Add Unit Testing for development

[jiweiqi]

As the package becomes more and more complex, it is important to adopt unit testing. We can following the example of RMS.jl at https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl/blob/ac2a3bd88504b86d5bc60dedc09533839a9c9cbb/src/Calculators/TestThermo.jl#L1-L60.

Some thoughts:

• We could put the test files inside the src folder, with a consistent prefix, so that one can easily spot the actual source file.
• We can test the functions against Cantera via PyCall. This should work well for most of the functionality.
• @test Cps ≈ Cpexplist rtol=1e-3 where 1e-3 is a good default value for tolerance.

[TJP-Karpowski]

That sound like a good ideal.
I can add that for the thermo interface.

I think the naming "test_.jl" sounds great. I also agree, that we can test a lot against Cantera.
But could you explain, why you would put the test files in the source folder? I would prefer those test files either in the toplevel test dir (e.g. test/test_Thermo.jl) or in a separate folder in the src directory (src/tests/test_Thermo.jl) as I fear, that the src dir becomes cluttered over time. I also find it conceptually odd to place things which are not actually src files in the src toplevel. But maybe I am just unaware of some advantages of the shared folder (especially if they are unique to Julia). In that case please let me know :).

[jiweiqi]

Hi @TJP-Karpowski , I agree with you that we should make the top level of src being clean. Indeed, putting them into either ./test/ or ./src/test is a good idea.

As for the current test files, which are put at the level of src, the reason is that I haven't figured out a good pipeline for debugging code during the development phase. As you probably know, if I import Arrhenius.jl via using Arrhenius, every time I change the source code, I will have to restart the Julia terminal. Instead, I currently import Arrhenius.jl by directly executing the module file as done in

Arrhenius.jl/src/_transport_test.jl

Lines 5 to 43 in 3f77007

	module Arrhenius
	using YAML
	using NPZ
	using LinearAlgebra
	using SparseArrays
	include("Constants.jl")
	include("DataStructure.jl")
	include("Solution.jl")
	include("Magic.jl")
	include("Thermo.jl")
	include("Kinetics.jl")
	include("Transport.jl")
	end
	```
	Following codes are used during development phase only.
	```
	using LinearAlgebra
	using DifferentialEquations
	using Sundials
	using Profile
	using ForwardDiff
	using SparseArrays
	using PyCall
	using Test
	R = Arrhenius.R
	one_atm = Arrhenius.one_atm
	mech = "../mechanism/h2o2.yaml"
	gas = Arrhenius.CreateSolution(mech);
	ns = gas.n_species
	Y0 = zeros(ns);
	Y0[Arrhenius.species_index(gas, "H2")] = 0.1;
	Y0[Arrhenius.species_index(gas, "O2")] = 0.2;
	Y0[Arrhenius.species_index(gas, "AR")] = 0.7;

. I feel this is not a good way to do it. But at the current time being, I haven't tried other approaches.

Noting that, I have to call Arrhenius.R to access the member of the Arrhenius module. This is different from the standard test file, like

Arrhenius.jl/test/runtests.jl

Lines 1 to 38 in 3f77007

	using Arrhenius
	using ForwardDiff
	using LinearAlgebra
	using Test
	@testset "jl" begin
	# Write your tests here.
	gas = CreateSolution("../mechanism/gri30.yaml")
	ns = gas.n_species
	Y0 = ones(ns) ./ ns
	T0 = 1200.0
	P = one_atm
	wdot = set_states(gas, T0, P, Y0)
	@show size(wdot)
	@show wdot[1:3]
	u0 = vcat(Y0, T0)
	function f(u)
	T = u[end]
	Y = @view(u[1:ns])
	mean_MW = 1.0 / dot(Y, 1 ./ gas.MW)
	ρ_mass = P / R / T * mean_MW
	X = Y2X(gas, Y, mean_MW)
	C = Y2C(gas, Y, ρ_mass)
	cp_mole, cp_mass = get_cp(gas, T, X, mean_MW)
	h_mole = get_H(gas, T, Y, X)
	S0 = get_S(gas, T, P, X)
	wdot = wdot_func(gas.reaction, T, C, S0, h_mole)
	Tdot = -dot(h_mole, wdot) / ρ_mass / cp_mass
	return Tdot
	end
	grad = ForwardDiff.gradient(f, u0)
	@show size(grad)
	@show grad[1:3]
	end

.

[TJP-Karpowski]

I had the same problem with the Julia restart, luckily we are not the first to have that issue. You can use the revise package: https://timholy.github.io/Revise.jl/stable/ .
Just call using Revise before using Arrhenius and then revise will check for changes to the source files and will apply those changes in the running session :).