From 9fc50d50b52558c38389528c46308a6fc52b4932 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Thu, 14 Nov 2024 17:23:31 -0500
Subject: [PATCH 01/16] init

---
 src/dsl.jl              | 16 +++++++++++-----
 test/dsl/dsl_options.jl |  5 +++++
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index 91a2fa3851..4dae35b0b6 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -286,6 +286,11 @@ end
 ### DSL Internal Master Function ###
 
 # Function for creating a ReactionSystem structure (used by the @reaction_network macro).
+# What should no_infer do? We currently infer in:
+#   equations
+#   observables
+#   differentials
+# make it so that we no longer do so. 
 function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Handle interpolation of variables
@@ -308,6 +313,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
     compound_expr, compound_species = read_compound_options(options)
     continuous_events_expr = read_events_option(options, :continuous_events)
     discrete_events_expr = read_events_option(options, :discrete_events)
+    noinfer = haskey(options, :no_infer)
 
     # Parses reactions, species, and parameters.
     reactions = get_reactions(reaction_lines)
@@ -317,7 +323,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Reads equations. 
     vars_extracted, add_default_diff, equations = read_equations_options(
-        options, variables_declared)
+        options, variables_declared; noinfer = noinfer)
     variables = vcat(variables_declared, vars_extracted)
 
     # Handle independent variables
@@ -341,13 +347,13 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Reads observables.
     observed_vars, observed_eqs, obs_syms = read_observed_options(
-        options, [species_declared; variables], all_ivs)
+        options, [species_declared; variables], all_ivs; noinfer = noinfer)
 
     # Collect species and parameters, including ones inferred from the reactions. 
     declared_syms = Set(Iterators.flatten((parameters_declared, species_declared,
         variables)))
     species_extracted, parameters_extracted = extract_species_and_parameters!(
-        reactions, declared_syms)
+        reactions, declared_syms; noinfer = noinfer)
 
     species = vcat(species_declared, species_extracted)
     parameters = vcat(parameters_declared, parameters_extracted)
@@ -682,7 +688,7 @@ end
 # `vars_extracted`: A vector with extracted variables (lhs in pure differential equations only).
 # `dtexpr`: If a differential equation is defined, the default derivative (D ~ Differential(t)) must be defined.
 # `equations`: a vector with the equations provided.
-function read_equations_options(options, variables_declared)
+function read_equations_options(options, variables_declared; noinfer = false)
     # Prepares the equations. First, extracts equations from provided option (converting to block form if required).
     # Next, uses MTK's `parse_equations!` function to split input into a vector with the equations.
     eqs_input = haskey(options, :equations) ? options[:equations].args[3] : :(begin end)
@@ -752,7 +758,7 @@ function create_differential_expr(options, add_default_diff, used_syms, tiv)
 end
 
 # Reads the observables options. Outputs an expression ofr creating the observable variables, and a vector of observable equations.
-function read_observed_options(options, species_n_vars_declared, ivs_sorted)
+function read_observed_options(options, species_n_vars_declared, ivs_sorted; noinfer = false)
     if haskey(options, :observables)
         # Gets list of observable equations and prepares variable declaration expression.
         # (`options[:observables]` includes `@observables`, `.args[3]` removes this part)
diff --git a/test/dsl/dsl_options.jl b/test/dsl/dsl_options.jl
index 8174598fd4..3dbeabd6d4 100644
--- a/test/dsl/dsl_options.jl
+++ b/test/dsl/dsl_options.jl
@@ -1022,3 +1022,8 @@ let
     @parameters v n
     @test isequal(Catalyst.expand_registered_functions(equations(rn4)[1]), D(A) ~ v*(A^n))
 end
+
+### test that @no_infer properly throws errors when undeclared variables are written
+
+let
+end

From bd30f6528dd3c3e0f0fb8f29218553c153630352 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Thu, 14 Nov 2024 18:29:19 -0500
Subject: [PATCH 02/16] init no_option

---
 src/dsl.jl              | 17 ++++++++---
 test/dsl/dsl_options.jl | 62 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 75 insertions(+), 4 deletions(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index 4dae35b0b6..d6e5fffa49 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -71,7 +71,7 @@ const pure_rate_arrows = Set{Symbol}([:(=>), :(<=), :⇐, :⟽, :⇒, :⟾, :⇔
 # Declares the keys used for various options.
 const option_keys = (:species, :parameters, :variables, :ivs, :compounds, :observables,
     :default_noise_scaling, :differentials, :equations,
-    :continuous_events, :discrete_events, :combinatoric_ratelaws)
+    :continuous_events, :discrete_events, :combinatoric_ratelaws, :no_infer)
 
 ### `@species` Macro ###
 
@@ -517,11 +517,12 @@ end
 
 # Function looping through all reactions, to find undeclared symbols (species or
 # parameters), and assign them to the right category.
-function extract_species_and_parameters!(reactions, excluded_syms)
+function extract_species_and_parameters!(reactions, excluded_syms; noinfer = noinfer)
     species = OrderedSet{Union{Symbol, Expr}}()
     for reaction in reactions
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(species, reactant.reactant, excluded_syms)
+            (!isempty(species) && noinfer) && error("Unrecognized variables $(species) detected in reaction $(reaction). Since the flag @no_infer is declared, all species must be explicitly declared with the @species macro.")
         end
     end
 
@@ -529,8 +530,10 @@ function extract_species_and_parameters!(reactions, excluded_syms)
     parameters = OrderedSet{Union{Symbol, Expr}}()
     for reaction in reactions
         add_syms_from_expr!(parameters, reaction.rate, excluded_syms)
+        (!isempty(parameters) && noinfer) && error("Unrecognized parameter $(parameters) detected in reaction $(reaction.rate). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(parameters, reactant.stoichiometry, excluded_syms)
+            (!isempty(parameters) && noinfer) && error("Unrecognized parameter $(parameters) detected in reactant $(reactant). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
         end
     end
 
