These are chat archives for fiji/fiji

18th
Dec 2015
Curtis Rueden
@ctrueden
Dec 18 2015 05:50
Fiji components update: Nearly everything is released now. Left to do:
  • Add feature to the Updater UI to see the minimum required Java version of each JAR file.
  • Cut needed release of imagej-ui-swing (including that feature).
  • Push changes to Fiji_Developer (which depends on imagej-ui-swing) and cut a release.
  • Make sure fiji itself builds/assembles properly with the latest pom-fiji BOM.
  • Create Java-8 update site (actually, rename the 3D site, leaving behind a symlink redirect).
  • Upload all Java-7-or-8-based JARs to Java-8, and all Java-6-based JARs to the core ImageJ or Fiji update site as appropriate, testing both configurations first in respective installations locally.
May also want/need to cut a bigdataviewer_fiji release, since it is also affected by the Java 3D upgrade. (Already pushed the update to master, but it's not released.)
Curtis Rueden
@ctrueden
Dec 18 2015 06:10
May also want/need to cut a bigwarp_fiji release (even though 2.0.0 was just released!), since it is also affected by the Java 3D upgrade.
Curtis Rueden
@ctrueden
Dec 18 2015 06:20
And of course, there are still lots of components that need developers & contributors updated. But those updates are rolling along.
tpietzsch
@tpietzsch
Dec 18 2015 11:50
how is bigdataviewer_fiji affected?? It doesn't use Java3D?
tpietzsch
@tpietzsch
Dec 18 2015 12:02
oh right
transitively via SPIM_Registration
because SPIM_Registration depends on everything
Curtis Rueden
@ctrueden
Dec 18 2015 12:41
Yeah, bdv_fiji and bigwarp have some big dep chains! But it is ok: it is nice when components can be reused!
Stephan Saalfeld
@axtimwalde
Dec 18 2015 13:11
@ctrueden, we are planning to release and upload bigwarp_fiji since yesterday and we've been trying to do it right
Stephan Saalfeld
@axtimwalde
Dec 18 2015 13:16
i do not know if we actually need a 2.0.1 release for this as nothing changed in the bigwarp itself, it's just pom-modifications, no API
Curtis Rueden
@ctrueden
Dec 18 2015 13:19
@axtimwalde Then we may not, indeed. I will test.
@axtimwalde I am also going to lean on the melting pot today—plan is to test two configurations: a Java 6 one, and a Java 8 one.
(By which I mean: the latest versions of all Java-6-compatible components using a Java 6 VM.)
John Bogovic
@bogovicj
Dec 18 2015 13:22
Great, so I guess we'll hold off on releasing until we hear from you?
Curtis Rueden
@ctrueden
Dec 18 2015 13:24
@axtimwalde If you guys really want to "do it right" more easily, then I urge you to use release-version.sh. The only extra thing you need for that to work is an account on the ImageJ Nexus. And it works great for all single-component projects (i.e.: everything besides TrakEM2 and mpicbg).
Curtis Rueden
@ctrueden
Dec 18 2015 13:25
@bogovicj The double-push-to-master approach is too fragile. As an example: bigwarp_fiji 2.0.0 was never deployed, because you pushed the bump to 2.0.1-SNAPSHOT too fast. The ImageJ Jenkins only polls bigwarp every 5 minutes because we didn't add the Jenkins push notification to your repo.
Same for mpicbg I believe. You guys are more than welcome to do that though, and then it won't have to poll anymore.
@bogovicj Worry not about bigwarp_fiji 2.0.0 specifically though: I manually deployed it last night after I noticed you'd released it.
John Bogovic
@bogovicj
Dec 18 2015 13:28
@ctrueden , thanks for catching that. I noticed and had planned to contact you this morning - but you're just too on top of things :)
Curtis Rueden
@ctrueden
Dec 18 2015 13:28
As for the upload: I will take care of it today unless my testing finds a critical problem with the new soup of components.
John Bogovic
@bogovicj
Dec 18 2015 13:28
next release I do, I'll definitely use that script. thanks
Curtis Rueden
@ctrueden
Dec 18 2015 13:28
Yeah, I am working a little too much right now... trying to get this push finished before the holidays. ;-) I will be less responsive after next Wednesday.
@bogovicj Great, then I'll create a Nexus account for you right now.
@axtimwalde Hey, you already have an account. :-)
John Bogovic
@bogovicj
Dec 18 2015 13:29
oh! lovely
Stephan Saalfeld
@axtimwalde
Dec 18 2015 13:33
@ctrueden just a note on the most recent jenkins hickup, I can build bigwarp locally without complaints, so it's may be a configuration issue?
@ctrueden, i do have an account and i have been using it recently to fix stuff
Curtis Rueden
@ctrueden
Dec 18 2015 13:37
@bogovicj I PMed you the credentials and instructions. For simplicity, you have full control over all repos—use your power wisely!
(In particular: don't delete any release artifacts out of imagej.releases or imagej.thirdparty unless you really, really mean it. It will hose anyone who has previously downloaded those versions.)
@axtimwalde I haven't read mails yet today so didn't see that Jenkins failure. Looking now.
My bad, I forgot to switch that job to use OpenJDK 7.
Oops, gotta get off the bus. BBIAB.
Job switched.
John Bogovic
@bogovicj
Dec 18 2015 13:44
@ctrueden Got them, thanks. I'll be extra extra careful. (dont imagine I'll delete release artifacts ever)
Stephan Saalfeld
@axtimwalde
Dec 18 2015 14:09
@ctrueden, THANKS! You're awesome!
Stephan Saalfeld
@axtimwalde
Dec 18 2015 15:20
@bogovicj I predict that you will feel first like deleting a release artifact before tonight
(just teasing)
Mark Hiner
@hinerm
Dec 18 2015 15:29

