Chore: customize github workflows to correctly install system dependencies

[m-kolomanski]

Issue

Closes #149

Also resolves issues with checks in PR #146

Description

Reworks and customizes github workflows. Instead of relying on reusable workflows provided by admiralci, each of the needed workflows is inlined in the main workflow. This means that the jobs can be customizable in terms of correct installing of system deps, as well as efficiency. The drawback being that the workflows will need periodical, manual maintenance when updates are available.

How to test

Currently the PR also changes the DESCRIPTION, adding the units package, which has problematic system dependencies. With the changes, all checks pass. Before merging, changes to the DESCRIPTION file should be removed.

[Gotfrid]

Thank you for making this change, and confirming that it works!

Considering that #146 is still in review, let's wait - maybe we get some meaningful suggestions in pharmaverse/admiralci.

If #146 is ready before we get an answer, then let's proceed as we discussed - copy over the workflow files, modify them to install dependencies, and reference them from the main workflow.

[m-kolomanski]

@Gotfrid FYI, I have implemented the discussed workflow structure (copied files over, added minimal modifications, referenced in main file) and verified that everything works correctly with units package, the dependencies are being installed.

[Gotfrid]

LGTM, thanks!

[m-kolomanski]

So just for the record, we are now waiting for a response from admiralci to see if there is a better way of achieving that result.

Currently, this PR is blocking #146, as the checks are failing, but it is still in review. If #146 passes the review and we do not get the response, I will merge this PR to unblock #146 .

[m-kolomanski]

It does not look like we are going to get any meaningful answer. I am merging the PR. If any better solution arises, we can go back to this issue.