ci_find*: include sub and parent dirs

[bernt-matthias]

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fixes https://github.com/galaxyproject/planemo/issues/1129 and more:

include also tools/repos with:

• change of test data
• change of supplementary scripts (this already was the case for ci_find_repos)
• change of macros where the tools are in sub-directories (this failed for ci_find_repos if each tool has an individual shed file)
• change of a single tool in a collection where the shed file is in the parent

currently this will "fail" if the working dir of the planemo run is not the root of the repository: then changing for instance the README of the repository would lead to the inclusion of the all tools/repos in the repository. We could check if its the root by checking if there is a .git directory?

[mvdbeek]

currently this will "fail" if the working dir of the planemo run is not the root of the repository: then changing for instance the README of the repository would lead to the inclusion of the all tools/repos in the repository. We could check if its the root by checking if there is a .git directory?

To clarify, the problem here is if planemo's working dir is e.g tools-iuc/tools/minimap2, and not tools-iuc/ ? I think that's fine, planemo ci_find* is really meant for running within a CI system, and I think it's reasonable to expect that the working directory is the repository root.

On the other hand I don't think the presence of .git is a good proxy to check for this.

[bernt-matthias]

the problem here is if planemo's working dir is e.g tools-iuc/tools/minimap2, and not tools-iuc/ ?

This might also be a problem. But I thought more of the case when the working dir is the parent of tools-iuc/.

I think that's fine, planemo ci_find* is really meant for running within a CI system, and I think it's reasonable to expect that the working directory is the repository root.

Then everything should be fine.