From 51f03d04d19f19a62a4a789bc5cb362b71fc7693 Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 16:37:04 -0500
Subject: [PATCH 01/12] remove precommit ndev-settings stuff

---
 .pre-commit-config.yaml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e098778..5d89c4f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,8 +7,6 @@ repos:
       - id: trailing-whitespace
         exclude: ^\.napari-hub/.*
       - id: check-yaml # checks for correct yaml syntax for github actions ex.
-        exclude:
-          (?x)(^src/ndevio/ndev_settings\.yaml$)
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.14.8
     hooks:
@@ -18,7 +16,3 @@ repos:
     rev: v0.3.0
     hooks:
       - id: napari-plugin-checks
-  - repo: https://github.com/ndev-kit/ndev-settings
-    rev: v0.4.0
-    hooks:
-      - id: reset-settings-values

From d8282b1fd541aaacea15b61ea88c97227cfe9050 Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 16:37:20 -0500
Subject: [PATCH 02/12] remove ndev-settings from pyproject

---
 pyproject.toml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index a415afb..569c4bd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,6 @@ requires-python = ">=3.11"
 # See best practices: https://napari.org/stable/plugins/building_a_plugin/best_practices.html
 dependencies = [
     "napari",
-    "ndev-settings>=0.4.2",
     "nbatch>=0.0.4",
     "natsort",
     "magicgui",
@@ -64,9 +63,6 @@ dev = [
 [project.entry-points."napari.manifest"]
 ndevio = "ndevio:napari.yaml"
 
-[project.entry-points."ndev_settings.manifest"]
-ndevio = "ndevio:ndev_settings.yaml"
-
 [project.urls]
 "Bug Tracker" = "https://github.com/ndev-kit/ndevio/issues"
 "Documentation" = "https://github.com/ndev-kit/ndevio#README.md"

From d8736880aa36ae37787f639c676039af7d5e10c7 Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 16:38:07 -0500
Subject: [PATCH 03/12] move ndev-settings manifest to napari.yaml manifest

---
 src/ndevio/napari.yaml        | 69 +++++++++++++++++++++++++++++++++++
 src/ndevio/ndev_settings.yaml | 51 --------------------------
 2 files changed, 69 insertions(+), 51 deletions(-)
 delete mode 100644 src/ndevio/ndev_settings.yaml

diff --git a/src/ndevio/napari.yaml b/src/ndevio/napari.yaml
index caad56c..558bf89 100644
--- a/src/ndevio/napari.yaml
+++ b/src/ndevio/napari.yaml
@@ -59,6 +59,75 @@ contributions:
         '*.txt', '*.v', '*.vms', '*.vsi', '*.vws', '*.wat', '*.wlz', '*.xdce', '*.xml', '*.xqd',
         '*.xqf', '*.xv', '*.xvthumb', '*.xys', '*.zarr', '*.zarr*', '*.zfp', '*.zfr', '*.zif', '*.zvi',
       ]
+  configuration:
+    - title: Reader
+      properties:
+        ndevio.suggest_reader_plugins:
+          type: boolean
+          default: true
+          title: Suggest reader plugins
+          description: >-
+            Whether to suggest plugins to install when no reader can be found
+            for a file.
+        ndevio.scene_handling:
+          type: string
+          default: Open Scene Widget
+          title: Scene handling
+          description: >-
+            How to handle files with multiple scenes. Choose between showing
+            a scene-selection widget, viewing all scenes as layers, or viewing
+            only the first scene.
+          enum:
+            - Open Scene Widget
+            - View All Scenes
+            - View First Scene Only
+        ndevio.clear_layers_on_new_scene:
+          type: boolean
+          default: false
+          title: Clear layers on new scene
+          description: Whether to clear the viewer when selecting a new scene.
+        ndevio.max_in_mem_gb:
+          type: number
+          default: 8.0
+          title: Max in-memory size (GB)
+          description: >-
+            Maximum uncompressed image size in GB to load eagerly. Larger
+            images use dask.
+          minimum: 0.5
+          maximum: 128.0
+    - title: Export
+      properties:
+        ndevio.canvas_scale:
+          type: number
+          default: 1.0
+          title: Canvas scale
+          description: Scale factor for exported figures and screenshots.
+          minimum: 0.01
+          maximum: 100.0
+        ndevio.override_canvas_size:
+          type: boolean
+          default: false
+          title: Override canvas size
+          description: >-
+            Whether to override the canvas size when exporting screenshots.
+        ndevio.canvas_width:
+          type: integer
+          default: 1024
+          title: Canvas width
+          description: >-
+            Canvas width in pixels when exporting screenshots (if override
+            is enabled).
+          minimum: 1
+          maximum: 100000
+        ndevio.canvas_height:
+          type: integer
+          default: 1024
+          title: Canvas height
+          description: >-
+            Canvas height in pixels when exporting screenshots (if override
+            is enabled).
+          minimum: 1
+          maximum: 100000
   widgets:
     - command: ndevio.make_plugin_installer_widget
       display_name: Install BioIO Reader Plugins
diff --git a/src/ndevio/ndev_settings.yaml b/src/ndevio/ndev_settings.yaml
deleted file mode 100644
index ae77bfc..0000000
--- a/src/ndevio/ndev_settings.yaml
+++ /dev/null
@@ -1,51 +0,0 @@
-ndevio_reader:
-  suggest_reader_plugins:
-    default: true
-    tooltip: Whether to suggest plugins to install when no reader can be found.
-    value: true
-  preferred_reader:
-    default: null
-    dynamic_choices:
-      fallback_message: No readers found
-      provider: bioio.readers
-    tooltip: Preferred reader to try first when opening images.
-    value: null
-  scene_handling:
-    choices:
-    - Open Scene Widget
-    - View All Scenes
-    - View First Scene Only
-    default: Open Scene Widget
-    tooltip: How to handle files with multiple scenes.
-    value: Open Scene Widget
-  clear_layers_on_new_scene:
-    default: false
-    tooltip: Whether to clear the viewer when selecting a new scene.
-    value: false
-  max_in_mem_gb:
-    default: 8.0
-    min: 0.5
-    max: 128.0
-    step: 0.5
-    tooltip: Maximum uncompressed image size in GB to load eagerly. Larger images use dask.
-    value: 8.0
-
-ndevio_export:
-  canvas_scale:
-    default: 1.0
-    min: 0.01
-    max: 100.0
-    step: 1.0
-    tooltip: Scale factor for exported figures and screenshots
-    value: 1.0
-  override_canvas_size:
-    default: false
-    tooltip: Whether to override canvas size when exporting screenshots
-    value: false
-  canvas_size:
-    default: !!python/tuple [1024, 1024]
-    options:
-      min: 1
-      max: 100000
-    tooltip: Height x width of canvas when exporting (if override enabled)
-    value: !!python/tuple [1024, 1024]

From 18f4d9fc0f375b6d10f8880ebad95859b62a5013 Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 16:43:13 -0500
Subject: [PATCH 04/12] backwards compat settings for no get_plugin_settings

---
 src/ndevio/_settings.py |  82 ++++++++++++++++
 tests/test_settings.py  | 211 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 293 insertions(+)
 create mode 100644 src/ndevio/_settings.py
 create mode 100644 tests/test_settings.py

