Miscoto

Add

* Error message if SBML files have no reactions.

Add

* Merge all commands into one command with subcommands: e.g. `miscoto_scopes` becomes `miscoto scopes`
* Version can now be retrieved with `miscoto --version`
* Output messages are clearer than before

Update

* Documentation
* Help of subcommands

Fix

* Typos

New Features

* In `mincom -o soup` return in the json output a new predicate that contains all producible targets in a minimal community. This new predicate is stored as "producible" in the json output. This featyre is useful in 2 cases:
* In case there are compounds in targets that are also nutrients (seeds): they would not have appeared in `newly_producible`
* In case a host is provided: the target compounds that the host can produce by itself would not have been stored in the json

Fix

* Issue with the display of target producers in selected communities

CI & Tests

* Add a new test and its associated target file in `toy` related to returning all producible targets

Add

- final producers for the targets. Miscoto will search for the organisms able to activate the reaction producing each of the targets. This is computed in the full community with `miscoto_scopes` and in the selected minimal communities with `miscoto_mincom`. The information is stored in the `targets_producers` key in the json output.

CI

- test for the new final producer feature.

Modify mincom json ouput

- rename `optimum_inter` into `score_optimum_inter`

- rename `optimum_union` into `score_optimum_union`

- add result of --optsol in json with the `one_model` key.

- add `keystone_species`, `essential_symbionts` and `alternative_symbionts` in json if --union and --intersection are used together.

Fix
* minexch behaviour (missing solution) when running without host

CI
* add new tests for the above cases