trigger ci, deploy missing tools

[kostrykin]

trigger ci after #81 to deploy the tools which haven't been deployed from #76

xref #71

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FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the galaxy-image-analysis repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)
• - Tools added/updated by this PR (if any) comply with the Naming and Annotation Conventions for Tools in the Image Community in Galaxy (or please explain why they do not)

[bgruening]

What is different to IUC is that IUC is using the main branch and not the master branch. But I checked the CI and it respects both.

Maybe we can ask @bernt-matthias if he has any ideas why the deployment is skipped when linting is failing.

[kostrykin]

What is different to IUC is that IUC is using the main branch and not the master branch. But I checked the CI and it respects both.

Maybe we can ask @bernt-matthias if he has any ideas why the deployment is skipped when linting is failing.

Lets see whether it works now with the recent changes…

[kostrykin]

…nope. Deployment was skipped again: https://github.com/BMCV/galaxy-image-analysis/actions/runs/6811812716

Would be great if @bernt-matthias could have a look at this! Thanks…

[bernt-matthias]

CI is fine. Lint runs with --fail_level error on merge. This is decided here

Problem with the linked run is that there is really an error:

.. ERROR: Invalid XML found in file: tmpakqe62wn. Errors [/tmp/tmpakqe62wn:8:0:ERROR:SCHEMASV:SCHEMAV_CVC_ENUMERATION_VALID: Element 'xref', attribute 'type': [facet 'enumeration'] The value 'biii' is not an element of the set {'bio.tools', 'bioconductor'}.]

[kostrykin]

Yes, thanks @bernt-matthias, I think this is what I had just addressed in #83

[bernt-matthias]

Just to be sure: #83 will not help with the deployment since there is really an error in the tool that needs to be fixed.

[kostrykin]

How I understood @bgruening was that we want to deploy those tools regardless of the linting issue, until this is included in a release of Galaxy. Is skipping planemo lint during merge the way to go then?

[bernt-matthias]

Then you would need to skip linting completely during merge (which I would consider to be very dangerous .. since you need to check the linter output really careful in each and every PR).

The error because of the xref type biii (what is this btw?) will cause linting to fail in any case.

[bgruening]

@bernt-matthias we added this new type to the Galaxy 23.1 branch. its a bio.tools for imaging. http://biii.eu/
The problem is that we don't have new packages yet, so linting is failing - which is fine imho for a short period of time until we get new packages.