Allow add_legacy configuration in settings

dev-environment.yml

@@ -32,6 +32,7 @@ dependencies:
   - pyqt5-sip
   - pytest
   - pytest-cov
+  - pytest-env
   - pytest-qt
   - qtpy
   # Project from source

pyproject.toml

@@ -7,4 +7,9 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [tool.isort]
-profile = "black"
+profile = "black"
+
+[tool.pytest.ini_options]
+env = [
+    "NAPARI_IMAGEJ_TESTING=yes"
+]

setup.cfg

@@ -65,6 +65,7 @@ dev =
     pyqt5
     pytest
     pytest-cov
+    pytest-env
     pytest-qt
     qtpy
     numpy

src/napari_imagej/__init__.py

@@ -17,10 +17,23 @@
 napari-imagej is built upon the PyImageJ project:
 https://pyimagej.readthedocs.io/en/latest/
 """
+import os
+import sys
+
 import confuse
 
 __version__ = "0.0.1.dev0"
 
 # napari-imagej uses confuse (https://confuse.readthedocs.io/en/latest/) to configure
 # user settings.
-settings = confuse.Configuration(appname="napari-imagej", modname=__name__)
+settings = confuse.Configuration(appname="napari-imagej", modname=__name__, read=False)
+# Don't use user settings during the tests
+use_user_settings = os.environ["NAPARI_IMAGEJ_TESTING"] != "yes"
+settings.read(user=use_user_settings)
+
+# -- SETTING VALIDATION -- #
+
+# Ensure that the jvm mode is valid
+jvm_mode: str = settings["jvm_mode"].as_choice(["interactive", "headless"])
+if jvm_mode == "interactive" and sys.platform == "darwin":
+    settings["jvm_mode"] = "headless"

src/napari_imagej/config_default.yaml

@@ -15,6 +15,14 @@ imagej_directory_or_endpoint: 'net.imagej:imagej'
 # Iff True, original ImageJ functionality (ij.* packages) will be available.
 include_imagej_legacy: false
 
+# Designates the mode of execution for ImageJ2.
+# Allowed options are 'headless' and 'interactive'.
+# NB 'interactive' mode is unavailable on MacOS. More details can be found at
+# https://pyimagej.readthedocs.io/en/latest/Initialization.html#interactive-mode
+# If napari-imagej is launched on MacOS with this setting set to "interactive",
+# the setting will silently be reassigned to "headless"
+jvm_mode: 'interactive'
+
 # 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

@@ -16,8 +16,8 @@
         - object whose fields are lazily-loaded Java Class instances.
 """
 import os
-import sys
 from multiprocessing.pool import AsyncResult, ThreadPool
+from threading import Lock
 from typing import Callable
 
 import imagej
@@ -35,25 +35,14 @@ def ij():
     Returns the ImageJ instance.
     If it isn't ready yet, blocks until it is ready.
     """
-    return ij_future.get()
+    return imagej_init().get()
 
 
 def ensure_jvm_started() -> None:
     """
     Blocks until the ImageJ instance is ready.
     """
-    ij_future.wait()
-
-
-def _get_mode() -> str:
-    """
-    Returns the mode ImageJ will be run in
-    """
-    return "headless" if sys.platform == "darwin" else "interactive"
-
-
-def jvm_is_headless() -> bool:
-    return _get_mode() == "headless"
+    imagej_init().wait()
 
 
 def _imagej_init():
@@ -74,7 +63,7 @@ def _imagej_init():
     # Launch PyImageJ
     _ij = imagej.init(
         ij_dir_or_version_or_endpoint=settings["imagej_directory_or_endpoint"].get(str),
-        mode=_get_mode(),
+        mode=settings["jvm_mode"].get(str),
         add_legacy=settings["include_imagej_legacy"].get(bool),
     )
     log_debug(f"Initialized at version {_ij.getVersion()}")
@@ -83,21 +72,33 @@ def _imagej_init():
     return _ij
 