diff --git a/src/ndevio/_settings.py b/src/ndevio/_settings.py
new file mode 100644
index 0000000..796794d
--- /dev/null
+++ b/src/ndevio/_settings.py
@@ -0,0 +1,82 @@
+"""Access to ndevio's plugin settings.
+
+ndevio's user-configurable behavior is declared in ``napari.yaml`` under
+``contributions.configuration`` (two categories: ``reader`` and ``export``)
+and surfaces in napari's **Preferences** dialog.  At runtime the values are
+read through ``napari.settings.get_plugin_settings('ndevio')``.
+
+When napari is too old to expose plugin settings (i.e. it predates the
+``get_plugin_settings`` API), or when the ndevio plugin has not been
+discovered yet, :func:`get_ndevio_settings` falls back to the same defaults
+declared in the manifest so ndevio keeps working everywhere.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from napari.settings import PluginPreferences
+
+_PLUGIN_NAME = 'ndevio'
+
+# The defaults below mirror the ``contributions.configuration`` block in
+# ``napari.yaml``.  They are only used as a fallback when napari's plugin
+# settings are unavailable (old napari, or plugin not discovered yet).
+
+
+@dataclass(frozen=True)
+class ReaderDefaults:
+    """Default values for the ``reader`` configuration category."""
+
+    suggest_reader_plugins: bool = True
+    scene_handling: str = 'Open Scene Widget'
+    clear_layers_on_new_scene: bool = False
+    max_in_mem_gb: float = 8.0
+
+
+@dataclass(frozen=True)
+class ExportDefaults:
+    """Default values for the ``export`` configuration category."""
+
+    canvas_scale: float = 1.0
+    override_canvas_size: bool = False
+    canvas_width: int = 1024
+    canvas_height: int = 1024
+
+
+@dataclass(frozen=True)
+class _DefaultSettings:
+    """Fallback settings object exposing the same shape as napari's model.
+
+    Attributes are named to match the generated napari plugin preferences
+    (``.reader`` and ``.export``), so callers can use the fallback
+    interchangeably with the napari-managed model.
+    """
+
+    reader: ReaderDefaults = field(default_factory=ReaderDefaults)
+    export: ExportDefaults = field(default_factory=ExportDefaults)
+
+
+def get_ndevio_settings() -> PluginPreferences | _DefaultSettings:
+    """Return ndevio's plugin settings, falling back to defaults.
+
+    Returns
+    -------
+    PluginPreferences | _DefaultSettings
+        The napari-managed plugin preferences for ``ndevio`` when available,
+        otherwise a frozen dataclass carrying the manifest defaults.  Both
+        expose the same ``.reader`` and ``.export`` attributes.
+
+    """
+    try:
+        from napari.settings import get_plugin_settings
+    except ImportError:  # pragma: no cover - pre-plugin-settings napari
+        return _DefaultSettings()
+
+    try:
+        return get_plugin_settings(_PLUGIN_NAME)
+    except KeyError:
+        # ndevio is not registered/discovered (yet) -> manifest defaults
+        return _DefaultSettings()
diff --git a/tests/test_settings.py b/tests/test_settings.py
new file mode 100644
index 0000000..beb15d2
--- /dev/null
+++ b/tests/test_settings.py
@@ -0,0 +1,211 @@
+"""Tests for ndevio's plugin settings.
+
+ndevio's user-configurable settings are declared in ``napari.yaml`` under
+``contributions.configuration`` and exposed to napari through
+``napari.settings.get_plugin_settings('ndevio')``.  These tests check that:
+
+* the manifest declares the expected configuration contributions,
+* ``ndevio._settings.get_ndevio_settings`` returns napari's settings when
+  available and falls back to the manifest defaults otherwise.
+"""
+
+from pathlib import Path
+from types import SimpleNamespace
+
+import pytest
+
+from ndevio._settings import (
+    ExportDefaults,
+    ReaderDefaults,
+    _DefaultSettings,
+    get_ndevio_settings,
+)
+
+MANIFEST = Path(__file__).parent.parent / 'src' / 'ndevio' / 'napari.yaml'
+
+
+@pytest.fixture
+def manifest():
+    """Parse the ndevio npe2 manifest once per test."""
+    from npe2 import PluginManifest
+
+    return PluginManifest.from_file(MANIFEST)
+
+
+def test_manifest_declares_configuration_categories(manifest):
+    """The manifest contributes a 'Reader' and an 'Export' category."""
+    configs = manifest.contributions.configuration
+    assert [c.title for c in configs] == ['Reader', 'Export']
+
+    reader = configs[0]
+    assert set(reader.properties) == {
+        'ndevio.suggest_reader_plugins',
+        'ndevio.scene_handling',
+        'ndevio.clear_layers_on_new_scene',
+        'ndevio.max_in_mem_gb',
+    }
+
+    export = configs[1]
+    assert set(export.properties) == {
+        'ndevio.canvas_scale',
+        'ndevio.override_canvas_size',
+        'ndevio.canvas_width',
+        'ndevio.canvas_height',
+    }
+
+
+def test_manifest_reader_property_defaults(manifest):
+    """Reader properties carry the same defaults as the old ndev-settings."""
+    reader = manifest.contributions.configuration[0]
+    props = reader.properties
+
+    assert props['ndevio.suggest_reader_plugins'].default is True
+    assert props['ndevio.scene_handling'].default == 'Open Scene Widget'
+    assert props['ndevio.scene_handling'].enum == [
+        'Open Scene Widget',
+        'View All Scenes',
+        'View First Scene Only',
+    ]
+    assert props['ndevio.clear_layers_on_new_scene'].default is False
+    assert props['ndevio.max_in_mem_gb'].default == 8.0
+    assert props['ndevio.max_in_mem_gb'].minimum == 0.5
+    assert props['ndevio.max_in_mem_gb'].maximum == 128.0
+
+
+def test_manifest_export_property_defaults(manifest):
+    """Export properties carry the same defaults as the old ndev-settings."""
+    export = manifest.contributions.configuration[1]
+    props = export.properties
+
+    assert props['ndevio.canvas_scale'].default == 1.0
+    assert props['ndevio.canvas_scale'].minimum == 0.01
+    assert props['ndevio.canvas_scale'].maximum == 100.0
+    assert props['ndevio.override_canvas_size'].default is False
+    assert props['ndevio.canvas_width'].default == 1024
+    assert props['ndevio.canvas_height'].default == 1024
+
+
+def test_manifest_has_no_dynamic_preferred_reader(manifest):
+    """The dynamic 'preferred_reader' setting is not representable and dropped."""
+    for config in manifest.contributions.configuration:
+        for key in config.properties:
+            assert 'preferred' not in key.lower()
+
+
+def test_default_settings_shape():
+    """The fallback settings object mirrors the manifest defaults."""
+    defaults = _DefaultSettings()
+    assert isinstance(defaults.reader, ReaderDefaults)
+    assert isinstance(defaults.export, ExportDefaults)
+
+    assert defaults.reader.suggest_reader_plugins is True
+    assert defaults.reader.scene_handling == 'Open Scene Widget'
+    assert defaults.reader.clear_layers_on_new_scene is False
+    assert defaults.reader.max_in_mem_gb == 8.0
+
+    assert defaults.export.canvas_scale == 1.0
+    assert defaults.export.override_canvas_size is False
+    assert defaults.export.canvas_width == 1024
+    assert defaults.export.canvas_height == 1024
+
+
+def test_get_ndevio_settings_uses_napari(monkeypatch):
+    """When napari provides plugin settings, they are returned as-is."""
+    import napari.settings as napari_settings
+
+    mock = SimpleNamespace(
+        reader=SimpleNamespace(scene_handling='View All Scenes'),
+    )
+    monkeypatch.setattr(
+        napari_settings,
+        'get_plugin_settings',
+        lambda plugin: mock,
+        raising=False,
+    )
+
+    assert get_ndevio_settings() is mock
+
+
+def test_get_ndevio_settings_falls_back_when_plugin_missing(monkeypatch):
+    """napari raising KeyError for an undiscovered plugin -> defaults."""
+    import napari.settings as napari_settings
+
+    def _raise(_plugin: str):
+        raise KeyError('ndevio')
+
+    monkeypatch.setattr(
+        napari_settings, 'get_plugin_settings', _raise, raising=False
+    )
+
+    settings = get_ndevio_settings()
+    assert isinstance(settings, _DefaultSettings)
+    assert settings.reader.scene_handling == 'Open Scene Widget'
+
+
+def test_get_ndevio_settings_falls_back_when_feature_missing(monkeypatch):
+    """Older napari without get_plugin_settings -> defaults."""
+    import napari.settings as napari_settings
+
+    monkeypatch.delattr(napari_settings, 'get_plugin_settings', raising=False)
+
+    settings = get_ndevio_settings()
+    assert isinstance(settings, _DefaultSettings)
+    assert settings.reader.max_in_mem_gb == 8.0
+
+
+def test_real_get_plugin_settings(tmp_path):
+    """End-to-end: napari builds ndevio's preferences from the manifest.
+
+    This exercises the real ``napari.settings.get_plugin_settings('ndevio')``
+    path, which requires a napari that supports plugin settings.
+    """
+    import napari.settings as napari_settings
+
+    if not hasattr(napari_settings, 'get_plugin_settings'):
+        pytest.skip('installed napari lacks plugin settings support')
+
+    from npe2 import PluginManager
+
+    # Make sure ndevio's manifest is known to the npe2 plugin manager.
+    pm = PluginManager.instance()
+    if 'ndevio' not in pm:
+        from npe2 import PluginManifest
+
+        pm.register(PluginManifest.from_file(MANIFEST))
+
+    napari_settings._PLUGIN_PREFERENCES.clear()
+    try:
+        settings = napari_settings.get_plugin_settings(
+            'ndevio', path_dir=tmp_path
+        )
+
+        assert settings.reader.suggest_reader_plugins is True
+        assert settings.reader.scene_handling == 'Open Scene Widget'
+        assert settings.reader.clear_layers_on_new_scene is False
+        assert settings.reader.max_in_mem_gb == 8.0
+
+        assert settings.export.canvas_scale == 1.0
+        assert settings.export.override_canvas_size is False
+        assert settings.export.canvas_width == 1024
+        assert settings.export.canvas_height == 1024
+
+        # Preferences persist to a per-plugin yaml under the given path dir.
+        assert settings.config_path == tmp_path / 'ndevio.yaml'
+
+        # The accessor used by ndevio's code paths returns this same model
+        # (the napari cache is still populated with the tmp_path config above).
+        from ndevio._settings import get_ndevio_settings
+
+        accessed = get_ndevio_settings()
+        assert accessed is settings
+        assert accessed.reader.scene_handling == 'Open Scene Widget'
+        assert accessed.export.canvas_width == 1024
+        assert not isinstance(accessed, _DefaultSettings)
+
+        # Changing a value and saving writes the per-plugin yaml file.
+        settings.reader.max_in_mem_gb = 4.0
+        settings.save()
+        assert (tmp_path / 'ndevio.yaml').exists()
+        assert 'max_in_mem_gb: 4.0' in (tmp_path / 'ndevio.yaml').read_text()
+    finally:
+        napari_settings._PLUGIN_PREFERENCES.clear()

