remove Diagnostics module

[juliasloan25]

Purpose

Remove Diagnostics module in favor of ClimaDiagnostics and ClimaAnalysis

closes #

will supersede https://github.com/CliMA/ClimaCoupler.jl/issues/875 and https://github.com/CliMA/ClimaCoupler.jl/issues/517

note: debug_plots.jl still using plot_helper.jl but this is the only place - just move plot_helper functions into debug_plots ?

Current status

• atmos_extra_diags: when these are included in the output, default atmos diagnostics aren't
  • is this the intended behavior? to me "extra" implies we want to keep the defaults and add these as well.
  • if it is, how can I include default + extra diags? --> output_default_diagnostics = true
  • to do: check that toa_fluxes_net also output from extra_diags run
• amip_diagnostics: F_turb_energy not in any artifacts folders for any runs
  • does this need to be enabled somehow?
• plots also not in artifacts folders
  • but also no error - shouldn't this error if F_turb_energy file doesn't exist?

To-do

• [x] generalize make_ci_plots to work for AMIP plots as well; update amip_paperplots function to use this
• [x] recreate AMIP paperplots using existing ClimaAtmos diagnostics defined in https://github.com/CliMA/ClimaAtmos.jl/blob/main/src/diagnostics/core_diagnostics.jl
  • coupler symbol -> atmos symbol:
  • ":T" -> "ta"
  • ":u" -> "ua"
  • ":q_tot" -> "hus"
  • ":q_liq_ice" -> "clw"
  • ":precipitation_rate" -> "pr"
  • ":T_sfc" -> "ts"
• [x] remove output_short_name, output_long_name
• [x] for the few quantities that aren't already computed in ClimaAtmos diagnostics, add new variables in climaatmos_extra_diags.jl
  • ":toa_fluxes": sum fluxes that can be accessed from atmos cache
  • ":turbulent_energy_fluxes": access calculated value from CoupledSimulation (requires extending ClimaDiagnostics functions)
• [x] remove amip_visualizer.jl
• [x] remove diagnostics from CoupledSimulation object
• [x] remove use_coupler_diagnostics flag
• [x] remove Diagnostics module and tests

Output checks

• [x] check slabplanet_atmos_diags now outputs toa_fluxes_net, previous coupler-added atmos diagnostics, and default diagnostics from atmos
• [x] check all amip runs output F_turb_energy
• [ ] check plots are created for amip runs
  • atmos and coupled diagnostics

---

• [ ] I have read and checked the items on the review checklist.