Updated the yaml output to reference the toml file in the output

src/solver/type_getters.jl

@@ -988,12 +988,16 @@ function get_simulation(config::AtmosConfig)
     output_dir = sim_info.output_dir
     @info "Simulation info" job_id output_dir
 
+    output_toml_file = joinpath(output_dir, "$(job_id)_parameters.toml")
     CP.log_parameter_information(
         config.toml_dict,
-        joinpath(output_dir, "$(job_id)_parameters.toml"),
+        output_toml_file,
         strict = config.parsed_args["strict_params"],
     )
-    YAML.write_file(joinpath(output_dir, "$job_id.yml"), config.parsed_args)
+
+    output_args = copy(config.parsed_args)
+    output_args["toml"] = [abspath(output_toml_file)]
+    YAML.write_file(joinpath(output_dir, "$job_id.yml"), output_args)
 
     if sim_info.restart
         s = @timed_str begin

test/runtests.jl

@@ -33,6 +33,8 @@ if TEST_GROUP in ("infrastructure", "all")
     @safetestset "Variable manipulations" begin @time include("variable_manipulations_tests.jl") end
     @safetestset "Parameter tests" begin @time include("parameter_tests.jl") end
 
+    @safetestset "Check TOML path" begin @time include("test_output_yaml_path.jl") end
+
     # Interface tests
     @safetestset "Radiation interface tests" begin @time include("rrtmgp_interface.jl") end
     @safetestset "Coupler compatibility" begin @time include("coupler_compatibility.jl") end

test/test_output_yaml_path.jl

@@ -0,0 +1,39 @@
+import ClimaAtmos as CA
+import YAML
+using Test
+
+@testset "Output YAML Path Test" begin
+    mktempdir() do output_dir
+        job_id = "test_yaml_path_fix"
+
+        input_toml_path = joinpath(@__DIR__, "..", "toml", "bomex_box_rhoe.toml")
+
+        config_dict = Dict(
+            "job_id" => job_id,
+            "output_dir" => output_dir,
+            "config" => "box",
+            "toml" => [input_toml_path],
+            "x_elem" => 2,
+            "y_elem" => 2,
+            "z_elem" => 4,
+            "dt" => "1s",
+            "t_end" => "2s",
+            "dt_save_state_to_disk" => "2s",
+        )
+
+        config = CA.AtmosConfig(config_dict; job_id)
+
+        simulation = CA.get_simulation(config)
+        real_output_dir = simulation.output_dir
+
+        output_yaml_path = joinpath(real_output_dir, "$(job_id).yml")
+        output_toml_path = joinpath(real_output_dir, "$(job_id)_parameters.toml")
+
+        @test isfile(output_yaml_path)
+        @test isfile(output_toml_path)
+
+        yaml_data = YAML.load_file(output_yaml_path)
+        @test yaml_data["toml"] == [abspath(output_toml_path)]
+        @test yaml_data["toml"] != [input_toml_path]
+    end
+end