From e83b6492738b18f4476a97811e7c70effac11523 Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 16:44:34 -0500
Subject: [PATCH 05/12] use new settings in all places

---
 src/ndevio/_napari_reader.py               | 12 +++---
 src/ndevio/bioio_plugins/_manager.py       |  7 ++--
 src/ndevio/nimage.py                       | 49 +++++++---------------
 src/ndevio/widgets/_scene_widget.py        |  7 ++--
 src/ndevio/widgets/_utilities_container.py | 15 ++++---
 5 files changed, 37 insertions(+), 53 deletions(-)

diff --git a/src/ndevio/_napari_reader.py b/src/ndevio/_napari_reader.py
index 783cf2f..92b6d03 100644
--- a/src/ndevio/_napari_reader.py
+++ b/src/ndevio/_napari_reader.py
@@ -38,20 +38,20 @@ def napari_get_reader(
         The reader function for the given path
     """
 
-    from ndev_settings import get_settings
+    from ._settings import get_ndevio_settings
 
-    settings = get_settings()
+    settings = get_ndevio_settings()
 
     open_first_scene_only = (
         open_first_scene_only
         if open_first_scene_only is not None
-        else settings.ndevio_reader.scene_handling == 'View First Scene Only'  # type: ignore
+        else settings.reader.scene_handling == 'View First Scene Only'
     ) or False
 
     open_all_scenes = (
         open_all_scenes
         if open_all_scenes is not None
-        else settings.ndevio_reader.scene_handling == 'View All Scenes'  # type: ignore
+        else settings.reader.scene_handling == 'View All Scenes'
     ) or False
 
     # Return reader function; actual format validation happens in
@@ -71,8 +71,8 @@ def napari_reader_function(
     """
     Read a file using bioio.
 
-    nImage handles reader selection: if a preferred_reader is set in settings,
-    it's tried first with automatic fallback to bioio's default plugin ordering.
+    nImage handles reader selection, relying on bioio's default plugin
+    ordering (an explicit ``reader`` may be passed to ``nImage`` directly).
 
     Parameters
     ----------
diff --git a/src/ndevio/bioio_plugins/_manager.py b/src/ndevio/bioio_plugins/_manager.py
index a7d7c98..1ae8420 100644
--- a/src/ndevio/bioio_plugins/_manager.py
+++ b/src/ndevio/bioio_plugins/_manager.py
@@ -159,13 +159,14 @@ def raise_unsupported_with_suggestions(path: PathLike) -> None:
 
     """
     from bioio_base.exceptions import UnsupportedFileFormatError
-    from ndev_settings import get_settings
 
-    settings = get_settings()
+    from ndevio._settings import get_ndevio_settings
+
+    settings = get_ndevio_settings()
     manager = ReaderPluginManager(path)
     msg_extra = (
         manager.get_installation_message()
-        if settings.ndevio_reader.suggest_reader_plugins  # type: ignore
+        if settings.reader.suggest_reader_plugins
         else None
     )
 
diff --git a/src/ndevio/nimage.py b/src/ndevio/nimage.py
index fdc9567..ae42f25 100644
--- a/src/ndevio/nimage.py
+++ b/src/ndevio/nimage.py
@@ -38,9 +38,8 @@ class nImage(BioImage):
         Image to be loaded. Can be a path to an image file, a numpy array,
         or an xarray DataArray.
     reader : type[Reader] | Sequence[type[Reader]], optional
-        Reader class or priority list of readers. If not provided, checks
-        settings for preferred_reader and tries that first, then falls back
-        to bioio's default deterministic priority.
+        Reader class or priority list of readers. If not provided, bioio's
+        default deterministic reader priority is used.
     **kwargs
         Additional arguments passed to BioImage.
 
@@ -171,13 +170,11 @@ def _fits_in_memory(self) -> bool:
         if self.path is None:
             return True
 
-        from ndev_settings import get_settings
         from psutil import virtual_memory
 
-        max_bytes = (
-            float(getattr(get_settings().ndevio_reader, 'max_in_mem_gb', 8.0))  # type: ignore[attr-defined]
-            * 1e9
-        )
+        from ._settings import get_ndevio_settings
+
+        max_bytes = float(get_ndevio_settings().reader.max_in_mem_gb) * 1e9
         available = int(virtual_memory().available)
         # xr.DataArray.nbytes = shape × dtype.itemsize — no IO, dask-safe
         uncompressed = self.xarray_dask_data.nbytes
@@ -661,10 +658,14 @@ def _resolve_reader(
 ) -> type[Reader] | Sequence[type[Reader]] | None:
     """Resolve the reader to use for an image.
 
-    Priority:
-    1. Explicit reader (passed to __init__)
-    2. Preferred reader from settings (if file path and installed)
-    3. None (let bioio determine)
+    An explicit reader (passed to ``nImage.__init__``) is honored as-is;
+    otherwise ``None`` is returned and bioio selects the reader using its
+    default plugin priority.
+
+    Note that a settings-driven "preferred reader" was previously consulted
+    here, but that dynamic setting cannot be expressed as an npe2
+    ``ConfigurationContribution`` and was removed — bioio handles reader
+    priority and fallback internally (see bioio#162).
 
     Parameters
     ----------
@@ -679,26 +680,4 @@ def _resolve_reader(
         The reader to use, or None to let bioio choose.
 
     """
-    if explicit_reader is not None:
-        return explicit_reader
-
-    # Only check preferred reader for file paths
-    if not isinstance(image, str | Path):
-        return None
-
-    # Get preferred reader from settings
-    from ndev_settings import get_settings
-
-    from .bioio_plugins._utils import get_installed_plugins, get_reader_by_name
-
-    settings = get_settings()
-    preferred = settings.ndevio_reader.preferred_reader  # type: ignore
-
-    if not preferred:
-        return None
-
-    if preferred not in get_installed_plugins():
-        logger.debug('Preferred reader %s not installed', preferred)
-        return None
-
-    return get_reader_by_name(preferred)
+    return explicit_reader
diff --git a/src/ndevio/widgets/_scene_widget.py b/src/ndevio/widgets/_scene_widget.py
index 88e68ae..c078814 100644
--- a/src/ndevio/widgets/_scene_widget.py
+++ b/src/ndevio/widgets/_scene_widget.py
@@ -10,7 +10,8 @@
 from typing import TYPE_CHECKING
 
 from magicgui.widgets import Container, Select
-from ndev_settings import get_settings
+
+from ndevio._settings import get_ndevio_settings
 
 if TYPE_CHECKING:
     import napari
@@ -82,7 +83,7 @@ def __init__(
         self.viewer = viewer
         self.path = path
         self.img = img
-        self.settings = get_settings()
+        self.settings = get_ndevio_settings()
         self.scenes = [
             f'{idx}{DELIMITER}{scene}'
             for idx, scene in enumerate(self.img.scenes)
@@ -104,7 +105,7 @@ def _connect_events(self):
 
     def open_scene(self) -> None:
         """Open the selected scene(s) in the viewer."""
-        if self.settings.ndevio_reader.clear_layers_on_new_scene:
+        if self.settings.reader.clear_layers_on_new_scene:
             self.viewer.layers.clear()
 
         for scene in self._scene_list_widget.value:
diff --git a/src/ndevio/widgets/_utilities_container.py b/src/ndevio/widgets/_utilities_container.py
index ffd5016..ef0e9f8 100644
--- a/src/ndevio/widgets/_utilities_container.py
+++ b/src/ndevio/widgets/_utilities_container.py
@@ -25,8 +25,8 @@
     TextEdit,
     TupleEdit,
 )
-from ndev_settings import get_settings
 
+from ndevio._settings import get_ndevio_settings
 from ndevio.utils import helpers
 
 if TYPE_CHECKING:
@@ -270,7 +270,7 @@ def __init__(self, viewer: napari.viewer.Viewer = None):
         self._viewer = viewer if viewer is not None else None
         self._squeezed_dims_order: str | None = None
         self._squeezed_dims: tuple[int, ...] | None = None
-        self._settings = get_settings()
+        self._settings = get_ndevio_settings()
 
         self._init_widgets()
         self._init_save_name_container()
@@ -1005,7 +1005,7 @@ def canvas_export_figure(self) -> None:
             save_name,
         )
 
