Add linter exceptions for 24.2

[nilchia]

The skip lint is added based on the code provided in #6795

planemo ci_find_repos . > repos.txt
while read line
do
    echo $line;
    touch $line/.lint_skip;
    planemo l $line --skip_file $line/.lint_skip > t;
    egrep "WARN|ERROR" t | cut -d'(' -f2 | cut -d')' -f1 | sort -u >> $line/.lint_skip;
done < repos.txt

[bgruening]

@nilchia this was good? Are you still working on it?

[bgruening]

also ping @bernt-matthias

[bernt-matthias]

Looks quite good. I guess a find . -name .lint_skip -size 0 -delete should delete the empty files. Or in git find . -name .lint_skip -size 0 -exec git rm {} \;.

[nilchia]

@bernt-matthias, does this PR conflict with this? #1561

I closed it as I thought they might conflict.

[bernt-matthias]

@bernt-matthias, does this PR conflict with this? #1561

I closed it as I thought they might conflict.

Yours should be more up-to-date. We can close #1561.

Just remove the empty files and it should be good to go.

[nilchia]

I've removed the empty files.
It seems there are other linting problems as well.

[bernt-matthias]

It seems there are other linting problems as well.

All of them should be problems with URLs

The R linter problems could be fixed automatically with https://github.com/bgruening/galaxytools/blob/master/.github/styler.R .. but I would do this in a separate PR

[bernt-matthias]

No, this is not the problem. I guess your planemo is not up do date. You need to make sure that galaxy-tool-util 24.2 is used.

[bgruening]

is this needed?

[nilchia]

I don't think. It was a byproduct of the function.
I've removed it.

[bernt-matthias]

Should have been removed automatically by egrep "WARN|ERROR" .. maybe double check everything?

[nilchia]

I tried the code again, it didn't remove it. 🤔
I'm not sure if egrep "WARN|ERROR" t | cut -d'(' -f2 | cut -d')' -f1 | sort -u >> $line/.lint_skip; removes the file.

[bernt-matthias]

If you want you can compare with https://github.com/bernt-matthias/galaxytools/tree/lint-skip .. or just take my branch

[bgruening]

can this be removed