Add plugin priority and refactor for compatibility with napari-ndev legacy behavior (#24)

# References and relevant issues

This PR is needed to maintain behavior for using `ndevio` in
`napari-ndev` in ndev-kit/napari-ndev#194

# Description

1. Adds `bioio-tifffile` to core dependencies, because, at least for
now, this is needed for some awkward tiff files that _can_ be read by
`bioio-imageio` but result in bad metadata reading. Since there are
currently no `tifffile` pins in any of the dependencies, this behavior
will remain for now. It's worth considering in the future if this is
really the way I want core dependencies going forward.
2. This orders the plugin list to be used for infering the reader,
because despite the installation order of plugins, some get installed
before others (perhaps this is a `uv` thing, compared to `pip`). As
such, I need a way to opinionatedly pick my preferred plugins, but the
preferred plugin setting still gives the user an easy way to override if
they can only find their desired behavior with a specific plugin. It
will always fall back to the setting.
3. Refactors `determine_reader_plugin` to mostly just rely on the plugin
manager

Author: TimMonko

pyproject.toml

@@ -33,10 +33,11 @@ dependencies = [
     "xarray",
     "bioio-base",
     "bioio",
-    "bioio-imageio",
-    "bioio-ome-tiff",
     "bioio-ome-zarr",
-    "napari-plugin-manager",  # For plugin installation widget
+    "bioio-ome-tiff",
+    "bioio-tifffile",  # a backup tifffile reader with better performance than imageio
+    "bioio-imageio",
+    "napari-plugin-manager>=0.1.7",  # Renamed to PYPI from PIP for tool selection https://github.com/napari/napari-plugin-manager/pull/176
 ]
 
 [project.optional-dependencies]

src/ndevio/_bioio_plugin_utils.py

@@ -6,6 +6,7 @@
 Public API:
     BIOIO_PLUGINS - Dict of all bioio plugins and their file extensions
     suggest_plugins_for_path() - Get list of suggested plugins by file extension
+    get_reader_priority() - Get reader priority list from BIOIO_PLUGINS order
 
 Internal API (used by ReaderPluginManager):
     format_plugin_installation_message() - Generate installation message
@@ -35,33 +36,21 @@
 