@@ -717,9 +720,12 @@ function read_equations_options(options, variables_declared; noinfer = false)
             diff_var = lhs.args[2]
             if in(diff_var, forbidden_symbols_error)
                 error("A forbidden symbol ($(diff_var)) was used as an variable in this differential equation: $eq")
+            elseif (!in(diff_var, variables_declared)) && noinfer
+                error("Unrecognized symbol $(diff_var) was used as a variable in this differential equation. Since the @no_infer flag is set, all variables in equations must be explicitly declared via @variables, @species, or @parameters.")
+            else
+                add_default_diff = true
+                in(diff_var, variables_declared) || push!(vars_extracted, diff_var)
             end
-            add_default_diff = true
-            in(diff_var, variables_declared) || push!(vars_extracted, diff_var)
         end
     end
 
@@ -769,6 +775,9 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted; noi
         for (idx, obs_eq) in enumerate(observed_eqs.args)
             # Extract the observable, checks errors, and continues the loop if the observable has been declared.
             obs_name, ivs, defaults, metadata = find_varinfo_in_declaration(obs_eq.args[2])
+            if (noinfer && !in(obs_name, species_n_vars_declared))
+                error("An undeclared variable ($obs_name) was declared as an observable. Since the flag @no_infer is set, all variables must be declared with the @species, @parameters, or @variables macros.")
+            end
             isempty(ivs) ||
                 error("An observable ($obs_name) was given independent variable(s). These should not be given, as they are inferred automatically.")
             isnothing(defaults) ||
diff --git a/test/dsl/dsl_options.jl b/test/dsl/dsl_options.jl
index 3dbeabd6d4..a7de64a17c 100644
--- a/test/dsl/dsl_options.jl
+++ b/test/dsl/dsl_options.jl
@@ -1026,4 +1026,66 @@ end
 ### test that @no_infer properly throws errors when undeclared variables are written
 
 let
+    @test_throws LoadError rn = @reaction_network begin
+        @no_infer
+        (k, k1), A <--> B
+    end
+
+    @test_nowarn rn = @reaction_network begin
+        @no_infer
+        @species A(t) B(t)
+        @parameters k
+        k, A --> B
+    end
+
+    @test_throws LoadError rn = @reaction_network begin
+        @no_infer
+        @species A(t) B(t)
+        @parameters k
+        k*n, A --> B
+    end
+
+    @test_nowarn rn = @reaction_network begin
+        @no_infer
+        @parameters n k
+        @species A(t) B(t)
+        k*n, A --> B
+    end
+
+    @test_throws LoadError rn = @reaction_network begin
+        @no_infer
+        @species A(t) B(t)
+        k, n*A --> B
+    end
+
+    @test_nowarn rn = @reaction_network begin
+        @no_infer
+        @parameters n
+        @species A(t) B(t)
+        k, n*A --> B
+    end
+
+    @test_throws LoadError rn = @reaction_network begin
+        @no_infer
+        @equations D(V) ~ V^2
+    end
+
+    @test_nowarn rn = @reaction_network begin
+        @no_infer
+        @variables V(t)
+        @equations D(V) ~ V^2
+    end
+
+    @test_throws LoadError rn = @reaction_network begin
+        @no_infer
+        @variables X1(t)
+        @observables X2 ~ X1
+    end
+
+    @test_nowarn rn = @reaction_network begin
+        @no_infer
+        @variables X1(t) X2(t)
+        @observables X2 ~ X1
+    end
 end
+

From 56b4363cc819d14c6fae7df900d4535656b840f8 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Fri, 15 Nov 2024 15:24:22 -0500
Subject: [PATCH 03/16] test fix

---
 test/dsl/dsl_options.jl | 33 +++++++++++++++++----------------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/test/dsl/dsl_options.jl b/test/dsl/dsl_options.jl
index a7de64a17c..90aaed278e 100644
--- a/test/dsl/dsl_options.jl
+++ b/test/dsl/dsl_options.jl
@@ -1026,63 +1026,64 @@ end
 ### test that @no_infer properly throws errors when undeclared variables are written
 
 let
-    @test_throws LoadError rn = @reaction_network begin
+    # Test error when species are inferred
+    @test_throws LoadError @eval rn = @reaction_network begin
         @no_infer
-        (k, k1), A <--> B
+        @parameters k 
+        k, A --> B
     end
-
-    @test_nowarn rn = @reaction_network begin
+    @test_nowarn @eval rn = @reaction_network begin
         @no_infer
         @species A(t) B(t)
         @parameters k
         k, A --> B
     end
 
-    @test_throws LoadError rn = @reaction_network begin
+    # Test error when a parameter in rate is inferred
+    @test_throws LoadError @eval rn = @reaction_network begin
         @no_infer
         @species A(t) B(t)
         @parameters k
         k*n, A --> B
     end
-
-    @test_nowarn rn = @reaction_network begin
+    @test_nowarn @eval rn = @reaction_network begin
         @no_infer
         @parameters n k
         @species A(t) B(t)
         k*n, A --> B
     end
 
-    @test_throws LoadError rn = @reaction_network begin
+    # Test error when a parameter in stoichiometry is inferred
+    @test_throws LoadError @eval rn = @reaction_network begin
         @no_infer
         @species A(t) B(t)
         k, n*A --> B
     end
-
-    @test_nowarn rn = @reaction_network begin
+    @test_nowarn @eval rn = @reaction_network begin
         @no_infer
         @parameters n
         @species A(t) B(t)
         k, n*A --> B
     end
 
-    @test_throws LoadError rn = @reaction_network begin
+    # Test error when a variable in an equation is inferred
+    @test_throws LoadError @eval rn = @reaction_network begin
         @no_infer
         @equations D(V) ~ V^2
     end
-
-    @test_nowarn rn = @reaction_network begin
+    @test_nowarn @eval rn = @reaction_network begin
         @no_infer
         @variables V(t)
         @equations D(V) ~ V^2
     end
 
