Planemo test is ignoring --failed

[bernt-matthias]

planemo, version 0.75.2

I guess this came with #1232

Also it seems that GalaxyTestCommand is not used anymore

[wm75]

yeah, #1352 is another case where an option became non-functional with that refactoring.
@simonbray rescued --update_test_data via https://github.com/galaxyproject/planemo/pull/1232/files#r885840184, but --failed and --job_output_files that also got handled through run_in_config were less lucky :(

[wm75]

Since an aspect of --skip-venv handling was also part of run_in_config, I am now wondering whether the broken behavior of that option that I mentioned in #1343 (comment) is also related.

[mvdbeek]

To start, i have added --update_test_data back in, for the sake of making progress with important work. Otherwise we'd still be stuck with 22.01. It was a deliberate choice to not keep this, and I'd rather we delete it for all the problem it has that i don't think are solvable, but y'all made the case that you want it, so that's ok. --skip-venv is such a niche flag that only bloats the options and makes reasoning about what people are doing with planemo more complicated, i hope we can just remove this (and maybe add this back when it really makes sense, that is when we have fully packaged galaxy).

The other flags are reasonable, and we can add them back, but this time with tests.

Note that none of this would work with the other engine types.

[wm75]

Cool! My own ordering by importance of these options is very similar:
--update_test_data == --failed > --job_output_files > --skip-venv
for the last, I don't have any actual use and would not mind if it was removed permanently.
For --job_output_files, there are workarounds like --update_test_data and git restoring what you want to keep unaltered, or --no_cleanup and taking files out of the job's work dir directly, but the option simplifies things.