These are chat archives for fiji/fiji

22nd
Mar 2016
Ignacio Arganda-Carreras
@iarganda
Mar 22 2016 08:26
OK, makes sense, thanks a lot @imagejan and @ctrueden !
Curtis Rueden
@ctrueden
Mar 22 2016 13:20
@iarganda Be sure to check the <description> tag of the POM parent you are using, since it lists all the XML elements you should override. Otherwise, you might inherit some erroneous configuration (e.g., the wrong license declaration).
You can use mvn help:effective-pom on your project to verify that everything looks good.
Stefan Helfrich
@stelfrich
Mar 22 2016 14:48
@tinevez: I just stumbled over a TrackMate_-3.0.0.jar in one my user’s Fiji installations. How did that happen?
Jean-Yves Tinevez
@tinevez
Mar 22 2016 14:51
Automatic version changed when everything was updated with java8 and 3D.
I don't know what to do with it.
Stefan Helfrich
@stelfrich
Mar 22 2016 14:51
Ah ok. So it’s TrackMate(2)-3.0.0 instead of TrackMate3-1.0.0?
Jean-Yves Tinevez
@tinevez
Mar 22 2016 14:52
Yep.
Stefan Helfrich
@stelfrich
Mar 22 2016 14:53
Hmm. That’s.. unfortunate.. but oke. I was just wondering
Jean-Yves Tinevez
@tinevez
Mar 22 2016 15:21
@ctrueden Is it something I could do about the 3.0.0 version of TrackMate? Could I release a new version with a proper 2.9.0 (for instance) without breaking everything?
Curtis Rueden
@ctrueden
Mar 22 2016 15:22
It comes down to the fact that SemVer is incompatible with "romantic versioning"
In other words: you cannot hold off on 3.0.0 forever—SemVer demands the major version bump whenever some backwards incompatible change occurs.
One way people get around this is to use four digits: with the leftmost being the "romantic" one.
I.e.: the marketing one: big huge change with everything new!
I apologize that a TrackMate 3.0.0 was necessary, but IIRC it was needed due to the Java 3D changes.
One option is not to use the numeral for the new version of TrackMate, but instead "TrackMateX" or something. Or: just don't worry about it, and rebrand the artifact as TrackMate again once it is ready, with the next major version digit.
I don't have all the answers here: otherwise we wouldn't have a thing called "ImageJ2" ... :worried:
Stefan Helfrich
@stelfrich
Mar 22 2016 15:26
Thanks to you @ctrueden, I will never stop learning new things, like "sentimental versioning”. :clap:
Curtis Rueden
@ctrueden
Mar 22 2016 15:33
Hehehe
tpietzsch
@tpietzsch
Mar 22 2016 15:35
Speaking of TrackMate3: YEsterday, trying to demo it, I ran into the Java8-Fiji issue
I had told people to update Fiji beforehand, but that doesn't bring in the java8 updates.
Can someone point me to best practices or something on the wiki?
I guess: Reinstall Fiji?
Stefan Helfrich
@stelfrich
Mar 22 2016 15:36
Had a similar issue today. Only solution: reinstall
tpietzsch
@tpietzsch
Mar 22 2016 15:37
Ok
I thought so
...
Stefan Helfrich
@stelfrich
Mar 22 2016 15:37
I couldn’t even get any error message..
tpietzsch
@tpietzsch
Mar 22 2016 15:38
Oh... then you ran into something different
Stefan Helfrich
@stelfrich
Mar 22 2016 15:38
Oh.. nice..
tpietzsch
@tpietzsch
Mar 22 2016 15:38
for me the issue was clearly that Fiji was still running with java 1.6
:-D
major.minor version exception thingie
Stefan Helfrich
@stelfrich
Mar 22 2016 15:39
Then hope might not be lost.. I had a Fiji that did not start at all after enabling the Java8 update site..
Jean-Yves Tinevez
@tinevez
Mar 22 2016 16:50
@ctrueden The Jenkins job is in Java8 right?
Because I have a couple of Eclipse warnings like for example
JList is a raw type. References to generic type JList<E> should be parameterized
I would like to get rid of. Is it safe for an artifact that is under Jenkins supervision?
Curtis Rueden
@ctrueden
Mar 22 2016 17:20
@tinevez Which Jenkins job?
Looks like that job is currently set to build using Java 6.
@tpietzsch @stelfrich There is no migration guide from Java 6 to Java 8 yet.
The easiest solution is to redownload Fiji. Alternately, you can download Fiji then rip out the java folder and stuff it into your existing installation, overwriting the old one (or renaming the old one to e.g. java6).
Then you can turn on the Java-8 update site and it should work without needing to reinstall. This is nice if your Fiji is complex with lots of manually added stuff.
I do not have time to make the updater support Java version upgrades, unfortunately.
Curtis Rueden
@ctrueden
Mar 22 2016 18:41
@tinevez I changed the MaMuT Jenkins job to use Java 8 now, since it looks like the latest code requires it.
Jean-Yves Tinevez
@tinevez
Mar 22 2016 19:26
thanks @ctrueden .
I might crash things in the next hours.
Jean-Yves Tinevez
@tinevez
Mar 22 2016 21:52
Turns out things are really smooth with the Java8 thingie. This is the first time the 3D Viewer in TrackMate and MaMuT works in a long time.
Plus it made me review the code a bit. Thanks @ctrueden
Curtis Rueden
@ctrueden
Mar 22 2016 21:52
Very glad to hear that!
BTW, I saw that the TrackMate job failed, so I bumped it to use Java 8 instead of 7 now, which addressed the issue.