-    @test_throws LoadError rn = @reaction_network begin
+    # Test error when a variable in an observable is inferred
+    @test_throws LoadError @eval rn = @reaction_network begin
         @no_infer
         @variables X1(t)
         @observables X2 ~ X1
     end
-
-    @test_nowarn rn = @reaction_network begin
+    @test_nowarn @eval rn = @reaction_network begin
         @no_infer
         @variables X1(t) X2(t)
         @observables X2 ~ X1

From 4b26cc4972436c936631c3ef60e50e5fdea08c24 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Fri, 15 Nov 2024 15:42:37 -0500
Subject: [PATCH 04/16] up

---
 src/dsl.jl              | 6 +++---
 test/dsl/dsl_options.jl | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index d6e5fffa49..78b0a570de 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -522,7 +522,7 @@ function extract_species_and_parameters!(reactions, excluded_syms; noinfer = noi
     for reaction in reactions
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(species, reactant.reactant, excluded_syms)
-            (!isempty(species) && noinfer) && error("Unrecognized variables $(species) detected in reaction $(reaction). Since the flag @no_infer is declared, all species must be explicitly declared with the @species macro.")
+            (!isempty(species) && noinfer) && error("Unrecognized variables $(species[1]) detected in reaction reaction expression. Since the flag @no_infer is declared, all species must be explicitly declared with the @species macro.")
         end
     end
 
@@ -530,10 +530,10 @@ function extract_species_and_parameters!(reactions, excluded_syms; noinfer = noi
     parameters = OrderedSet{Union{Symbol, Expr}}()
     for reaction in reactions
         add_syms_from_expr!(parameters, reaction.rate, excluded_syms)
-        (!isempty(parameters) && noinfer) && error("Unrecognized parameter $(parameters) detected in reaction $(reaction.rate). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
+        (!isempty(parameters) && noinfer) && error("Unrecognized parameter $(parameters[1]) detected in rate expression $(reaction.rate). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(parameters, reactant.stoichiometry, excluded_syms)
-            (!isempty(parameters) && noinfer) && error("Unrecognized parameter $(parameters) detected in reactant $(reactant). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
+            (!isempty(parameters) && noinfer) && error("Unrecognized parameters $(parameters[1]) detected in the stoichiometry for reactant $(reactant.reactant). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
         end
     end
 
diff --git a/test/dsl/dsl_options.jl b/test/dsl/dsl_options.jl
index 90aaed278e..892d844cc0 100644
--- a/test/dsl/dsl_options.jl
+++ b/test/dsl/dsl_options.jl
@@ -1056,12 +1056,13 @@ let
     # Test error when a parameter in stoichiometry is inferred
     @test_throws LoadError @eval rn = @reaction_network begin
         @no_infer
+        @parameters k
         @species A(t) B(t)
         k, n*A --> B
     end
     @test_nowarn @eval rn = @reaction_network begin
         @no_infer
-        @parameters n
+        @parameters k n
         @species A(t) B(t)
         k, n*A --> B
     end

From 13d236ecba87be701e173691ed6c8b6b89ca30bb Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Fri, 15 Nov 2024 15:45:56 -0500
Subject: [PATCH 05/16] up

---
 src/dsl.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index 78b0a570de..ff97abd746 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -517,12 +517,12 @@ end
 
 # Function looping through all reactions, to find undeclared symbols (species or
 # parameters), and assign them to the right category.
-function extract_species_and_parameters!(reactions, excluded_syms; noinfer = noinfer)
+function extract_species_and_parameters!(reactions, excluded_syms; noinfer = false)
     species = OrderedSet{Union{Symbol, Expr}}()
     for reaction in reactions
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(species, reactant.reactant, excluded_syms)
-            (!isempty(species) && noinfer) && error("Unrecognized variables $(species[1]) detected in reaction reaction expression. Since the flag @no_infer is declared, all species must be explicitly declared with the @species macro.")
+            (!isempty(species) && noinfer) && error("Unrecognized variables $(species[1]) detected in reaction expression. Since the flag @no_infer is declared, all species must be explicitly declared with the @species macro.")
         end
     end
 

From e2b423e6c9a589f50b7941cd925c15eb57f76a2b Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 10:18:36 -0500
Subject: [PATCH 06/16] Update src/dsl.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 src/dsl.jl | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index ff97abd746..0b2535930e 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -286,11 +286,6 @@ end
 ### DSL Internal Master Function ###
 
 # Function for creating a ReactionSystem structure (used by the @reaction_network macro).
-# What should no_infer do? We currently infer in:
-#   equations
-#   observables
-#   differentials
-# make it so that we no longer do so. 
 function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Handle interpolation of variables

From 71fd89f73a5969070638342131b63a8bc5084870 Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 10:18:44 -0500
Subject: [PATCH 07/16] Update src/dsl.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 src/dsl.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index 0b2535930e..9e76f01138 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -318,7 +318,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Reads equations. 
     vars_extracted, add_default_diff, equations = read_equations_options(
-        options, variables_declared; noinfer = noinfer)
+        options, variables_declared; noinfer)
     variables = vcat(variables_declared, vars_extracted)
 
     # Handle independent variables

From 3e5b66920c11612a445d8e63760613802bd16dda Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 10:18:50 -0500
Subject: [PATCH 08/16] Update src/dsl.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 src/dsl.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index 9e76f01138..a8d6de3f79 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -342,7 +342,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Reads observables.
     observed_vars, observed_eqs, obs_syms = read_observed_options(
-        options, [species_declared; variables], all_ivs; noinfer = noinfer)
+        options, [species_declared; variables], all_ivs; noinfer)
 
     # Collect species and parameters, including ones inferred from the reactions. 
     declared_syms = Set(Iterators.flatten((parameters_declared, species_declared,

