Pass reader to ImageConverter.to_tiledb() instead of creating custom ImageConverter subclasses

napari_tiledb_bioimg/_reader.py

@@ -10,8 +10,8 @@ def napari_get_reader(path):
         warnings.warn(f"Not a single path: {path}")
         return None
 
-    if not os.path.isdir(path):
-        warnings.warn(f"Not a directory: {path}")
+    if tiledb.object_type(path) != "group":
+        warnings.warn(f"Not a tiledb group: {path}")
         return None
 
     try:

napari_tiledb_bioimg/_writer.py

@@ -108,14 +108,6 @@ def level_metadata(self, level: int) -> Dict[str, Any]:
         return {}
 
 
-class NapariSingleScaleConverter(ImageConverter):
-    _ImageReaderType = NapariSingleScaleDataReader
-
-
-class NapariMultiScaleConverter(ImageConverter):
-    _ImageReaderType = NapariMultiScaleDataReader
-
-
 def napari_write_image_lossless(path, data, attributes):
     return _napari_write_image(path, data, lossless=True)
 
@@ -128,8 +120,8 @@ def _napari_write_image(path, data, lossless):
     kwargs = dict(compressor=tiledb.WebpFilter(lossless=lossless))
     if isinstance(data, MultiScaleData):
         kwargs.update(chunked=True, max_workers=os.cpu_count())
-        converter = NapariMultiScaleConverter
+        reader = NapariMultiScaleDataReader(data)
     else:
-        converter = NapariSingleScaleConverter
-    converter.to_tiledb(data, path, **kwargs)
+        reader = NapariSingleScaleDataReader(data)
+    ImageConverter.to_tiledb(reader, path, **kwargs)
     return [path]

napari_tiledb_bioimg/napari.yaml

@@ -14,7 +14,7 @@ contributions:
   readers:
     - command: napari-tiledb-bioimg.get_reader
       accepts_directories: true
-      filename_patterns: []
+      filename_patterns: ['*.tdb', '*.tiledb']
   writers:
     - command: napari-tiledb-bioimg.write_image_lossless
       layer_types: ['image']

tests/test_reader.py

@@ -16,13 +16,13 @@ def test_get_reader_not_dir_fail(tmp_path):
     f.write_text("")
     assert f.is_file()
 
-    with pytest.warns(UserWarning, match="Not a directory"):
+    with pytest.warns(UserWarning, match="Not a tiledb group"):
         assert napari_get_reader(str(f)) is None
 
 
 def test_get_reader_invalid_dir_fail(tmp_path):
     """Not receiving a proper TileDB group directory"""
-    with pytest.warns(UserWarning, match="Failed to open"):
+    with pytest.warns(UserWarning, match="Not a tiledb group"):
         assert napari_get_reader(str(tmp_path)) is None
 
 

tox.ini

@@ -1,7 +1,7 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
 envlist = py{38,39,310}-{linux,macos,windows}
-isolated_build=true
+isolated_build = true
 
 [gh-actions]
 python =
@@ -20,13 +20,9 @@ platform =
     macos: darwin
     linux: linux
     windows: win32
-passenv =
-    CI
-    GITHUB_ACTIONS
-    DISPLAY
-    XAUTHORITY
-    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
-    PYVISTA_OFF_SCREEN
-extras =
-    testing
-commands = pytest -v --color=yes --cov=napari_tiledb_bioimg --cov-report=xml
+passenv = CI,GITHUB_ACTIONS,DISPLAY,XAUTHORITY,NUMPY_EXPERIMENTAL_ARRAY_FUNCTION,PYVISTA_OFF_SCREEN
+extras = testing
+
+commands =
+    {linux,macos}: pytest -v --color=yes --cov=napari_tiledb_bioimg --cov-report=xml
+    windows: pytest --basetemp={envtmpdir} -v --color=yes --cov=napari_tiledb_bioimg --cov-report=xml