refactor: use Python 3, has latest pip for cobra

[mihai-sysbio]

Main improvements in this PR:

This PR migrates Python to version 3, which removes the need to upgrade pip before installing cobra. It also addresses the FutureWarning message which cobrapy outputs.

[mihai-sysbio]

Great improvement @Hao-Chalmers 👍 for the action to pass it needs the model file in the new location, ie #188 should be merged first.

[JonathanRob]

Agreed, nice addition, @Hao-Chalmers.

A small question - should this new basicCheck.py script be placed in the .github/workflows/ directory?

[haowang-bioinfo]

@JonathanRob not sure about the location. @mihai-sysbio what do you think?

Some thoughts about basicCheck: now it has checks for cobrapy import and consistency with annotation files. More tests may be added later either by curator or user, to whom the code/test folder probably is better to work with?

[mihai-sysbio]

Imho tests should be designed to run on their own, and just called in the workflow, so that users can have the freedom of testing whenever they prefer; I'd leave tests in code/test.

[JonathanRob]

Ok, sounds good @mihai-sysbio @Hao-Chalmers! No need to move things around then.