These are chat archives for fiji/fiji

21st
Mar 2017
Stefan Helfrich
@stelfrich
Mar 21 2017 07:38
Hi @nabalab. Could you please post this to http://forum.imagej.net? Sounds like a Bio-Formats-related issue..
Curtis Rueden
@ctrueden
Mar 21 2017 11:26
@stelfrich IIRC there is already an issue for that in the SCIFIO issue tracker. Can you search for it and crosslink here please?
Stefan Helfrich
@stelfrich
Mar 21 2017 11:38
@ctrueden I couldn't find such issue (neither by search nor by manually checking the issue names)..
Curtis Rueden
@ctrueden
Mar 21 2017 12:21
@stelfrich You are right; I was misled by the drag-and-drop nature. This is not the same bug.
This is indeed a Bio-Formats bug, which should be reported to the Bio-Formats team.
Jan Eglinger
@imagejan
Mar 21 2017 12:49
@ctrueden @tinevez when cutting releases next time (for SPIM_Registration etc.), can we also include a new release of TrackMate, to include the new ShapeRoi support into a non-SNAPSHOT version?
Jean-Yves Tinevez
@tinevez
Mar 21 2017 13:05
@imagejan Ok let's release TrackMate.
I do it? Now? I have time.
Hum there are a couple of outstanding issues I would like to investigate. Please give me a deadline, even today.
Curtis Rueden
@ctrueden
Mar 21 2017 13:33
@tinevez How about you investigate your issues today and tomorrow, with the plan to cut releases either tomorrow afternoon/evening, or Thursday morning. I have to fix HTTPS for maven.imagej.net, to fix the builds, so that new releases can be cut again. Then I can fix Descriptor_based_registration to use the new Bio-Formats and newly released SPIM_Registration. I am happy to also cut a new TrackMate around that same time.
Jean-Yves Tinevez
@tinevez
Mar 21 2017 13:34
Deal!
Curtis Rueden
@ctrueden
Mar 21 2017 14:45
Hooray, SSL is fixed.
Jean-Yves Tinevez
@tinevez
Mar 21 2017 15:26
@ctrueden : Following your recommendations: how pass the imagej.app.directory in a ~/.m2/settings.xml? Things I have tried failed so far (properties tag, etc...)
Curtis Rueden
@ctrueden
Mar 21 2017 15:35
@tinevez Here is an example:
<settings>
    <profiles>
        <profile>
            <id>imagej</id>
            <activation>
                <file>
                    <exists>${env.HOME}/Desktop/Fiji.app</exists>
                </file>
            </activation>
            <properties>
                <imagej.app.directory>${env.HOME}/Desktop/Fiji.app</imagej.app.directory>
            </properties>
        </profile>
    </profiles>
</settings>
Haven't tested that in a while, though.
Jean-Yves Tinevez
@tinevez
Mar 21 2017 15:38
Thanks! Works as expected:
[INFO] --- imagej-maven-plugin:0.6.0:copy-jars (copy-jars) @ TrackMate_ ---
[INFO] Copying TrackMate_-3.4.3-SNAPSHOT.jar to /Users/tinevez/Development/Fiji.app/plugins
Curtis Rueden
@ctrueden
Mar 21 2017 15:38
Cool.
Philipp Hanslovsky
@hanslovsky
Mar 21 2017 18:46

@ctrueden do you know how I can print the version of a maven artifact using maven?
I tried:

mvn help:evaluate -Dexpression=project.version
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ImgLib2 Algorithms 0.6.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-help-plugin:2.2:evaluate (default-cli) @ imglib2-algorithm ---
[INFO] No artifact parameter specified, using 'net.imglib2:imglib2-algorithm:jar:0.6.4-SNAPSHOT' as project.
[INFO] 
0.6.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.862 s
[INFO] Finished at: 2017-03-21T14:45:17-04:00
[INFO] Final Memory: 19M/491M
[INFO] ------------------------------------------------------------------------

But I don't wanna have the [INFO] logs
I also tried with the --quiet option but then I don't see any output at all. The same is true for MAVEN_OPTS=-Dorg.slf4j.simpleLogger.defaultLogLevel=warn mvn help:evaluate -Dexpression=project.version

I could just inverse grep for [INFO] but when maven downloads dependencies it is also very vocal about it and does not add [INFO] to those lines. I would need to inverse grep for ^Download as well and I don't know if there are any other outputs that I would not capture with that grep. So I would like to have the version printed only and nothing else, if possible.
Philipp Hanslovsky
@hanslovsky
Mar 21 2017 18:53
This is the grep I use:
grep -Ev '(^\[|Download\w+:)'
Or this, assuming there is only one line of output starting with a number (and that line prints the version):
grep -Ev '(^[^0-9])'
Curtis Rueden
@ctrueden
Mar 21 2017 18:57
@hanslovsky Something like this?
: curtis@sirius ~/code/imagej/imagej (master) »
maven-helper.sh gav-from-pom pom.xml
net.imagej:imagej:2.0.0-rc-60-SNAPSHOT
: curtis@sirius ~/code/imagej/imagej (master) »
which maven-helper.sh
/Users/curtis/code/scijava/scijava-scripts/maven-helper.sh
Philipp Hanslovsky
@hanslovsky
Mar 21 2017 18:58
Yes, that looks exactly like what I'd like to have!
Is that script on github?
Curtis Rueden
@ctrueden
Mar 21 2017 18:59
Sure. All my code is organized in $HOME/code/<org>/<repo> folders. So you can deduce from the above where that script lives. :-)
Philipp Hanslovsky
@hanslovsky
Mar 21 2017 18:59
great, thanks :D
:+1:
Curtis Rueden
@ctrueden
Mar 21 2017 19:03
Another way:
xmllint --xpath '/*[local-name()="project"]/*[local-name()="version"]/text()' pom.xml
(Too bad about the local-name() junk, but Maven POMs use namespaces so you have to do it.)
Philipp Hanslovsky
@hanslovsky
Mar 21 2017 20:01
Even better @ctrueden I think I'll use that