Allow add_legacy configuration in settings

src/napari_imagej/config_default.yaml

@@ -11,6 +11,10 @@
 # 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 include original ImageJ functionality.
+# Iff True, original ImageJ functionality (ij.* packages) will be available.
+include_imagej_legacy: false
+
 # 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.

src/napari_imagej/java.py

@@ -6,10 +6,8 @@
         - used to access the ImageJ instance
     * ensure_jvm_started()
         - used to block execution until the ImageJ instance is ready
-    * running_headless()
+    * jvm_is_headless()
         - reports whether the JVM is being run headlessly
-    * setting()
-        - used to obtain values of configuration settings
     * log_debug()
         - used for logging in a standardized way
 
@@ -47,15 +45,15 @@ def ensure_jvm_started() -> None:
     ij_future.wait()
 
 
-def get_mode() -> str:
+def _get_mode() -> str:
     """
     Returns the mode ImageJ will be run in
     """
     return "headless" if sys.platform == "darwin" else "interactive"
 
 
-def running_headless() -> bool:
-    return get_mode() == "headless"
+def jvm_is_headless() -> bool:
+    return _get_mode() == "headless"
 
 
 def _imagej_init():
@@ -73,15 +71,12 @@ def _imagej_init():
     config.endpoints.append("io.scif:scifio:0.43.1")
     log_debug("Completed JVM Configuration")
 
-    # Configure PyImageJ settings
-    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(**ij_settings)
+    _ij = imagej.init(
+        ij_dir_or_version_or_endpoint=settings["imagej_directory_or_endpoint"].get(str),
+        mode=_get_mode(),
+        add_legacy=settings["include_imagej_legacy"].get(bool),
+    )
     log_debug(f"Initialized at version {_ij.getVersion()}")
 
     # Return the ImageJ gateway

src/napari_imagej/widgets/menu.py

@@ -15,7 +15,7 @@
 from qtpy.QtWidgets import QHBoxLayout, QMessageBox, QPushButton, QWidget
 
 from napari_imagej import settings
-from napari_imagej.java import ensure_jvm_started, ij, jc, log_debug, running_headless
+from napari_imagej.java import ensure_jvm_started, ij, jc, jvm_is_headless, log_debug
 from napari_imagej.resources import resource_path
 from napari_imagej.utilities._module_utils import _get_layers_hack
 
@@ -38,7 +38,7 @@ def __init__(self, viewer: Viewer):
         self.settings_button: SettingsButton = SettingsButton(viewer)
         self.layout().addWidget(self.settings_button)
 
-        if running_headless():
+        if jvm_is_headless():
             self.gui_button.clicked.connect(self.gui_button.disable_popup)
         else:
             self.gui_button.clicked.connect(self._showUI)
@@ -241,12 +241,12 @@ def get_active_layer(self) -> None:
 class GUIButton(QPushButton):
     def __init__(self):
         super().__init__()
-        running_headful = not running_headless()
         self.setEnabled(False)
-        if running_headful:
-            self._setup_headful()
-        else:
+
+        if jvm_is_headless():
             self._setup_headless()
+        else:
+            self._setup_headful()
 
     def _set_icon(self, path: str):
         icon: QIcon = QIcon(QPixmap(path))

tests/widgets/test_menu.py

@@ -14,7 +14,7 @@
 from qtpy.QtWidgets import QApplication, QHBoxLayout, QMessageBox
 
 from napari_imagej import settings
-from napari_imagej.java import running_headless
+from napari_imagej.java import jvm_is_headless
 from napari_imagej.resources import resource_path
 from napari_imagej.widgets import menu
 from napari_imagej.widgets.menu import (
@@ -26,6 +26,9 @@
 )
 from tests.utils import jc
 
+# Determine whether we are testing headlessly
+TESTING_HEADLESS: bool = jvm_is_headless()
+
 
 @pytest.fixture(autouse=True)
 def clean_settings():
@@ -132,9 +135,7 @@ def test_widget_layout(gui_widget: NapariImageJMenu):
     assert isinstance(subwidgets[4], SettingsButton)
 
 
-@pytest.mark.skipif(
-    running_headless(), reason="Only applies when not running headlessly"
-)
+@pytest.mark.skipif(TESTING_HEADLESS, reason="Only applies when not running headlessly")
 def test_GUIButton_layout_headful(qtbot, asserter, ij, gui_widget: NapariImageJMenu):
     """Tests headful-specific settings of GUIButton"""
     button: GUIButton = gui_widget.gui_button
@@ -155,9 +156,7 @@ def test_GUIButton_layout_headful(qtbot, asserter, ij, gui_widget: NapariImageJM
     asserter(ij.ui().isVisible)
 
 
-@pytest.mark.skipif(
-    not running_headless(), reason="Only applies when running headlessly"
-)
+@pytest.mark.skipif(not TESTING_HEADLESS, reason="Only applies when running headlessly")
 def test_GUIButton_layout_headless(asserter, gui_widget: NapariImageJMenu):
     """Tests headless-specific settings of GUIButton"""
     # Wait until the JVM starts to test settings
@@ -214,9 +213,7 @@ def passed(self) -> bool:
     assert runnable.passed()
 
 
-@pytest.mark.skipif(
-    running_headless(), reason="Only applies when not running headlessly"
-)
+@pytest.mark.skipif(TESTING_HEADLESS, reason="Only applies when not running headlessly")
 def test_active_data_send(asserter, qtbot, ij, gui_widget: NapariImageJMenu):
     button: ToIJButton = gui_widget.to_ij
     assert not button.isEnabled()
@@ -240,9 +237,7 @@ def test_active_data_send(asserter, qtbot, ij, gui_widget: NapariImageJMenu):
     assert "test_to" == active_display.getName()
 
 
-@pytest.mark.skipif(
-    running_headless(), reason="Only applies when not running headlessly"
-)
+@pytest.mark.skipif(TESTING_HEADLESS, reason="Only applies when not running headlessly")
 def test_active_data_receive(asserter, qtbot, ij, gui_widget: NapariImageJMenu):
     button: FromIJButton = gui_widget.from_ij
     assert not button.isEnabled()
@@ -267,9 +262,7 @@ def test_active_data_receive(asserter, qtbot, ij, gui_widget: NapariImageJMenu):
     assert (10, 10, 10) == layer.data.shape
 
 
-@pytest.mark.skipif(
-    running_headless(), reason="Only applies when not running headlessly"
-)
+@pytest.mark.skipif(TESTING_HEADLESS, reason="Only applies when not running headlessly")
 def test_data_choosers(asserter, qtbot, ij, gui_widget_chooser):
     button_to: ToIJButton = gui_widget_chooser.to_ij
     button_from: FromIJButton = gui_widget_chooser.from_ij