Use dynaconf for user preferences

[gselzer]

This PR introduces dynaconf as a preferences management tool, and removes bugs associated with relative paths.

[codecov-commenter]

Codecov Report

Merging #99 (f901740) into main (99a115c) will decrease coverage by 0.40%.
The diff coverage is 76.73%.

@@            Coverage Diff             @@
##             main      #99      +/-   ##
==========================================
- Coverage   92.30%   91.89%   -0.41%     
==========================================
  Files          39       40       +1     
  Lines        3078     3233     +155     
==========================================
+ Hits         2841     2971     +130     
- Misses        237      262      +25     

Impacted Files	Coverage Δ
tests/widgets/test_menu.py	75.82% <61.53%> (+0.33%)	⬆️
tests/conftest.py	87.50% <71.42%> (-10.18%)	⬇️
src/napari_imagej/__init__.py	82.60% <81.81%> (-17.40%)	⬇️
src/napari_imagej/resources/__init__.py	85.71% <85.71%> (ø)
src/napari_imagej/widgets/menu.py	85.95% <91.54%> (+3.99%)	⬆️
src/napari_imagej/java.py	95.23% <100.00%> (-0.07%)	⬇️
src/napari_imagej/widgets/napari_imagej.py	88.37% <100.00%> (+0.56%)	⬆️
tests/utils.py	96.33% <100.00%> (+0.10%)	⬆️

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

[ctrueden]

Nice! Just some minor comments. Feel free to act on or ignore them as you see fit.

[ctrueden]

@gselzer This is looking really nice!

I ran into a couple of problems, like one does:

JVMNotRunning

I tried changing net.imagej:imagej to sc.fiji:fiji and restarting napari. Then when I run napari-imagej, I get the following stack trace:

---------------------------------------------------------------------------
JVMNotRunning                             Traceback (most recent call last)
File ~/mambaforge/envs/napari-imagej-dev/lib/python3.10/threading.py:1016, in Thread._bootstrap_inner(self=<Thread(Thread-8 (_init_producer), stopped 123145615675392)>)
   1013     _sys.setprofile(_profile_hook)
   1015 try:
-> 1016     self.run()
        self = <Thread(Thread-8 (_init_producer), stopped 123145615675392)>
   1017 except:
   1018     self._invoke_excepthook(self)

File ~/mambaforge/envs/napari-imagej-dev/lib/python3.10/threading.py:953, in Thread.run(self=<Thread(Thread-8 (_init_producer), stopped 123145615675392)>)
    951 try:
    952     if self._target is not None:
--> 953         self._target(*self._args, **self._kwargs)
        self = <Thread(Thread-8 (_init_producer), stopped 123145615675392)>
    954 finally:
    955     # Avoid a refcycle if the thread is running a function with
    956     # an argument that has a member that points to the thread.
    957     del self._target, self._args, self._kwargs

File /Volumes/Code/napari/napari-imagej/src/napari_imagej/widgets/result_tree.py:156, in SearchResultTree._init_producer(self=<napari_imagej.widgets.result_tree.SearchResultTree object>)
    152 ensure_jvm_started()
    154 # Then, define our SearchListener
    155 @JImplements("org.scijava.search.SearchListener")
--> 156 class NapariImageJSearchListener:
    157     def __init__(self, event_handler: Signal):
    158         super().__init__()

File ~/mambaforge/envs/napari-imagej-dev/lib/python3.10/site-packages/jpype/_jproxy.py:136, in JImplements.<locals>.JProxyCreator(cls=<class 'napari_imagej.widgets.result_tree.Search...it_producer.<locals>.NapariImageJSearchListener'>)
    135 def JProxyCreator(cls):
--> 136     return _createJProxy(cls, *interfaces, **kwargs)
        cls = <class 'napari_imagej.widgets.result_tree.SearchResultTree._init_producer.<locals>.NapariImageJSearchListener'>
        interfaces = ('org.scijava.search.SearchListener',)
        kwargs = {}

File ~/mambaforge/envs/napari-imagej-dev/lib/python3.10/site-packages/jpype/_jproxy.py:80, in _createJProxy(cls=<class 'napari_imagej.widgets.result_tree.Search...it_producer.<locals>.NapariImageJSearchListener'>, *intf=('org.scijava.search.SearchListener',))
     76 def _createJProxy(cls, *intf):
     77     """ (internal) Create a proxy from a Python class with
     78     @JOverride notation on methods evaluated at declaration.
     79     """
---> 80     actualIntf = _prepareInterfaces(cls, intf)
        cls = <class 'napari_imagej.widgets.result_tree.SearchResultTree._init_producer.<locals>.NapariImageJSearchListener'>
        intf = ('org.scijava.search.SearchListener',)
     82     def new(tp, *args, **kwargs):
     83         self = _jpype._JProxy.__new__(tp, None, actualIntf)

File ~/mambaforge/envs/napari-imagej-dev/lib/python3.10/site-packages/jpype/_jproxy.py:51, in _prepareInterfaces(cls=<class 'napari_imagej.widgets.result_tree.Search...it_producer.<locals>.NapariImageJSearchListener'>, intf=('org.scijava.search.SearchListener',))
     49 def _prepareInterfaces(cls, intf):
     50     # Convert the interfaces list
---> 51     actualIntf = _convertInterfaces(intf)
        intf = ('org.scijava.search.SearchListener',)
     52     overrides = _classOverrides(cls)
     53     _checkInterfaceOverrides(actualIntf, overrides)