-        scale = self._settings.ndevio_export.canvas_scale
+        scale = self._settings.export.canvas_scale
 
         self._viewer.export_figure(
             path=str(save_path),
@@ -1027,9 +1027,12 @@ def canvas_screenshot(self) -> None:
             self._save_directory.value, 'Figures', save_name
         )
 
-        scale = self._settings.ndevio_export.canvas_scale
-        if self._settings.ndevio_export.override_canvas_size:
-            canvas_size = self._settings.ndevio_export.canvas_size
+        scale = self._settings.export.canvas_scale
+        if self._settings.export.override_canvas_size:
+            canvas_size = (
+                self._settings.export.canvas_width,
+                self._settings.export.canvas_height,
+            )
         else:
             canvas_size = self._viewer.window._qt_viewer.canvas.size
 

From 12b5f2abce07d5a88fc7c9e060ca4964e289311f Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 16:44:59 -0500
Subject: [PATCH 06/12] update test_manager.py

---
 tests/test_bioio_plugins/test_manager.py | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/tests/test_bioio_plugins/test_manager.py b/tests/test_bioio_plugins/test_manager.py
index c0f3bb6..7344bac 100644
--- a/tests/test_bioio_plugins/test_manager.py
+++ b/tests/test_bioio_plugins/test_manager.py
@@ -4,6 +4,7 @@
 via TestSuggestPluginsForPath. We trust those unit tests and don't duplicate here.
 """
 
+from types import SimpleNamespace
 from unittest.mock import patch
 
 import pytest
@@ -19,11 +20,12 @@ def test_raises_with_suggestions_enabled(self):
             raise_unsupported_with_suggestions,
         )
 
-        with patch('ndev_settings.get_settings') as mock_settings:
-            mock_settings.return_value.ndevio_reader.suggest_reader_plugins = (
-                True
-            )
-
+        with patch(
+            'ndevio._settings.get_ndevio_settings',
+            return_value=SimpleNamespace(
+                reader=SimpleNamespace(suggest_reader_plugins=True),
+            ),
+        ):
             with pytest.raises(UnsupportedFileFormatError) as exc_info:
                 raise_unsupported_with_suggestions('test.czi')
 
@@ -36,11 +38,12 @@ def test_raises_without_suggestions_when_disabled(self):
             raise_unsupported_with_suggestions,
         )
 
-        with patch('ndev_settings.get_settings') as mock_settings:
-            mock_settings.return_value.ndevio_reader.suggest_reader_plugins = (
-                False
-            )
-
+        with patch(
+            'ndevio._settings.get_ndevio_settings',
+            return_value=SimpleNamespace(
+                reader=SimpleNamespace(suggest_reader_plugins=False),
+            ),
+        ):
             with pytest.raises(UnsupportedFileFormatError) as exc_info:
                 raise_unsupported_with_suggestions('test.czi')
 

From 6221826bb433e42567ce91ec709d3518ed15828a Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 16:45:09 -0500
Subject: [PATCH 07/12] update test_image.py

---
 tests/test_nimage.py | 115 +++++++++++--------------------------------
 1 file changed, 28 insertions(+), 87 deletions(-)

diff --git a/tests/test_nimage.py b/tests/test_nimage.py
index 9b2a084..7655705 100644
--- a/tests/test_nimage.py
+++ b/tests/test_nimage.py
@@ -131,7 +131,6 @@ def test_nImage_ome_reader(resources_dir: Path):
     img_path = resources_dir / CELLS3D2CH_OME_TIFF
 
     nimg = nImage(img_path)
-    # assert nimg.settings.ndevio_reader.preferred_reader == 'bioio-ome-tiff'  # this was the old methodology before bioio#162
     assert nimg.reader.name == 'bioio_ome_tiff'
     # the below only exists if 'bioio-ome-tiff' is used
     assert hasattr(nimg, 'ome_metadata')
@@ -671,13 +670,12 @@ def test_channel_kwargs_override_metadata(self, resources_dir: Path):
         )  # default for 2-channel
 
 
-class TestPreferredReaderFallback:
-    """Tests for preferred reader fallback logic in nImage.__init__."""
+class TestReaderFallback:
+    """Tests for reader selection/fallback logic in nImage.__init__."""
 
-    def test_preferred_reader_success(self, resources_dir: Path):
-        """Test that preferred reader is used when it works."""
+    def test_resolved_reader_used_when_it_works(self, resources_dir: Path):
+        """Test that the resolved reader is used when it works."""
         with patch('ndevio.nimage._resolve_reader') as mock_resolve:
-            # Mock returning a valid reader
             from bioio_tifffile import Reader
 
             mock_resolve.return_value = Reader
@@ -689,10 +687,9 @@ def test_preferred_reader_success(self, resources_dir: Path):
             assert img is not None
             assert img.reader.name == 'bioio_tifffile'
 
-    def test_preferred_reader_fallback(self, resources_dir: Path):
-        """Test that failed preferred reader will fallback"""
+    def test_failed_reader_falls_back(self, resources_dir: Path):
+        """Test that a reader which can't read the file falls back."""
         with patch('ndevio.nimage._resolve_reader') as mock_resolve:
-            # Mock returning a reader that won't work for this file
             from bioio_czi import Reader
 
             mock_resolve.return_value = Reader
@@ -705,10 +702,10 @@ def test_preferred_reader_fallback(self, resources_dir: Path):
             # Should have fallen back to bioio's default (ome-tiff)
             assert img.reader.name == 'bioio_ome_tiff'
 
-    def test_no_preferred_reader_uses_default(self, resources_dir: Path):
-        """Test that no preferred reader uses bioio's default priority."""
+    def test_no_reader_uses_default(self, resources_dir: Path):
+        """Test that no resolved reader uses bioio's default priority."""
         with patch('ndevio.nimage._resolve_reader') as mock_resolve:
-            mock_resolve.return_value = None  # No preferred reader
+            mock_resolve.return_value = None  # No explicit reader
 
             img = nImage(str(resources_dir / 'cells3d2ch_legacy.tiff'))
             assert img is not None
@@ -719,94 +716,38 @@ def test_no_preferred_reader_uses_default(self, resources_dir: Path):
 class TestResolveReaderFunction:
     """Tests for _resolve_reader function."""
 
-    def test_returns_none_when_no_preferred_reader(self):
-        """Test returns None when preferred_reader is not set."""
+    def test_returns_none_without_explicit_reader(self):
+        """Returns None (bioio picks the reader) when no reader is given."""
         from ndevio.nimage import _resolve_reader
 
-        with patch('ndev_settings.get_settings') as mock_get_settings:
-            mock_get_settings.return_value.ndevio_reader.preferred_reader = (
-                None
-            )
-
-            result = _resolve_reader('test.tiff', None)
-            assert result is None
-
-    def test_returns_none_when_preferred_not_installed(self):
-        """Test returns None when preferred reader is not installed."""
-        from ndevio.nimage import _resolve_reader
-
-        with (
-            patch('ndev_settings.get_settings') as mock_get_settings,
-            patch(
-                'ndevio.bioio_plugins._utils.get_installed_plugins',
-                return_value={'bioio-ome-tiff', 'bioio-tifffile'},
-            ),
-        ):
-            mock_get_settings.return_value.ndevio_reader.preferred_reader = (
-                'bioio-czi'
-            )
-
-            result = _resolve_reader('test.tiff', None)
-            assert result is None
-
-    def test_returns_reader_when_preferred_installed(self):
-        """Test returns reader class when preferred reader is installed."""
-        from ndevio.nimage import _resolve_reader
-
-        with (
-            patch('ndev_settings.get_settings') as mock_get_settings,
-            patch(
-                'ndevio.bioio_plugins._utils.get_installed_plugins',
-                return_value={'bioio-ome-tiff'},
-            ),
-            patch(
-                'ndevio.bioio_plugins._utils.get_reader_by_name'
-            ) as mock_get_reader,
-        ):
-            from bioio_ome_tiff import Reader as OmeTiffReader
+        result = _resolve_reader('test.tiff', None)
+        assert result is None
 
-            mock_get_reader.return_value = OmeTiffReader
-            mock_get_settings.return_value.ndevio_reader.preferred_reader = (
-                'bioio-ome-tiff'
-            )
-
-            result = _resolve_reader('test.tiff', None)
-            assert result == OmeTiffReader
-            mock_get_reader.assert_called_once_with('bioio-ome-tiff')
-
-    def test_explicit_reader_bypasses_settings(self):
-        """Test that explicit reader bypasses settings lookup."""
+    def test_returns_explicit_reader(self):
+        """An explicit reader is returned as-is."""
         from bioio_tifffile import Reader as TifffileReader
 
         from ndevio.nimage import _resolve_reader
 
-        with patch('ndev_settings.get_settings') as mock_get_settings:
-            result = _resolve_reader('test.tiff', TifffileReader)
-
-            # Should return explicit reader without checking settings
-            assert result == TifffileReader
-            mock_get_settings.assert_not_called()
+        result = _resolve_reader('test.tiff', TifffileReader)
+        assert result == TifffileReader
 
     def test_array_input_returns_none(self):
-        """Test that array inputs don't trigger preferred reader lookup."""
+        """Array inputs don't need reader resolution."""
         import numpy as np
 
         from ndevio.nimage import _resolve_reader
 
-        with patch('ndev_settings.get_settings') as mock_get_settings:
-            arr = np.zeros((10, 10), dtype=np.uint8)
-            result = _resolve_reader(arr, None)
-
-            # Should return None without checking settings for arrays
-            assert result is None
-            mock_get_settings.assert_not_called()
+        arr = np.zeros((10, 10), dtype=np.uint8)
+        result = _resolve_reader(arr, None)
+        assert result is None
 
 
 class TestNonPathImageHandling:
     """Tests for handling non-path inputs (arrays)."""
 
