Merge pull request #140 from ChrisRackauckas/fix-formatting

Apply JuliaFormatter to fix code formatting

Author: ChrisRackauckas

README.md

@@ -121,7 +121,7 @@ prodstoich = [0 2 0 1 3;
               1 0 0 1 0;
               0 0 1 0 0]
 mn = MatrixNetwork(pars, substoich, prodstoich; species = species,
-                   params = pars) # a matrix network
+    params = pars) # a matrix network
 prn = loadrxnetwork(mn; name = :testnetwork) # dense version
 
 # test the two networks are the same
@@ -138,7 +138,7 @@ incidencemat = [-1 1 0 0 0;
                 0 0 0 0 -1;
                 0 0 0 0 1]
 cmn = ComplexMatrixNetwork(pars, stoichmat, incidencemat; species = species,
-                           params = pars)  # a complex matrix network
+    params = pars)  # a complex matrix network
 prn = loadrxnetwork(cmn)
 
 # test the two networks are the same
@@ -149,11 +149,11 @@ The basic usages are
 
 ```julia
 mn = MatrixNetwork(rateexprs, substoich, prodstoich; species = Any[],
-                   params = Any[], t = nothing)
+    params = Any[], t = nothing)
 prn = loadrxnetwork(mn::MatrixNetwork)
 
 cmn = ComplexMatrixNetwork(rateexprs, stoichmat, incidencemat; species = Any[],
-                           params = Any[], t = nothing)
+    params = Any[], t = nothing)
 prn = loadrxnetwork(cmn::ComplexMatrixNetwork)
 ```
 
@@ -171,18 +171,18 @@ reaction rate expressions. These two types have the following fields:
     involving parameters and species like `k*A`.
 
   - matrix inputs
-
+    
       + For `MatrixNetwork`
-
+        
           * `substoich`, a number of species by number of reactions matrix with entry
             `(i,j)` giving the stoichiometric coefficient of species `i` as a
             substrate in reaction `j`.
           * `prodstoich`, a number of species by number of reactions matrix with entry
             `(i,j)` giving the stoichiometric coefficient of species `i` as a product
             in reaction `j`.
-
+    
       + For `ComplexMatrixNetwork`
-
+        
           * `stoichmat`, the complex stoichiometry matrix [defined
             here](https://docs.sciml.ai/Catalyst/stable/api/catalyst_api/#Catalyst.complexstoichmat).
           * `incidencemat`, the complex incidence matrix [defined

docs/make.jl

@@ -9,25 +9,25 @@ cp(joinpath(docpath, "Project.toml"), joinpath(assetpath, "Project.toml"), force
 include("pages.jl")
 
 mathengine = MathJax3(Dict(:loader => Dict("load" => ["[tex]/require", "[tex]/mathtools"]),
-                           :tex => Dict("inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
-                                        "packages" => [
-                                            "base",
-                                            "ams",
-                                            "autoload",
-                                            "mathtools",
-                                            "require",
-                                        ])))
+    :tex => Dict("inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
+        "packages" => [
+            "base",
+            "ams",
+            "autoload",
+            "mathtools",
+            "require"
+        ])))
 
 makedocs(sitename = "ReactionNetworkImporters.jl",
-         authors = "Samuel Isaacson",
-         format = Documenter.HTML(; analytics = "UA-90474609-3",
-                                  assets = ["assets/favicon.ico"],
-                                  mathengine,
-                                  prettyurls = (get(ENV, "CI", nothing) == "true"),
-                                  canonical = "https://docs.sciml.ai/ReactionNetworkImporters/stable/"),
-         modules = [ReactionNetworkImporters],
-         checkdocs = :exports, warnonly = [:missing_docs],
-         clean = true, doctest = false, pages = pages)
+    authors = "Samuel Isaacson",
+    format = Documenter.HTML(; analytics = "UA-90474609-3",
+        assets = ["assets/favicon.ico"],
+        mathengine,
+        prettyurls = (get(ENV, "CI", nothing) == "true"),
+        canonical = "https://docs.sciml.ai/ReactionNetworkImporters/stable/"),
+    modules = [ReactionNetworkImporters],
+    checkdocs = :exports, warnonly = [:missing_docs],
+    clean = true, doctest = false, pages = pages)
 
 deploydocs(repo = "github.com/SciML/ReactionNetworkImporters.jl.git";
-           push_preview = true)
+    push_preview = true)

docs/src/index.md

@@ -35,7 +35,7 @@ Pkg.add("ReactionNetworkImporters")
 
