Caching settings, editable install support, and better validation

README.md

@@ -117,6 +117,48 @@ print(settings.Canvas.canvas_scale)
 # Access settings from external libraries (if installed)
 print(settings.Reader.preferred_reader)  # From ndevio
 print(settings.Export.compression_level)  # From ndevio
+
+# Modify and save settings
+settings.Canvas.canvas_scale = 2.0
+settings.save()  # Persists across sessions
+
+# Reset to defaults
+settings.reset_to_default("canvas_scale")  # Reset single setting
+settings.reset_to_default(group="Canvas")  # Reset entire group
+settings.reset_to_default()  # Reset all settings
+```
+
+## Performance Note: npe1 Plugin Compatibility
+
+If you have many legacy npe1 plugins installed (e.g., `napari-assistant`, `napari-segment-blobs-and-things-with-membranes`, `napari-simpleitk-image-processing`), you may experience slow widget loading times (10+ seconds) the first time you open the settings plugin widget in a napari session. This is a known issue in napari's npe1 compatibility layer, not specific to ndev-settings. The npe1 adapter iterates through all plugin widgets and performs expensive metadata lookups for each legacy plugin.
+
+**Workaround**: If you don't need npe1 runtime behavior plugins, you can disable the adapter in napari:
+
+1. Go to `File` -> `Preferences` -> `Plugins`
+2. Uncheck "Use npe2 adapter"
+3. Restart napari
+
+This dramatically improves widget loading times since only pure npe2 plugins are discovered.
+
+## How Settings Persistence Works
+
+Settings are automatically cached to improve startup performance:
+
+1. **First load**: Settings are discovered from all installed packages via entry points, merged together, and saved to a user config file
+2. **Subsequent loads**: Settings are loaded directly from the cached file (much faster)
+3. **Package changes**: When packages are installed/removed, settings are re-discovered and merged while preserving your customizations
+
+**Storage location**: Settings are stored in a platform-appropriate config directory:
+
+- **Windows**: `%LOCALAPPDATA%\ndev-settings\settings.yaml`
+- **macOS**: `~/Library/Application Support/ndev-settings/settings.yaml`
+- **Linux**: `~/.config/ndev-settings/settings.yaml`
+
+**Clearing the cache**: To force re-discovery of settings (e.g., after manual edits to package YAML files):
+
+```python
+from ndev_settings import clear_settings
+clear_settings()  # Deletes cached settings, next load will re-discover
 ```
 
 ## Pre-commit hook

pyproject.toml

@@ -29,6 +29,7 @@ requires-python = ">=3.10"
 # or any other Qt bindings directly (e.g. PyQt5, PySide2).
 # See best practices: https://napari.org/stable/plugins/building_a_plugin/best_practices.html
 dependencies = [
+    "appdirs",
     "magicgui",
     "magic-class",
     "pyyaml",
@@ -37,15 +38,16 @@ dependencies = [
 [project.optional-dependencies]
 # Allow easily installation with the full, default napari installation
 # (including Qt backend) using ndev-settings[all].
-all = ["napari[all]"]
+all = ["napari[pyqt6]"]
 
 [dependency-groups]
-testing = [
+dev = [
     "tox-uv",
     "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/
     "pyqt6",
+    "napari",
 ]
 
 [project.entry-points."napari.manifest"]

src/ndev_settings/__init__.py

@@ -1,7 +1,7 @@
-from ._settings import Settings
+from ._settings import Settings, clear_settings
 from ._version import version as __version__
 
-__all__ = ["get_settings", "__version__"]
+__all__ = ["get_settings", "clear_settings", "__version__"]
 
 # Singleton instance
 _settings_instance = None

src/ndev_settings/_cli.py

@@ -9,6 +9,9 @@
 def reset_values_to_defaults(settings_file: Path | str) -> bool:
     """Reset all 'value' fields to match 'default' fields in a settings YAML file.
 
+    Works with flat format settings files where groups are at the top level.
+    Metadata keys starting with '_' (e.g., _entry_points_hash) are preserved.
+
     Parameters
     ----------
     settings_file : Path | str
@@ -26,14 +29,20 @@ def reset_values_to_defaults(settings_file: Path | str) -> bool:
         return False
 
     with open(settings_file) as f:
-        settings = yaml.safe_load(f)
+        settings_data = yaml.load(f, Loader=yaml.FullLoader)
 
-    if not settings:
+    if not settings_data:
         return False
 
     modified = False
 
-    for group_name, group_settings in settings.items():
+    for group_name, group_settings in settings_data.items():
+        # Skip metadata keys (e.g., _entry_points_hash)
+        if group_name.startswith("_"):
+            continue
+        if not isinstance(group_settings, dict):
+            continue
+
         for setting_name, setting_data in group_settings.items():
             if (
                 isinstance(setting_data, dict)
@@ -50,7 +59,9 @@ def reset_values_to_defaults(settings_file: Path | str) -> bool:
 
     if modified:
         with open(settings_file, "w") as f:
-            yaml.dump(settings, f, default_flow_style=False, sort_keys=False)
+            yaml.dump(
+                settings_data, f, default_flow_style=False, sort_keys=False
+            )
 
     return modified