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trackmate-sc / TrackMate-CTCRunner

Batch measurements of the Cell-Tracking-Challenge metrics using TrackMate.
GNU Affero General Public License v3.0
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Deploy to maven.scijava.org #5

Closed imagejan closed 1 year ago

imagejan commented 2 years ago

The page https://imagej.net/plugins/trackmate/extensions/trackmate-helper is currently pointing to the wrong source code on GitHub, because the artifact is set as sc.fiji:TrackMate where it should be sc.fiji:TrackMate-CTCRunner. But the maven artifact of this repository here is not deployed.

I suggest:

That would have made it much easier for me to find the source code when troubleshooting for users of our core facility 🙂.

tinevez commented 2 years ago

We should do this for all TrackMate-* stuff I maintain.

imagejan commented 2 years ago

@tinevez do you want to move all to the fiji org? Or do you prefer an own organization such as trackmate? In any case, I'll be happy to run the github-actionify.sh and submit pull requests for all repos, once they are in their final location.

tinevez commented 2 years ago

Hello @imagejan We started a discussion on zulip on this very topic: https://imagesc.zulipchat.com/#narrow/stream/327238-Fiji/topic/Move.20tinevez.20TrackMate.20extensions.20to.20Fiji.3F

As you can see it reached a bit beyond but we have a plan that will implement your suggestions.

ctrueden commented 2 years ago

An update on this issue: since the above discussion, we migrated TrackMate and its extensions to a dedicated trackmate-sc org. I thought the components were all set up with GitHub Actions, but taking a look again now, I saw that the configuration were outdated and/or wrong, so I have now fixed them all to have a single identical /.github/workflows/build.yml according to current best practices.

Some of the components have already deployed snapshots to maven.scijava.org automatically, but others have dependency issues. This component (TrackMate-CTCRunner) in particular depends on most of the others, so it has not yet deployed successfully due to these issues:

The following artifacts could not be resolved: sc.fiji:TrackMate-StarDist:jar:1.1.2, sc.fiji:TrackMate-MorphoLibJ:jar:1.1.0, sc.fiji:TrackMate-Cellpose:jar:0.0.5, sc.fiji:TrackMate-Ilastik:jar:1.1.0, sc.fiji:TrackMate-Weka:jar:1.1.0, net.celltrackingchallenge:CTC-measures:jar:0.9.0

And digging down into those builds:

TrackMate-StarDist

Missing dependency:

Could not resolve dependencies for project sc.fiji:TrackMate-StarDist:jar:1.1.3: Could not find artifact de.csbdresden:StarDist_:jar:0.3.0

Solution: get de.csbdresden:StarDist_ deployed to maven.scijava.org. See trackmate-sc/TrackMate-StarDist#5.

TrackMate-MorphLibJ

Build was passing, but no release had been done with the current infrastructure. Released version 1.1.2.

TrackMate-Cellpose

Build was passing, but no release had been done with the current infrastructure. Released TrackMate-Cellpose 0.0.7.

TrackMate-Ilastik

Was using unreleased TrackMate features. Released TrackMate 7.9.0. Then released TrackMate-Ilastik 1.2.2.

TrackMate-Weka

Build was passing, but no release had been done with the current infrastructure. Released TrackMate-Weka 1.1.1.

Remaining issues

The following components need a release deployed to maven.scijava.org before TrackMate-CTCRunner can be released and deployed:

Other TrackMate component releases

Even though they are not dependencies of TrackMate-CTCRunner, I also made initial releases of the other TrackMate extensions:

Component management in the BOM

All components released thus far have been added to pom-scijava version management (scijava/pom-scijava@9ec5bc2380334e1d9ce9bb479b0141e2fecd8363). We can add the rest once the above issues have been resolved and the remaining components have been released.

tinevez commented 1 year ago

Update:

This still fails because the build fails on the CI for every changes we make. The reason for the CI build to fail is that it cannot find the CTC measures artifact on the maven repo. I will write to Vlado about this.

ctrueden commented 1 year ago

@tinevez In the meantime, if you are impatient, we could hack the CI in this repository to also build and deploy the CTC measures artifact first. :smiling_imp:

ctrueden commented 1 year ago

On second thought... I just checked out the existing release tags/branches from the measures repo, and deployed them to maven.scijava.org myself. So @tinevez we can now depend on 0.9.6, 0.9.7, 1.0.0, or 1.0.1. I have now updated this repository to depend on 1.0.1. The build passes locally for me; we'll see how CI does!

ctrueden commented 1 year ago

Build passed, and TrackMate-CTCRunner artifact is now deployed. :smile:

xulman commented 1 year ago

sorry @ctrueden and @tinevez for the CTC measures mess (and for my silence recently)

I will work with Curtis to publish (the current and future versions of) the measures to scijava.maven