From 56baddebfdd126725640868ac240f0c503b50819 Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 10:18:56 -0500
Subject: [PATCH 09/16] Update src/dsl.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 src/dsl.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index a8d6de3f79..0e3b4ee59c 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -348,7 +348,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
     declared_syms = Set(Iterators.flatten((parameters_declared, species_declared,
         variables)))
     species_extracted, parameters_extracted = extract_species_and_parameters!(
-        reactions, declared_syms; noinfer = noinfer)
+        reactions, declared_syms)
 
     species = vcat(species_declared, species_extracted)
     parameters = vcat(parameters_declared, parameters_extracted)

From 4d02ba26048bb77f095c869270bc0340cfae015a Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 10:19:05 -0500
Subject: [PATCH 10/16] Update src/dsl.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 src/dsl.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index 0e3b4ee59c..f7dc40d468 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -716,7 +716,7 @@ function read_equations_options(options, variables_declared; noinfer = false)
             if in(diff_var, forbidden_symbols_error)
                 error("A forbidden symbol ($(diff_var)) was used as an variable in this differential equation: $eq")
             elseif (!in(diff_var, variables_declared)) && noinfer
-                error("Unrecognized symbol $(diff_var) was used as a variable in this differential equation. Since the @no_infer flag is set, all variables in equations must be explicitly declared via @variables, @species, or @parameters.")
+                error("Unrecognized symbol $(diff_var) was used as a variable in an equation. Since the @no_infer flag is set, all variables in equations must be explicitly declared via @variables, @species, or @parameters.")
             else
                 add_default_diff = true
                 in(diff_var, variables_declared) || push!(vars_extracted, diff_var)

From 64dab974edf43f99d94f1bb68be0f97296d6f133 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Sat, 16 Nov 2024 11:06:13 -0500
Subject: [PATCH 11/16] rename + error

---
 src/dsl.jl | 35 ++++++++++++++++++++++-------------
 1 file changed, 22 insertions(+), 13 deletions(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index f7dc40d468..17bb53a6b3 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -71,7 +71,7 @@ const pure_rate_arrows = Set{Symbol}([:(=>), :(<=), :⇐, :⟽, :⇒, :⟾, :⇔
 # Declares the keys used for various options.
 const option_keys = (:species, :parameters, :variables, :ivs, :compounds, :observables,
     :default_noise_scaling, :differentials, :equations,
-    :continuous_events, :discrete_events, :combinatoric_ratelaws, :no_infer)
+    :continuous_events, :discrete_events, :combinatoric_ratelaws, :require_declaration)
 
 ### `@species` Macro ###
 
@@ -230,6 +230,9 @@ struct ReactionStruct
     end
 end
 
+#function Base.show(io::IO, rx::ReactionStruct) #    
+#end
+
 # Recursive function that loops through the reaction line and finds the reactants and their
 # stoichiometry. Recursion makes it able to handle weird cases like 2(X+Y+3(Z+XY)).
 function recursive_find_reactants!(ex::ExprValues, mult::ExprValues,
@@ -283,6 +286,12 @@ function extract_metadata(metadata_line::Expr)
     return metadata
 end
 
+
+
+struct UndeclaredSymbolicError <: Exception
+    msg::String
+end
+
 ### DSL Internal Master Function ###
 
 # Function for creating a ReactionSystem structure (used by the @reaction_network macro).
@@ -308,7 +317,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
     compound_expr, compound_species = read_compound_options(options)
     continuous_events_expr = read_events_option(options, :continuous_events)
     discrete_events_expr = read_events_option(options, :discrete_events)
-    noinfer = haskey(options, :no_infer)
+    requiredec = haskey(options, :require_declaration)
 
     # Parses reactions, species, and parameters.
     reactions = get_reactions(reaction_lines)
@@ -318,7 +327,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Reads equations. 
     vars_extracted, add_default_diff, equations = read_equations_options(
-        options, variables_declared; noinfer)
+        options, variables_declared; requiredec)
     variables = vcat(variables_declared, vars_extracted)
 
     # Handle independent variables
@@ -342,13 +351,13 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Reads observables.
     observed_vars, observed_eqs, obs_syms = read_observed_options(
-        options, [species_declared; variables], all_ivs; noinfer)
+        options, [species_declared; variables], all_ivs; requiredec)
 
     # Collect species and parameters, including ones inferred from the reactions. 
     declared_syms = Set(Iterators.flatten((parameters_declared, species_declared,
         variables)))
     species_extracted, parameters_extracted = extract_species_and_parameters!(
-        reactions, declared_syms)
+        reactions, declared_syms; requiredec)
 
     species = vcat(species_declared, species_extracted)
     parameters = vcat(parameters_declared, parameters_extracted)
@@ -512,12 +521,12 @@ end
 
 # Function looping through all reactions, to find undeclared symbols (species or
 # parameters), and assign them to the right category.
-function extract_species_and_parameters!(reactions, excluded_syms; noinfer = false)
+function extract_species_and_parameters!(reactions, excluded_syms; requiredec = false)
     species = OrderedSet{Union{Symbol, Expr}}()
     for reaction in reactions
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(species, reactant.reactant, excluded_syms)
-            (!isempty(species) && noinfer) && error("Unrecognized variables $(species[1]) detected in reaction expression. Since the flag @no_infer is declared, all species must be explicitly declared with the @species macro.")
+            (!isempty(species) && requiredec) && error("Unrecognized variables $(species[1]) detected in reaction expression. Since the flag @no_infer is declared, all species must be explicitly declared with the @species macro.")
         end
     end
 
