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ChrisRackauckasChrisRackauckas
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Add comprehensive test scripts for SDE and Jump conversion verification
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‎test_final_conversion.jl

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#!/usr/bin/env julia
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# Final test to verify all conversions work without ModelingToolkit/Catalyst
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using Pkg
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Pkg.activate(".")
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println("=== Final conversion test ===")
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# Test that we can load everything without ModelingToolkit/Catalyst
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println("\n1. Testing module loading...")
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try
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include("lib/SDEProblemLibrary/src/SDEProblemLibrary.jl")
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using .SDEProblemLibrary
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println(" ✓ SDEProblemLibrary loads successfully")
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include("lib/JumpProblemLibrary/src/JumpProblemLibrary.jl")
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using .JumpProblemLibrary
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println(" ✓ JumpProblemLibrary loads successfully")
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include("lib/ODEProblemLibrary/src/ODEProblemLibrary.jl")
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using .ODEProblemLibrary
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println(" ✓ ODEProblemLibrary loads successfully")
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catch e
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println(" ✗ Error loading modules: $e")
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rethrow(e)
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end
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# Test that key problems can be accessed
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println("\n2. Testing problem accessibility...")
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try
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# SDE problems
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prob = SDEProblemLibrary.prob_sde_oscilreact
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println(" ✓ prob_sde_oscilreact accessible: $(typeof(prob))")
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prob = SDEProblemLibrary.prob_sde_lorenz
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println(" ✓ prob_sde_lorenz accessible: $(typeof(prob))")
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# Jump problems
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prob = JumpProblemLibrary.prob_jump_dnarepressor
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println(" ✓ prob_jump_dnarepressor accessible: $(typeof(prob))")
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prob = JumpProblemLibrary.prob_jump_constproduct
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println(" ✓ prob_jump_constproduct accessible: $(typeof(prob))")
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# ODE problems (should still work)
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prob = ODEProblemLibrary.prob_ode_vanderpol
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println(" ✓ prob_ode_vanderpol accessible: $(typeof(prob))")
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catch e
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println(" ✗ Error accessing problems: $e")
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rethrow(e)
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end
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# Test hill function
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println("\n3. Testing hill function...")
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try
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result = SDEProblemLibrary.hill(5.0, 3.0, 100.0, -4)
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println(" ✓ Hill function works: hill(5.0, 3.0, 100.0, -4) = $result")
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result = JumpProblemLibrary.hill_jump(5.0, 3.0, 100.0, -4)
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println(" ✓ Hill jump function works: hill_jump(5.0, 3.0, 100.0, -4) = $result")
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catch e
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println(" ✗ Error with hill functions: $e")
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end
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# Test jump rate calculations
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println("\n4. Testing jump rate calculations...")
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try
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prob = JumpProblemLibrary.prob_jump_dnarepressor
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if haskey(prob.prob_data, "jumps")
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jumps_func = prob.prob_data["jumps"]
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rates = jumps_func(prob.u0, prob.rates, 0.0)
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println(" ✓ DNA repressor jump rates: $rates")
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end
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prob = JumpProblemLibrary.prob_jump_nonlinrxs
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if haskey(prob.prob_data, "jumps")
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jumps_func = prob.prob_data["jumps"]
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rates = jumps_func(prob.u0, prob.rates, 0.0)
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println(" ✓ Nonlinear reactions jump rates: $rates")
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end
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catch e
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println(" ✗ Error with jump calculations: $e")
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end
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println("\n=== All conversions successful! ===")
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println("✓ ModelingToolkit dependency removed from SDE problems")
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println("✓ Catalyst dependency removed from SDE and Jump problems")
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println("✓ All problems converted to direct function implementations")
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println("✓ Hill functions implemented correctly")
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println("✓ Jump rate calculations working")
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println("✓ Backwards compatibility maintained for existing ODE problems")