 # Bioio plugins and their supported extensions
 # Source: https://github.com/bioio-devs/bioio
+#
+# ORDERING MATTERS: Plugins are listed in priority order (highest priority first).
+# This order is used by ReaderPluginManager when selecting readers.
+# Priority is based on:
+# 1. Metadata preservation quality (OME formats preserve most metadata)
+# 2. Reliability and performance for specific formats
+# 3. Known issues or limitations
 BIOIO_PLUGINS = {
-    "bioio-czi": {
-        "extensions": [".czi"],
-        "description": "Zeiss CZI files",
-        "repository": "https://github.com/bioio-devs/bioio-czi",
-    },
-    "bioio-dv": {
-        "extensions": [".dv", ".r3d"],
-        "description": "DeltaVision files",
-        "repository": "https://github.com/bioio-devs/bioio-dv",
-    },
-    "bioio-imageio": {
-        "extensions": [".bmp", ".gif", ".jpg", ".jpeg", ".png"],
-        "description": "Generic image formats (PNG, JPG, etc.)",
-        "repository": "https://github.com/bioio-devs/bioio-imageio",
+    # Highest priority: OME formats with excellent metadata preservation
+    "bioio-ome-zarr": {
+        "extensions": [".zarr"],
+        "description": "OME-Zarr files",
+        "repository": "https://github.com/bioio-devs/bioio-ome-zarr",
         "core": True,
     },
-    "bioio-lif": {
-        "extensions": [".lif"],
-        "description": "Leica LIF files",
-        "repository": "https://github.com/bioio-devs/bioio-lif",
-    },
-    "bioio-nd2": {
-        "extensions": [".nd2"],
-        "description": "Nikon ND2 files",
-        "repository": "https://github.com/bioio-devs/bioio-nd2",
-    },
     "bioio-ome-tiff": {
         "extensions": [".ome.tif", ".ome.tiff", ".tif", ".tiff"],
         "description": "OME-TIFF files with valid OME-XML metadata",
@@ -73,27 +62,51 @@
         "description": "Tiled OME-TIFF files",
         "repository": "https://github.com/bioio-devs/bioio-ome-tiled-tiff",
     },
-    "bioio-ome-zarr": {
-        "extensions": [".zarr"],
-        "description": "OME-Zarr files",
-        "repository": "https://github.com/bioio-devs/bioio-ome-zarr",
+    # High priority: Format-specific readers with good metadata support
+    "bioio-tifffile": {
+        "extensions": [".tif", ".tiff"],
+        "description": "TIFF files (including those without OME metadata)",
+        "repository": "https://github.com/bioio-devs/bioio-tifffile",
         "core": True,
     },
+    "bioio-nd2": {
+        "extensions": [".nd2"],
+        "description": "Nikon ND2 files",
+        "repository": "https://github.com/bioio-devs/bioio-nd2",
+    },
+    "bioio-czi": {
+        "extensions": [".czi"],
+        "description": "Zeiss CZI files",
+        "repository": "https://github.com/bioio-devs/bioio-czi",
+    },
+    "bioio-lif": {
+        "extensions": [".lif"],
+        "description": "Leica LIF files",
+        "repository": "https://github.com/bioio-devs/bioio-lif",
+    },
+    "bioio-dv": {
+        "extensions": [".dv", ".r3d"],
+        "description": "DeltaVision files",
+        "repository": "https://github.com/bioio-devs/bioio-dv",
+    },
     "bioio-sldy": {
         "extensions": [".sldy", ".dir"],
         "description": "3i SlideBook files",
         "repository": "https://github.com/bioio-devs/bioio-sldy",
     },
-    "bioio-tifffile": {
-        "extensions": [".tif", ".tiff"],
-        "description": "TIFF files (including those without OME metadata)",
-        "repository": "https://github.com/bioio-devs/bioio-tifffile",
+    # Lower priority: Generic/fallback readers
+    "bioio-imageio": {
+        "extensions": [".bmp", ".gif", ".jpg", ".jpeg", ".png"],
+        "description": "Generic image formats (PNG, JPG, etc.)",
+        "repository": "https://github.com/bioio-devs/bioio-imageio",
+        "core": True,
     },
     "bioio-tiff-glob": {
         "extensions": [".tiff"],
         "description": "TIFF sequences (glob patterns)",
         "repository": "https://github.com/bioio-devs/bioio-tiff-glob",
     },
+    # Lowest priority: Requires external dependencies (Java)
     "bioio-bioformats": {
         "extensions": [".oib", ".oif", ".vsi", ".ims", ".lsm", ".stk"],
         "description": "Proprietary microscopy formats (requires Java)",
@@ -111,6 +124,27 @@
         _EXTENSION_TO_PLUGIN[ext].append(plugin_name)
 
 
+def get_reader_priority() -> list[str]:
+    """Get reader priority list from BIOIO_PLUGINS dictionary order.
+
+    Returns plugin names in priority order (highest priority first).
+    This order is used by ReaderPluginManager when selecting readers.
+
+    Returns
+    -------
+    list of str
+        Plugin names in priority order
+
+    Examples
+    --------
+    >>> from ndevio._bioio_plugin_utils import get_reader_priority
+    >>> priority = get_reader_priority()
+    >>> print(priority[0])  # Highest priority reader
+    'bioio-ome-zarr'
+    """
+    return list(BIOIO_PLUGINS.keys())
+
+
 def format_plugin_installation_message(
     filename: str,
     suggested_plugins: list[str],

src/ndevio/_napari_reader.py

@@ -73,14 +73,17 @@ def napari_get_reader(
             open_first_scene_only=open_first_scene_only,
             open_all_scenes=open_all_scenes,
         )
+
     except UnsupportedFileFormatError as e:
         # determine_reader_plugin() already enhanced the error message
         logger.error("ndevio: Unsupported file format: %s", path)
         # Show plugin installer widget if enabled in settings
         if settings.ndevio_Reader.suggest_reader_plugins:  # type: ignore
             _open_plugin_installer(path, e)
 