@@ -525,10 +534,10 @@ function extract_species_and_parameters!(reactions, excluded_syms; noinfer = fal
     parameters = OrderedSet{Union{Symbol, Expr}}()
     for reaction in reactions
         add_syms_from_expr!(parameters, reaction.rate, excluded_syms)
-        (!isempty(parameters) && noinfer) && error("Unrecognized parameter $(parameters[1]) detected in rate expression $(reaction.rate). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
+        (!isempty(parameters) && requiredec) && error("Unrecognized parameter $(parameters[1]) detected in rate expression $(reaction.rate). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(parameters, reactant.stoichiometry, excluded_syms)
-            (!isempty(parameters) && noinfer) && error("Unrecognized parameters $(parameters[1]) detected in the stoichiometry for reactant $(reactant.reactant). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
+            (!isempty(parameters) && requiredec) && error("Unrecognized parameters $(parameters[1]) detected in the stoichiometry for reactant $(reactant.reactant). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
         end
     end
 
@@ -686,7 +695,7 @@ end
 # `vars_extracted`: A vector with extracted variables (lhs in pure differential equations only).
 # `dtexpr`: If a differential equation is defined, the default derivative (D ~ Differential(t)) must be defined.
 # `equations`: a vector with the equations provided.
-function read_equations_options(options, variables_declared; noinfer = false)
+function read_equations_options(options, variables_declared; requiredec = false)
     # Prepares the equations. First, extracts equations from provided option (converting to block form if required).
     # Next, uses MTK's `parse_equations!` function to split input into a vector with the equations.
     eqs_input = haskey(options, :equations) ? options[:equations].args[3] : :(begin end)
@@ -715,7 +724,7 @@ function read_equations_options(options, variables_declared; noinfer = false)
             diff_var = lhs.args[2]
             if in(diff_var, forbidden_symbols_error)
                 error("A forbidden symbol ($(diff_var)) was used as an variable in this differential equation: $eq")
-            elseif (!in(diff_var, variables_declared)) && noinfer
+            elseif (!in(diff_var, variables_declared)) && requiredec
                 error("Unrecognized symbol $(diff_var) was used as a variable in an equation. Since the @no_infer flag is set, all variables in equations must be explicitly declared via @variables, @species, or @parameters.")
             else
                 add_default_diff = true
@@ -759,7 +768,7 @@ function create_differential_expr(options, add_default_diff, used_syms, tiv)
 end
 
 # Reads the observables options. Outputs an expression ofr creating the observable variables, and a vector of observable equations.
-function read_observed_options(options, species_n_vars_declared, ivs_sorted; noinfer = false)
+function read_observed_options(options, species_n_vars_declared, ivs_sorted; requiredec = false)
     if haskey(options, :observables)
         # Gets list of observable equations and prepares variable declaration expression.
         # (`options[:observables]` includes `@observables`, `.args[3]` removes this part)
@@ -770,7 +779,7 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted; noi
         for (idx, obs_eq) in enumerate(observed_eqs.args)
             # Extract the observable, checks errors, and continues the loop if the observable has been declared.
             obs_name, ivs, defaults, metadata = find_varinfo_in_declaration(obs_eq.args[2])
-            if (noinfer && !in(obs_name, species_n_vars_declared))
+            if (requiredec && !in(obs_name, species_n_vars_declared))
                 error("An undeclared variable ($obs_name) was declared as an observable. Since the flag @no_infer is set, all variables must be declared with the @species, @parameters, or @variables macros.")
             end
             isempty(ivs) ||

From 3aa68ad01d5e63b3ef7ad6c1d5233fb25ce2d6f8 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Sat, 16 Nov 2024 11:58:53 -0500
Subject: [PATCH 12/16] fixes

---
 src/Catalyst.jl         |  2 +-
 src/dsl.jl              | 20 +++++++++++++++-----
 test/dsl/dsl_options.jl | 40 ++++++++++++++++++++--------------------
 3 files changed, 36 insertions(+), 26 deletions(-)

diff --git a/src/Catalyst.jl b/src/Catalyst.jl
index 047747da71..499493c362 100644
--- a/src/Catalyst.jl
+++ b/src/Catalyst.jl
@@ -122,7 +122,7 @@ export symmap_to_varmap
 # reaction_network macro
 include("expression_utils.jl")
 include("dsl.jl")
-export @reaction_network, @network_component, @reaction, @species
+export @reaction_network, @network_component, @reaction, @species, UndeclaredSymbolicError
 
 # Network analysis functionality.
 include("network_analysis.jl")
diff --git a/src/dsl.jl b/src/dsl.jl
index 17bb53a6b3..6248a4442f 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -292,6 +292,11 @@ struct UndeclaredSymbolicError <: Exception
     msg::String
 end
 
+function Base.showerror(io::IO, err::UndeclaredSymbolicError) 
+    print(io, "UndeclaredSymbolicError: ")
+    print(io, err.msg)
+end
+
 ### DSL Internal Master Function ###
 
 # Function for creating a ReactionSystem structure (used by the @reaction_network macro).
@@ -526,7 +531,8 @@ function extract_species_and_parameters!(reactions, excluded_syms; requiredec =
     for reaction in reactions
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(species, reactant.reactant, excluded_syms)
-            (!isempty(species) && requiredec) && error("Unrecognized variables $(species[1]) detected in reaction expression. Since the flag @no_infer is declared, all species must be explicitly declared with the @species macro.")
+            (!isempty(species) && requiredec) && throw(UndeclaredSymbolicError(
+                                                                               "Unrecognized variables $(species[1]) detected in reaction expression. Since the flag @require_declaration is declared, all species must be explicitly declared with the @species macro."))
         end
     end
 
