Use submodules

Author: YingboMa

src/DiffEqProblemLibrary.jl

@@ -1,59 +1,23 @@
-__precompile__(false)
+__precompile__(true)
 
 module DiffEqProblemLibrary
 
-using DiffEqBase, ParameterizedFunctions, DiffEqOperators, DiffEqBiological,
-      LinearAlgebra
+const file = @__FILE__
 
-include("ode/ode_premade_problems.jl")
-include("dae_premade_problems.jl")
-include("dde_premade_problems.jl")
-include("sde_premade_problems.jl")
-include("jump_premade_problems.jl")
-
-#ODE Example Problems
-export prob_ode_linear, prob_ode_bigfloatlinear, prob_ode_2Dlinear,
-       prob_ode_large2Dlinear, prob_ode_bigfloat2Dlinear, prob_ode_rigidbody,
-       prob_ode_2Dlinear_notinplace, prob_ode_vanderpol, prob_ode_vanderpol_stiff,
-       prob_ode_lorenz, prob_ode_rober, prob_ode_threebody, prob_ode_mm_linear, prob_ode_pleiades,
-       prob_ode_brusselator_1d, prob_ode_brusselator_2d, prob_ode_orego,
-       prob_ode_hires, prob_ode_pollution, prob_ode_filament,
-       SolverDiffEq, filament_prob
-
- #SDE Example Problems
- export prob_sde_wave, prob_sde_linear, prob_sde_cubic, prob_sde_2Dlinear,
-        prob_sde_lorenz, prob_sde_2Dlinear, prob_sde_additive,
-        prob_sde_additivesystem, oval2ModelExample, prob_sde_bistable,
-        prob_sde_bruss, prob_sde_oscilreact
-
- #SDE Stratonovich Example Problems
- export prob_sde_linear_stratonovich, prob_sde_2Dlinear_stratonovich
-
- #DAE Example Problems
- export prob_dae_resrob
-
-# DDE Example Problems
-# examples with constant delays
-export prob_dde_1delay, prob_dde_1delay_notinplace, prob_dde_1delay_scalar_notinplace,
-       prob_dde_2delays, prob_dde_2delays_notinplace, prob_dde_2delays_scalar_notinplace,
-       prob_dde_1delay_long, prob_dde_1delay_long_notinplace,
-       prob_dde_1delay_long_scalar_notinplace, prob_dde_2delays_long,
-       prob_dde_2delays_long_notinplace, prob_dde_2delays_long_scalar_notinplace,
-       prob_dde_mackey, prob_dde_wheldon, prob_dde_qs,
-# examples with vanishing time dependent delays
-       prob_ddde_neves1, prob_dde_neves_thompson,
-# examples with state dependent delays
-       prob_dde_paul1, prob_dde_paul2, prob_dde_mahaffy1, prob_dde_mahaffy2,
-# examples with vanishing state dependent delays
-       prob_neves2, prob_dde_gatica
-
-# Jump Example Problems
-export prob_jump_dnarepressor, prob_jump_constproduct, prob_jump_nonlinrxs,
-# examples mixing mass action and constant rate jumps
-       prob_jump_osc_mixed_jumptypes,
-# examples used in published benchmarks / comparisions
-       prob_jump_multistate, prob_jump_twentygenes, prob_jump_dnadimer_repressor,
-# examples approximating diffusion by continuous time random walks
-       prob_jump_diffnetwork
+module ODEProblemLibrary
+importodeproblems() = @eval ODEProblemLibrary include(joinpath(@__DIR__, "ode/ode_premade_problems.jl"))
+end # module
+module DAEProblemLibrary
+importdaeproblems() = @eval DAEProblemLibrary include(joinpath(@__DIR__, "dae_premade_problems.jl"))
+end # module
+module DDEProblemLibrary
+importddeproblems() = @eval DDEProblemLibrary include(joinpath(@__DIR__, "dde_premade_problems.jl"))
+end # module
+module SDEProblemLibrary
+importsdeproblems() = @eval SDEProblemLibrary include(joinpath(@__DIR__, "sde_premade_problems.jl"))
+end # module
+module JumpProblemLibrary
+importjumpproblems() = @eval JumpProblemLibrary include(joinpath(@__DIR__, "src/jump_premade_problems.jl"))
+end # module
 
