CliMA · bors · Jul 19, 2021 · Jul 19, 2021
diff --git a/.gitignore b/.gitignore
@@ -10,6 +10,8 @@
 !docs/src/assets/*.png
 *.nc
 *.png
+*.json
+*.in
 
 # System-specific files and directories generated by the BinaryProvider and BinDeps packages
 # They contain absolute paths specific to the host computer, and so should not be committed

diff --git a/Project.toml b/Project.toml
@@ -4,10 +4,12 @@ authors = ["Charles Kawczynski <[email protected]>"]
 version = "0.1.0"
 
 [deps]
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 ArtifactWrappers = "a14bc488-3040-4b00-9dc1-f6467924858a"
 Dierckx = "39dd38d3-220a-591b-8e3c-4c3a8c710a94"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LambertW = "984bce1d-4616-540c-a9ee-88d1112d94c9"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ An extended eddy-diffusivity mass-flux scheme for unified representation of
 subgrid-scale turbulence and convection. Journal of Advances in Modeling Earth Systems, 2018.
 (see [Tan et al., 2018](https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017MS001162)).
 
-The code is written in Julia, and was translated from [SCAMPy](https://github.com/CliMA/SCAMPy) on 7/13/2021.
+The code is written in Julia, and was translated from [SCAMPy](https://github.com/CliMA/SCAMPy) for the commit 496dad0c2438235684823511cacbf5761d6a237c.
 
 Code Contributors:
 	Colleen Kaul (PNNL) --initial/primary developer,
@@ -50,7 +50,7 @@ pkg> instantiate
 $ cd TurbulenceConvection.jl
 ```
 
-Note that, we will soon support running TurbulenceConvection.jl in the same way that SCAMPy used to. For now, run one of the cases:
+TurbulenceConvection.jl can be run in the same way that SCAMPy used to, given one of the following cases:
 
  - Bomex
  - life_cycle_Tan2018
@@ -63,10 +63,13 @@ Note that, we will soon support running TurbulenceConvection.jl in the same way
  - GABLS
  - SP
 
-with
+with, for example:
 
 ```
-julia --project integration_tests/Soares.jl
+julia --project integration_tests/utils/generate_namelist.jl Soares
+julia --project integration_tests/utils/generate_paramlist.jl Soares
+julia --project integration_tests/utils/main.jl Soares
+
 ```
 or, interactively, with
 ```julia-repl

diff --git a/integration_tests/ARM_SGP.jl b/integration_tests/ARM_SGP.jl
@@ -5,16 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
 include(joinpath("utils", "compute_mse.jl"))
-using .Cases
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 best_mse = OrderedDict()
 best_mse["qt_mean"] = 6.7939652328911526e+00
 best_mse["updraft_area"] = 2.6728907094911216e+02

diff --git a/integration_tests/Bomex.jl b/integration_tests/Bomex.jl
@@ -5,16 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
 include(joinpath("utils", "compute_mse.jl"))
-using .Cases
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 best_mse = OrderedDict()
 best_mse["qt_mean"] = 8.3714605287379840e-02
 best_mse["updraft_area"] = 7.0261471608838769e+02

diff --git a/integration_tests/DYCOMS_RF01.jl b/integration_tests/DYCOMS_RF01.jl
@@ -5,16 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
 include(joinpath("utils", "compute_mse.jl"))
-using .Cases
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 best_mse = OrderedDict()
 best_mse["qt_mean"] = 3.8001673126194867e-02
 best_mse["ql_mean"] = 8.4578478184878048e+00

diff --git a/integration_tests/DryBubble.jl b/integration_tests/DryBubble.jl
@@ -5,15 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
-using .Cases
+include(joinpath("utils", "compute_mse.jl"))
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 @testset "DryBubble" begin
     println("Running DryBubble...")
     namelist = NameList.DryBubble(default_namelist("DryBubble"))

diff --git a/integration_tests/GABLS.jl b/integration_tests/GABLS.jl
@@ -5,16 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
 include(joinpath("utils", "compute_mse.jl"))
-using .Cases
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 best_mse = OrderedDict()
 
 best_mse["updraft_thetal"] = 5.0418613105717345e+00

diff --git a/integration_tests/GATE_III.jl b/integration_tests/GATE_III.jl
@@ -5,15 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
-using .Cases
+include(joinpath("utils", "compute_mse.jl"))
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 @testset "GATE_III" begin
     println("Running GATE_III...")
     namelist = NameList.GATE_III(default_namelist("GATE_III"))

diff --git a/integration_tests/Nieuwstadt.jl b/integration_tests/Nieuwstadt.jl
@@ -5,16 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
 include(joinpath("utils", "compute_mse.jl"))
-using .Cases
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 best_mse = OrderedDict()
 best_mse["qt_mean"] = 1.1424341230332884e-01
 best_mse["updraft_area"] = 1.1765062251021085e+02

