use npe2 ConfigurationContribution for settings, with fallback

.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

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.configurations` 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.configurations`) for user-configurable behavior rather than hardcoding choices
 4. **bioio compatibility**: Stay aligned with bioio's data model and avoid reinventing functionality
 
 ## Testing

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.configurations`),
+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

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",
@@ -56,17 +55,14 @@ 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
 ]
 
 [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"

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
     ----------

src/ndevio/_settings.py

@@ -0,0 +1,57 @@
+"""Access to ndevio's plugin settings.
+
+ndevio's user-configurable behavior is declared in ``napari.yaml`` under
+``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')``.
+
+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 types import SimpleNamespace
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from napari.settings import PluginPreferences
+
+_PLUGIN_NAME = 'ndevio'
+
+# Defaults mirroring the ``contributions.configurations`` 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
+
+        return get_plugin_settings(_PLUGIN_NAME)
+    except ImportError:  # pragma: no cover - napari < 0.9.0
+        return _DEFAULTS

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
     )
 

src/ndevio/napari.yaml

@@ -59,6 +59,77 @@ contributions:
         '*.txt', '*.v', '*.vms', '*.vsi', '*.vws', '*.wat', '*.wlz', '*.xdce', '*.xml', '*.xqd',
         '*.xqf', '*.xv', '*.xvthumb', '*.xys', '*.zarr', '*.zarr*', '*.zfp', '*.zfr', '*.zif', '*.zvi',
       ]
+  configurations:
+    reader:
+      title: Reader
+      properties:
+        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.
+        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
+        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.
+        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
+    export:
+      title: Export
+      properties:
+        canvas_scale:
+          type: number
+          default: 1.0
+          title: Canvas scale
+          description: Scale factor for exported figures and screenshots.
+          minimum: 0.01
+          maximum: 100.0
+        override_canvas_size:
+          type: boolean
+          default: false
+          title: Override canvas size
+          description: >-
+            Whether to override the canvas size when exporting screenshots.
+        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
+        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