Make IUC workflows reusable

[bernt-matthias]

This PR adds:

1. Reusable Workflows which can be used in all IUC style repos
   • The hope/aim is that users of these workflows will need to update/sync their workflows less often. In particular the galaxy-branch will be updated automatically per default once its updated at IUC. Still users can fix the branch if they like. Also parameters for linting and testing are by default as they are at IUC, but can be overwritten.
   • Bugs in Galaxy (tool-util,...) and planemo will impact more repos by default (if repos do not fix the for and branch). I would argue that this is good because it might help to detect bugs early.
   • TODO it would be handy if we could do the switch from master to main, since called worflows apparently can't refer to the default branch. otherwise we would need to change the calling workflows again.
2. Adds report-level and fail-level
   • supersedes add report/error level for linting galaxy-tool-repository-template#8
3. Add planemo-version parameter to slash command which should allow to test planemo releases
   • usage, e.g. planemo-version="planemo==0.74"
4. Update all called actions
   • checkout v2 -> v3
   • cache v2 -> v3
   • upload-artifact v2 -> v3
   • download-artifact v2 -> v3
   • setup-python v1 -> v4
   • peter-evans/create-or-update-comment v1 -> v2
   • peter-evans/slash-command-dispatch v2 -> v3
5. Make used flake8 plugins configurable fixes Make flake8 plugins configurable #4988
6. Execute slash command only if PAT is defined (only relevant for template repo .. once synced .. there the problem is that the slash workflow always fails until PAT is defined .. which is a bit annoying since it runs on every comment)

The PR can also be seen in action here: galaxyproject/galaxy-tool-repository-template#11

TODOs:

• test to use from devteam / template repo (Reuse IUC worklows galaxy-tool-repository-template#11)
• decide if the called workflows should live at the IUC repo / template repo

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc 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)

[nsoranzo]

@bernt-matthias Can you take a look at the conflicts please?

[bernt-matthias]

Will do. Seems that two PR were merged during my vacation:

• remove deprecated set-output syntax and update create-or-update-comment #4892 the set-output things need to be incorporated here .. one moment
• Update version of GitHub actions used #4850 I think I also updated all versions here .. I will recheck

[bernt-matthias]

Reminder:

• remove test bumps of tools before merging

Note that the WF does not run because of error parsing called workflow "galaxyproject/tools-iuc/.github/workflows/wf_lint.yaml@master": failed to fetch workflow: workflow was not found. .. If you like I could change it temporarily to the branch in my for to see it in action?

[bernt-matthias]

Integrate peterjc/galaxy_blast#151

[mvdbeek]

Awesome, let's do this!

[bernt-matthias]

As discussed on gitter I will try to add the called workflows to the planemo-ci-action repo. Putting this to draft until it is done.