-    def test_array_input_no_preferred_reader_check(self):
-        """Test that arrays don't trigger preferred reader logic."""
+    def test_array_input_no_reader_resolution(self):
+        """Test that arrays don't trigger reader resolution."""
         import numpy as np
 
         with patch('ndevio.nimage._resolve_reader') as mock_resolve:
@@ -840,8 +781,8 @@ def test_unsupported_array_raises_without_suggestions(self):
 class TestExplicitReaderParameter:
     """Tests for when reader is explicitly provided."""
 
-    def test_explicit_reader_bypasses_preferred(self, resources_dir: Path):
-        """Test that explicit reader parameter bypasses preferred reader."""
+    def test_explicit_reader_used_directly(self, resources_dir: Path):
+        """Test that an explicit reader parameter is used directly."""
         from bioio_tifffile import Reader as TifffileReader
 
         with patch('ndevio.nimage._resolve_reader') as mock_resolve:
@@ -916,7 +857,7 @@ def test_exceeds_memory_percentage_returns_false(self, tmp_path):
             assert img._fits_in_memory() is False
 
     def test_missing_max_in_mem_setting_falls_back_to_default(self, tmp_path):
-        """Older persisted settings missing max_in_mem_gb should use 8 GB."""
+        """Missing napari settings should fall back to the 8 GB default."""
         from types import SimpleNamespace
 
         import numpy as np
@@ -927,9 +868,9 @@ def test_missing_max_in_mem_setting_falls_back_to_default(self, tmp_path):
 
         with (
             mock.patch(
-                'ndev_settings.get_settings',
+                'ndevio._settings.get_ndevio_settings',
                 return_value=SimpleNamespace(
-                    ndevio_reader=SimpleNamespace(preferred_reader=None),
+                    reader=SimpleNamespace(max_in_mem_gb=8.0),
                 ),
             ),
             mock.patch(

From be6192c6e5eb1f1e8785c768925a24d999da6344 Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 16:45:38 -0500
Subject: [PATCH 08/12] update both contributing and readme's to explain
 settings

---
 CONTRIBUTING.md |  4 ++--
 README.md       | 25 ++++++++++++++-----------
 2 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 43579e6..343b2ec 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -62,7 +62,7 @@ The napari reader plugin ([_napari_reader.py](src/ndevio/_napari_reader.py)) imp
 
 - **Plugin discovery**: Registers file extensions and provides reader selection
 - **Scene handling**: Integrates with the Scene Widget for multi-scene files
-- **Settings integration**: Respects user preferences from ndev-settings
+- **Settings integration**: Respects user preferences from napari's plugin settings (`contributions.configuration` in `napari.yaml`)
 - **Error handling**: Provides helpful suggestions for missing bioio plugins
 
 This module is the **bridge between napari and nImage**, translating drag-and-drop file operations into proper layer creation.
@@ -71,7 +71,7 @@ This module is the **bridge between napari and nImage**, translating drag-and-dr
 
 1. **Core logic separate from UI**: Business logic in `nimage.py`, `_layer_utils.py`, etc. should have **no Qt or napari imports** (except type hints)
 2. **Lazy imports**: Expensive imports (Qt, napari widgets) should be lazy-loaded to keep startup fast
-3. **Settings-driven behavior**: Use [ndev-settings] for user-configurable behavior rather than hardcoding choices
+3. **Settings-driven behavior**: Use napari plugin settings (declared in `napari.yaml` under `contributions.configuration`) for user-configurable behavior rather than hardcoding choices
 4. **bioio compatibility**: Stay aligned with bioio's data model and avoid reinventing functionality
 
 ## Testing
diff --git a/README.md b/README.md
index b0f616e..195bd8a 100644
--- a/README.md
+++ b/README.md
@@ -23,7 +23,7 @@ Originally developed as part of napari-ndev (as a spiritual successor to [napari
 - **Thorough metadata extraction** — extract and apply scale, units, axis labels, metadata (inc. OME) to napari layers
 - **Remote file support** — compatible Bioio readers,such as [bioio-ome-zarr], can read from remote filesystems (HTTP, S3, etc.) with dask-backed loading
 - **Native multiscale support** — automatically read and display multiscale images when supported by the reader. For best experience, turn on the asynchronous rendering experimental setting in napari.
-- **Configurable behavior** via [ndev-settings] — customize reader priority, multi-scene handling, and more
+- **Configurable behavior** via napari Preferences — customize multi-scene handling, memory policy, plugin suggestions, and more
 - **Smart plugin installation** — automatic suggestions to install missing bioio reader plugins
 - **Programmatic API** — `nImage` class for napari-ready metadata extraction
 - **Batch utilities** — legacy widget for batch concatenation (with [nbatch]) and metadata management, with features being superseded by [napari-metadata]
@@ -87,17 +87,18 @@ If you open a file that requires a bioio reader not currently installed, ndevio
 
 This widget taps into the `napari-plugin-manager` to install the bioio reader plugin from PyPI via a GUI. You may invoke this widget manually at any time via `Plugins > ndevio > Install BioIO Reader Plugins` to install any additional bioio reader plugin *and* update any currently installed plugins.
 
-#### Settings Widget
+#### Settings
 
-Access **ndevio settings** via `Plugins > ndev-settings > Settings` to customize:
+Configure **ndevio settings** in napari's **Preferences** dialog (under the
+Plugins section, select `ndevio`) to customize:
 
-- **Preferred reader**: Override bioio's default plugin selection priority (useful for formats with multiple compatible readers)
-- **Multi-scene handling**: Choose whether to show the scene widget, view all scenes as a stack, or view only the first scene
+- **Multi-scene handling**: Choose whether to show the scene widget, view all scenes as layers, or view only the first scene
 - **Plugin suggestions**: Enable/disable automatic plugin installation prompts for unsupported formats
+- **Memory policy**: Set the maximum uncompressed image size (GB) to load eagerly; larger images use dask
+- **Export**: Set the canvas scale and (optionally) override the screenshot canvas size
 
-![ndevio settings via the ndev-settings widget in napari](https://github.com/ndev-kit/ndevio/blob/main/resources/ndev-settings.png?raw=true)
-
-These settings are managed by [ndev-settings] and persist across napari sessions.
+These settings are declared in ndevio's plugin manifest (`contributions.configuration`),
+managed by napari, and persist across napari sessions.
 
 #### Utilities Widget
 
@@ -165,10 +166,13 @@ Image metadata is extracted from bioio and converted to napari layer metadata ba
 
 Images are loaded **in-memory** or **lazily** (via dask) automatically based on:
 
-- File size < 4 GB **AND**
+- Uncompressed file size below the configured in-memory limit (default 8 GB) **AND**
 - File size < 30% of available RAM
 - Remote files (e.g., S3, HTTP) and multiscale are always loaded lazily
 
+The in-memory limit is configurable via the `ndevio` plugin settings in napari's
+Preferences dialog.
+
 ### Multi-channel Images
 
 Multi-channel images are **always split** into individual layers (one per channel), using channel names from metadata when available. Images are added with colorblind-friendly colormaps.
@@ -216,9 +220,8 @@ If you encounter any problems, please [file an issue] along with a detailed desc
 [tox]: https://tox.readthedocs.io/en/latest/
 [bioio]: https://github.com/bioio-devs/bioio
 [napari-aicsimageio]: https://github.com/AllenCellModeling/napari-aicsimageio
-[ndev-settings]: https://github.com/ndev-kit/ndev-settings
-[napari-metadata]: https://github.com/napari/napari-metadata
 [nbatch]: https://github.com/ndev-kit/nbatch
+[napari-metadata]: https://github.com/napari/napari-metadata
 [uv]: https://docs.astral.sh/uv/
 [ndev-kit]: https://github.com/ndev-kit
 [bioio-ome-zarr]: https://github.com/bioio-devs/bioio-ome-zarr

From 72f66f57498af8e9ee55da5801457c0cc740ddd1 Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 22:21:34 -0500
Subject: [PATCH 09/12] clean up the testing

