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  • Feb 28 11:04
    guillaume-ferry opened #244
  • Feb 26 22:14
    SandorAlbert opened #243
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  • Feb 21 10:49

    tinevez on master

    Better logo color scheme. (compare)

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  • Feb 18 21:45
    kant commented #196
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    ctrueden on master

    Add JFreeSVG library to the Fij… (compare)

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    WIP: Add JFreeSVG library to th… (compare)

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    Travis: fix uploading of compon… (compare)

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    ctrueden commented #196
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    Format Image.sh command in back… Merge pull request #196 from ka… (compare)

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Varun Kapoor
@kapoorlab
Ah let me check
odinsbane
@odinsbane
When I go into the Fiji.app folder, they're under jars/macosx/ Then there are four of them.
Varun Kapoor
@kapoorlab
Oh yeah the 3D viewer works in Fiji, just not on eclipse
odinsbane
@odinsbane
I spent a little time trying to get Intellij to work with the native jar files and not unpack them, but I just ended up unpacking them and it worked.
Varun Kapoor
@kapoorlab
I c, so I have to point these jars on the java build path for the repo I want to use the 3D viewer in, right?
odinsbane
@odinsbane
The only way I could get it to work was to unpack the jarfiles and then when I run the program include an argument to the jvm. -Djava.library.path=/path/to/folder/with/jnilibs
Hopefully somebody chimes in with the correct way to do this. I would much prefer to just include the jarfiles.
Varun Kapoor
@kapoorlab
No it works that way, I just did this to trackmate in eclipse: Right click on repo, -> Build Path -> Add external Archives -> Then add all the four jars in the Fiji macos folder that you mentioned and then it works
Curtis Rueden
@ctrueden
@odinsbane It should not be necessary to manually unpack natives from JARs in IntelliJ. The Java code is supposed to provide magic to take care of that for you. Maybe @skalarproduktraum has some insight?
Jean-Yves Tinevez
@tinevez
Hi all.
I am having troubles creating a new update site for Fiji.
I successfully created the TrackMateCSVImporteraccount on the wiki, and validated my email. But when I try to create the corresponding update site in Fiji updater, it does not work.
I cliked on Add my site in the updater, and input TrackMateCSVImporter as account name. The updater then asks me for my password, but it rejects it and this message appears in the console:
Did not get a token!
Did I do something wrong?
Jan Eglinger
@imagejan
You did set the upload password in addition to your wiki password, right?
Jean-Yves Tinevez
@tinevez

And another question: (sorry for the spam).
I meet a enforcer-related compile error for this very project.
It depends on the bioformats_plugin artifact, and it generate the following error:

[WARNING] Rule 3: org.apache.maven.plugins.enforcer.BanDuplicateClasses failed with message:
No Duplicate Classes Allowed!
- For duplicate transitive dependencies, add dependency exclusions.
- For duplications between direct dependencies, resolve or add
  ignored classes to this rule's configuration.

  Found in:
    commons-io:commons-io:jar:2.6:compile
    ch.systems.cisd:jhdf5:jar:14.12.0:compile
  Duplicate classes:
    org/apache/commons/io/FileCleaningTracker.class
    org/apache/commons/io/comparator/SizeFileComparator.class
    org/apache/commons/io/output/ProxyWriter.class

which is fine I guess. But how to skip this?

@imagejan .... no
Where do you do this?
Jan Eglinger
@imagejan
Also note that it's better to ask @ctrueden to add upload permissions to your existing personal account, instead of creating a new account...
Sorry, on mobile. ...
Jean-Yves Tinevez
@tinevez
ok.
Jan Eglinger
@imagejan
Special page set upload password on the wiki.
Jean-Yves Tinevez
@tinevez
aaaaaaah
Jan Eglinger
@imagejan
Re enforcer: you can add exclude statements to your pom, no?
It should all be documented somewhere on the wiki :smile:
Jean-Yves Tinevez
@tinevez
this one is a tough nut to crack even with google.
Curtis Rueden
@ctrueden
<properties><enforcer.skip>true</enforcer.skip></properties>
But then we come to your house with torches and pitchforks.
For testing and development, it is temporarily OK. But better to fix with exclusions as mentioned in the error message.
The problem is that ch.systems.cisd:jhdf5 is an uber-JAR.