 end # module

src/dae_premade_problems.jl

@@ -1,3 +1,8 @@
+using DiffEqBase
+
+#DAE Example Problems
+export prob_dae_resrob
+
 ### DAE Problems
 
 f = function (r, yp, y, p, tres)

src/dde_premade_problems.jl

@@ -1,3 +1,21 @@
+module DAEProblemLibrary
+using DiffEqBase
+# DDE Example Problems
+# examples with constant delays
+export prob_dde_1delay, prob_dde_1delay_notinplace, prob_dde_1delay_scalar_notinplace,
+       prob_dde_2delays, prob_dde_2delays_notinplace, prob_dde_2delays_scalar_notinplace,
+       prob_dde_1delay_long, prob_dde_1delay_long_notinplace,
+       prob_dde_1delay_long_scalar_notinplace, prob_dde_2delays_long,
+       prob_dde_2delays_long_notinplace, prob_dde_2delays_long_scalar_notinplace,
+       prob_dde_mackey, prob_dde_wheldon, prob_dde_qs,
+# examples with vanishing time dependent delays
+       prob_ddde_neves1, prob_dde_neves_thompson,
+# examples with state dependent delays
+       prob_dde_paul1, prob_dde_paul2, prob_dde_mahaffy1, prob_dde_mahaffy2,
+# examples with vanishing state dependent delays
+       prob_neves2, prob_dde_gatica
+
+
 # DDE examples with analytical solution
 
 ## Single constant delay
@@ -640,3 +658,4 @@ prob_dde_qs = build_prob_dde_qs([1; 8.4e8; 2.5e-9; 7.6e-8; 5e-15], # initial val
                                 0.1, 1.3e-12, 0.38, 1.3, 0.66, 2.3e-19, 2.3e-18, 70e-9,
                                 2.3, 0.05, 4e4, 5e-7, 0.080, 1.5e-4, 1.1e-8, 70e-9, 2.5,
                                 0.005)
+end # module

src/jump_premade_problems.jl

@@ -1,9 +1,19 @@
-""" 
+using DiffEqBase, DiffEqBiological
+# Jump Example Problems
+export prob_jump_dnarepressor, prob_jump_constproduct, prob_jump_nonlinrxs,
+# examples mixing mass action and constant rate jumps
+       prob_jump_osc_mixed_jumptypes,
+# examples used in published benchmarks / comparisions
+       prob_jump_multistate, prob_jump_twentygenes, prob_jump_dnadimer_repressor,
+# examples approximating diffusion by continuous time random walks
+       prob_jump_diffnetwork
+
+"""
     General structure to hold JumpProblem info. Needed since
-    the JumpProblem constructor requires the algorithm, so we 
+    the JumpProblem constructor requires the algorithm, so we
     don't create the JumpProblem here.
 """
-struct JumpProblemNetwork 
+struct JumpProblemNetwork
     network         # DiffEqBiological network
     rates           # vector of rate constants or nothing
     tstop           # time to end simulation
@@ -28,7 +38,7 @@ Nsims = 8000
 expected_avg = 5.926553750000000e+02
 prob_data = Dict("num_sims_for_mean" => Nsims, "expected_mean" => expected_avg)
 """
-    DNA negative feedback autoregulatory model. Protein acts as repressor.    
+    DNA negative feedback autoregulatory model. Protein acts as repressor.
 """
 prob_jump_dnarepressor = JumpProblemNetwork(dna_rs, rates, tf, u0, prob, prob_data)
 
@@ -50,7 +60,7 @@ prob_jump_constproduct = JumpProblemNetwork(bd_rs, rates, tf, u0, prob, prob_dat
 
 nonlin_rs = @reaction_network dtype begin
     k1, 2A --> B
-    k2, B --> 2A 
+    k2, B --> 2A
     k3, A + B --> C
     k4, C --> A + B
     k5, 3C --> 3A
@@ -132,12 +142,12 @@ u0[ findfirst(rs.syms, :S3) ] = params[3]
 tf    = 100.
 prob = DiscreteProblem(u0, (0., tf), rates)
 """
-    Multistate model from Gupta and Mendes, 
+    Multistate model from Gupta and Mendes,
     "An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems",
     Computation 2018, 6, 9; doi:10.3390/computation6010009
     Translated from supplementary data file: Models/Multi-state/fixed_multistate.xml
 """
-prob_jump_multistate = JumpProblemNetwork(rs, rates, tf, u0, prob, 
+prob_jump_multistate = JumpProblemNetwork(rs, rates, tf, u0, prob,
                 Dict("specs_to_sym_name" => specs_sym_to_name, "rates_sym_to_idx" => rates_sym_to_idx, "params" => params))
 
