Fix CI fails

[bernt-matthias]

Try to fix tools failing in the first run of the CI workflow: https://github.com/galaxyproject/tools-devteam/actions/runs/120951902

Other changes to testing framework:

• adds --no_dependency_resolution to planemo test
• PR: make test only depend on setup
• setup.cfg
• remove outdated tools from .tt_skip

TODO:

• dwt_var1, cufflinks: [20.05] Move some tools that no longer need galaxy on the PATH galaxy#9850
• cummerbund:

+1: In png(filename = args$filename, width = args$width, height = args$height,  :
+  unable to load shared object '/usr/local/lib/R/library/grDevices/libs//cairo.so':
+  libXrender.so.1: cannot open shared object file: No such file or directory

• sam_pileup
• adapt https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/__init__.py#L176 and https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/__init__.py#L127 for affected tools

[bernt-matthias]

@nsoranzo note that I increased the allowed cyclomatic complexity (for lintr) to 25 which seems to the the documented default ..

still, 1 is failing: tools/dwt_var_perclass/execute_dwt_var_perClass.R:21:1 functions should have cyclomatic complexity of less than 25, this has 27.

any ideas .. I just don't want to touch the code more than necessary

[nsoranzo]

What about cyclocomp_linter = NULL ?

[bernt-matthias]

What about cyclocomp_linter = NULL ?

This is an option. But, actually I found it a useful indicator of bad code. Maybe its acceptable to simply ignore such errors if submitter has done everything to improve the code...

[nsoranzo]

I agree it's a useful indicator, but maybe it's a bit too invasive compared to space and indentation style changes. No strong opinion any way.

[bernt-matthias]

Ready from my side.

[nsoranzo]

Thanks @bernt-matthias , fantastic work!