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
+  - dynaconf
   - labeling >= 0.1.12
   - magicgui >= 0.5.1
   - napari

environment.yml

@@ -14,6 +14,7 @@ channels:
   - defaults
 dependencies:
   # Project depenencies
+  - dynaconf
   - 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

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.settings import preferences
 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
@@ -87,7 +75,7 @@ def _imagej_init():
 
     # Configure PyImageJ settings
     settings = {
-        "ij_dir_or_version_or_endpoint": setting("imagej_installation"),
+        "ij_dir_or_version_or_endpoint": preferences.imagej_directory_or_endpoint,
         "mode": get_mode(),
         "add_legacy": False,
     }

src/napari_imagej/settings.py

@@ -0,0 +1,13 @@
+from pathlib import Path
+
+from dynaconf import Dynaconf
+
+# Preferences settings
+
+# The settings are in the root directory, three directories up
+SETTINGS_PATH = (Path(__file__).parent / "settings.toml").resolve()
+
+preferences = Dynaconf(
+    envvar_prefix="DYNACONF",
+    settings_files=SETTINGS_PATH,
+)

src/napari_imagej/settings.toml

@@ -0,0 +1,18 @@
+# napari-imagej Settings
+
+# USERS BEWARE:
+# This toml 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 is the latest version of ImageJ2.
+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/widgets/menu.py

@@ -14,15 +14,10 @@
 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.java import ensure_jvm_started, ij, jc, log_debug, running_headless
+from napari_imagej.settings import preferences
 from napari_imagej.utilities._module_utils import _get_layers_hack
+from napari_imagej.widgets.resources import resource_path
 
 
 class NapariImageJMenu(QWidget):
@@ -134,7 +129,7 @@ def __init__(self, viewer: Viewer):
         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 preferences.choose_active_layer:
             self.clicked.connect(self.send_active_layer)
         else:
             self.clicked.connect(self.send_chosen_layer)
@@ -179,7 +174,7 @@ def __init__(self, viewer: Viewer):
         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 preferences.choose_active_layer:
             self.clicked.connect(self.get_active_layer)
         else:
             self.clicked.connect(self.get_chosen_layer)
@@ -259,19 +254,19 @@ 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):

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]

tests/conftest.py

@@ -7,7 +7,7 @@
 import pytest
 from napari import Viewer
 
-from napari_imagej.widgets import menu
+from napari_imagej.settings import preferences
 from napari_imagej.widgets.menu import NapariImageJMenu
 from napari_imagej.widgets.napari_imagej import NapariImageJWidget
 
@@ -46,10 +46,8 @@ def gui_widget(viewer) -> Generator[NapariImageJMenu, None, None]:
 
     # Define GUIWidget settings for this particular feature.
     # In particular, we want to enforce active layer selection
-    def mock_setting(value: str):
-        return {"imagej_installation": None, "choose_active_layer": True}[value]
-
-    menu.setting = mock_setting
+    previous = preferences.choose_active_layer
+    preferences.choose_active_layer = True
 
     # Create widget
     widget: NapariImageJMenu = NapariImageJMenu(viewer)
@@ -58,6 +56,7 @@ def mock_setting(value: str):
 
     # Cleanup -> Close the widget, trigger ImageJ shutdown
     widget.close()
+    preferences.choose_active_layer = previous
 
 
 @pytest.fixture
@@ -68,10 +67,8 @@ def gui_widget_chooser(viewer) -> Generator[NapariImageJMenu, None, None]:
 
     # Define GUIWidget settings for this particular feature.
     # In particular, we want to enforce user layer selection via Dialog
-    def mock_setting(value: str):
-        return {"imagej_installation": None, "choose_active_layer": False}[value]
-
-    menu.setting = mock_setting
+    previous = preferences.choose_active_layer
+    preferences.choose_active_layer = False
 
     # Create widget
     widget: NapariImageJMenu = NapariImageJMenu(viewer)
@@ -80,6 +77,7 @@ def mock_setting(value: str):
 
     # Cleanup -> Close the widget, trigger ImageJ shutdown
     widget.close()
+    preferences.choose_active_layer = previous
 
 
 @pytest.fixture()

tests/widgets/test_menu.py

@@ -18,6 +18,7 @@
     NapariImageJMenu,
     ToIJButton,
 )
+from napari_imagej.widgets.resources import resource_path
 
 
 class JavaClassesTest(JavaClasses):
@@ -119,7 +120,7 @@ def test_GUIButton_layout_headful(qtbot, asserter, ij, gui_widget: NapariImageJM
     """Tests headful-specific settings of GUIButton"""
     button: GUIButton = gui_widget.gui_button
 
-    expected: QPixmap = QPixmap("resources/16x16-flat.png")
+    expected: QPixmap = QPixmap(resource_path("imagej2-16x16-flat"))
     actual: QPixmap = button.icon().pixmap(expected.size())
     assert expected.toImage() == actual.toImage()
 
@@ -142,7 +143,7 @@ def test_GUIButton_layout_headless(asserter, gui_widget: NapariImageJMenu):
     """Tests headless-specific settings of GUIButton"""
     button: GUIButton = gui_widget.gui_button
 
-    expected: QPixmap = QPixmap("resources/16x16-flat-disabled.png")
+    expected: QPixmap = QPixmap(resource_path("imagej2-16x16-flat-disabled"))
     actual: QPixmap = button.icon().pixmap(expected.size())
     assert expected.toImage() == actual.toImage()