
 description = "DataJoint codecs for Zarr array storage"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = {text = "MIT"}
 authors = [
     {name = "Davis Bennett", email = "davis.v.bennett@gmail.com"},
@@ -24,14 +24,15 @@ classifiers = [
 dependencies = [
     "datajoint>=2.0.0a22",
     "zarr>=2.0",
-    "numpy>=1.20",
+    "numpy>=2.0",
 ]
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
     "pytest>=7.0",
     "pytest-cov>=4.0",
     "ruff>=0.1.0",
+    "testcontainers[mysql]>=4.14.0",
 ]
 
 [project.urls]
@@ -47,12 +48,14 @@ zarr = "dj_zarr_codecs:ZarrCodec"
 requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
+[tool.uv.sources]
+datajoint = {git = "https://github.com/datajoint/datajoint-python.git"}
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
-addopts = "-v --cov=dj_zarr_codecs --cov-report=term-missing"
 
 [tool.ruff]
 line-length = 100

src/dj_zarr_codecs/__init__.py

@@ -1,6 +1,6 @@
 """DataJoint codecs for Zarr array storage."""
 
-from .codecs import ZarrCodec
+from .codecs import ZarrArrayCodec
 
 __version__ = "0.1.0"
-__all__ = ["ZarrCodec"]
+__all__ = ["ZarrArrayCodec"]

src/dj_zarr_codecs/codecs.py

@@ -6,18 +6,11 @@
 
 import numpy as np
 import zarr
+import datajoint as dj
+from datajoint import DataJointError
+from datajoint.builtin_codecs import SchemaCodec
 
-try:
-    import datajoint as dj
-    from datajoint import DataJointError
-    from datajoint.builtin_codecs import SchemaCodec
-except ImportError as e:
-    raise ImportError(
-        "datajoint>=2.0.0a22 is required. Install with: pip install 'datajoint>=2.0.0a22'"
-    ) from e
-
-
-class ZarrCodec(SchemaCodec):
+class ZarrArrayCodec(SchemaCodec):
     """
     Store numpy arrays in Zarr format with schema-addressed paths.
 
@@ -78,7 +71,6 @@ class Recording(dj.Manual):
     """
 
     name = "zarr"
-    CODEC_VERSION = "1.0"  # Data format version for backward compatibility
 
     def validate(self, value: Any) -> None:
         """
@@ -94,16 +86,16 @@ def validate(self, value: Any) -> None:
         DataJointError
             If value is not a numpy array or has object dtype.
         """
-        if not isinstance(value, np.ndarray):
-            raise DataJointError(
-                f"<zarr> requires numpy.ndarray, got {type(value).__name__}"
+        if not isinstance(value, np.ndarray | zarr.Array):
+            raise TypeError(
+                f"<zarr> requires a Numpy array or Zarr array, got {type(value).__name__}"
             )
         if value.dtype == object:
             raise DataJointError("<zarr> does not support object dtype arrays")
 
     def encode(
         self,
-        value: np.ndarray,
+        value: np.ndarray | zarr.Array,
         *,
         key: dict | None = None,
         store_name: str | None = None,
@@ -130,40 +122,35 @@ def encode(
         DataJointError
             If encoding fails.
         """
-        try:
-            # Extract context from key
-            schema, table, field, primary_key = self._extract_context(key)
-
-            # Build schema-addressed path
-            path, _token = self._build_path(
-                schema, table, field, primary_key, ext=".zarr", store_name=store_name
-            )
-
-            # Get storage backend
-            backend = self._get_backend(store_name)
-
-            # Get fsspec mapper for direct Zarr write
-            store_map = backend.get_fsmap(path)
-
-            # Write array to Zarr format
-            zarr.save_array(store_map, value)
-
-            # Store version metadata in Zarr attributes
-            z = zarr.open(store_map, mode="r+")
-            z.attrs["codec_version"] = self.CODEC_VERSION
-            z.attrs["codec_name"] = self.name
-
-            # Return metadata for database storage
-            return {
-                "path": path,
-                "store": store_name,
-                "codec_version": self.CODEC_VERSION,
-                "shape": list(value.shape),
-                "dtype": str(value.dtype),
-            }
-
-        except Exception as e:
-            raise DataJointError(f"Failed to encode Zarr array: {e}") from e
+        # import here to avoid circular import
+        from dj_zarr_codecs import __version__
+        # Extract context from key
+        schema, table, field, primary_key = self._extract_context(key)
+
+        # Build schema-addressed path
+        path, _token = self._build_path(
+            schema, table, field, primary_key, ext=".zarr", store_name=store_name
+        )
+
+        # Get storage backend
+        backend = self._get_backend(store_name)
+
+        # Get fsspec mapper for direct Zarr write
+        store_map = backend.get_fsmap(path)
+
+        zarr.create_array(store=store_map, data=value, write_data=True)
+
+        # Return metadata for database storage (stored as JSON column)
+        return {
+            "path": path,
+            "store": store_name,
+            "shape": list(value.shape),
+            "dtype": str(value.dtype),
+            "provenance": {
+                "datajoint-python": dj.__version__,
+                "dj-zarr-codecs": __version__,
+            },
+        }
 
     def decode(self, stored: dict, *, key: dict | None = None) -> zarr.Array:
         """
@@ -187,30 +174,11 @@ def decode(self, stored: dict, *, key: dict | None = None) -> zarr.Array:
         DataJointError
             If decoding fails.
         """
-        try:
-            # Get storage backend
-            backend = self._get_backend(stored.get("store"))
+        # Get storage backend
+        backend = self._get_backend(stored.get("store"))
 
-            # Get fsspec mapper for Zarr path
-            store_map = backend.get_fsmap(stored["path"])
-
-            # Open Zarr array (read-only)
-            z = zarr.open(store_map, mode="r")
-
-            # Check codec version for backward compatibility
-            # Priority: Zarr attrs > DB metadata > default "1.0"
-            version = z.attrs.get(
-                "codec_version", stored.get("codec_version", "1.0")
-            )
+        # Get fsspec mapper for Zarr path
+        store_map = backend.get_fsmap(stored["path"])
 
-            # All v1.x versions are compatible
-            if version.startswith("1."):
-                return z
-            else:
-                raise DataJointError(
-                    f"Unsupported zarr codec version: {version}. "
-                    f"Upgrade dj-zarr-codecs or migrate data."
-                )
-
-        except Exception as e:
-            raise DataJointError(f"Failed to decode Zarr array: {e}") from e
+        # Open Zarr array (read-only)
+        return zarr.open(store_map, mode="r")