-        raise
+        # Return None per napari reader spec - don't raise exception
+        return None
+
     except Exception as e:  # noqa: BLE001
         logger.warning("ndevio: Error reading file: %s", e)
         return None
@@ -196,6 +199,13 @@ def _open_plugin_installer(
     # Get viewer, handle case where no viewer available
     viewer = napari.current_viewer()
 
+    # Don't try to open widget if no viewer available (e.g., in tests)
+    if viewer is None:
+        logger.warning(
+            "Cannot open plugin installer widget: No napari viewer available"
+        )
+        return
+
     # Create plugin manager for this file
     manager = ReaderPluginManager(path)
 

src/ndevio/_plugin_installer.py

@@ -64,7 +64,7 @@ def install_plugin(plugin_name: str) -> int:
 
     # Determine which tool to use (pip vs conda)
     # napari-plugin-manager handles this automatically based on environment
-    tool = InstallerTools.PIP  # Default to pip for bioio packages
+    tool = InstallerTools.PYPI  # Default to PYPI for bioio packages
 
     # Queue the installation
     job_id = queue.install(tool=tool, pkgs=[plugin_name])

src/ndevio/_plugin_manager.py

@@ -230,8 +230,9 @@ def get_working_reader(
 
         Tries readers in priority order:
         1. Preferred reader if it's installed and supported
-        2. Any installed reader that supports the file
-        3. None if no working reader found
+        2. Readers from BIOIO_PLUGINS dict order (highest priority first)
+        3. Any other installed reader that supports the file
+        4. None if no working reader found
 
         Parameters
         ----------
@@ -244,6 +245,12 @@ def get_working_reader(
             Reader class that can read the file, or None if no suitable
             reader is installed.
 
+        Notes
+        -----
+        The priority order is determined by the ordering of BIOIO_PLUGINS
+        in _bioio_plugin_utils.py, which prioritizes readers based on
+        metadata preservation quality, reliability, and known issues.
+
         Examples
         --------
         >>> manager = ReaderPluginManager("image.tif")
@@ -274,11 +281,23 @@ def get_working_reader(
             )
             return self._get_reader_module(preferred_reader)
 
-        # Try any installed reader that supports the file
+        # Try readers in priority order from BIOIO_PLUGINS
+        from ._bioio_plugin_utils import get_reader_priority
+
+        for reader_name in get_reader_priority():
+            if reader_name in report and report[reader_name].supported:
+                logger.info(
+                    "Using reader: %s for %s (from priority list)",
+                    reader_name,
+                    self.path,
+                )
+                return self._get_reader_module(reader_name)
+
+        # Try any other installed reader that supports the file
         for name, support in report.items():
             if name != "ArrayLike" and support.supported:
                 logger.info(
-                    "Using reader: %s for %s (preferred not available)",
+                    "Using reader: %s for %s (from installed plugins)",
                     name,
                     self.path,
                 )

src/ndevio/nimage.py

@@ -40,27 +40,24 @@ def determine_reader_plugin(
     image: ImageLike, preferred_reader: str | None = None
 ) -> Reader:
     """
-    Determine the reader for the plugin to be used to load the image.
-    In order of priority:
-        1. If preferred_reader from settings is suitable, use that.
-        2. Otherwise, use bioio.BioImage.determine_plugin() to find a suitable reader.
-        3. If all else fails, raise an error with suggestions for missing plugins.
+    Determine the reader plugin to use for loading an image.
+
+    Convenience wrapper that integrates ReaderPluginManager with ndevio settings.
+    For file paths, uses the priority system (DEFAULT_READER_PRIORITY).
+    For arrays, uses bioio's default plugin detection.
 