   - See the [SciML Style Guide](https://github.com/SciML/SciMLStyle) for common coding practices and other style decisions.
   - There are a few community forums:
-
+    
       + The #diffeq-bridged and #sciml-bridged channels in the
         [Julia Slack](https://julialang.org/slack/)
       + The #diffeq-bridged and #sciml-bridged channels in the
@@ -133,7 +133,7 @@ prodstoich = [0 2 0 1 3;
               1 0 0 1 0;
               0 0 1 0 0]
 mn = MatrixNetwork(pars, substoich, prodstoich; species = species,
-                   params = pars) # a matrix network
+    params = pars) # a matrix network
 prn = loadrxnetwork(mn) # dense version
 
 # test the two networks are the same
@@ -150,7 +150,7 @@ incidencemat = [-1 1 0 0 0;
                 0 0 0 0 -1;
                 0 0 0 0 1]
 cmn = ComplexMatrixNetwork(pars, stoichmat, incidencemat; species = species,
-                           params = pars)  # a complex matrix network
+    params = pars)  # a complex matrix network
 prn = loadrxnetwork(cmn; name = :testnetwork)
 
 # test the two networks are the same
@@ -161,11 +161,11 @@ The basic usages are
 
 ```julia
 mn = MatrixNetwork(rateexprs, substoich, prodstoich; species = Any[],
-                   params = Any[], t = nothing)
+    params = Any[], t = nothing)
 prn = loadrxnetwork(mn::MatrixNetwork)
 
 cmn = ComplexMatrixNetwork(rateexprs, stoichmat, incidencemat; species = Any[],
-                           params = Any[], t = nothing)
+    params = Any[], t = nothing)
 prn = loadrxnetwork(cmn::ComplexMatrixNetwork)
 ```
 
@@ -183,18 +183,18 @@ reaction rate expressions. These two types have the following fields:
     involving parameters and species like `k*A`.
 
   - matrix inputs
-
+    
       + For `MatrixNetwork`
-
+        
           * `substoich`, a number of species by number of reactions matrix, with entry
             `(i,j)` giving the stoichiometric coefficient of species `i` as a
             substrate in reaction `j`.
           * `prodstoich`, a number of species by number of reactions matrix, with entry
             `(i,j)` giving the stoichiometric coefficient of species `i` as a product
             in reaction `j`.
-
+    
       + For `ComplexMatrixNetwork`
-
+        
           * `stoichmat`, the complex stoichiometry matrix [defined
             here](https://docs.sciml.ai/Catalyst/stable/api/catalyst_api/#Catalyst.complexstoichmat).
           * `incidencemat`, the complex incidence matrix [defined

examples/bcrssa_bench.jl

@@ -28,7 +28,7 @@ rn = prn.rn
 tf = 20000.0
 jsys = convert(JumpSystem, rn)
 u0 = convert.(Int,
-              ModelingToolkit.varmap_to_vars(ModelingToolkit.defaults(jsys), states(jsys)))
+    ModelingToolkit.varmap_to_vars(ModelingToolkit.defaults(jsys), states(jsys)))
 dprob = DiscreteProblem(jsys, u0, (0.0, tf), [])
 @assert eltype(dprob.u0) <: Int
 jprob = JumpProblem(jsys, dprob, RSSACR(), save_positions = (false, false))

examples/not_updated_yet/bcr_odes_sparse.jl

@@ -35,8 +35,8 @@ rnbng = prnbng.rn;
 u0 = prnbng.u0;
 p = prnbng.p;
 @timeit to "baddodes" addodes!(rnbng; build_jac = build_jac, zeroout_jac = zeroout_jac,
-                               sparse_jac = sparse_jac, build_symfuncs = false,
-                               build_paramjac = false)
+    sparse_jac = sparse_jac, build_symfuncs = false,
+    build_paramjac = false)
 @timeit to "bODEProb" boprob=ODEProblem(rnbng, u0, (0.0, tf), p)
 u = copy(u0);
 du = similar(u);
@@ -52,13 +52,17 @@ function solve_dense(boprob, u, p, build_jac)
     show(to)
     println()
 
-    @timeit to "KenCarp4-LU-1" begin bsol = solve(boprob, KenCarp4(autodiff = false),
-                                                  abstol = 1e-8, reltol = 1e-8,
-                                                  saveat = 1.0) end
+    @timeit to "KenCarp4-LU-1" begin
+        bsol = solve(boprob, KenCarp4(autodiff = false),
+            abstol = 1e-8, reltol = 1e-8,
+            saveat = 1.0)
+    end
     show(to)
-    @timeit to "KenCarp4-LU-2" begin bsol = solve(boprob, KenCarp4(autodiff = false),
-                                                  abstol = 1e-8, reltol = 1e-8,
-                                                  saveat = 1.0) end
+    @timeit to "KenCarp4-LU-2" begin
+        bsol = solve(boprob, KenCarp4(autodiff = false),
+            abstol = 1e-8, reltol = 1e-8,
+            saveat = 1.0)
+    end
     show(to)
 
     bsol
@@ -71,17 +75,21 @@ function solve_sparse(boprob, u, p)
     show(to)
     println()
 