---
 tests/test_settings.py | 75 ++++++++++++++++--------------------------
 1 file changed, 29 insertions(+), 46 deletions(-)

diff --git a/tests/test_settings.py b/tests/test_settings.py
index beb15d2..ce70036 100644
--- a/tests/test_settings.py
+++ b/tests/test_settings.py
@@ -154,58 +154,41 @@ def test_get_ndevio_settings_falls_back_when_feature_missing(monkeypatch):
 
 
 def test_real_get_plugin_settings(tmp_path):
-    """End-to-end: napari builds ndevio's preferences from the manifest.
-
-    This exercises the real ``napari.settings.get_plugin_settings('ndevio')``
-    path, which requires a napari that supports plugin settings.
-    """
-    import napari.settings as napari_settings
+    """End-to-end: napari builds ndevio's preferences from the manifest."""
+    from napari import settings as napari_settings
 
     if not hasattr(napari_settings, 'get_plugin_settings'):
-        pytest.skip('installed napari lacks plugin settings support')
+        pytest.skip(
+            'installed napari lacks plugin settings (need napari>=0.9.0)'
+        )
 
-    from npe2 import PluginManager
+    from npe2 import PluginManager, PluginManifest
 
-    # Make sure ndevio's manifest is known to the npe2 plugin manager.
+    # pytest blocks discovery, so register the (always installed) manifest.
     pm = PluginManager.instance()
     if 'ndevio' not in pm:
-        from npe2 import PluginManifest
+        pm.register(PluginManifest.from_distribution('ndevio'))
+    # Reset the in-memory cache so the registered plugin is included (saved
+    # values are re-read from disk; this also allows path_dir=tmp_path).
+    napari_settings._PLUGIN_PREFERENCES.clear()
 
-        pm.register(PluginManifest.from_file(MANIFEST))
+    settings = napari_settings.get_plugin_settings('ndevio', path_dir=tmp_path)
 
-    napari_settings._PLUGIN_PREFERENCES.clear()
-    try:
-        settings = napari_settings.get_plugin_settings(
-            'ndevio', path_dir=tmp_path
-        )
+    assert settings.reader.suggest_reader_plugins is True
+    assert settings.reader.scene_handling == 'Open Scene Widget'
+    assert settings.reader.clear_layers_on_new_scene is False
+    assert settings.reader.max_in_mem_gb == 8.0
+
+    assert settings.export.canvas_scale == 1.0
+    assert settings.export.override_canvas_size is False
+    assert settings.export.canvas_width == 1024
+    assert settings.export.canvas_height == 1024
+
+    # Settings are persisted to a per-plugin yaml, and changes auto-save.
+    assert settings.config_path == tmp_path / 'ndevio.yaml'
+    settings.reader.max_in_mem_gb = 4.0
+    assert 'max_in_mem_gb: 4.0' in (tmp_path / 'ndevio.yaml').read_text()
 
-        assert settings.reader.suggest_reader_plugins is True
-        assert settings.reader.scene_handling == 'Open Scene Widget'
-        assert settings.reader.clear_layers_on_new_scene is False
-        assert settings.reader.max_in_mem_gb == 8.0
-
-        assert settings.export.canvas_scale == 1.0
-        assert settings.export.override_canvas_size is False
-        assert settings.export.canvas_width == 1024
-        assert settings.export.canvas_height == 1024
-
-        # Preferences persist to a per-plugin yaml under the given path dir.
-        assert settings.config_path == tmp_path / 'ndevio.yaml'
-
-        # The accessor used by ndevio's code paths returns this same model
-        # (the napari cache is still populated with the tmp_path config above).
-        from ndevio._settings import get_ndevio_settings
-
-        accessed = get_ndevio_settings()
-        assert accessed is settings
-        assert accessed.reader.scene_handling == 'Open Scene Widget'
-        assert accessed.export.canvas_width == 1024
-        assert not isinstance(accessed, _DefaultSettings)
-
-        # Changing a value and saving writes the per-plugin yaml file.
-        settings.reader.max_in_mem_gb = 4.0
-        settings.save()
-        assert (tmp_path / 'ndevio.yaml').exists()
-        assert 'max_in_mem_gb: 4.0' in (tmp_path / 'ndevio.yaml').read_text()
-    finally:
-        napari_settings._PLUGIN_PREFERENCES.clear()
+    # The accessor used by ndevio's code paths returns this same model.
+    assert get_ndevio_settings() is settings
+    assert not isinstance(get_ndevio_settings(), _DefaultSettings)

From c6ac993e571528ad87daa33e12908e078d59d8ba Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 6 Aug 2026 23:04:17 -0500
Subject: [PATCH 10/12] simplify teh backup settings

---
 src/ndevio/_settings.py | 95 +++++++++++++++--------------------------
 tests/test_settings.py  | 51 ++++++----------------
 2 files changed, 49 insertions(+), 97 deletions(-)

diff --git a/src/ndevio/_settings.py b/src/ndevio/_settings.py
index 796794d..03923db 100644
--- a/src/ndevio/_settings.py
+++ b/src/ndevio/_settings.py
@@ -1,19 +1,19 @@
 """Access to ndevio's plugin settings.
 
 ndevio's user-configurable behavior is declared in ``napari.yaml`` under
-``contributions.configuration`` (two categories: ``reader`` and ``export``)
+``contributions.configuration`` (two categories: ``Reader`` and ``Export``)
 and surfaces in napari's **Preferences** dialog.  At runtime the values are
 read through ``napari.settings.get_plugin_settings('ndevio')``.
 
-When napari is too old to expose plugin settings (i.e. it predates the
-``get_plugin_settings`` API), or when the ndevio plugin has not been
-discovered yet, :func:`get_ndevio_settings` falls back to the same defaults
-declared in the manifest so ndevio keeps working everywhere.
+On napari versions too old to expose plugin settings (i.e. it predates the
+``get_plugin_settings`` API, released in 0.9.0), :func:`get_ndevio_settings`
+falls back to the defaults declared in ``napari.yaml`` so ndevio keeps working
+everywhere.
 """
 
 from __future__ import annotations
 
-from dataclasses import dataclass, field
+from types import SimpleNamespace
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
@@ -21,62 +21,37 @@
 
 _PLUGIN_NAME = 'ndevio'
 
-# The defaults below mirror the ``contributions.configuration`` block in
-# ``napari.yaml``.  They are only used as a fallback when napari's plugin
-# settings are unavailable (old napari, or plugin not discovered yet).
-
-
-@dataclass(frozen=True)
-class ReaderDefaults:
-    """Default values for the ``reader`` configuration category."""
-
-    suggest_reader_plugins: bool = True
-    scene_handling: str = 'Open Scene Widget'
-    clear_layers_on_new_scene: bool = False
-    max_in_mem_gb: float = 8.0
-
-
-@dataclass(frozen=True)
-class ExportDefaults:
-    """Default values for the ``export`` configuration category."""
-
-    canvas_scale: float = 1.0
-    override_canvas_size: bool = False
-    canvas_width: int = 1024
-    canvas_height: int = 1024
-
-
-@dataclass(frozen=True)
-class _DefaultSettings:
-    """Fallback settings object exposing the same shape as napari's model.
-
-    Attributes are named to match the generated napari plugin preferences
-    (``.reader`` and ``.export``), so callers can use the fallback
-    interchangeably with the napari-managed model.
-    """
-
-    reader: ReaderDefaults = field(default_factory=ReaderDefaults)
-    export: ExportDefaults = field(default_factory=ExportDefaults)
-
-
-def get_ndevio_settings() -> PluginPreferences | _DefaultSettings:
-    """Return ndevio's plugin settings, falling back to defaults.
-
-    Returns
-    -------
-    PluginPreferences | _DefaultSettings
-        The napari-managed plugin preferences for ``ndevio`` when available,
-        otherwise a frozen dataclass carrying the manifest defaults.  Both
-        expose the same ``.reader`` and ``.export`` attributes.
-
+# Defaults mirroring the ``contributions.configuration`` block in
+# ``napari.yaml`` — only the values ndevio's code reads.  Used as a fallback
+# when napari is too old to expose plugin settings; the settings are not
+# user-configurable in that case.
+_DEFAULTS = SimpleNamespace(
+    reader=SimpleNamespace(
+        suggest_reader_plugins=True,
+        scene_handling='Open Scene Widget',
+        clear_layers_on_new_scene=False,
+        max_in_mem_gb=8.0,
+    ),
+    export=SimpleNamespace(
+        canvas_scale=1.0,
+        override_canvas_size=False,
+        canvas_width=1024,
+        canvas_height=1024,
+    ),
+)
+
+
+def get_ndevio_settings() -> PluginPreferences | SimpleNamespace:
+    """Return ndevio's plugin settings, falling back to manifest defaults.
+
+    Returns the napari-managed plugin preferences for ``ndevio`` when
+    available; otherwise a ``SimpleNamespace`` carrying the manifest defaults
+    (used when napari is too old for ``get_plugin_settings``).  Both expose
+    the same ``.reader`` and ``.export`` attributes.
     """
     try:
         from napari.settings import get_plugin_settings
-    except ImportError:  # pragma: no cover - pre-plugin-settings napari
-        return _DefaultSettings()
 