@@ -534,10 +540,12 @@ function extract_species_and_parameters!(reactions, excluded_syms; requiredec =
     parameters = OrderedSet{Union{Symbol, Expr}}()
     for reaction in reactions
         add_syms_from_expr!(parameters, reaction.rate, excluded_syms)
-        (!isempty(parameters) && requiredec) && error("Unrecognized parameter $(parameters[1]) detected in rate expression $(reaction.rate). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
+        (!isempty(parameters) && requiredec) && throw(UndeclaredSymbolicError(
+                                                                              "Unrecognized parameter $(parameters[1]) detected in rate expression $(reaction.rate). Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(parameters, reactant.stoichiometry, excluded_syms)
-            (!isempty(parameters) && requiredec) && error("Unrecognized parameters $(parameters[1]) detected in the stoichiometry for reactant $(reactant.reactant). Since the flag @no_infer is declared, all parameters must be explicitly declared with the @parameters macro.")
+            (!isempty(parameters) && requiredec) && throw(UndeclaredSymbolicError(
+                                                                                  "Unrecognized parameters $(parameters[1]) detected in the stoichiometry for reactant $(reactant.reactant). Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
         end
     end
 
@@ -725,7 +733,8 @@ function read_equations_options(options, variables_declared; requiredec = false)
             if in(diff_var, forbidden_symbols_error)
                 error("A forbidden symbol ($(diff_var)) was used as an variable in this differential equation: $eq")
             elseif (!in(diff_var, variables_declared)) && requiredec
-                error("Unrecognized symbol $(diff_var) was used as a variable in an equation. Since the @no_infer flag is set, all variables in equations must be explicitly declared via @variables, @species, or @parameters.")
+                throw(UndeclaredSymbolicError(
+                                              "Unrecognized symbol $(diff_var) was used as a variable in an equation. Since the @require_declaration flag is set, all variables in equations must be explicitly declared via @variables, @species, or @parameters."))
             else
                 add_default_diff = true
                 in(diff_var, variables_declared) || push!(vars_extracted, diff_var)
@@ -780,7 +789,8 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted; req
             # Extract the observable, checks errors, and continues the loop if the observable has been declared.
             obs_name, ivs, defaults, metadata = find_varinfo_in_declaration(obs_eq.args[2])
             if (requiredec && !in(obs_name, species_n_vars_declared))
-                error("An undeclared variable ($obs_name) was declared as an observable. Since the flag @no_infer is set, all variables must be declared with the @species, @parameters, or @variables macros.")
+                throw(UndeclaredSymbolicError(
+                                              "An undeclared variable ($obs_name) was declared as an observable. Since the flag @require_declaration is set, all variables must be declared with the @species, @parameters, or @variables macros."))
             end
             isempty(ivs) ||
                 error("An observable ($obs_name) was given independent variable(s). These should not be given, as they are inferred automatically.")
diff --git a/test/dsl/dsl_options.jl b/test/dsl/dsl_options.jl
index 892d844cc0..36d3afff38 100644
--- a/test/dsl/dsl_options.jl
+++ b/test/dsl/dsl_options.jl
@@ -1027,65 +1027,65 @@ end
 
 let
     # Test error when species are inferred
-    @test_throws LoadError @eval rn = @reaction_network begin
-        @no_infer
+    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+        @require_declaration
         @parameters k 
         k, A --> B
     end
-    @test_nowarn @eval rn = @reaction_network begin
-        @no_infer
+    @test_nowarn @macroexpand rn = @reaction_network begin
+        @require_declaration
         @species A(t) B(t)
         @parameters k
         k, A --> B
     end
 
     # Test error when a parameter in rate is inferred
-    @test_throws LoadError @eval rn = @reaction_network begin
-        @no_infer
+    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+        @require_declaration
         @species A(t) B(t)
         @parameters k
         k*n, A --> B
     end
-    @test_nowarn @eval rn = @reaction_network begin
-        @no_infer
+    @test_nowarn @macroexpand rn = @reaction_network begin
+        @require_declaration
         @parameters n k
         @species A(t) B(t)
         k*n, A --> B
     end
 
     # Test error when a parameter in stoichiometry is inferred
-    @test_throws LoadError @eval rn = @reaction_network begin
-        @no_infer
+    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+        @require_declaration
         @parameters k
         @species A(t) B(t)
         k, n*A --> B
     end
-    @test_nowarn @eval rn = @reaction_network begin
-        @no_infer
+    @test_nowarn @macroexpand rn = @reaction_network begin
+        @require_declaration
         @parameters k n
         @species A(t) B(t)
         k, n*A --> B
     end
 
     # Test error when a variable in an equation is inferred
-    @test_throws LoadError @eval rn = @reaction_network begin
-        @no_infer
+    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+        @require_declaration
         @equations D(V) ~ V^2
     end
-    @test_nowarn @eval rn = @reaction_network begin
-        @no_infer
+    @test_nowarn @macroexpand rn = @reaction_network begin
+        @require_declaration
         @variables V(t)
         @equations D(V) ~ V^2
     end
 
     # Test error when a variable in an observable is inferred
-    @test_throws LoadError @eval rn = @reaction_network begin
-        @no_infer
+    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+        @require_declaration
         @variables X1(t)
         @observables X2 ~ X1
     end
-    @test_nowarn @eval rn = @reaction_network begin
-        @no_infer
+    @test_nowarn @macroexpand rn = @reaction_network begin
+        @require_declaration
         @variables X1(t) X2(t)
         @observables X2 ~ X1
     end

From 54ea053f8f2cab5477a8fa61ef0079f4f9a4c1d0 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Mon, 18 Nov 2024 18:42:01 -0500
Subject: [PATCH 13/16] add reaction/equation printing

---
 src/Catalyst.jl         |  3 ++-
 src/dsl.jl              | 30 ++++++++++++++----------------
 test/dsl/dsl_options.jl |  1 +
 3 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/src/Catalyst.jl b/src/Catalyst.jl
index 499493c362..04bb436b48 100644
--- a/src/Catalyst.jl
+++ b/src/Catalyst.jl
@@ -122,7 +122,8 @@ export symmap_to_varmap
 # reaction_network macro
 include("expression_utils.jl")
 include("dsl.jl")
-export @reaction_network, @network_component, @reaction, @species, UndeclaredSymbolicError
+export @reaction_network, @network_component, @reaction, @species
+
 