-    @timeit to "KenCarp4-SLU-1" begin bsol = solve(boprob,
-                                                   KenCarp4(autodiff = false,
-                                                            linsolve = LinSolveFactorize(lu)),
-                                                   saveat = 1.0, abstol = 1e-8,
-                                                   reltol = 1e-8) end
+    @timeit to "KenCarp4-SLU-1" begin
+        bsol = solve(boprob,
+            KenCarp4(autodiff = false,
+                linsolve = LinSolveFactorize(lu)),
+            saveat = 1.0, abstol = 1e-8,
+            reltol = 1e-8)
+    end
     show(to)
-    @timeit to "KenCarp4-SLU-2" begin bsol = solve(boprob,
-                                                   KenCarp4(autodiff = false,
-                                                            linsolve = LinSolveFactorize(lu)),
-                                                   saveat = 1.0, abstol = 1e-8,
-                                                   reltol = 1e-8) end
+    @timeit to "KenCarp4-SLU-2" begin
+        bsol = solve(boprob,
+            KenCarp4(autodiff = false,
+                linsolve = LinSolveFactorize(lu)),
+            saveat = 1.0, abstol = 1e-8,
+            reltol = 1e-8)
+    end
     show(to)
 
     bsol

examples/not_updated_yet/test_network.jl

@@ -19,14 +19,14 @@ tf = 10.0
 # get the RSSA reaction network
 reset_timer!(to)
 @timeit to "netgen" prn=loadrxnetwork(RSSANetwork(), networkname, speciesf, rxsf;
-                                      printrxs = false)
+    printrxs = false)
 rn = prn.rn
 initialpop = prn.u0
 println("network parsed")
 
 # get the BioNetGen reaction network
 @timeit to "bionetgen" prnbng=loadrxnetwork(BNGNetwork(), string(networkname, "bng"),
-                                            bngfname)
+    bngfname)
 rnbng = prnbng.rn;
 u0 = prnbng.u0;
 p = prnbng.p;

examples/not_updated_yet/test_odes.jl

@@ -19,7 +19,7 @@ rn = prnbng.rn;
 u0 = prnbng.u0;
 p = prnbng.p;
 @timeit to "addodes" addodes!(rn; build_jac = build_jac, sparse_jac = sparse_jac,
-                              build_symfuncs = false, build_paramjac = false)
+    build_symfuncs = false, build_paramjac = false)
 @timeit to "ODEProb" oprob=ODEProblem(rn, u0, (0.0, tf), p)
 u = copy(u0);
 du = similar(u);
@@ -47,16 +47,24 @@ calck = true
 # @timeit to "CVODE_BDF-GMRES-2" begin sol = solve(oprob,CVODE_BDF(linear_solver=:GMRES),dense=dense, abstol=1e-8, reltol=1e-8); end; 
 
 # CVODE_BDF with LU 
-@timeit to "CVODE_BDF-1" begin sol = solve(oprob, CVODE_BDF(), dense = dense, abstol = 1e-8,
-                                           reltol = 1e-8) end;
+@timeit to "CVODE_BDF-1" begin
+    sol = solve(oprob, CVODE_BDF(), dense = dense, abstol = 1e-8,
+        reltol = 1e-8)
+end;
 show(to);
-@timeit to "CVODE_BDF-2" begin sol = solve(oprob, CVODE_BDF(), dense = dense, abstol = 1e-8,
-                                           reltol = 1e-8) end;
+@timeit to "CVODE_BDF-2" begin
+    sol = solve(oprob, CVODE_BDF(), dense = dense, abstol = 1e-8,
+        reltol = 1e-8)
+end;
 show(to);
-@timeit to "KenCarp4-1" begin sol = solve(oprob, KenCarp4(autodiff = false), dense = dense,
-                                          calck = calck, abstol = 1e-8, reltol = 1e-8) end;
+@timeit to "KenCarp4-1" begin
+    sol = solve(oprob, KenCarp4(autodiff = false), dense = dense,
+        calck = calck, abstol = 1e-8, reltol = 1e-8)
+end;
 show(to);
-@timeit to "KenCarp4-2" begin sol = solve(oprob, KenCarp4(autodiff = false), dense = dense,
-                                          calck = calck, abstol = 1e-8, reltol = 1e-8) end;
+@timeit to "KenCarp4-2" begin
+    sol = solve(oprob, KenCarp4(autodiff = false), dense = dense,
+        calck = calck, abstol = 1e-8, reltol = 1e-8)
+end;
 
 show(to)

examples/not_updated_yet/test_odes_rssa.jl

@@ -18,11 +18,11 @@ reset_timer!(to)
 
