Merge branch 'main' into 15-functional-full-model

.github/workflows/test-EpiAware.yaml

@@ -14,4 +14,4 @@ jobs:
       with:
         version: '1.10.0'
     - name: Run unit tests for EpiAware
-      run: julia --project=EpiAware -e 'using Pkg; Pkg.test()'
+      run: julia --project=EpiAware -e 'using Pkg; Pkg.test(coverage = true)'

EpiAware/test/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.0"
 manifest_format = "2.0"
-project_hash = "4e801d137527f7d9f5c027430e922fb6b4f9c643"
+project_hash = "0b01aa91e53bb772f02a49192dfa1019eaa23f4b"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245"
@@ -1263,6 +1263,17 @@ version = "0.1.7"
 deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
+[[deps.TestItemRunner]]
+deps = ["Pkg", "TOML", "Test", "TestItems", "UUIDs"]
+git-tree-sha1 = "7351f1f7389e048ce974b2c176513b817c94b15f"
+uuid = "f8b46487-2199-4994-9208-9a1283c18c0a"
+version = "0.2.2"
+
+[[deps.TestItems]]
+git-tree-sha1 = "8621ba2637b49748e2dc43ba3d84340be2938022"
+uuid = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
+version = "0.1.1"
+
 [[deps.Tracker]]
 deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"]
 git-tree-sha1 = "5c942be30a85ac75d14e9e527b55504031e1bbd3"

EpiAware/test/Project.toml

@@ -3,4 +3,6 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
+TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"

EpiAware/test/runtests.jl

@@ -1,9 +1,3 @@
-using Test
-using EpiAware
-using Distributions
-using LinearAlgebra
-using Turing, DynamicPPL
+using TestItemRunner
 
-include("test_utilities.jl")
-include("test_epimodel.jl")
-include("test_latent-processes.jl")
+@run_package_tests

EpiAware/test/test_epimodel.jl

@@ -1,25 +1,5 @@
 
-@testset "EpiModel constructor" begin
-    gen_int = [0.2, 0.3, 0.5]
-    delay_int = [0.1, 0.4, 0.5]
-    cluster_coeff = 0.8
-    time_horizon = 10
-
-    model = EpiModel(gen_int, delay_int, cluster_coeff, time_horizon)
-
-    @test length(model.gen_int) == 3
-    @test length(model.delay_int) == 3
-    @test model.cluster_coeff == 0.8
-    @test model.len_gen_int == 3
-    @test model.len_delay_int == 3
-
-    @test sum(model.gen_int) ≈ 1
-    @test sum(model.delay_int) ≈ 1
-
-    @test size(model.delay_kernel) == (time_horizon, time_horizon)
-end
-
-@testset "EpiModel constructor" begin
+@testitem "EpiModel constructor" begin
     gen_int = [0.2, 0.3, 0.5]
     delay_int = [0.1, 0.4, 0.5]
     cluster_coeff = 0.8
@@ -39,7 +19,8 @@ end
     @test size(model.delay_kernel) == (time_horizon, time_horizon)
 end
 
-@testset "EpiModel function" begin
+@testitem "EpiModel function" begin
+    using LinearAlgebra
     recent_incidence = [10, 20, 30]
     Rt = 1.5
 

EpiAware/test/test_latent-processes.jl

@@ -1,31 +1,27 @@
 
+@testitem "Testing random_walk against theoretical properties" begin
+    using DynamicPPL, Turing
+    n = 5
+    model = random_walk(n)
+    fixed_model = fix(model, (σ²_RW = 1.0,)) #Fixing the standard deviation of the random walk process
+    n_samples = 1000
+    samples_day_5 =
+        sample(fixed_model, Prior(), n_samples) |>
+        chn -> mapreduce(vcat, generated_quantities(fixed_model, chn)) do gen
+            gen[1][5] #Extracting day 5 samples
+        end
+    #Check statistics are within 5 sigma
+    #Theoretically, after 5 steps distribution is N(0, var = 5)
+    theoretical_std_of_empiral_mean = sqrt(5 / n_samples)
+    @test mean(samples_day_5) < 5 * theoretical_std_of_empiral_mean &&
+          mean(samples_day_5) > -5 * theoretical_std_of_empiral_mean
 
-@testset "Testing random_walk function" begin
-    # Test case 1: Testing against theoretical properties
-    @testset "Test case 1" begin
-        n = 5
-        model = random_walk(n)
-        fixed_model = fix(model, (σ²_RW = 1.0,)) #Fixing the standard deviation of the random walk process
-        n_samples = 1000
-        samples_day_5 =
-            sample(fixed_model, Prior(), n_samples) |>
-            chn -> mapreduce(vcat, generated_quantities(fixed_model, chn)) do gen
-                gen[1][5] #Extracting day 5 samples
-            end
-        #Check statistics are within 5 sigma
-        #Theoretically, after 5 steps distribution is N(0, var = 5)
-        theoretical_std_of_empiral_mean = sqrt(5 / n_samples)
-        @test mean(samples_day_5) < 5 * theoretical_std_of_empiral_mean &&
-              mean(samples_day_5) > -5 * theoretical_std_of_empiral_mean
+    #Theoretically, after 5 steps distribution is N(0, var = 5)
 
-        #Theoretically, after 5 steps distribution is N(0, var = 5)
+    theoretical_std_of_empiral_var = std(Chisq(5)) / sqrt(n_samples)
 
-        theoretical_std_of_empiral_var = std(Chisq(5)) / sqrt(n_samples)
-
-        @info "var = $(var(samples_day_5)); theoretical_std_of_empiral_var = $(theoretical_std_of_empiral_var)"
-        @test (var(samples_day_5) - 5) < 5 * theoretical_std_of_empiral_var &&
-              (var(samples_day_5) - 5) > -5 * theoretical_std_of_empiral_var
-
-    end
+    @info "var = $(var(samples_day_5)); theoretical_std_of_empiral_var = $(theoretical_std_of_empiral_var)"
+    @test (var(samples_day_5) - 5) < 5 * theoretical_std_of_empiral_var &&
+          (var(samples_day_5) - 5) > -5 * theoretical_std_of_empiral_var
 
 end

EpiAware/test/test_utilities.jl

@@ -1,4 +1,4 @@
-@testset "Testing scan function with addition" begin
+@testitem "Testing scan function with addition" begin
     # Test case 1: Testing with addition function
     function add(a, b)
         return a + b, a + b
@@ -12,7 +12,7 @@
     @test carry == expected_carry
 end
 
-@testset "Testing scan function with multiplication" begin
+@testitem "Testing scan function with multiplication" begin
     # Test case 2: Testing with multiplication function
     function multiply(a, b)
         return a * b, a * b
@@ -27,7 +27,8 @@ end
     @test carry == expected_carry
 end
 
-@testset "Testing create_discrete_pmf function" begin
+@testitem "Testing create_discrete_pmf function" begin
+    using Distributions
     # Test case 1: Testing with a non-negative distribution
     @testset "Test case 1" begin
         dist = Normal()
@@ -79,7 +80,8 @@ end
     end
 
 end
-@testset "Testing growth_rate_to_reproductive_ratio function" begin
+
+@testitem"Testing growth_rate_to_reproductive_ratio function" begin
     #Test that zero exp growth rate imples R0 = 1
     @testset "Test case 1" begin
         r = 0