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  • Aug 22 17:44
    ctrueden commented #205
  • Aug 16 17:34
    acardona opened #231
  • Aug 07 13:48
    chalkie666 opened #230
  • Aug 02 13:33
    tinevez labeled #107
  • Aug 02 13:33
    tinevez labeled #107
  • Aug 02 13:32
    tinevez opened #107
  • Aug 02 13:30
    tinevez commented #106
  • Aug 02 13:29
    tinevez synchronize #106
  • Aug 02 13:29

    tinevez on serialize-feature-model2

    Avoid feature name inflation wh… Update the MaMuT exporter examp… (compare)

  • Jul 18 11:57
    tpietzsch commented #106
  • Jul 18 11:44
    tinevez commented #106
  • Jul 18 11:41
    tpietzsch commented #106
  • Jul 18 11:32
    tinevez commented #106
  • Jul 18 11:31
    tpietzsch commented #106
  • Jul 18 11:20
    tpietzsch synchronize #106
  • Jul 18 11:20

    tpietzsch on serialize-feature-model2

    formatting Demonstrate that feature names … Add TODO and 2 more (compare)

  • Jul 10 13:08
    tinevez closed #104
  • Jul 10 13:08
    tinevez commented #104
  • Jul 10 13:08
    tinevez opened #106
  • Jul 10 10:56

    tinevez on serialize-feature-model2

    Fix weird compile error with Op… Make some static methods of MaM… JUnit test for the TrackMate im… and 5 more (compare)

Hadrien Mary
@hadim
Sweet. Congrats !
Curtis Rueden
@ctrueden
@aneevel It looks like our cert auto-renew scheme is not working: https://fiji.sc/ says the cert expired 6 days ago. :frowning:
Hadrien Mary
@hadim
I don't know your setup @ctrueden but I found the following to work very well in the past and I use it in production : https://github.com/JrCs/docker-letsencrypt-nginx-proxy-companion
Curtis Rueden
@ctrueden
Thanks @hadim. @aneevel is indeed currently working to Dockerize everything. And we do use Let's Encrypt. But we use Apache, not nginx.
@aneevel Also https://sites.imagej.net/ is expired now.
Hadrien Mary
@hadim
Well you can have your servers in apache and only use this nginx proxy (https://github.com/jwilder/nginx-proxy) to redirect traffic where you want.
But homemade solution are maybe the best for you :-)
Alec Neevel
@aneevel
@ctrueden This is just a problem with the auto-renew script I set up. It should be a very simple fix that I can handle tomorrow morning.
Curtis Rueden
@ctrueden
@aneevel Great.
Kyle I S Harrington
@kephale
for the record, as more folks shift to travis, it will probably be worth thinking harder about how to manage dependencies for both maven deployment and update sites, the bootstrap script has some hardcoded stuff that is bitrotting and i believe there is some redundancy in package fetching
Curtis Rueden
@ctrueden
@kephale Definitely. My goal is to migrate the bootstrapping to instead use mvn -Dimagej.app.directory rather than pulling down the state of an update site.
The reason for the hardcoded stuff was to ensure a working base state before updating... there is little reason to update those versions often. Though Johannes used to do so occasionally, and now I never do.
Kyle I S Harrington
@kephale
gotcha, the mvn w/ directory param solution sounds awesome
Curtis Rueden
@ctrueden
@kephale Keep buggin' me to finish that. This comes down to fully solving fiji/fiji#39, which I have pursued on and off for years now.
(and fiji/fiji#37 and fiji/fiji#38, intrinsically related work)
nstifani
@nstifani
Hi there, I was wondering how useful or complex should a script be to be considered as a potential plugin? I have written few things (useful but no rocket-science) and I believe it could be interesting to share it... Any suggestions?
Curtis Rueden
@ctrueden
@nstifani When you say "considered as a potential plugin" do you mean: at what point should you port it to a Command plugin written in Java, instead of keeping it as a script?
I would say "maybe never"... scripts are really good. One consideration is if you are doing a lot of control structures like loops... that might be slower depending on the script language. Worth testing.
Of course, there are many other types of plugins besides Commands, which cannot be written as scripts currently.
One consideration at the moment is that it is currently not possible to annotate a script with metadata such as "can this script run headless" whereas with a Command, you can via the @Plugin annotation.
However, I want to change that.
nstifani
@nstifani
@ctrueden Well In my non-specialist word plugin = .jar
I guess I meant macros regrouped in a .jar. How do I know that it is worth sharing them?
Jan Eglinger
@imagejan
@nstifani it's not required to put scripts into a jar file for sharing them and uploading to an update site. That depends more on how many scripts that are and if you want to manage dependencies centrally.
How about making them available on github.com first, and announcing them on the forum or the wiki?
Jean-Yves Tinevez
@tinevez
(the TrackMate paper is accepted for publication!! :wine_glass: )
Jan Eglinger
@imagejan
@tinevez congrats! :clap: :wine_glass:
Hadrien Mary
@hadim
Bravo !!!
Curtis Rueden
@ctrueden
@tinevez :fireworks: :beers:
@nstifani Ah, I understand what you are asking now. Whether to share some work you did... my inclination is to say yes whenever possible—and no only when necessary (e.g., legal issues). As long as you communicate the status of the project, so users have the right expectations, I'd say go ahead and announce it.
E.g.: If it's something you did quickly, and do not have time to support, then certainly say that in the README.
This is how my group does it: https://github.com/uw-loci/loci-scripts
Not a lot there—my point is just the README, which hopefully makes clear that these are not general solutions for everyone, but which we share just in case they help.
Philipp Hanslovsky
@hanslovsky
Congrats @tinevez !
Ulrik Günther
@skalarproduktraum
@tinevez: awesome, congratulations! do you already know when it’s going to be published?
Jean-Yves Tinevez
@tinevez
Thanks! It's planned for March 2017.
It is a special issue of Methods on software tools, but I do not know what are the other articles about.
Curtis Rueden
@ctrueden