 
@@ -162,14 +172,14 @@ genenetwork *= "end"
 rs = eval( parse(genenetwork) )
 u0 = zeros(Int, length(rs.syms))
 for i = 1:(2*N)
-    u0[findfirst(rs.syms, Symbol("G$(i)"))] = 1    
+    u0[findfirst(rs.syms, Symbol("G$(i)"))] = 1
 end
 tf = 2000.0
 prob = DiscreteProblem(u0, (0.0, tf))
 """
-    Twenty-gene model from McCollum et al, 
+    Twenty-gene model from McCollum et al,
     "The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior"
-    Comp. Bio. and Chem., 30, pg. 39-49 (2006). 
+    Comp. Bio. and Chem., 30, pg. 39-49 (2006).
 """
 prob_jump_twentygenes = JumpProblemNetwork(rs, nothing, tf, u0, prob, nothing)
 
@@ -191,11 +201,11 @@ tf = 4000.
 prob = DiscreteProblem(u0, (0.0, tf), rnpar)
 """
     Negative feedback autoregulatory gene expression model. Dimer is the repressor.
-    Taken from Marchetti, Priami and Thanh, 
-    "Simulation Algorithms for Comptuational Systems Biology", 
+    Taken from Marchetti, Priami and Thanh,
+    "Simulation Algorithms for Comptuational Systems Biology",
     Springer (2017).
 """
-prob_jump_dnadimer_repressor = JumpProblemNetwork(rn, rnpar, tf, u0, prob, 
+prob_jump_dnadimer_repressor = JumpProblemNetwork(rn, rnpar, tf, u0, prob,
                                                 Dict("specs_names" => varlabels))
 
 
@@ -217,7 +227,7 @@ end
 tf = 10.
 """
     Continuous time random walk (i.e. diffusion approximation) example.
-    Here the network in the JumpProblemNetwork is a function that returns a 
+    Here the network in the JumpProblemNetwork is a function that returns a
     network given the number of lattice sites.
     u0 is a similar function that returns the initial condition vector.
 """

src/ode/ode_premade_problems.jl

@@ -1,5 +1,16 @@
+using DiffEqBase, ParameterizedFunctions, DiffEqOperators, Random, LinearAlgebra
+
 srand(100)
 
+#ODE Example Problems
+export prob_ode_linear, prob_ode_bigfloatlinear, prob_ode_2Dlinear,
+       prob_ode_large2Dlinear, prob_ode_bigfloat2Dlinear, prob_ode_rigidbody,
+       prob_ode_2Dlinear_notinplace, prob_ode_vanderpol, prob_ode_vanderpol_stiff,
+       prob_ode_lorenz, prob_ode_rober, prob_ode_threebody, prob_ode_mm_linear, prob_ode_pleiades,
+       prob_ode_brusselator_1d, prob_ode_brusselator_2d, prob_ode_orego,
+       prob_ode_hires, prob_ode_pollution, prob_ode_filament,
+       SolverDiffEq, filament_prob
+
 include("ode_linear_prob.jl")
 include("ode_simple_nonlinear_prob.jl")
 include("brusselator_prob.jl")

src/sde_premade_problems.jl

@@ -1,3 +1,13 @@
+using DiffEqBase, ParameterizedFunctions, DiffEqBiological
+#SDE Example Problems
+export prob_sde_wave, prob_sde_linear, prob_sde_cubic, prob_sde_2Dlinear,
+      prob_sde_lorenz, prob_sde_2Dlinear, prob_sde_additive,
+      prob_sde_additivesystem, oval2ModelExample, prob_sde_bistable,
+      prob_sde_bruss, prob_sde_oscilreact
+#SDE Stratonovich Example Problems
+export prob_sde_linear_stratonovich, prob_sde_2Dlinear_stratonovich
+
+
 ### SDE Examples
 
 f = (u,p,t) -> 1.01u