Check for missing containers failing, no planemo shed_lint -s option

[peterjc]

I'm tracing a CI failure on https://github.com/peterjc/galaxy_blast/ after recently updating to the tools-iuc GitHub Actions, under "Check for missing containers (3.7)". It turns out the IUC repo is also failing here (cross reference #5499):

planemo shed_lint --tools --ensure_metadata --urls --report_level all --fail_level error --recursive tools/blast_rbh --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd
Usage: planemo shed_lint [OPTIONS] PROJECT
Try 'planemo shed_lint --help' for help.

Error: No such option: -s

That is coming from here the ci.yaml block added in pull request #5242:

    - name: Planemo lint
      uses: galaxyproject/planemo-ci-action@v1
      id: lint
      with:
        mode: lint
        repository-list: ${{ needs.setup.outputs.repository-list }}
        tool-list: ${{ needs.setup.outputs.tool-list }}
        additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd

My local copy of planemo 0.75.12 does indeed lack a documented -s switch, and I don't see any evidence of this existing in the source code here:

https://github.com/galaxyproject/planemo/blob/master/planemo/commands/cmd_shed_lint.py

Was this a typo for -r (recursive)?

[bernt-matthias]

shed_lint misses the -s/--skip option. I hope that galaxyproject/planemo#1394 fixes this

[peterjc]

Should be fixed as of planemo 0.75.13 - thanks!