These are chat archives for fiji/fiji

29th
Dec 2017
Jean-Yves Tinevez
@tinevez
Dec 29 2017 12:19
Just uploaded TrackMate v3.6.0, that fixes problems caused by JFreeChart being updated from 1.0.19 to 1.5.0. This update permits to remove a dependency on JCommon.
It is likely that other Fiji plugins that depends on JFreeChart will report similar problems.
Checking MaMuT immediately.
Curtis Rueden
@ctrueden
Dec 29 2017 13:37
Thank you @tinevez. Sorry for rocking the boat with that.
The following projects in my sphere of awareness depend on it directly:
  • PreibischLab/MTV_Tracker
  • PreibischLab/MTrack
  • PreibischLab/multiview-reconstruction
  • fiji/Directionality
  • fiji/SPIM_Registration
  • fiji/Simple_Neurite_Tracer
  • fiji/TrackMate
  • fiji/legacy-imglib1
  • imagej/imagej-ui-swing
  • imglib/imglib2-script
  • maarzt/imagej-plot-service
  • uw-loci/sonification
  • scijava/pom-scijava
  • slim/slim-plugin
Jean-Yves Tinevez
@tinevez
Dec 29 2017 14:44
Woops forgot about Directionality. I think that's the last one on my maintainer list.
I can help if people tell (explicitely).
Curtis Rueden
@ctrueden
Dec 29 2017 21:25
@tinevez Please use the updated release-version.sh script to release new versions of plugins from now on. It is as simple as running release-version.sh with no arguments. See here for details.
Any component that has been "Travisified" will support doing releases this way.
Curtis Rueden
@ctrueden
Dec 29 2017 21:46
@tferr I pushed an update to Simple_Neurite_Tracer upgrading to JFreeChart 1.5.0 accordingly. Code still compiles with passing tests. If you have time to briefly test chart-related features, I would greatly appreciate it. If anything is broken, we'll fix it ASAP.
Jean-Yves Tinevez
@tinevez
Dec 29 2017 21:50
@ctrueden Oooooooh....
Does it upload to ImageJ repo too?
Curtis Rueden
@ctrueden
Dec 29 2017 21:50
Still passing the build: Directionality, legacy-imglib1, imagej-ui-swing, imglib2-script.
@tinevez Travis will deploy the release to Maven. But it does not upload anything to the update site.
The eventual goal is for the update site to be driven by what's in certain POMs on GitHub. But not yet.
Jean-Yves Tinevez
@tinevez
Dec 29 2017 21:53
ok! Anyway this is going to be much better with this now. I cannot count how many time I forgot to tag properly or pushed with the wrong version...
thx
Curtis Rueden
@ctrueden
Dec 29 2017 21:53
:+1:
Also still passing: imagej-plot-service.
Also still passing: uw-loci/sonification.
Failing: PreibischLab/MTrack, PreibischLab/multiview-reconstruction, fiji/SPIM_Registration, slim/slim-plugin
So now I study the fixes in TrackMate to understand them, then do the same for the above. -_-
Jean-Yves Tinevez
@tinevez
Dec 29 2017 21:56
@ctrueden I can help.
Curtis Rueden
@ctrueden
Dec 29 2017 21:56
It's late for you now, no?
Jean-Yves Tinevez
@tinevez
Dec 29 2017 21:56
heuh thatt's ok actually the kids are playing and I am chatting on the computer. A cool evening.
Curtis Rueden
@ctrueden
Dec 29 2017 21:58
OK! It looks like the fixes were quite easy? Just RectangleEdge changing package, and ChartUtilities renamed to ChartUtils?
You want to fix fiji/SPIM_Registration? I'll do the others since I have push access to them.
Jean-Yves Tinevez
@tinevez
Dec 29 2017 22:00
Ok so here is briefly what I understood from the changes involved in the JFreeChart v1.5.0:
There is 2 main changes:
  • ChartUtilities must be renamed to ChartUtils
  • they want to get rid of jcommon so some of the classes they return have been moved from jcommon to jfreechart. So many core classes and interfaces like Rectangle2D and PublicClonable have to change packages.
Once you fixed the compile errors, you should be able to remove the jcommon dependency from your project.
Ok I go for SPIM_registration. I do it in a branch for safety.
Curtis Rueden
@ctrueden
Dec 29 2017 22:03
Then next, check that this example still works?
Jean-Yves Tinevez
@tinevez
Dec 29 2017 22:04
Most likely yes because it does not intersect with the changes involved.
Curtis Rueden
@ctrueden
Dec 29 2017 22:04
I figured, but just wanted to be safe. If you are confident, then that is good enough for me.
Curtis Rueden
@ctrueden
Dec 29 2017 22:09
One down: PreibischLab/MTrack#3
@tinevez Got multiview-reconstruction to build, but it still leans on JCommon because of RefineryUtilities. Did you read anything about what happened to that?
Jean-Yves Tinevez
@tinevez
Dec 29 2017 22:13
Nope. This one stayed on jcommon. The SPIM_registration also uses it, but I copy/pasted the methods used (5 liners)
is fiji/SPIM_Registration#133 ok?
Jean-Yves Tinevez
@tinevez
Dec 29 2017 22:20
Comparison-1.png
@ctrueden : the example still works.
Curtis Rueden
@ctrueden
Dec 29 2017 22:21
Awesome, thanks! I squashed and merged it, so that we don't have a commit in the history that fails to build.
I finished slim_plugin. I have multiview-reconstruction fixed locally but did not push yet due to the continued usage of RefineryUtilities. I will inline it as you suggest, then commit and push.
And that is everything I know of which broke. All the other projects I listed above still compile.
Thanks again for your help! And sorry again for causing trouble. I should have run the melting-pot.sh. I am looking forward to automating that integration test in the future, to catch these things proactively.
Jean-Yves Tinevez
@tinevez
Dec 29 2017 22:25
Good! So we are back with normal operations in the Fiji distribution. Maybe when we killed the last RefineryUtilities uses we can remove one jar from the distribution?
That was fun!
Curtis Rueden
@ctrueden
Dec 29 2017 23:06
New SPIM_Registration 5.0.18 released and uploaded to Java-8 update site. The others are not part of the core Fiji update site, so I think all is well now for core Fiji distro.
@StephanPreibisch @hoerldavid You will need to update the BigStitcher update site. I already released multiview-reconstruction 0.1.3, and updated BigStitcher master, accordingly. You just have to upload the JARs I expect.