 # get the reaction network
 @timeit to "netgen" prn=loadrxnetwork(RSSAFile(), networkname, speciesf, rxsf;
-                                      printrxs = false)
+    printrxs = false)
 rn = prn.rn;
 initialpop = prn.u0;
 @timeit to "addodes" addodes!(rn; build_jac = false, build_symfuncs = false,
-                              build_paramjac = false)
+    build_paramjac = false)
 @timeit to "ODEProb" oprob=ODEProblem(rn, convert.(Float64, initialpop), (0.0, tf))
 show(to)
 println()
@@ -40,8 +40,12 @@ println()
 
 # CVODE_BDF with LU seems to finish, on my machine it takes upwards of 500 seconds
 reset_timer!(to);
-@timeit to "CVODE_BDF" begin sol = solve(oprob, CVODE_BDF(), dense = false) end;
+@timeit to "CVODE_BDF" begin
+    sol = solve(oprob, CVODE_BDF(), dense = false)
+end;
 show(to);
 reset_timer!(to);
-@timeit to "CVODE_BDF" begin sol = solve(oprob, CVODE_BDF(), dense = false) end;
+@timeit to "CVODE_BDF" begin
+    sol = solve(oprob, CVODE_BDF(), dense = false)
+end;
 show(to);

examples/test_bcr_odes.jl

@@ -19,7 +19,7 @@ fname = joinpath(datadir, "bcr.net")
 gdatfile = joinpath(datadir, "bcr.gdat")
 print("getting gdat file...")
 gdatdf = DataFrame(load(File(format"CSV", gdatfile), header_exists = true,
-                        spacedelim = true))
+    spacedelim = true))
 println("done")
 
 # we'll time the DiffEq solvers 
@@ -57,11 +57,15 @@ println()
 # #reset_timer!(to); @timeit to "BNG_RODAS5_BDF" begin bsol2 = solve(boprob, rodas5(autodiff=false), saveat=1., abstol=1e-8, reltol=1e-8); end; show(to)
 #@timeit to "KenCarp4-1" begin sol = solve(boprob,KenCarp4(autodiff=false,linsolve=LinSolveFactorize(lu)), saveat=1., abstol=1e-8, reltol=1e-8); end; show(to)
 #@timeit to "KenCarp4-2" begin bsol = solve(boprob,KenCarp4(autodiff=false,linsolve=LinSolveFactorize(lu)), saveat=1., abstol=1e-8, reltol=1e-8); end; show(to)
-@timeit to "KenCarp4-1" begin sol = solve(boprob, KenCarp4(autodiff = false), abstol = 1e-8,
-                                          reltol = 1e-8, saveat = 1.0) end;
+@timeit to "KenCarp4-1" begin
+    sol = solve(boprob, KenCarp4(autodiff = false), abstol = 1e-8,
+        reltol = 1e-8, saveat = 1.0)
+end;
 show(to);
-@timeit to "KenCarp4-2" begin bsol = solve(boprob, KenCarp4(autodiff = false),
-                                           abstol = 1e-8, reltol = 1e-8, saveat = 1.0) end;
+@timeit to "KenCarp4-2" begin
+    bsol = solve(boprob, KenCarp4(autodiff = false),
+        abstol = 1e-8, reltol = 1e-8, saveat = 1.0)
+end;
 show(to);
 
 # Activated Syk from DiffEq
@@ -70,9 +74,9 @@ show(to);
 if doplot
     plotlyjs()
     plot(gdatdf[!, :time][2:end], gdatdf[!, :Activated_Syk][2:end], xscale = :log10,
-         label = "AsykGroup", linestyle = :dot)
+        label = "AsykGroup", linestyle = :dot)
     plot!(bsol.t[2:end], sol[Activated_Syk][2:end], label = "Activated_Syk",
-          xscale = :log10)
+        xscale = :log10)
 end
 
 # test the error, note may be large in abs value though small relatively

src/ReactionNetworkImporters.jl

@@ -57,7 +57,7 @@ struct ParsedReactionNetwork
     groupstosyms::Any
 end
 function ParsedReactionNetwork(rn::ReactionSystem; u0 = nothing, p = nothing,
-                               varstonames = nothing, groupstosyms = nothing)
+        varstonames = nothing, groupstosyms = nothing)
     ParsedReactionNetwork(rn, u0, p, varstonames, groupstosyms)
 end
 
@@ -69,7 +69,6 @@ include("parsing_routines_matrixnetworks.jl")
 
 export loadrxnetwork
 
-
 # Overload ensuring that u0 and u₀ can be used interchangeably.
 # (introduced when the u₀ field was changed to u0)
 # Should be deleted whenever u₀ is fully deprecated.