Gempyor CLI

[jcblemai]

With #105 , we can have a commandline interface based on click command, where e.g build this new command-line interface (CLI) for flepimop, where each object (seeding, initial_conditions, compartments, parameters, seir/outcomes-modifiers) is a submodule of the flepimop command and allow the user to plot, to import and export a csv/parquet, and so on. It should allow one to check a config very fast without having to spin-up a notebook and all the current state (also plan on adding flepimop resume download , ...)

gempyor compartment plot would plot the transitions graph between compartments (same for seeding, ic, ...) which would greatly help debuging.

[jcblemai]

Documentation on click command group: https://click.palletsprojects.com/en/8.1.x/commands/

flepimop -c config_SMH_Flu_2023_R1_medVax_H3_simple.yml compartments export export two csv files: one with all compartments, and one with every transitions, with it's rate and exponent. Moreovoer, if you have graphviz installed, you can get the transitions graph as flepimop -c config_SMH_Flu_2023_R1_medVax_H3_simple.yml compartments plot

TODO: documentation, help, think hard about namespace canibalization (compartements.compartments really ?) and context passing, for the config argument e.g.

Also improve these with filename arguments and filtering options

[fang19911030]

This one should also be a subclass of SimulationComponent?