Install system dependencies in the workflows

[Gotfrid]

Hi, in aNCA project we need to take a dependency on the units package - which requires a corresponding system dependency (libudunits2-dev).

This project uses admiralci workflows, however most of these workflows have run-system-dependencies: false, which makes it impossible for us to run even spellcheck.

I'm opening this issue seeking for advice on how to best solve this problem. We can either inline all the workflows that we currently use and toggle system dependency installation, or we can change admiralci workflows.

The former might be a short-term remedy, but is very undesirable as we would instantly fall behind if any updates are to happen here.

Would it make sense to add something like install-system-dependencies to the workflow inputs with a default false value, so that it doesn't affect existing projects? Ofc I'd be willing to open a PR for that.

cc @m-kolomanski

[cicdguy]

Looks like you copied the core workflow verbatim in pharmaverse/aNCA#151 and modified it there. No action needed here.

[Gotfrid]

Indeed, we copied the workflow as a temporary suboptimal solution.

To solve this problem properly, my suggestion is to parametrize run-system-dependencies and make it an input in every workflow that uses insightsengineering/staged-dependencies-action. This way, you can keep it false by default to ensure backwards compatibility with the projects that already use this repository to run actions, but also give some flexibility to some projects that need it.

In my opinion, unit conversion is not an uncommon thing in biological, chemical, pharmaceutical projects, which often requires a dependency on a system library libudunits2-dev. Currently, a fellow pharmaverse project aNCA needs it, hence this issue.