save_reaction_network -> save_reactionsystem

Author: TorkelE

src/Catalyst.jl

@@ -188,6 +188,6 @@ include("spatial_reaction_systems/lattice_jump_systems.jl")
 include("reactionsystem_serialisation/serialisation_support.jl")
 include("reactionsystem_serialisation/serialise_fields.jl")
 include("reactionsystem_serialisation/serialise_reactionsystem.jl")
-export save_reaction_network
+export save_reactionsystem
 
 end # module

src/reactionsystem.jl

@@ -209,10 +209,10 @@ end
 
 # Constant storing all reaction system fields (in order). Used to check whether the `ReactionSystem`
 # structure have been updated (in the `reactionsystem_uptodate` function).
-const reactionsystem_fields = [:eqs, :rxs, :iv, :sivs, :unknowns, :species, :ps, :var_to_name, 
+const reactionsystem_fields = (:eqs, :rxs, :iv, :sivs, :unknowns, :species, :ps, :var_to_name, 
                                :observed, :name, :systems, :defaults, :connection_type, 
                                :networkproperties, :combinatoric_ratelaws, :continuous_events, 
-                               :discrete_events, :metadata, :complete]
+                               :discrete_events, :metadata, :complete)
 
 """
 $(TYPEDEF)

src/reactionsystem_serialisation/serialise_reactionsystem.jl

@@ -1,5 +1,5 @@
 """
-    save_reaction_network(filename::String, rn::ReactionSystem; annotate = true, safety_check = true)
+    save_reactionsystem(filename::String, rn::ReactionSystem; annotate = true, safety_check = true)
 
 Save a `ReactionSystem` model to a file. The `ReactionSystem` is saved as runnable Julia code. This
 can both be used to save a `ReactionSystem` model, but also to write it to a file for easy inspection.
@@ -18,7 +18,7 @@ Example:
 rn = @reaction_network begin
     (p,d), 0 <--> X
 end
-save_reaction_network("rn.jls", rn)
+save_reactionsystem("rn.jls", rn)
 ```
 The model can now be loaded using
 ```julia
@@ -32,14 +32,14 @@ Notes:
 - Reaction systems with components that have units cannot currently be saved.
 - The `ReactionSystem` is saved using *programmatic* (not DSL) format for model creation.
 """
-function save_reaction_network(filename::String, rn::ReactionSystem; annotate = true, safety_check = true)
+function save_reactionsystem(filename::String, rn::ReactionSystem; annotate = true, safety_check = true)
     open(filename, "w") do file
         write(file, get_full_system_string(rn, annotate, true))
     end
     if safety_check 
         if !isequal(rn, include(joinpath(pwd(), filename)))
             rm(filename)
-            error("The serialised `ReactionSystem` is not equal to the original one. Please make a report (including the full system) at https://github.com/SciML/Catalyst.jl/issues. To disable this behaviour, please pass the `safety_check = false` argument to `save_reaction_network` (warning, this will permit the serialisation of an erroneous system).")
+            error("The serialised `ReactionSystem` is not equal to the original one. Please make a report (including the full system) at https://github.com/SciML/Catalyst.jl/issues. To disable this behaviour, please pass the `safety_check = false` argument to `save_reactionsystem` (warning, this will permit the serialisation of an erroneous system).")
         end
     end
     return nothing

test/miscellaneous_tests/reactionsystem_serialisation.jl

@@ -26,8 +26,8 @@ let
         @equations D(V) ~ 1 - V
         d, X --> 0
     end
-    save_reaction_network("test_serialisation_annotated.jl", rn; safety_check = false)
-    save_reaction_network("test_serialisation.jl", rn; annotate = false, safety_check = false)
+    save_reactionsystem("test_serialisation_annotated.jl", rn; safety_check = false)
+    save_reactionsystem("test_serialisation.jl", rn; annotate = false, safety_check = false)
 
     # Checks equivalence.
     file_string_annotated = read("test_serialisation_annotated.jl", String)
@@ -159,7 +159,7 @@ let
     rs = complete(rs1)
 
     # Loads the model and checks that it is correct. Removes the saved file
-    save_reaction_network("serialised_rs.jl", rs; safety_check = false)
+    save_reactionsystem("serialised_rs.jl", rs; safety_check = false)
     rs_loaded = include("../serialised_rs.jl")
     @test rs == rs_loaded
     rm("serialised_rs.jl")
@@ -247,7 +247,7 @@ let
 
     # Creates model and checks it against serialised version.
     @named rs = ReactionSystem([], τ, [X, Y, Z, U, V, W, A, B, C, D, E, F, G], [a, b, c, d, e, f])
-    save_reaction_network("serialised_rs.jl", rs; safety_check = false)
+    save_reactionsystem("serialised_rs.jl", rs; safety_check = false)
     @test rs == include("../serialised_rs.jl")
     rm("serialised_rs.jl")
 end
@@ -348,9 +348,9 @@ let
     rs = complete(rs_1)
 
     # Checks that the correct system is saved (both complete and incomplete ones).
-    save_reaction_network("serialised_rs_incomplete.jl", rs_1; safety_check = false)
+    save_reactionsystem("serialised_rs_incomplete.jl", rs_1; safety_check = false)
     @test isequal(rs_1, include("../serialised_rs_incomplete.jl"))
-    save_reaction_network("serialised_rs_complete.jl", rs; safety_check = false)
+    save_reactionsystem("serialised_rs_complete.jl", rs; safety_check = false)
     @test isequal(rs, include("../serialised_rs_complete.jl"))
     rm("serialised_rs_incomplete.jl")
     rm("serialised_rs_complete.jl")
@@ -379,7 +379,7 @@ let
     end
 
     # Checks that serialisation works.
-    save_reaction_network("serialised_rs.jl", rs; safety_check = false)
+    save_reactionsystem("serialised_rs.jl", rs; safety_check = false)
     @test_broken isequal(rs, include("../serialised_rs.jl"))
     rm("serialised_rs.jl")
 end
@@ -400,7 +400,7 @@ let
 
     @named osys = ODESystem([eq], t)
     @named rs = ReactionSystem(rxs, t; systems = [osys])
-    @test_throws Exception save_reaction_network("failed_serialisation.jl", rs)
+    @test_throws Exception save_reactionsystem("failed_serialisation.jl", rs)
 end
 
 # Checks that completeness is recorded correctly.
@@ -410,7 +410,7 @@ let
     rs_complete = @reaction_network begin
         (p,d), 0 <--> X
     end
-    save_reaction_network("serialised_rs_complete.jl", rs_complete)
+    save_reactionsystem("serialised_rs_complete.jl", rs_complete)
     rs_complete_loaded = include("../serialised_rs_complete.jl")
     @test ModelingToolkit.iscomplete(rs_complete_loaded)
     rm("serialised_rs_complete.jl")
@@ -419,7 +419,7 @@ let
     rs_incomplete = @network_component begin
         (p,d), 0 <--> X
     end
-    save_reaction_network("serialised_rs_incomplete.jl", rs_incomplete)
+    save_reactionsystem("serialised_rs_incomplete.jl", rs_incomplete)
     rs_incomplete_loaded = include("../serialised_rs_incomplete.jl")
     @test !ModelingToolkit.iscomplete(rs_incomplete_loaded)
     rm("serialised_rs_incomplete.jl")