Merge pull request #25 from PALEOtoolkit/fix_empty_parameters

bugfix for config file with empty parameters:

Project.toml

@@ -1,7 +1,7 @@
 name = "PALEOboxes"
 uuid = "804b410e-d900-4b2a-9ecd-f5a06d4c1fd4"
 authors = ["Stuart Daines <[email protected]>"]
-version = "0.18.5"
+version = "0.18.6"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"

src/Reaction.jl

@@ -361,15 +361,16 @@ function create_reaction_from_config(
 
     # set parameters
     allpars = get_parameters(newreaction)
-    conf_parameters = copy(get(conf_reaction, "parameters", Dict{Any,Any}()))
+    conf_parameters_raw = get(conf_reaction, "parameters", Dict{Any,Any}())  # empty 'parameters:' will return nothing
+    conf_parameters = isnothing(conf_parameters_raw) ? Dict{Any, Any}() : copy(conf_parameters_raw)
     for par in allpars
         rawvalue = par.v
         par_modified = false
         if par.external && haskey(newreaction.base.external_parameters, par.name)
             rawvalue = newreaction.base.external_parameters[par.name]
             par_modified = true
         end
-        if !isnothing(conf_parameters) && haskey(conf_parameters, par.name) # empty 'parameters:' will return nothing
+        if haskey(conf_parameters, par.name)
             rawvalue = pop!(conf_parameters, par.name)
             par_modified = true
         end

test/configbase.yaml

@@ -61,7 +61,6 @@ model_with_loop:
             reactions:
 
 
-# two reactions that depend on each other - sort_reactions! should fail
 model_with_invalid_parameter:
     domains:
         ocean:
@@ -81,3 +80,21 @@ model_with_invalid_parameter:
         oceanfloor:
             reactions:
 
+model_with_empty_parameters:
+    domains:
+        ocean:
+
+            reactions:
+                julia_paleo_mock:
+                    class: ReactionPaleoMock
+                    parameters:
+
+                    variable_links:
+                        phy*:      mock_phy*
+
+        oceansurface:
+            reactions:
+
+        oceanfloor:
+            reactions:
+

test/runbasetests.jl

@@ -100,4 +100,12 @@ end
 
     @test_throws ErrorException("reaction ocean.julia_paleo_mock has no Parameter(s):\n    misspelt_par:    something\n") PB.create_model_from_config("configbase.yaml", "model_with_invalid_parameter")
 
+end
+
+@testset "PALEOboxes base empty parameters" begin
+
+    model = PB.create_model_from_config("configbase.yaml", "model_with_empty_parameters")
+
+    @test length(model.domains) == 3
+
 end