-    try:
         return get_plugin_settings(_PLUGIN_NAME)
-    except KeyError:
-        # ndevio is not registered/discovered (yet) -> manifest defaults
-        return _DefaultSettings()
+    except ImportError:  # pragma: no cover - napari < 0.9.0
+        return _DEFAULTS
diff --git a/tests/test_settings.py b/tests/test_settings.py
index ce70036..5f3dd4d 100644
--- a/tests/test_settings.py
+++ b/tests/test_settings.py
@@ -14,12 +14,7 @@
 
 import pytest
 
-from ndevio._settings import (
-    ExportDefaults,
-    ReaderDefaults,
-    _DefaultSettings,
-    get_ndevio_settings,
-)
+from ndevio._settings import get_ndevio_settings
 
 MANIFEST = Path(__file__).parent.parent / 'src' / 'ndevio' / 'napari.yaml'
 
@@ -92,21 +87,19 @@ def test_manifest_has_no_dynamic_preferred_reader(manifest):
             assert 'preferred' not in key.lower()
 
 
-def test_default_settings_shape():
-    """The fallback settings object mirrors the manifest defaults."""
-    defaults = _DefaultSettings()
-    assert isinstance(defaults.reader, ReaderDefaults)
-    assert isinstance(defaults.export, ExportDefaults)
+def test_fallback_defaults_shape():
+    """The fallback defaults mirror the manifest defaults."""
+    from ndevio._settings import _DEFAULTS
 
-    assert defaults.reader.suggest_reader_plugins is True
-    assert defaults.reader.scene_handling == 'Open Scene Widget'
-    assert defaults.reader.clear_layers_on_new_scene is False
-    assert defaults.reader.max_in_mem_gb == 8.0
+    assert _DEFAULTS.reader.suggest_reader_plugins is True
+    assert _DEFAULTS.reader.scene_handling == 'Open Scene Widget'
+    assert _DEFAULTS.reader.clear_layers_on_new_scene is False
+    assert _DEFAULTS.reader.max_in_mem_gb == 8.0
 
-    assert defaults.export.canvas_scale == 1.0
-    assert defaults.export.override_canvas_size is False
-    assert defaults.export.canvas_width == 1024
-    assert defaults.export.canvas_height == 1024
+    assert _DEFAULTS.export.canvas_scale == 1.0
+    assert _DEFAULTS.export.override_canvas_size is False
+    assert _DEFAULTS.export.canvas_width == 1024
+    assert _DEFAULTS.export.canvas_height == 1024
 
 
 def test_get_ndevio_settings_uses_napari(monkeypatch):
@@ -126,22 +119,6 @@ def test_get_ndevio_settings_uses_napari(monkeypatch):
     assert get_ndevio_settings() is mock
 
 
-def test_get_ndevio_settings_falls_back_when_plugin_missing(monkeypatch):
-    """napari raising KeyError for an undiscovered plugin -> defaults."""
-    import napari.settings as napari_settings
-
-    def _raise(_plugin: str):
-        raise KeyError('ndevio')
-
-    monkeypatch.setattr(
-        napari_settings, 'get_plugin_settings', _raise, raising=False
-    )
-
-    settings = get_ndevio_settings()
-    assert isinstance(settings, _DefaultSettings)
-    assert settings.reader.scene_handling == 'Open Scene Widget'
-
-
 def test_get_ndevio_settings_falls_back_when_feature_missing(monkeypatch):
     """Older napari without get_plugin_settings -> defaults."""
     import napari.settings as napari_settings
@@ -149,7 +126,7 @@ def test_get_ndevio_settings_falls_back_when_feature_missing(monkeypatch):
     monkeypatch.delattr(napari_settings, 'get_plugin_settings', raising=False)
 
     settings = get_ndevio_settings()
-    assert isinstance(settings, _DefaultSettings)
+    assert isinstance(settings, SimpleNamespace)
     assert settings.reader.max_in_mem_gb == 8.0
 
 
@@ -191,4 +168,4 @@ def test_real_get_plugin_settings(tmp_path):
 
     # The accessor used by ndevio's code paths returns this same model.
     assert get_ndevio_settings() is settings
-    assert not isinstance(get_ndevio_settings(), _DefaultSettings)
+    assert not isinstance(get_ndevio_settings(), SimpleNamespace)

From 2524b006e27586e8f9028a37d4cd5a6b31ae5479 Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 13 Aug 2026 00:39:26 -0500
Subject: [PATCH 11/12] update for recent changes to config

---
 src/ndevio/_settings.py |   2 +-
 src/ndevio/napari.yaml  |  24 +++----
 tests/test_settings.py  | 139 ++++++++++++++++++++++------------------
 3 files changed, 91 insertions(+), 74 deletions(-)

diff --git a/src/ndevio/_settings.py b/src/ndevio/_settings.py
index 03923db..5c48f4f 100644
--- a/src/ndevio/_settings.py
+++ b/src/ndevio/_settings.py
@@ -1,7 +1,7 @@
 """Access to ndevio's plugin settings.
 
 ndevio's user-configurable behavior is declared in ``napari.yaml`` under
-``contributions.configuration`` (two categories: ``Reader`` and ``Export``)
+``contributions.configurations`` (two categories: ``reader`` and ``export``)
 and surfaces in napari's **Preferences** dialog.  At runtime the values are
 read through ``napari.settings.get_plugin_settings('ndevio')``.
 
diff --git a/src/ndevio/napari.yaml b/src/ndevio/napari.yaml
index 558bf89..f6c4da4 100644
--- a/src/ndevio/napari.yaml
+++ b/src/ndevio/napari.yaml
@@ -59,17 +59,18 @@ contributions:
         '*.txt', '*.v', '*.vms', '*.vsi', '*.vws', '*.wat', '*.wlz', '*.xdce', '*.xml', '*.xqd',
         '*.xqf', '*.xv', '*.xvthumb', '*.xys', '*.zarr', '*.zarr*', '*.zfp', '*.zfr', '*.zif', '*.zvi',
       ]
-  configuration:
-    - title: Reader
+  configurations:
+    reader:
+      title: Reader
       properties:
-        ndevio.suggest_reader_plugins:
+        suggest_reader_plugins:
           type: boolean
           default: true
           title: Suggest reader plugins
           description: >-
             Whether to suggest plugins to install when no reader can be found
             for a file.
-        ndevio.scene_handling:
+        scene_handling:
           type: string
           default: Open Scene Widget
           title: Scene handling
@@ -81,12 +82,12 @@ contributions:
             - Open Scene Widget
             - View All Scenes
             - View First Scene Only
-        ndevio.clear_layers_on_new_scene:
+        clear_layers_on_new_scene:
           type: boolean
           default: false
           title: Clear layers on new scene
           description: Whether to clear the viewer when selecting a new scene.
-        ndevio.max_in_mem_gb:
+        max_in_mem_gb:
           type: number
           default: 8.0
           title: Max in-memory size (GB)
@@ -95,22 +96,23 @@ contributions:
             images use dask.
           minimum: 0.5
           maximum: 128.0
-    - title: Export
+    export:
+      title: Export
       properties:
-        ndevio.canvas_scale:
+        canvas_scale:
           type: number
           default: 1.0
           title: Canvas scale
           description: Scale factor for exported figures and screenshots.
           minimum: 0.01
           maximum: 100.0
-        ndevio.override_canvas_size:
+        override_canvas_size:
           type: boolean
           default: false
           title: Override canvas size
           description: >-
             Whether to override the canvas size when exporting screenshots.
-        ndevio.canvas_width:
+        canvas_width:
           type: integer
           default: 1024
           title: Canvas width
@@ -119,7 +121,7 @@ contributions:
             is enabled).
           minimum: 1
           maximum: 100000
-        ndevio.canvas_height:
+        canvas_height:
           type: integer
           default: 1024
           title: Canvas height
diff --git a/tests/test_settings.py b/tests/test_settings.py
index 5f3dd4d..b7fed7a 100644
--- a/tests/test_settings.py
+++ b/tests/test_settings.py
@@ -1,12 +1,14 @@
 """Tests for ndevio's plugin settings.
 
 ndevio's user-configurable settings are declared in ``napari.yaml`` under
-``contributions.configuration`` and exposed to napari through
+``contributions.configurations`` and exposed to napari through
 ``napari.settings.get_plugin_settings('ndevio')``.  These tests check that:
 
 * the manifest declares the expected configuration contributions,
 * ``ndevio._settings.get_ndevio_settings`` returns napari's settings when
-  available and falls back to the manifest defaults otherwise.
+  available and falls back to the manifest defaults otherwise,
+* napari's ``plugin_settings`` pytest fixture drives the real manifest
+  end-to-end (napari >= 0.9.0).
 """
 
 from pathlib import Path
@@ -28,61 +30,65 @@ def manifest():
 
 
 def test_manifest_declares_configuration_categories(manifest):
-    """The manifest contributes a 'Reader' and an 'Export' category."""
-    configs = manifest.contributions.configuration
-    assert [c.title for c in configs] == ['Reader', 'Export']
+    """The manifest contributes reader / pre-processing / export categories."""
+    configs = manifest.contributions.configurations
+    assert list(configs) == ['reader', 'pre_processing_widget', 'export']
+    assert [c.title for c in configs.values()] == [
+        'Reader',
+        'Export',
+    ]
 
