Update CLI arguments

There are two modes:

• check a pair of bio files with the --annot and --predict arguments,
• check several pairs of bio files with the --csv and --folder arguments.

There is a mutually exclusive group between the --annot and --csv arguments but we can still mix other parameters (and use this command for example nerval -c demo/mapping_file.csv -f demo -p demo/toy_test_predict.bio).

Can we use a mutually exclusive group between groups (and not just between parameters)? Or perhaps we can revise this command by always using a folder?

changed milestone to %0.4.0

Can we use a mutually exclusive group between groups (and not just between parameters)?

No, this is something that used to be possible but was removed in 3.11. You could however do all these checks in a dedicated function, ran after argument parsing.

Or perhaps we can revise this command by always using a folder?

We should folder inputs. Make it so that --annot and --predict may be folders (if one of them is, both should be). If there are, there should be one prediction file per label.