You can avoid the error by adding:

<exclusions>
  <exclusion>
    <groupId>commons-io</groupId>
    <artifactId>commons-io</artifactId>
  </exclusion>
</exclusions>

in the <dependency> block of whatever dependency is pulling in commons-io.

Best fix would be for us to deploy a new jhdf5 that does not do this evilness.
Jean-Yves Tinevez
@tinevez
ok thanks this is clear.
Curtis Rueden
@ctrueden
Regarding the update site: as @imagejan said, I can create whatever update site you want, without you needing to make a wiki account, if you ask. And I can grant JeanYvesTinevez and/or other users permission to push to it .
Jean-Yves Tinevez
@tinevez
I did not know. What do you favor?
Curtis Rueden
@ctrueden
I have a weak preference to avoid creating dummy wiki accounts solely for the side effect of making an update site. But I do not care a lot—I fully appreciate that you can do it right now without waiting for other humans by doing that.
Jean-Yves Tinevez
@tinevez
Agreed.
Curtis Rueden
@ctrueden
@tinevez It looks like you already were able to successfully upload to TrackMateCSVImporter?
But just in case, I granted JeanYvesTinevez user the permission as well, for the future.
Jean-Yves Tinevez
@tinevez
yep. I had forgotten about the upload password. @imagejan reminded me and everything rolled.
Jean-Yves Tinevez
@tinevez
The exclusions fix does not have an effect. I think I may have to live with -Dskip.enforcer=true for a while.
Curtis Rueden
@ctrueden
I'd suggest checking the dependency tree using the Dependency Hierarchy tab of the pom.xml in Eclipse.
You can search it for where the commons-io is coming in.
You need to plug all holes in your metaphorical boat.
Jean-Yves Tinevez
@tinevez
I should frame this and hang it in the lab.
Jean-Yves Tinevez
@tinevez
@ctrueden fixed, thanks!
Curtis Rueden
@ctrueden
👍
Philipp Hanslovsky
@hanslovsky
:plus1:
For people who prefer command line, you can also run:
mvn dependency:tree
Curtis Rueden
@ctrueden
@hanslovsky Beware: mvn dependency:tree does pruning, unlike the Eclipse UI.
Philipp Hanslovsky
@hanslovsky
@ctrueden I am not 100% sure what that means but definitely good to know (and somewhat unexpected).
Curtis Rueden
@ctrueden

@hanslovsky It means the dependency tree listed by dependency:tree can be incomplete compared to the one given by Eclipse. For example, the dependency:tree for net.imagej:imagej says:

[INFO] +- net.imagej:imagej-legacy:jar:0.29.0:runtime (optional)
[INFO] |  +- net.imagej:ij1-patcher:jar:0.12.8:runtime (optional)
[INFO] |  +- net.imagej:ij:jar:1.51s:runtime (optional)
[INFO] |  +- net.imglib2:imglib2-ij:jar:2.0.0-beta-39:runtime (optional)
[INFO] |  +- org.scijava:scijava-search:jar:0.4.0:runtime (optional)
[INFO] |  +- org.scijava:scijava-ui-awt:jar:0.1.6:runtime
[INFO] |  +- org.scijava:scijava-ui-swing:jar:0.9.5:runtime
[INFO] |  |  +- org.scijava:swing-checkbox-tree:jar:1.0.2:runtime
[INFO] |  |  \- net.sourceforge.jdatepicker:jdatepicker:jar:1.3.2:runtime
[INFO] |  \- org.javassist:javassist:jar:3.22.0-GA:runtime (optional)

But imagej-legacy has additional dependencies such as imagej-common. The imagej-common dependency is not shown because it is already a direct dependency of imagej. So even though it is also inherited transitively, this fact is not visible from the output. So if your goal is to add exclusions to stop all leakage of a particular dependency, this tool is only sufficient if you check the tree iteratively.

Philipp Hanslovsky
@hanslovsky
Ugh, that's frustrating. Thanks for the clarification @ctrueden