fix depwarns

Author: ChrisRackauckas

src/jump_premade_problems.jl

@@ -136,9 +136,9 @@ end kon kAon koff kAoff kAp kAdp
 rsi   = rates_sym_to_idx
 rates = params[[rsi[:kon], rsi[:kAon], rsi[:koff], rsi[:kAoff], rsi[:kAp], rsi[:kAdp]]]
 u0    = zeros(Int,9)
-u0[ findfirst(rs.syms, :S1) ] = params[1]
-u0[ findfirst(rs.syms, :S2) ] = params[2]
-u0[ findfirst(rs.syms, :S3) ] = params[3]
+u0[ something(findfirst(isequal(:S1), rs.syms),0)] = params[1]
+u0[ something(findfirst(isequal(:S2), rs.syms),0)] = params[2]
+u0[ something(findfirst(isequal(:S3), rs.syms),0)] = params[3]
 tf    = 100.
 prob = DiscreteProblem(u0, (0., tf), rates)
 """
@@ -153,23 +153,26 @@ prob_jump_multistate = JumpProblemNetwork(rs, rates, tf, u0, prob,
 
 # generate the network
 N = 10  # number of genes
-genenetwork = "@reaction_network twentgtype begin\n"
-for i in 1:N
-    genenetwork *= "\t 10.0, G$(2*i-1) --> G$(2*i-1) + M$(2*i-1)\n"
-    genenetwork *= "\t 10.0, M$(2*i-1) --> M$(2*i-1) + P$(2*i-1)\n"
-    genenetwork *= "\t 1.0,  M$(2*i-1) --> 0\n"
-    genenetwork *= "\t 1.0,  P$(2*i-1) --> 0\n"
-
-    genenetwork *= "\t 5.0, G$(2*i) --> G$(2*i) + M$(2*i)\n"
-    genenetwork *= "\t 5.0, M$(2*i) --> M$(2*i) + P$(2*i)\n"
-    genenetwork *= "\t 1.0,  M$(2*i) --> 0\n"
-    genenetwork *= "\t 1.0,  P$(2*i) --> 0\n"
-
-    genenetwork *= "\t 0.0001, G$(2*i) + P$(2*i-1) --> G$(2*i)_ind \n"
-    genenetwork *= "\t 100., G$(2*i)_ind --> G$(2*i)_ind + M$(2*i)\n"
+function construct_genenetwork(N)
+  genenetwork = "@reaction_network twentgtype begin\n"
+  for i in 1:N
+      genenetwork *= "\t 10.0, G$(2*i-1) --> G$(2*i-1) + M$(2*i-1)\n"
+      genenetwork *= "\t 10.0, M$(2*i-1) --> M$(2*i-1) + P$(2*i-1)\n"
+      genenetwork *= "\t 1.0,  M$(2*i-1) --> 0\n"
+      genenetwork *= "\t 1.0,  P$(2*i-1) --> 0\n"
+
+      genenetwork *= "\t 5.0, G$(2*i) --> G$(2*i) + M$(2*i)\n"
+      genenetwork *= "\t 5.0, M$(2*i) --> M$(2*i) + P$(2*i)\n"
+      genenetwork *= "\t 1.0,  M$(2*i) --> 0\n"
+      genenetwork *= "\t 1.0,  P$(2*i) --> 0\n"
+
+      genenetwork *= "\t 0.0001, G$(2*i) + P$(2*i-1) --> G$(2*i)_ind \n"
+      genenetwork *= "\t 100., G$(2*i)_ind --> G$(2*i)_ind + M$(2*i)\n"
+  end
+  genenetwork *= "end"
 end
-genenetwork *= "end"
-rs = eval( parse(genenetwork) )
+genenetwork = construct_genenetwork(N)
+rs = eval( Meta.parse(genenetwork) )
 u0 = zeros(Int, length(rs.syms))
 for i = 1:(2*N)
     u0[findfirst(rs.syms, Symbol("G$(i)"))] = 1
@@ -217,7 +220,7 @@ function getDiffNetwork(N)
         diffnetwork *= "\t K, X$(i+1) --> X$(i)\n"
     end
     diffnetwork *= "end K"
-    rs = eval( parse(diffnetwork) )
+    rs = eval( Meta.parse(diffnetwork) )
     rs
 end
 params = (1.,)