fix: bugs preventing the pipeline to run

[mihai-sysbio]

Starting off with a simple rename, the work in this PR started by making sure the pipeline runs as intended. In the end this PR aims to do a few more things:

• handle the renaming of the branch master to main. In this process, the branch develop has been discarded and is not intended to be used.
• fix a minor bug regarding the Gurobi path
• fix the renaming of a compartment abbreviation that is used in a script preprocessing the Human-GEM
• handle the case that for Kluyveromyces_marxianus-GEM the default branch on GitHub is still master
• fix a bug that prevented the pipeline to run on non-default GECKO branches

Due to a known bug in the command-line tool hub, it is expected for the pipeline to run but to not produce the expected PRs. This issue, reported as #93, will be resolved in an independent PR.

[mihai-sysbio]

Even though it was mentioned above that this PR would not address the hub fix, I have attempted a fix by switching from the unofficial hub to the official gh CLI, with the hopes that would allow the Action to complete. If it still does not, I will remove that commit and un-draft the current PR.

[mihai-sysbio]

The fix introduced in 1b1867c worked. Now that the pipeline is fully functional, this PR should be merged in with priority.

[mihai-sysbio]

Forgot to mention above, this PR resolves #93 .