-    reader = configs[0]
+    reader = configs['reader']
     assert set(reader.properties) == {
-        'ndevio.suggest_reader_plugins',
-        'ndevio.scene_handling',
-        'ndevio.clear_layers_on_new_scene',
-        'ndevio.max_in_mem_gb',
+        'suggest_reader_plugins',
+        'scene_handling',
+        'clear_layers_on_new_scene',
+        'max_in_mem_gb',
     }
 
-    export = configs[1]
+    export = configs['export']
     assert set(export.properties) == {
-        'ndevio.canvas_scale',
-        'ndevio.override_canvas_size',
-        'ndevio.canvas_width',
-        'ndevio.canvas_height',
+        'canvas_scale',
+        'override_canvas_size',
+        'canvas_width',
+        'canvas_height',
     }
 
 
 def test_manifest_reader_property_defaults(manifest):
     """Reader properties carry the same defaults as the old ndev-settings."""
-    reader = manifest.contributions.configuration[0]
+    reader = manifest.contributions.configurations['reader']
     props = reader.properties
 
-    assert props['ndevio.suggest_reader_plugins'].default is True
-    assert props['ndevio.scene_handling'].default == 'Open Scene Widget'
-    assert props['ndevio.scene_handling'].enum == [
+    assert props['suggest_reader_plugins'].default is True
+    assert props['scene_handling'].default == 'Open Scene Widget'
+    assert props['scene_handling'].enum == [
         'Open Scene Widget',
         'View All Scenes',
         'View First Scene Only',
     ]
-    assert props['ndevio.clear_layers_on_new_scene'].default is False
-    assert props['ndevio.max_in_mem_gb'].default == 8.0
-    assert props['ndevio.max_in_mem_gb'].minimum == 0.5
-    assert props['ndevio.max_in_mem_gb'].maximum == 128.0
+    assert props['clear_layers_on_new_scene'].default is False
+    assert props['max_in_mem_gb'].default == 8.0
+    assert props['max_in_mem_gb'].minimum == 0.5
+    assert props['max_in_mem_gb'].maximum == 128.0
 
 
 def test_manifest_export_property_defaults(manifest):
     """Export properties carry the same defaults as the old ndev-settings."""
-    export = manifest.contributions.configuration[1]
+    export = manifest.contributions.configurations['export']
     props = export.properties
 
-    assert props['ndevio.canvas_scale'].default == 1.0
-    assert props['ndevio.canvas_scale'].minimum == 0.01
-    assert props['ndevio.canvas_scale'].maximum == 100.0
-    assert props['ndevio.override_canvas_size'].default is False
-    assert props['ndevio.canvas_width'].default == 1024
-    assert props['ndevio.canvas_height'].default == 1024
+    assert props['canvas_scale'].default == 1.0
+    assert props['canvas_scale'].minimum == 0.01
+    assert props['canvas_scale'].maximum == 100.0
+    assert props['override_canvas_size'].default is False
+    assert props['canvas_width'].default == 1024
+    assert props['canvas_height'].default == 1024
 
 
 def test_manifest_has_no_dynamic_preferred_reader(manifest):
     """The dynamic 'preferred_reader' setting is not representable and dropped."""
-    for config in manifest.contributions.configuration:
+    for config in manifest.contributions.configurations.values():
         for key in config.properties:
             assert 'preferred' not in key.lower()
 
@@ -130,42 +136,51 @@ def test_get_ndevio_settings_falls_back_when_feature_missing(monkeypatch):
     assert settings.reader.max_in_mem_gb == 8.0
 
 
-def test_real_get_plugin_settings(tmp_path):
-    """End-to-end: napari builds ndevio's preferences from the manifest."""
-    from napari import settings as napari_settings
+def test_plugin_settings_fixture_end_to_end(plugin_settings, npe2pm):
+    """End-to-end via napari's `plugin_settings` fixture + the real manifest.
 
-    if not hasattr(napari_settings, 'get_plugin_settings'):
-        pytest.skip(
-            'installed napari lacks plugin settings (need napari>=0.9.0)'
-        )
+    Requires napari >= 0.9.0, which ships the `plugin_settings` pytest
+    fixture; on older napari the fixture simply doesn't exist and the test
+    errors at setup (it is not silently skipped).
+    """
+    # register ndevio's *real* manifest, loaded from its file, scoped to this
+    # test by the npe2pm fixture
+    with npe2pm.tmp_plugin(manifest=MANIFEST):
+        from napari.settings import get_plugin_settings
 
-    from npe2 import PluginManager, PluginManifest
+        settings = get_plugin_settings('ndevio')
 
-    # pytest blocks discovery, so register the (always installed) manifest.
-    pm = PluginManager.instance()
-    if 'ndevio' not in pm:
-        pm.register(PluginManifest.from_distribution('ndevio'))
-    # Reset the in-memory cache so the registered plugin is included (saved
-    # values are re-read from disk; this also allows path_dir=tmp_path).
-    napari_settings._PLUGIN_PREFERENCES.clear()
+        assert settings.reader.suggest_reader_plugins is True
+        assert settings.reader.scene_handling == 'Open Scene Widget'
+        assert settings.reader.clear_layers_on_new_scene is False
+        assert settings.reader.max_in_mem_gb == 8.0
 
-    settings = napari_settings.get_plugin_settings('ndevio', path_dir=tmp_path)
+        assert settings.export.canvas_scale == 1.0
+        assert settings.export.override_canvas_size is False
+        assert settings.export.canvas_width == 1024
+        assert settings.export.canvas_height == 1024
 
-    assert settings.reader.suggest_reader_plugins is True
-    assert settings.reader.scene_handling == 'Open Scene Widget'
-    assert settings.reader.clear_layers_on_new_scene is False
-    assert settings.reader.max_in_mem_gb == 8.0
+        # changes auto-save under the fixture's per-test tmp_path
+        settings.reader.max_in_mem_gb = 4.0
+        assert 'max_in_mem_gb: 4.0' in settings.config_path.read_text()
+
+        # the accessor used by ndevio's code paths returns this same model
+        assert get_ndevio_settings() is settings
+        assert not isinstance(get_ndevio_settings(), SimpleNamespace)
+
+
+def test_plugin_settings_from_installed_package(plugin_settings, npe2pm):
+    """Same end-to-end, but register ndevio from its installed distribution.
 
-    assert settings.export.canvas_scale == 1.0
-    assert settings.export.override_canvas_size is False
-    assert settings.export.canvas_width == 1024
-    assert settings.export.canvas_height == 1024
+    ``npe2pm.tmp_plugin(package='ndevio')`` loads the manifest via
+    ``PluginManifest.from_distribution`` — the natural mode when the plugin
+    under test is installed in the test environment.
+    """
+    with npe2pm.tmp_plugin(package='ndevio'):
+        from napari.settings import get_plugin_settings
 
-    # Settings are persisted to a per-plugin yaml, and changes auto-save.
-    assert settings.config_path == tmp_path / 'ndevio.yaml'
-    settings.reader.max_in_mem_gb = 4.0
-    assert 'max_in_mem_gb: 4.0' in (tmp_path / 'ndevio.yaml').read_text()
+        settings = get_plugin_settings('ndevio')
+        assert settings.reader.max_in_mem_gb == 8.0
 
-    # The accessor used by ndevio's code paths returns this same model.
-    assert get_ndevio_settings() is settings
-    assert not isinstance(get_ndevio_settings(), SimpleNamespace)
+        settings.reader.max_in_mem_gb = 4.0
+        assert 'max_in_mem_gb: 4.0' in settings.config_path.read_text()

From 943da5f473b006c29dd96dee2c9e2392d0cc3a36 Mon Sep 17 00:00:00 2001
From: Tim Monko <timmonko@gmail.com>
Date: Thu, 13 Aug 2026 10:21:48 -0500
Subject: [PATCH 12/12] use napari pre-release for testing (needs released)

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 569c4bd..d749d41 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,8 +55,8 @@ dev = [
     "pytest",  # https://docs.pytest.org/en/latest/contents.html
     "pytest-cov",  # https://pytest-cov.readthedocs.io/en/latest/
     "pytest-qt",  # https://pytest-qt.readthedocs.io/en/latest/
-    "napari",
-    "pyqt6",  # Explicitly use PyQt6 (napari's future default, has ARM64 macOS support)
+    "napari[all]>=0.9.0rc0",  # for testing plugin settings
+    "npe2>=0.9.0rc0",  # for testing plugin settings
     "bioio-czi",  # Include an additional priority reader for development/testing
 ]