planemo
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galaxyproject
Run local galaxy via gravity
This drops the run_tests.sh mode completely and leads to a lot of simplification of the code.
@mvdbeek The unit test failures are legit, I think you mention you already have fixes for them?
Q: with this, we are dropping support for serving/testing on Galaxy pre 22.01, right?
In that case, we should replace unit-nonredundant-noclientbuild-noshed-gx-2105 and unit-nonredundant-noclientbuild-noshed-gx-2109 tox envs with unit-nonredundant-noclientbuild-noshed-gx-2201 in .github/workflows/ci.yaml (and similarly in tox.ini).
Q: with this, we are dropping support for serving/testing on Galaxy pre 22.01, right?
No, I will re-introduce the necessary parts. That shouldn't be a big deal, that was just for me to get started.
It is used in _run for Galaxy Engines via https://github.com/galaxyproject/planemo/blob/36eb798ef41528571717b646c380ba2798cba948/planemo/engine/galaxy.py#L49. If we pass the kwds explicitly we'd have to make a copy of the dict so we're not passing the argument twice ... my first version did pass the timeout argument to _run but that didn't look much better to me.
I remember now that one of the concerns I had at the time is that I'm not sure we're always correctly shutting down all processes managed by gravity ... unit tests seemed to leave me with lingering processes IIRC.
Thanks for pushing us forward @mvdbeek - these are really really important changes and simplify things very nicely.