File ~/mambaforge/envs/napari-imagej-dev/lib/python3.10/site-packages/jpype/_jproxy.py:156, in _convertInterfaces(intf=('org.scijava.search.SearchListener',))
    154 for item in intflist:
    155     if isinstance(item, str):
--> 156         actualIntf.add(_jpype.JClass(item))
        item = 'org.scijava.search.SearchListener'
        actualIntf = set()
        _jpype.JClass = <class 'jpype._jclass.JClass'>
    157     else:
    158         actualIntf.add(item)

File ~/mambaforge/envs/napari-imagej-dev/lib/python3.10/site-packages/jpype/_jclass.py:99, in JClass.__new__(cls=<class 'jpype._jclass.JClass'>, jc='org.scijava.search.SearchListener', loader=None, initialize=True)
     96     return ret
     98 # Pass to class factory to create the type
---> 99 return _jpype._getClass(jc)
        jc = 'org.scijava.search.SearchListener'

JVMNotRunning: Java Virtual Machine is not running

Something weird with the multithreading, perhaps? Edit: it's just a symptom of the actual problem, which was emitted on the console:

Console error

16:32:26 DEBUG napari-imagej: Initializing ImageJ2
16:32:26 DEBUG napari-imagej: Completed JVM Configuration
16:32:27 ERROR Failed to bootstrap the artifact.
16:32:27 ERROR
16:32:27 ERROR Possible solutions:
16:32:27 ERROR * Double check the endpoint for correctness (https://search.maven.org/).
16:32:27 ERROR * Add needed repositories to ~/.jgorc [repositories] block (see README).
16:32:27 ERROR * Try with an explicit version number (release metadata might be wrong).
16:32:27 ERROR
16:32:27 ERROR Full Maven error output:
16:32:27 ERROR 	[ERROR] [ERROR] Some problems were encountered while processing the POMs:
16:32:27 ERROR 	[ERROR] Non-resolvable import POM: Failed to resolve version for sc.fiji:fiji:pom:RELEASE @ line 8, column 29
16:32:27 ERROR 	[ERROR] The build could not read 1 project -> [Help 1]
16:32:27 ERROR 	[ERROR]
16:32:27 ERROR 	[ERROR]   The project sc.fiji-BOOTSTRAPPER:fiji-BOOTSTRAPPER:0 (/Users/curtis/.jgo/sc.fiji/fiji/RELEASE/b616c577c2873bd4b5338a8fad1280c9b5448e17fda031f6b7a4fc8612418b0b/pom.xml) has 1 error
16:32:27 ERROR 	[ERROR]     Non-resolvable import POM: Failed to resolve version for sc.fiji:fiji:pom:RELEASE @ line 8, column 29 -> [Help 2]
16:32:27 ERROR 	[ERROR]
16:32:27 ERROR 	[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
16:32:27 ERROR 	[ERROR] Re-run Maven using the -X switch to enable full debug logging.
16:32:27 ERROR 	[ERROR]
16:32:27 ERROR 	[ERROR] For more information about the errors and possible solutions, please read the following articles:
16:32:27 ERROR 	[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
16:32:27 ERROR 	[ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
16:32:27 ERROR

Suboptimal dialog message when clicking ImageJ GUI button on macOS

The message I receive is: "The ImageJ2 user interface cannot be opened when running PyImageJ headlessly. Visit this site for more information." Which is correct, but what is not explained is that because I'm on macOS, napari-imagej has no choice but to run in headless mode, and interactive mode is not available. I think this could be better communicated to users.

Relatedly: I'm not sure if on non-Mac platforms, the settings dialog has a toggle between headless and interactive, but I don't see it on macOS.

[ctrueden]

I looked into why the sc.fiji:fiji endpoint failed to resolve with Maven.

If I change RELEASE to 2.6.0 in the generated pom.xml, it works.

I was worried that Maven finally killed support for the special RELEASE keyword once and for all... but after rm -rf ~/.m2/repository/sc/fiji/fiji, doing mvn dependency:get -Dartifact=sc.fiji:fiji:RELEASE fetched the previously missing maven-metadata.xml and the resolution worked. So 🤷, not actually an issue.

[ctrueden]

LGTM!

[gselzer]

A couple things I'd like to add before merge:

• For some reason, the ordering of the settings is not the same every time. It seems to change based on the value of the settings. If I start out with choose_active_layer (ordered second in the list) checked, and uncheck it, the next time I click the settings button it will appear first! And then, if I check it again, it will then appear second if I click on the settings button a third time!
• I'd like to add a disclaimer that settings changes will only take effect on restart. But I'm not sure that napari's request_values dialog has the option for this, so maybe I'll add this disclaimer in a popup that spawns only if the user makes any changes to the settings.
• I'd like to test that pressing the settings button and making a change will actually affect the file.

[gselzer]

I only got through part of it, but gotta run now. Will do the rest later!

[gselzer]

Finished the review!