diff --git a/integration_tests/Rico.jl b/integration_tests/Rico.jl
@@ -5,16 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
 include(joinpath("utils", "compute_mse.jl"))
-using .Cases
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 best_mse = OrderedDict()
 best_mse["qt_mean"] = 4.0432375728696790e-01
 best_mse["updraft_area"] = 1.8875614747005029e+03

diff --git a/integration_tests/SP.jl b/integration_tests/SP.jl
@@ -5,15 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
-using .Cases
+include(joinpath("utils", "compute_mse.jl"))
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 @testset "SP" begin
     println("Running SP...")
     namelist = NameList.SP(default_namelist("SP"))

diff --git a/integration_tests/Soares.jl b/integration_tests/Soares.jl
@@ -5,16 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
 include(joinpath("utils", "compute_mse.jl"))
-using .Cases
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 best_mse = OrderedDict()
 best_mse["qt_mean"] = 2.5654529603089010e-01
 best_mse["updraft_area"] = 7.7772077592145229e+02

diff --git a/integration_tests/TRMM_LBA.jl b/integration_tests/TRMM_LBA.jl
@@ -5,16 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
 include(joinpath("utils", "compute_mse.jl"))
-using .Cases
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 best_mse = OrderedDict()
 best_mse["qt_mean"] = 3.0653862333906230e+00
 best_mse["updraft_area"] = 2.7495023710812657e+04

diff --git a/integration_tests/life_cycle_Tan2018.jl b/integration_tests/life_cycle_Tan2018.jl
@@ -5,15 +5,13 @@ import TurbulenceConvection
 using TurbulenceConvection
 using Test
 
-include(joinpath("utils", "Cases.jl"))
+include(joinpath("utils", "main.jl"))
 include(joinpath("utils", "generate_paramlist.jl"))
 include(joinpath("utils", "generate_namelist.jl"))
-using .Cases
+include(joinpath("utils", "compute_mse.jl"))
 using .NameList
 using .ParamList
 
-include(joinpath("utils", "main.jl"))
-
 @testset "life_cycle_Tan2018" begin
     println("Running life_cycle_Tan2018...")
     namelist = NameList.life_cycle_Tan2018(default_namelist("life_cycle_Tan2018"))

diff --git a/integration_tests/utils/generate_namelist.jl b/integration_tests/utils/generate_namelist.jl
@@ -1,7 +1,33 @@
 module NameList
+
 #Adapated from PyCLES: https://github.com/pressel/pycles
+
+using ArgParse
+import JSON
+
 export default_namelist
-function default_namelist(case_name)
+
+function parse_commandline()
+    s = ArgParseSettings(;description="Namelist Generator")
+
+    @add_arg_table! s begin
+        "case_name"
+            help = "The case name"
+            arg_type = String
+            required = true
+    end
+
+    return parse_args(s)
+end
+
+function default_namelist(::Nothing)
+    args = parse_commandline()
+    case_name = args["case_name"]
+    return default_namelist(case_name)
+end
+
+function default_namelist(case_name::String)
+
     namelist_defaults = Dict()
     namelist_defaults["grid"] = Dict()
     namelist_defaults["grid"]["dims"] = 1
@@ -71,9 +97,10 @@ function default_namelist(case_name)
     elseif case_name == "DryBubble"
         namelist = DryBubble(namelist_defaults)
     else
-        error("Not a valid case name")
+        error("Not a valid case name in namelist")
     end
-    # write_file(namelist)
+    write_file(namelist)
+    return namelist
 end
 
 
@@ -273,27 +300,22 @@ function DryBubble(namelist_defaults)
     return namelist
 end
 
-# function write_file(namelist)
+function write_file(namelist)
 
-#     try
-#         type(namelist["meta"]["simname"])
-#     catch
-#         print("Casename not specified in namelist dictionary!")
-#         print("FatalError")
-#         exit()
-#     end
+    @assert haskey(namelist, "meta")
+    @assert haskey(namelist["meta"], "simname")
 
-#     namelist["meta"]["uuid"] = str(uuid.uuid4())
+    namelist["meta"]["uuid"] = basename(tempname())
 
-#     fh = open(namelist["meta"]["simname"] + ".in", "w")
-#     #pprint.pprint(namelist)
-#     json.dump(namelist, fh, sort_keys=true, indent=4)
-#     fh.close()
+    open(namelist["meta"]["simname"]*".in", "w") do io
+        JSON.print(io, namelist, 4)
+    end
 
-#     return
-# end
+    return
+end
 
-# if __name__ == "__main__"
-#     main()
+if abspath(PROGRAM_FILE) == @__FILE__
+    default_namelist(nothing)
+end
 
 end