Isolate config and argument parsing

[juliasloan25]

Purpose

closes #678

This PR isolates the argument and configuration file parsing to functions. Since we have one configuration file each for the coupled simulation and for the atmosphere, we end up with the following functions, as well as smaller helper functions. These are located in the new experiments/ClimaEarth/arg_parsing.jl file.

• get_coupler_config, get_coupler_args, get_atmos_args

These functions are called from the driver run_amip.jl, where the returned arguments are unpacked. After that point, the config files are not accessed further down in the driver, so we have isolated the config file access to the initial step.

Many files are changed in this PR because argument changes are propagated to many config files. The main files to look at for review are: run_amip.jl, arg_parsing.jl, cli_options.jl, and climaatmos.jl.

Note that this PR introduces some very minor behavioral changes in buildkite runs because the atmos config is no longer added to the coupler config. This will allow us to have better separation of and control over the two in the future.

To-do

• Add function to read in config file and job id
• Add function to parse input arguments (from config file)
  • Separate functions for coupler and atmos?
• Update atmos config function to not modify coupler (make these two independent)
• Unify argparse and get_args functions - want same parameters available from command line and from config files
• Allow t_start as an argument
• Unify dt_cpl to use same format as all other times
• Change restart_dir default to nothing
• Rename "diagnostics" -> "extra_atmos_diagnostics" for clarity
• Check CI outputs

Notes

• Separate PR: Remove atmos-related args from coupler configs, and move them into atmos configs
  • extra_atmos_diagnostics, EDMF-related arguments
  • This PR will become very large if we do this here, and I'd prefer to change that logic in an isolated PR

[juliasloan25]

Removed because 400secs is the default for dt and dt_cpl

[Sbozzolo]

This is a good step in the direction of isolating config/argument parsing. The next step would be to make sure that we don't use the parsed_args anywhere after the initial parsing. This would entail making everything types/symbols and ensuring that we are not matching strings after the initial parsing

[juliasloan25]

This is a good step in the direction of isolating config/argument parsing. The next step would be to make sure that we don't use the parsed_args anywhere after the initial parsing. This would entail making everything types/symbols and ensuring that we are not matching strings after the initial parsing

If we did this, wouldn't we still use the args we've read in after the initial parsing? We would just use them for dispatch instead of matching strings

[Sbozzolo]

This is a good step in the direction of isolating config/argument parsing. The next step would be to make sure that we don't use the parsed_args anywhere after the initial parsing. This would entail making everything types/symbols and ensuring that we are not matching strings after the initial parsing

If we did this, wouldn't we still use the args we've read in after the initial parsing? We would just use them for dispatch instead of matching strings

Yes, but this would allow users to run without any argument parsing at all, just setting up the correct types (and only the relevant types, as we might want to do in a CI context). It would also allow users to extend the behavior of functions with their custom types, whereas it is not possible to extend string-matching without changing the source code.