 # Network analysis functionality.
 include("network_analysis.jl")
diff --git a/src/dsl.jl b/src/dsl.jl
index 6248a4442f..22a6fbc3f0 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -220,19 +220,17 @@ struct ReactionStruct
     products::Vector{ReactantStruct}
     rate::ExprValues
     metadata::Expr
+    rxexpr::Expr
 
     function ReactionStruct(sub_line::ExprValues, prod_line::ExprValues, rate::ExprValues,
-            metadata_line::ExprValues)
+            metadata_line::ExprValues, rx_line::Expr)
         sub = recursive_find_reactants!(sub_line, 1, Vector{ReactantStruct}(undef, 0))
         prod = recursive_find_reactants!(prod_line, 1, Vector{ReactantStruct}(undef, 0))
         metadata = extract_metadata(metadata_line)
-        new(sub, prod, rate, metadata)
+        new(sub, prod, rate, metadata, rx_line)
     end
 end
 
-#function Base.show(io::IO, rx::ReactionStruct) #    
-#end
-
 # Recursive function that loops through the reaction line and finds the reactants and their
 # stoichiometry. Recursion makes it able to handle weird cases like 2(X+Y+3(Z+XY)).
 function recursive_find_reactants!(ex::ExprValues, mult::ExprValues,
@@ -440,15 +438,15 @@ function get_reactions(exprs::Vector{Expr}, reactions = Vector{ReactionStruct}(u
                 error("Error: Must provide a tuple of reaction rates when declaring a bi-directional reaction.")
             end
             push_reactions!(reactions, reaction.args[2], reaction.args[3],
-                rate.args[1], metadata.args[1], arrow)
+                rate.args[1], metadata.args[1], arrow, line)
             push_reactions!(reactions, reaction.args[3], reaction.args[2],
-                rate.args[2], metadata.args[2], arrow)
+                rate.args[2], metadata.args[2], arrow, line)
         elseif in(arrow, fwd_arrows)
             push_reactions!(reactions, reaction.args[2], reaction.args[3],
-                rate, metadata, arrow)
+                rate, metadata, arrow, line)
         elseif in(arrow, bwd_arrows)
             push_reactions!(reactions, reaction.args[3], reaction.args[2],
-                rate, metadata, arrow)
+                rate, metadata, arrow, line)
         else
             throw("Malformed reaction, invalid arrow type used in: $(MacroTools.striplines(line))")
         end
@@ -482,7 +480,7 @@ end
 # Takes a reaction line and creates reaction(s) from it and pushes those to the reaction array.
 # Used to create multiple reactions from, for instance, `k, (X,Y) --> 0`.
 function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues,
-        prod_line::ExprValues, rate::ExprValues, metadata::ExprValues, arrow::Symbol)
+        prod_line::ExprValues, rate::ExprValues, metadata::ExprValues, arrow::Symbol, line::Expr)
     # The rates, substrates, products, and metadata may be in a tupple form (e.g. `k, (X,Y) --> 0`).
     # This finds the length of these tuples (or 1 if not in tuple forms). Errors if lengs inconsistent.
     lengs = (tup_leng(sub_line), tup_leng(prod_line), tup_leng(rate), tup_leng(metadata))
@@ -505,7 +503,7 @@ function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues
 
         push!(reactions,
             ReactionStruct(get_tup_arg(sub_line, i),
-                get_tup_arg(prod_line, i), get_tup_arg(rate, i), metadata_i))
+                get_tup_arg(prod_line, i), get_tup_arg(rate, i), metadata_i, line))
     end
 end
 
@@ -532,7 +530,7 @@ function extract_species_and_parameters!(reactions, excluded_syms; requiredec =
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(species, reactant.reactant, excluded_syms)
             (!isempty(species) && requiredec) && throw(UndeclaredSymbolicError(
-                                                                               "Unrecognized variables $(species[1]) detected in reaction expression. Since the flag @require_declaration is declared, all species must be explicitly declared with the @species macro."))
+                                                                               "Unrecognized variables $(join(species, ", ")) detected in reaction expression: \"$(string(reaction.rxexpr))\". Since the flag @require_declaration is declared, all species must be explicitly declared with the @species macro."))
         end
     end
 
@@ -541,11 +539,11 @@ function extract_species_and_parameters!(reactions, excluded_syms; requiredec =
     for reaction in reactions
         add_syms_from_expr!(parameters, reaction.rate, excluded_syms)
         (!isempty(parameters) && requiredec) && throw(UndeclaredSymbolicError(
-                                                                              "Unrecognized parameter $(parameters[1]) detected in rate expression $(reaction.rate). Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
+                                                                              "Unrecognized parameter $(join(parameters, ", ")) detected in rate expression: $(reaction.rate) for the following reaction expression: \"$(string(reaction.rxexpr))\". Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(parameters, reactant.stoichiometry, excluded_syms)
             (!isempty(parameters) && requiredec) && throw(UndeclaredSymbolicError(
-                                                                                  "Unrecognized parameters $(parameters[1]) detected in the stoichiometry for reactant $(reactant.reactant). Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
+                                                                                  "Unrecognized parameters $(join(parameters, ", ")) detected in the stoichiometry for reactant $(reactant.reactant) in the following reaction expression: \"$(string(reaction.rxpexpr))\". Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
         end
     end
 
