Merge #536 #1079

536: apply JuliaFormatter.jl r=simonbyrne a=simonbyrne

This applies [JuliaFormatter.jl](https://github.com/domluna/JuliaFormatter.jl) to the whole repository.

Any thoughts/comments?

- [x] Testing?

1079: Fix some broken docs r=charleskawczynski a=charleskawczynski

# Description

Fixes several broken docs:

 - Microphysics: had missing variables / function arguments
 - RTB/Turbulence/Tracers: switched `@example` to `julia` blocks, since they are split across scope blocks (which breaks), or does not include sufficient code for an example.

 - Fixes the
```
connect: Connection refused
GKS: can't connect to GKS socket application

GKS: Open failed in routine OPEN_WS
GKS: GKS not in proper state. GKS must be either in the state WSOP or WSAC in routine ACTIVATE_WS
```
error by [installing](https://gr-framework.org/julia.html#installation) required libraries as suggested [here](jheinen/GR.jl#278 (comment)) and [here](jheinen/GR.jl#278 (comment))



Co-authored-by: Simon Byrne <simonbyrne@gmail.com>
Co-authored-by: Charles Kawczynski <kawczynski.charles@gmail.com>

.github/pull_request_template.md

@@ -7,7 +7,7 @@ A clear and concise description of the code with usage.
 I have
 
 - [ ] Written and run all necessary tests with CLIMA by including `tests/runtests.jl`
-- [ ] Followed all necessary [style guidelines](https://CliMA.github.io/CLIMA/latest/CodingConventions.html) and run `julia .dev/format.jl`
+- [ ] Followed all necessary [style guidelines](https://CliMA.github.io/CLIMA/latest/CodingConventions.html) and run `julia .dev/climaformat.jl .`
 - [ ] Updated the documentation to reflect changes from this PR.
 
 <!--- Please leave the following section --->

.github/workflows/Documenter.yaml

@@ -22,7 +22,9 @@ jobs:
           sudo apt-get update
           sudo apt-get install mpich libmpich-dev
       - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.instantiate()'
+        run: |
+          sudo apt install libxt6 libxrender1 libxext6 libgl1-mesa-glx libqt5widgets5
+          julia --project=docs/ -e 'using Pkg; Pkg.instantiate()'
       - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/JuliaFormatter.yml

@@ -15,7 +15,7 @@ jobs:
         version: 1.3
     - name: Apply JuliaFormatter
       run: |
-        julia --project=.dev .dev/format.jl origin/master
+        julia --project=.dev .dev/climaformat.jl .
     - name: Check formatting diff
       run: |
         git diff --color=always --exit-code

docs/make.jl

@@ -1,6 +1,7 @@
 Base.HOME_PROJECT[] = abspath(Base.HOME_PROJECT[]) # JuliaLang/julia/pull/28625
 
 using ClimateMachine, Documenter, Literate
+ENV["GKSwstype"] = "100" # https://github.com/jheinen/GR.jl/issues/278#issuecomment-587090846
 
 generated_dir = joinpath(@__DIR__, "src", "generated") # generated files directory
 mkpath(generated_dir)

docs/src/HowToGuides/Atmos/Microphysics.md

@@ -98,8 +98,9 @@ The default value of ``C_{drag}`` is chosen such that the ``v_t`` is close to th
 using ClimateMachine.Microphysics
 using Plots
 using CLIMAParameters
-abstract type EarthParameterSet <: AbstractParameterSet end
-param_set = EarthParameterSet()
+using CLIMAParameters.Atmos.Microphysics
+struct EarthParameterSet <: AbstractEarthParameterSet end
+const param_set = EarthParameterSet()
 
 # eq. 5d in Smolarkiewicz and Grabowski 1996
 # https://doi.org/10.1175/1520-0493(1996)124<0487:TTLSLM>2.0.CO;2
@@ -172,7 +173,7 @@ using ClimateMachine.Microphysics
 using Plots
 using CLIMAParameters
 struct EarthParameterSet <: AbstractEarthParameterSet end
-param_set = EarthParameterSet()
+const param_set = EarthParameterSet()
 
 # eq. 5b in Smolarkiewicz and Grabowski 1996
 # https://doi.org/10.1175/1520-0493(1996)124<0487:TTLSLM>2.0.CO;2
@@ -271,7 +272,7 @@ using ClimateMachine.Microphysics
 using ClimateMachine.MoistThermodynamics
 
 using CLIMAParameters
-using CLIMAParameters.Planet: R_d, planet_radius, grav, MSLP
+using CLIMAParameters.Planet: R_d, planet_radius, grav, MSLP, molmass_ratio
 struct EarthParameterSet <: AbstractEarthParameterSet end
 const param_set = EarthParameterSet()
 
@@ -310,7 +311,7 @@ q = PhasePartition(q_tot, q_liq, q_ice)
 R = gas_constant_air(param_set, q)
 ρ = p / R / T
 
-plot(q_rain_range * 1e3,  [conv_q_rai_to_q_vap(q_rai, q, T, p, ρ) for q_rai in q_rain_range], xlabel="q_rain [g/kg]", ylabel="rain evaporation rate [1/s]", title="Rain evaporation", label="ClimateMachine")
+plot(q_rain_range * 1e3,  [conv_q_rai_to_q_vap(param_set, q_rai, q, T, p, ρ) for q_rai in q_rain_range], xlabel="q_rain [g/kg]", ylabel="rain evaporation rate [1/s]", title="Rain evaporation", label="ClimateMachine")
 plot!(q_rain_range * 1e3, [rain_evap_empirical(q_rai, q, T, p, ρ) for q_rai in q_rain_range], label="empirical")
 savefig("rain_evaporation_rate.svg") # hide
 nothing # hide