Add plots to CLI

[stefsmeets]

This PR refactors the plots and exposes them through the CLI. The plots can also be invoked directly.

Example:

$ proteus plot interior global --config init_coupler.toml
Plotting: global
Plotting: interior

which is the equivalent of:

python src/plot/cpl_interior.py init_coupler.toml

List all plots:

$ proteus plot --list
atmosphere atmosphere_cbar elements escape fluxes_atmosphere
fluxes_global global heatingrates interior interior_cbar
interior_cmesh observables offchem_grid_cross offchem_species
offchem_time offchem_year sflux sflux_cross stacked

Closes #143

Todo

• [x] Check if it is possible to add some tests
• [x] Test on real data

Tested:

• atmosphere
• elements
• escape
• fluxes_atmosphere
• fluxes_global
• global
• interior
• interior_cbar
• interior_cmesh
• observables
• sflux
• sflux_cross
• stacked

Not tested (data not available, needs vulcan run):

• atmosphere_cbar
• offchem_species
• offchem_time
• offchem_year

Not available through CLI yet:

• heatingrates
• offchem_grid_cross

[stefsmeets]

For testing the plots, in the absence of a full dataset, I would like to follow-up with a sample output dataset to work with, e.g. from proteus start --config inputs/default.toml. The data can be hosted in a separate repo, and we can use the matplotlib.testing module to help regression test the outputs.

[stefsmeets]

Hi @lsoucasse @nichollsh , this PR is ready. could you have a look at this PR and let me know what you think?

I changed all the plotting codes so that they have a consistent entry point (plot_xxx_entry), so that they take a Proteus object. There are no functional changes. All functions can still be invoked directly.

Other than that, most of the changes are of this kind:

• Remove dead code, separators
• Add types to plot functions
• Move the code from if __name__ == '__main__' block to entry.