@bogovicj I predict that you will feel first like deleting a release artifact before tonight

:laughing:

John Bogovic
@bogovicj
Dec 18 2015 15:32
Resisting the urge!! >.<
Kyle I S Harrington
@kephale
Dec 18 2015 18:33
any Janelia folks want to hang out a bit on the 22nd? i'll be swinging by campus to meet with some folks
John Bogovic
@bogovicj
Dec 18 2015 18:49
@kephale Would be great to meet you!
Curtis Rueden
@ctrueden
Dec 18 2015 20:38
@bogovicj @axtimwalde Quick dependency question: I just noticed that bigwarp_fiji 1.1.0 requires au.com.bytecode:opencsv:2.4, and trakem2_tps 1.1.1 requires net.sf.opencsv:opencsv:2.0.
These two opencsv artifacts clash. Can this be fixed to be consistent?
I could fix it on the Fiji side by adding an exclusion to trakem2_tps, but it would be good to make the two POMs consistent. We can also add version management for that artifact to pom-fiji to avoid version skew (but it won't fix the groupId skew).
Update: I did fix it on the Fiji side by doing that. ;-) But we should still fix it some time.
Curtis Rueden
@ctrueden
Dec 18 2015 20:45
Hey, we already are managing au.com.bytecode:opencsv in pom-fiji. So I'll file a PR to trakem2-tps OH WAIT @hinerm ALREADY FIXED IT saalfeldlab/trakem2-tps@7655e37
Thank you @hinerm!
So we just need a trakem2-tps 1.1.2 release at some point.
John Bogovic
@bogovicj
Dec 18 2015 20:45
Ah, nice catch!
I'll get a release going for that ( itll be nice to see if i have everything setup correctly for the release script)
and opencsv2.0 is fine
Curtis Rueden
@ctrueden
Dec 18 2015 21:06
@bogovicj Well, it will be 2.4.
Both your components declare au.com.bytecode:opencsv:2.4 now.
John Bogovic
@bogovicj
Dec 18 2015 21:08
oops, yes, my mistake.
Stephan Saalfeld
@axtimwalde
Dec 18 2015 23:31
@ctrueden, regarding the Java 1.6 vs >= 1.7 issue
I believe that we currently do not depend on 1.7 features and would like to compile for 1.6, but we failed in an apocalyptic pile of rule complaints that we did not understand
this is obviously failure on our side, but it'd be great if we could get a hint
Curtis Rueden
@ctrueden
Dec 18 2015 23:34
Bigwarp does depend on 1.7-specific artifacts, and is thus 1.7-specific now.
I explained this in the relevant commit message.
Java version granularity is at the level of artifacts only. If you want otherwise we will need to cut one or more artifacts in half.
Stephan Saalfeld
@axtimwalde
Dec 18 2015 23:43
does that mean we cannot have bigwarp in fiji short term?
Curtis Rueden
@ctrueden
Dec 18 2015 23:49
It is already in fiji. And the latest version(s) will go on the Java-8 update site within the next couple of days.
And we will update the Fiji continuous release to include Java 8 with that update site enabled ASAP.
Curtis Rueden
@ctrueden
Dec 18 2015 23:59
I am planning a news and/or forum post explaining this plan very soon. Does it make sense to you guys?
This way existing users csn opt in to Java 8 to get latest updates of affected components. And new usera get a correct installation with java 8 bundled out od the box.