@@ -734,7 +732,7 @@ function read_equations_options(options, variables_declared; requiredec = false)
                 error("A forbidden symbol ($(diff_var)) was used as an variable in this differential equation: $eq")
             elseif (!in(diff_var, variables_declared)) && requiredec
                 throw(UndeclaredSymbolicError(
-                                              "Unrecognized symbol $(diff_var) was used as a variable in an equation. Since the @require_declaration flag is set, all variables in equations must be explicitly declared via @variables, @species, or @parameters."))
+                                              "Unrecognized symbol $(diff_var) was used as a variable in an equation: \"$eq\". Since the @require_declaration flag is set, all variables in equations must be explicitly declared via @variables, @species, or @parameters."))
             else
                 add_default_diff = true
                 in(diff_var, variables_declared) || push!(vars_extracted, diff_var)
@@ -790,7 +788,7 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted; req
             obs_name, ivs, defaults, metadata = find_varinfo_in_declaration(obs_eq.args[2])
             if (requiredec && !in(obs_name, species_n_vars_declared))
                 throw(UndeclaredSymbolicError(
-                                              "An undeclared variable ($obs_name) was declared as an observable. Since the flag @require_declaration is set, all variables must be declared with the @species, @parameters, or @variables macros."))
+                                              "An undeclared variable ($obs_name) was declared as an observable in the following observable equation: \"$obs_eq\". Since the flag @require_declaration is set, all variables must be declared with the @species, @parameters, or @variables macros."))
             end
             isempty(ivs) ||
                 error("An observable ($obs_name) was given independent variable(s). These should not be given, as they are inferred automatically.")
diff --git a/test/dsl/dsl_options.jl b/test/dsl/dsl_options.jl
index 36d3afff38..14d9432fa5 100644
--- a/test/dsl/dsl_options.jl
+++ b/test/dsl/dsl_options.jl
@@ -1025,6 +1025,7 @@ end
 
 ### test that @no_infer properly throws errors when undeclared variables are written
 
+import Catalyst: UndeclaredSymbolicError
 let
     # Test error when species are inferred
     @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin

From 81d4a10671b7030e5f715f76b603245905769fd5 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Mon, 18 Nov 2024 18:43:13 -0500
Subject: [PATCH 14/16] fix

---
 src/Catalyst.jl | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/Catalyst.jl b/src/Catalyst.jl
index 04bb436b48..047747da71 100644
--- a/src/Catalyst.jl
+++ b/src/Catalyst.jl
@@ -124,7 +124,6 @@ include("expression_utils.jl")
 include("dsl.jl")
 export @reaction_network, @network_component, @reaction, @species
 
-
 # Network analysis functionality.
 include("network_analysis.jl")
 export reactioncomplexmap, reactioncomplexes, incidencemat

From fbf7a295a98e8f46d4fd018f5889fedfe4b86163 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Mon, 18 Nov 2024 18:51:58 -0500
Subject: [PATCH 15/16] typo

---
 src/dsl.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dsl.jl b/src/dsl.jl
index 22a6fbc3f0..f17c17522c 100644
--- a/src/dsl.jl
+++ b/src/dsl.jl
@@ -543,7 +543,7 @@ function extract_species_and_parameters!(reactions, excluded_syms; requiredec =
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(parameters, reactant.stoichiometry, excluded_syms)
             (!isempty(parameters) && requiredec) && throw(UndeclaredSymbolicError(
-                                                                                  "Unrecognized parameters $(join(parameters, ", ")) detected in the stoichiometry for reactant $(reactant.reactant) in the following reaction expression: \"$(string(reaction.rxpexpr))\". Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
+                                                                                  "Unrecognized parameters $(join(parameters, ", ")) detected in the stoichiometry for reactant $(reactant.reactant) in the following reaction expression: \"$(string(reaction.rxexpr))\". Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
         end
     end
 

From c7108148a8baa7ea804a0599ac29d64f288e4b30 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Wed, 20 Nov 2024 10:26:58 -0500
Subject: [PATCH 16/16] remove rn

---
 test/dsl/dsl_options.jl | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/test/dsl/dsl_options.jl b/test/dsl/dsl_options.jl
index 14d9432fa5..872ba4f0b2 100644
--- a/test/dsl/dsl_options.jl
+++ b/test/dsl/dsl_options.jl
@@ -1028,12 +1028,12 @@ end
 import Catalyst: UndeclaredSymbolicError
 let
     # Test error when species are inferred
-    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
         @require_declaration
         @parameters k 
         k, A --> B
     end
-    @test_nowarn @macroexpand rn = @reaction_network begin
+    @test_nowarn @macroexpand @reaction_network begin
         @require_declaration
         @species A(t) B(t)
         @parameters k
@@ -1041,13 +1041,13 @@ let
     end
 
     # Test error when a parameter in rate is inferred
-    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
         @require_declaration
         @species A(t) B(t)
         @parameters k
         k*n, A --> B
     end
-    @test_nowarn @macroexpand rn = @reaction_network begin
+    @test_nowarn @macroexpand @reaction_network begin
         @require_declaration
         @parameters n k
         @species A(t) B(t)
@@ -1055,13 +1055,13 @@ let
     end
 
     # Test error when a parameter in stoichiometry is inferred
-    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
         @require_declaration
         @parameters k
         @species A(t) B(t)
         k, n*A --> B
     end
-    @test_nowarn @macroexpand rn = @reaction_network begin
+    @test_nowarn @macroexpand @reaction_network begin
         @require_declaration
         @parameters k n
         @species A(t) B(t)
@@ -1069,23 +1069,23 @@ let
     end
 
     # Test error when a variable in an equation is inferred
-    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
         @require_declaration
         @equations D(V) ~ V^2
     end
-    @test_nowarn @macroexpand rn = @reaction_network begin
+    @test_nowarn @macroexpand @reaction_network begin
         @require_declaration
         @variables V(t)
         @equations D(V) ~ V^2
     end
 
     # Test error when a variable in an observable is inferred
-    @test_throws UndeclaredSymbolicError @macroexpand rn = @reaction_network begin
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
         @require_declaration
         @variables X1(t)
         @observables X2 ~ X1
     end
-    @test_nowarn @macroexpand rn = @reaction_network begin
+    @test_nowarn @macroexpand @reaction_network begin
         @require_declaration
         @variables X1(t) X2(t)
         @observables X2 ~ X1