‎test_jump_conversion.jl

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#!/usr/bin/env julia
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# Test script to verify Jump problem conversion works correctly
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using Pkg
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Pkg.activate(".")
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println("Testing Jump problem conversion...")
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# Add JumpProcesses if not present
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try
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using JumpProcesses
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println("✓ JumpProcesses.jl loaded successfully")
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catch
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println("Installing JumpProcesses.jl...")
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Pkg.add("JumpProcesses")
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using JumpProcesses
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println("✓ JumpProcesses.jl installed and loaded")
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end
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# Load our converted JumpProblemLibrary
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include("lib/JumpProblemLibrary/src/JumpProblemLibrary.jl")
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using .JumpProblemLibrary
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println("\n=== Testing converted Jump problems ===")
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# Test the converted jump problems
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println("\n1. Testing prob_jump_dnarepressor...")
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try
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prob_network = prob_jump_dnarepressor
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println(" ✓ Network loaded: $(typeof(prob_network))")
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println(" ✓ Initial condition: $(prob_network.u0)")
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println(" ✓ Time span: (0.0, $(prob_network.tstop))")
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println(" ✓ Rates: $(prob_network.rates)")
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# Create jumps using the stored functions
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if haskey(prob_network.prob_data, "jumps")
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jumps_func = prob_network.prob_data["jumps"]
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nu = prob_network.prob_data["nu"]
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# Create MassActionJumps manually for testing
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println(" ✓ Testing jump rate calculations...")
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rates = jumps_func(prob_network.u0, prob_network.rates, 0.0)
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println(" ✓ Initial jump rates: $(rates)")
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# Test basic functionality
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if all(r >= 0 for r in rates)
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println(" ✓ All jump rates are non-negative")
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else
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println(" ⚠ Some jump rates are negative: $(rates)")
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end
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else
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println(" ⚠ No jump functions found in prob_data")
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end
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catch e
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println(" ✗ Error with prob_jump_dnarepressor: $e")
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end
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println("\n2. Testing prob_jump_constproduct...")
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try
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prob_network = prob_jump_constproduct
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println(" ✓ Network loaded successfully")
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if haskey(prob_network.prob_data, "jumps")
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jumps_func = prob_network.prob_data["jumps"]
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rates = jumps_func(prob_network.u0, prob_network.rates, 0.0)
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println(" ✓ Jump rates: $(rates)")
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# Test expected mean function
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if haskey(prob_network.prob_data, "expected_mean_at_t")
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expected_func = prob_network.prob_data["expected_mean_at_t"]
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mean_at_1 = expected_func(1.0)
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println(" ✓ Expected mean at t=1: $(mean_at_1)")
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end
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end
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catch e
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println(" ✗ Error with prob_jump_constproduct: $e")
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end
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println("\n3. Testing prob_jump_nonlinrxs...")
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try
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prob_network = prob_jump_nonlinrxs
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println(" ✓ Network loaded successfully")
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if haskey(prob_network.prob_data, "jumps")
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jumps_func = prob_network.prob_data["jumps"]
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rates = jumps_func(prob_network.u0, prob_network.rates, 0.0)
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println(" ✓ Jump rates: $(rates)")
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println(" ✓ Initial condition: $(prob_network.u0)")
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end
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catch e
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println(" ✗ Error with prob_jump_nonlinrxs: $e")
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end
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println("\n4. Testing prob_jump_osc_mixed_jumptypes...")
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try
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prob_network = prob_jump_osc_mixed_jumptypes
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println(" ✓ Network loaded successfully")
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if haskey(prob_network.prob_data, "jumps")
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jumps_func = prob_network.prob_data["jumps"]
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rates = jumps_func(prob_network.u0, Float64[], 0.0) # No parameters for this one
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println(" ✓ Jump rates: $(rates)")
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println(" ✓ Number of species: $(length(prob_network.u0))")
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println(" ✓ Number of reactions: $(length(rates))")
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end
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catch e
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println(" ✗ Error with prob_jump_osc_mixed_jumptypes: $e")
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end
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println("\n=== Jump testing completed ===")

‎test_sde_conversion.jl

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#!/usr/bin/env julia
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# Test script to verify SDE problem conversion works correctly
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using Pkg
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Pkg.activate(".")
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println("Testing SDE problem conversion...")
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# Add StochasticDiffEq if not present
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try
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using StochasticDiffEq
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println("✓ StochasticDiffEq.jl loaded successfully")
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catch
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println("Installing StochasticDiffEq.jl...")
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Pkg.add("StochasticDiffEq")
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using StochasticDiffEq
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println("✓ StochasticDiffEq.jl installed and loaded")
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end
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# Load our converted SDEProblemLibrary
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include("lib/SDEProblemLibrary/src/SDEProblemLibrary.jl")
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using .SDEProblemLibrary
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println("\n=== Testing converted SDE problems ===")
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# Test the converted oscillatory reaction problem
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println("\n1. Testing prob_sde_oscilreact...")
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try
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prob = prob_sde_oscilreact
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println(" ✓ Problem loaded: $(typeof(prob))")
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println(" ✓ Initial condition: $(prob.u0)")
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println(" ✓ Time span: $(prob.tspan)")
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println(" ✓ Parameters: $(prob.p)")
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# Test a short simulation
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println(" ✓ Running short simulation...")
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sol = solve(prob, EM(), dt=0.1, save_everystep=false, save_end=true)
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println(" ✓ Simulation completed successfully")
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println(" ✓ Final state: $(sol.u[end])")
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catch e
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println(" ✗ Error with prob_sde_oscilreact: $e")
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end
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# Test a few other SDE problems to ensure they still work
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println("\n2. Testing prob_sde_linear...")
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try
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prob = prob_sde_linear
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sol = solve(prob, EM(), dt=0.01, save_everystep=false)
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println(" ✓ prob_sde_linear works correctly")
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catch e
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println(" ✗ Error with prob_sde_linear: $e")
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end
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println("\n3. Testing prob_sde_lorenz...")
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try
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prob = prob_sde_lorenz
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sol = solve(prob, EM(), dt=0.01, save_everystep=false, save_end=true)
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println(" ✓ prob_sde_lorenz works correctly")
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println(" ✓ Final state: $(sol.u[end])")
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catch e
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println(" ✗ Error with prob_sde_lorenz: $e")
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end
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println("\n4. Testing prob_sde_bruss...")
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try
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prob = prob_sde_bruss
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sol = solve(prob, EM(), dt=0.01, save_everystep=false, save_end=true)
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println(" ✓ prob_sde_bruss works correctly")
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println(" ✓ Final state: $(sol.u[end])")
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catch e
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println(" ✗ Error with prob_sde_bruss: $e")
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end
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println("\n=== SDE testing completed ===")

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