@tinevez When searching the archives just now, I came across this comment from you circa one year ago:

And use this version to publish this #$%#$ nonexistant paper, which is like the Ragnarok.

So it seems we survived the apocalypse! It is the dawn of a new era.

Jean-Yves Tinevez
@tinevez
Aha :) I completely forgot about this.
By the way the unedited, un-proofed version is online, but the supplemental information including the docs are not there yet.
Robert Haase
@haesleinhuepf
@ctrueden Hi Curtis, may I get a user account for imagejs maven repository? We would like to push artifacts there to allow other developers to reuse our stuff. I guess the deployment strategy described here http://imagej.net/Travis is the way to go, right? Thanks!
Curtis Rueden
@ctrueden
@haesleinhuepf Very sorry for the delay in reply. I was out of the office yesterday and today. Yes, of course you can have an account.
Going for the Travis-based deployment would be excellent, yeah. We are moving that direction.
Robert Haase
@haesleinhuepf
@ctrueden There was no hurry… And the account works - thanks a lot!
Curtis Rueden
@ctrueden
@haesleinhuepf :sunglasses:
Robert Haase
@haesleinhuepf
@ctrueden Hi again Curtis, I’m currently trying to deploy something to the nexus, but I’m not very successful. I tried with maven deploy, but also using the scijava release_version script… I’m always getting an error message like:[INFO] --- maven-deploy-plugin:2.8.2:deploy (default-deploy) @ SCF_ImgTools_binaryops ---
Uploading: http://maven.imagej.net/content/groups/public/de/mpicbg/scf/SCF_ImgTools_binaryops/1.0.1/SCF_ImgTools_binaryops-1.0.1.jar
Uploading: http://maven.imagej.net/content/groups/public/de/mpicbg/scf/SCF_ImgTools_binaryops/1.0.1/SCF_ImgTools_binaryops-1.0.1.pom
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 33.885 s
[INFO] Finished at: 2016-10-10T17:20:55+02:00
[INFO] Final Memory: 50M/1636M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-deploy-plugin:2.8.2:deploy (default-deploy) on project SCF_ImgTools_binaryops: Failed to deploy artifacts: Could not transfer artifact de.mpicbg.scf:SCF_ImgTools_binaryops:jar:1.0.1 from/to imagej.releases (http://maven.imagej.net/content/groups/public): Failed to transfer file: http://maven.imagej.net/content/groups/public/de/mpicbg/scf/SCF_ImgTools_binaryops/1.0.1/SCF_ImgTools_binaryops-1.0.1.jar. Return code is: 400, ReasonPhrase: Bad Request. -> [Help 1]
It’s very hard to guess, what I’m doing wrong here...
Any help is appreciated :-/
Curtis Rueden
@ctrueden
You cannot deploy the same version more than once. Use a -SNAPSHOT suffix in your POM.
Robert Haase
@haesleinhuepf
@ctrueden Thanks for the hint, but I was trying SNAPSHOTs as well. Furthermore, there is no 1.0.1 version in the repository.
Robert Haase
@haesleinhuepf
Ok, I just figured out: "maven deploy" did not work, "release_version.sh 1.0.1-SNAPSHOT" did not work. But mvn -U -Pdeploy-to-imagej clean deploy --settings settings.xml does! Furthermore, suprisingly I need no <DistributionManagement> node in my Pom… Thanks to @skalarproduktraum and @ctrueden ! <3
Curtis Rueden
@ctrueden
Sorry @haesleinhuepf, I should have thought of that profile. Yes, you need it -- it adds the proper distributionManagement.