Needs pom dependency updates

PreibischLab / RS-FISH

Tool for precise, interactive, fast and scalable FISH spot detection

GNU General Public License v2.0

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Needs pom dependency updates #11

Closed kephale closed 2 years ago

kephale commented 2 years ago

I was working pushing to the update site in response to @LauraBreimann's request.

It looks like RS-FISH is falling behind on versions:

[INFO] Uploading 38 (removing 91) to RadialSymmetry (webdav:RadialSymmetry:<password>:./)

[ERROR] There are conflicts:

jars/jaxb-api-2.3.0.jar: Is not installed but a dependency of

jars/scijava-common-2.87.1.jar

jars/scijava-common-2.87.1.jar: Depends on jars/jaxb-api.jar which is about to be removed.

This is also an older scijava-common and made me notice that the pom-scijava version needs to be updated. I haven't started this and am putting this on my queue. It might be a quick job but in case someone wants to take care of it before I do, I'm posting this issue.

LauraBreimann commented 2 years ago

Thank you @kephale! Maybe @mzouink could have a look at these conflicts?

mzouink commented 2 years ago

I found that we were using pom-scijava 30.0.0 I just upgraded it to scijava 31.1.0 which uses scijava-common 2.87.0 (still behind scijava-common 2.87.1 but it is the last scijava release ) I hope the problem is solved. Else, we need to force dependency.

kephale commented 2 years ago

Great, thank you @mzouink.

For some reason jitpack doesn't like the maven release flag: https://jitpack.io/com/github/PreibischLab/RS-FISH/e9db74a/build.log

The trivial fix is in this branch: https://github.com/PreibischLab/RS-FISH/tree/remove-maven-release-flag and it looks like it works: https://jitpack.io/com/github/PreibischLab/RS-FISH/742f6a3/build.log

It looks like the everything works from there. If you merge that branch or undo the release flag in the pom, then I can point to the latest main branch. Otherwise, it is still using the same code anyway.

LauraBreimann commented 2 years ago

The updated version seems to work for the normal RS-FISH function and the newly added Mask filtering.

However @StephanPreibisch added some spot intensity refinement back in January (bc19ed231394bfe49cbbc9f33b1d36acb81e83b3) and if I select that it throws an exception.

java.lang.ArrayIndexOutOfBoundsException

LauraBreimann commented 2 years ago

Ok the new bugs should be fixed now! @kephale could you release a new version?

Thank you!