 
-# There is a good debate to be had whether to multithread or multiprocess.
-# From what I (Gabe) have read, it seems that threading is preferrable for
-# network / IO bottlenecking, while multiprocessing is preferrable for CPU
-# bottlenecking.
-# While multiprocessing might theoretically be a better choice for JVM startup,
-# there are two reasons we instead choose multithreading:
-# 1) Multiprocessing is not supported without additional libraries on MacOS.
-# See https://docs.python.org/3/library/multiprocessing.html#introduction
-# 2) JPype items cannot (currently) be passed between processes due to an
-# issue with pickling. See
-# https://github.com/imagej/napari-imagej/issues/27#issuecomment-1130102033
-threadpool: ThreadPool = ThreadPool(processes=1)
-# ij_future is not very pythonic, but we are dealing with a Java Object
-# and it better conveys the object's meaning than e.g. ij_result
-ij_future: AsyncResult = threadpool.apply_async(func=_imagej_init)
+init_lock = Lock()
+_ij_future: AsyncResult = None
+
+
+def imagej_init() -> AsyncResult:
+    """Function that"""
+    global _ij_future
+    if not _ij_future:
+        with init_lock:
+            if not _ij_future:
+                # There is a good debate to be had whether to multithread or
+                # multiprocess. From what I (Gabe) have read, it seems that threading
+                # is preferrable for network / IO bottlenecking, while multiprocessing
+                # is preferrable for CPU bottlenecking. While multiprocessing might
+                # theoretically be a better choice for JVM startup, there are two
+                # reasons we instead choose multithreading:
+                # 1) Multiprocessing is not supported without additional libraries on
+                # MacOS. See
+                # https://docs.python.org/3/library/multiprocessing.html#introduction
+                # 2) JPype items cannot (currently) be passed between processes due to
+                # an issue with pickling. See
+                # https://github.com/imagej/napari-imagej/issues/27#issuecomment-1130102033
+                threadpool: ThreadPool = ThreadPool(processes=1)
+                # ij_future is not very pythonic, but we are dealing with a Java Object
+                # and it better conveys the object's meaning than e.g. ij_result
+                _ij_future = threadpool.apply_async(func=_imagej_init)
+    return _ij_future
 
 
 class JavaClasses(object):

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, jvm_is_headless, log_debug
+from napari_imagej.java import ensure_jvm_started, ij, jc, 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 jvm_is_headless():
+        if settings["jvm_mode"].get(str) == "headless":
             self.gui_button.clicked.connect(self.gui_button.disable_popup)
         else:
             self.gui_button.clicked.connect(self._showUI)
@@ -243,7 +243,7 @@ def __init__(self):
         super().__init__()
         self.setEnabled(False)
 
-        if jvm_is_headless():
+        if settings["jvm_mode"].get(str) == "headless":
             self._setup_headless()
         else:
             self._setup_headful()

src/napari_imagej/widgets/napari_imagej.py

@@ -7,6 +7,7 @@
 from napari import Viewer
 from qtpy.QtWidgets import QTreeWidgetItem, QVBoxLayout, QWidget
 
+from napari_imagej.java import imagej_init
 from napari_imagej.widgets.menu import NapariImageJMenu
 from napari_imagej.widgets.result_runner import ResultRunner
 from napari_imagej.widgets.result_tree import SearchResultTree, SearchResultTreeItem
@@ -20,6 +21,9 @@ def __init__(self, napari_viewer: Viewer):
         super().__init__()
         self.setLayout(QVBoxLayout())
 
+        # First things first, let's start up imagej (in the background)
+        imagej_init()
+
         # -- NapariImageJWidget construction -- #
 
         # At the top: the napari-imagej menu

tests/conftest.py

@@ -13,8 +13,8 @@
 
 
 @pytest.fixture(autouse=True)
-def confuse_settings():
-    """Fixture ensuring user settings are not used in tests"""
+def install_default_settings():
+    """Fixture ensuring any changes made earlier to the settings are reversed"""
     napari_imagej.settings.clear()
     napari_imagej.settings.read(user=False)
 

tests/widgets/test_menu.py

@@ -14,7 +14,6 @@
 from qtpy.QtWidgets import QApplication, QHBoxLayout, QMessageBox
 
 from napari_imagej import settings
-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 (
@@ -27,7 +26,7 @@
 from tests.utils import jc
 
 # Determine whether we are testing headlessly
-TESTING_HEADLESS: bool = jvm_is_headless()
+TESTING_HEADLESS: bool = settings["jvm_mode"].get(str) == "headless"
 
 
 @pytest.fixture(autouse=True)