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imagej / napari-imagej

Use ImageJ functionality from napari
https://napari-imagej.readthedocs.io
BSD 2-Clause "Simplified" License
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Error with SNT endpoint #211

Closed kephale closed 1 year ago

kephale commented 1 year ago

Testing endpoint: net.imagej:imagej:2.9.0+org.morphonets:SNT:4.1.16

Gives this error:

[Errno 2] No such file or directory: '/Users/kharrington/.m2/repository/org/jzy3d/jzy3d-native-jogl-core/2.2.1/jzy3d-native-jogl-core-2.2.1-tests.test-jar' -> '/Users/kharrington/.jgo/net.imagej/imagej/2.9.0/e54008d79786f76ac454ef21e0ab51eea30a2b1fbc5b0bb5bd8586e5c1534414/jzy3d-native-jogl-core-2.2.1-tests.test-jar'

I guess this is probably either a SNT issue or jgo, but it wasn't obvious so I'm starting the issue here.

gselzer commented 1 year ago

Hmm, I was able to repeat this initially @kephale, but I reset my environment while trying to debug into jgo and now I can't reproduce this anymore. napari-imagej prevents the usage of net.imagej:imagej:2.9.0 because we need bugfixes in new components, and net.imagej:imagej:2.11.0+org.morphonets:SNT:4.1.16 works without errors.

Can you try to reproduce after running git checkout main; git pull; mamba env update -f <whatever_file_you_were_using.yml> --prune? If it persists, I'd guess it's a jgo failure, as your endpoint looks correct, and I was getting the error within jgo.resolve_dependencies...

kephale commented 1 year ago

This endpoint works: org.scijava:scijava-common:2.94.0+io.scif:scifio:0.45.0+org.scijava:scijava-search:2.0.2+net.imagej:imagej-legacy:1.1.0+net.imagej:imagej:2.11.0+org.morphonets:SNT:4.1.17, aside from an error I get from jzy3d-core-2.2.1-tests.test-jar missing (which seems like an odd file). That missing file error is clearly from SNT, and I was able to resolve it by creating a duplicate of jzy3d-core-2.2.1-tests.jar as jzy3d-core-2.2.1-tests.test-jar

ctrueden commented 1 year ago

Simpler endpoints which might work:

Version 2.13.0 (of either) comes with scijava-common 2.94.0, scifio 0.45.0, scijava-search 2.0.3, and imagej-legacy 1.1.0, so you wouldn't have to declare those upgrades manually anymore.