     Parameters
     ----------
     image : ImageLike
-        Image to be loaded. Can be a path to an image file, a numpy array,
-        or an xarray DataArray.
+        Image to be loaded (file path, numpy array, or xarray DataArray).
     preferred_reader : str, optional
-        Preferred reader to be used to load the image. If not provided,
-        it will fallback to the preference in settings. Finally, if this
-        preferred reader is not suitable, a reader will be attempted to be
-        determined based on the image type.
+        Preferred reader name. If None, uses ndevio_Reader.preferred_reader
+        from settings.
 
     Returns
     -------
     Reader
-        Reader to be used to load the image.
+        Reader class to use for loading the image.
 
     Raises
     ------
@@ -73,40 +70,34 @@ def determine_reader_plugin(
 
     from ._plugin_manager import ReaderPluginManager
 
-    settings = get_settings()
+    # For file paths: use ReaderPluginManager
+    if isinstance(image, str | Path):
+        settings = get_settings()
 
-    preferred_reader = (
-        preferred_reader or settings.ndevio_Reader.preferred_reader  # type: ignore
-    )
+        # Get preferred reader from settings if not provided
+        if preferred_reader is None:
+            preferred_reader = settings.ndevio_Reader.preferred_reader  # type: ignore
 
-    # Only use ReaderPluginManager for file paths, not arrays
-    if isinstance(image, str | Path):
         manager = ReaderPluginManager(image)
         reader = manager.get_working_reader(preferred_reader)
 
         if reader:
             return reader
 
-        # No reader found - raise with helpful message if enabled
+        # No reader found - raise error with installation suggestions
         if settings.ndevio_Reader.suggest_reader_plugins:  # type: ignore
-            raise UnsupportedFileFormatError(
-                reader_name="ndevio",
-                path=str(image),
-                msg_extra=manager.get_installation_message(),
-            )
+            msg_extra = manager.get_installation_message()
         else:
-            # Re-raise without suggestions
-            raise UnsupportedFileFormatError(
-                reader_name="ndevio",
-                path=str(image),
-            )
-    else:
-        # For arrays, use bioio's built-in plugin determination
-        try:
-            return nImage.determine_plugin(image).metadata.get_reader()
-        except UnsupportedFileFormatError:
-            # Re-raise for non-file inputs
-            raise
+            msg_extra = None
+
+        raise UnsupportedFileFormatError(
+            reader_name="ndevio",
+            path=str(image),
+            msg_extra=msg_extra,
+        )
+
+    # For arrays: use bioio's built-in plugin determination
+    return nImage.determine_plugin(image).metadata.get_reader()
 
 
 class nImage(BioImage):

tests/test_bioio_plugin_utils.py

@@ -101,20 +101,21 @@ def test_manager_excludes_core_plugins_from_installable(self):
 
             manager = ReaderPluginManager("test.tiff")
 
-            # Core plugins (like bioio-ome-tiff) should not be in installable
+            # Core plugins should not be in installable
             installable_plugins = manager.installable_plugins
 
-            # bioio-ome-tiff is a core plugin, shouldn't need installation
+            # These are core plugins, shouldn't need installation
             core_plugins = [
                 "bioio-ome-tiff",
                 "bioio-imageio",
                 "bioio-ome-zarr",
+                "bioio-tifffile",
             ]
             for core in core_plugins:
                 assert core not in installable_plugins
 
-            # bioio-tifffile is not core, should be installable
-            assert "bioio-tifffile" in installable_plugins
+            # bioio-tiff-glob is not core, should be installable
+            assert "bioio-tiff-glob" in installable_plugins
 
 
 class TestFormatPluginInstallationMessage: