Use dynaconf for user preferences

.gitignore

@@ -86,3 +86,6 @@ venv/
 # Scripts
 /scripts/*
 !/scripts/examples
+
+# Ignore dynaconf secret files
+.secrets.*

dev-environment.yml

@@ -14,6 +14,7 @@ channels:
   - defaults
 dependencies:
   # Project dependencies
+  - confuse
   - labeling >= 0.1.12
   - magicgui >= 0.5.1
   - napari

environment.yml

@@ -14,6 +14,7 @@ channels:
   - defaults
 dependencies:
   # Project depenencies
+  - confuse
   - labeling >= 0.1.12
   - magicgui >= 0.5.1
   - napari

setup.cfg

@@ -37,6 +37,7 @@ package_dir =
 
 # add your package requirements here
 install_requires =
+    dynaconf
     labeling >= 0.1.12
     napari
     magicgui >= 0.5.1
@@ -59,6 +60,7 @@ dev =
     autopep8
     black
     build
+    confuse
     flake8
     isort
     pyqt5

src/napari_imagej/__init__.py

@@ -17,4 +17,8 @@
 napari-imagej is built upon the PyImageJ project:
 https://pyimagej.readthedocs.io/en/latest/
 """
+import confuse
+
 __version__ = "0.0.1.dev0"
+
+settings = confuse.Configuration(appname="napari-imagej", modname=__name__)

src/napari_imagej/config_default.yaml

@@ -0,0 +1,18 @@
+# napari-imagej Default Settings
+
+# USERS BEWARE:
+# This yaml file will soon be replaced with napari's contribution configuration.
+
+# Path to a local ImageJ2 installation (e.g. /Applications/Fiji.app),
+# OR version of net.imagej:imagej artifact to launch (e.g. 2.3.0),
+# OR endpoint of another artifact built on ImageJ2 (e.g. sc.fiji:fiji),
+# OR list of Maven artifacts to include (e.g.
+#   ['net.imagej:imagej:2.3.0', 'net.imagej:imagej-legacy', 'net.preibisch:BigStitcher']).
+# The default (null) will use the latest version of ImageJ2, downloading it if needed.
+imagej_directory_or_endpoint: 'net.imagej:imagej'
+
+# This can be used to identify whether transferred data between ImageJ2 and napari
+# should be selected via activation or by user selection via a dialog.
+# By default, the active layer/window is chosen for transfer between applications.
+# By setting this value to false, a popup will be shown instead.
+choose_active_layer: true

src/napari_imagej/java.py

@@ -19,15 +19,14 @@
 """
 import os
 import sys
-from functools import lru_cache
 from multiprocessing.pool import AsyncResult, ThreadPool
-from typing import Any, Callable, Dict
+from typing import Callable
 
 import imagej
-import yaml
 from jpype import JClass
 from scyjava import config, jimport
 
+from napari_imagej import settings
 from napari_imagej.utilities.logging import log_debug
 
 # -- ImageJ API -- #
@@ -48,17 +47,6 @@ def ensure_jvm_started() -> None:
     ij_future.wait()
 
 
-def setting(name: str):
-    """Gets the value of setting name"""
-    return settings().get(name, None)
-
-
-@lru_cache(maxsize=None)
-def settings() -> Dict[Any, Any]:
-    """Gets all plugin settings as a dictionary"""
-    return yaml.safe_load(open("settings.yml", "r"))
-
-
 def get_mode() -> str:
     """
     Returns the mode ImageJ will be run in
@@ -86,14 +74,14 @@ def _imagej_init():
     log_debug("Completed JVM Configuration")
 
     # Configure PyImageJ settings
-    settings = {
-        "ij_dir_or_version_or_endpoint": setting("imagej_installation"),
+    ij_settings = {
+        "ij_dir_or_version_or_endpoint": settings["imagej_directory_or_endpoint"].get(),
         "mode": get_mode(),
         "add_legacy": False,
     }
 
     # Launch PyImageJ
-    _ij = imagej.init(**settings)
+    _ij = imagej.init(**ij_settings)
     log_debug(f"Initialized at version {_ij.getVersion()}")
 
     # Return the ImageJ gateway

src/napari_imagej/widgets/menu.py

@@ -10,19 +10,14 @@
 from napari import Viewer
 from napari._qt.qt_resources import QColoredSVGIcon
 from napari.layers import Layer
-from qtpy.QtCore import Qt
+from qtpy.QtCore import Qt, Signal
 from qtpy.QtGui import QIcon, QPixmap
 from qtpy.QtWidgets import QHBoxLayout, QMessageBox, QPushButton, QWidget
 
-from napari_imagej.java import (
-    ensure_jvm_started,
-    ij,
-    jc,
-    log_debug,
-    running_headless,
-    setting,
-)
+from napari_imagej import settings
+from napari_imagej.java import ensure_jvm_started, ij, jc, log_debug, running_headless
 from napari_imagej.utilities._module_utils import _get_layers_hack
+from napari_imagej.widgets.resources import resource_path
 
 
 class NapariImageJMenu(QWidget):
@@ -40,6 +35,9 @@ def __init__(self, viewer: Viewer):
         self.gui_button: GUIButton = GUIButton()
         self.layout().addWidget(self.gui_button)
 
+        self.settings_button: SettingsButton = SettingsButton(viewer)
+        self.layout().addWidget(self.settings_button)
+
         if running_headless():
             self.gui_button.clicked.connect(self.gui_button.disable_popup)
         else:
@@ -133,10 +131,11 @@ def __init__(self, viewer: Viewer):
         self.setEnabled(False)
         icon = QColoredSVGIcon.from_resources("long_right_arrow")
         self.setIcon(icon.colored(theme=viewer.theme))
-        self.setToolTip("Export active napari layer to ImageJ2")
-        if setting("choose_active_layer"):
+        if settings["choose_active_layer"].get():
+            self.setToolTip("Export active napari layer to ImageJ2")
             self.clicked.connect(self.send_active_layer)
         else:
+            self.setToolTip("Export napari layer to ImageJ2")
             self.clicked.connect(self.send_chosen_layer)
 
     def _set_icon(self, path: str):
@@ -178,10 +177,11 @@ def __init__(self, viewer: Viewer):
         self.setEnabled(False)
         icon = QColoredSVGIcon.from_resources("long_left_arrow")
         self.setIcon(icon.colored(theme=viewer.theme))
-        self.setToolTip("Import active ImageJ2 Dataset to napari")
-        if setting("choose_active_layer"):
+        if settings["choose_active_layer"].get():
+            self.setToolTip("Import active ImageJ2 Dataset to napari")
             self.clicked.connect(self.get_active_layer)
         else:
+            self.setToolTip("Import ImageJ2 Dataset to napari")
             self.clicked.connect(self.get_chosen_layer)
 
     def _set_icon(self, path: str):
@@ -259,19 +259,19 @@ def post_setup():
         Thread(target=post_setup).start()
 
     def _setup_headful(self):
-        self._set_icon("resources/16x16-flat-disabled.png")
+        self._set_icon(resource_path("imagej2-16x16-flat-disabled"))
         self.setToolTip("Display ImageJ2 GUI (loading)")
 
         def post_setup():
             ensure_jvm_started()
-            self._set_icon("resources/16x16-flat.png")
+            self._set_icon(resource_path("imagej2-16x16-flat"))
             self.setEnabled(True)
             self.setToolTip("Display ImageJ2 GUI")
 
         Thread(target=post_setup).start()
 
     def _setup_headless(self):
-        self._set_icon("resources/16x16-flat-disabled.png")
+        self._set_icon(resource_path("imagej2-16x16-flat-disabled"))
         self.setToolTip("ImageJ2 GUI unavailable!")
 
     def disable_popup(self):
@@ -286,3 +286,50 @@ def disable_popup(self):
         msg.setTextFormat(Qt.RichText)
         msg.setTextInteractionFlags(Qt.TextBrowserInteraction)
         msg.exec()
+
+
+class SettingsButton(QPushButton):
+
+    # Signal used to identify changes to user settings
+    setting_change = Signal()
+
+    def __init__(self, viewer: Viewer):
+        super().__init__()
+        self.viewer = viewer
+
+        icon = QColoredSVGIcon(resource_path("gear"))
+        self.setIcon(icon.colored(theme=viewer.theme))
+
+        self.clicked.connect(self._update_settings)
+        self.setting_change.connect(self._notify_settings_change)
+
+    def _update_settings(self):
+        args = {}
+        default_source = next(s for s in settings.sources if s.default)
+        for k, v in default_source.items():
+            args[k] = {}
+            args[k]["value"] = settings[k].get()
+        choices = request_values(title="napari-imagej Settings", values=args)
+        if choices is not None:
+            any_changed = False
+            for k, v in choices.items():
+                if v != settings[k].get():
+                    any_changed = True
+                    settings[k] = v
+
+            if any_changed:
+                self.setting_change.emit()
+                output = settings.dump()
+                with open(settings.user_config_path(), "w") as f:
+                    f.write(output)
+
+    def _notify_settings_change(self):
+        """
+        Notifies (using a popup) that a restart is required for settings changes
+        to take effect
+        """
+        msg: QMessageBox = QMessageBox()
+        msg.setText(
+            "Please restart napari for napari-imagej settings changes to take effect!"
+        )
+        msg.exec()

src/napari_imagej/widgets/resources/__init__.py

@@ -0,0 +1,16 @@
+"""
+A module used to help find napari-imagej widget resources
+"""
+from pathlib import Path
+
+PATH = Path(__file__).parent.resolve()
+RESOURCES = {x.stem: str(x) for x in PATH.iterdir() if x.suffix != ".py"}
+
+
+def resource_path(name: str) -> str:
+    """Return path to a resource in this folder."""
+    if name not in RESOURCES:
+        raise ValueError(
+            f"{name} is not a known resource! Known resources: {RESOURCES}"
+        )
+    return RESOURCES[name]