Create run_testmode_pipeline.jl

pipeline/scripts/run_testmode_pipeline.jl

@@ -0,0 +1,31 @@
+# Local environment script to run the analysis pipeline
+using Pkg
+Pkg.activate(joinpath(@__DIR__(), ".."))
+using Dagger
+
+@assert !isempty(ARGS) "Test mode script requires the number of draws as an argument."
+ndraws = parse(Int64, ARGS[1])
+
+@info("""
+      Running the analysis pipeline in test mode with $(ndraws) draws per model.
+      --------------------------------------------
+      """)
+
+# Define the backend resources to use for the pipeline
+# in this case we are using distributed local workers with loaded modules
+using Distributed
+pids = addprocs(; exeflags = ["--project=$(Base.active_project())"])
+
+@everywhere using EpiAwarePipeline
+
+# Create an instance of the pipeline behaviour
+
+pipelines = [
+    SmoothOutbreakPipeline(ndraws = ndraws), MeasuresOutbreakPipeline(ndraws = ndraws),
+    SmoothEndemicPipeline(ndraws = ndraws), RoughEndemicPipeline(ndraws = ndraws)]
+
+# Run the pipeline
+do_pipeline(pipelines)
+
+# Remove the workers
+rmprocs(pids)

pipeline/src/infer/inference_prefix.jl

@@ -1,3 +1,26 @@
+"""
+This is an internal method that generates part of the prefix for the inference
+    results file name from the truth data and inference configuration.
+"""
+function _prefix_from_config(truthdata, inference_config)
+    igp_str = string(inference_config["igp"]) |> str -> split(str, ".")[end]
+
+    return "_igp_" * igp_str * "_latentmodel_" *
+           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
+           string(truthdata["truth_gi_mean"]) * "_inference_T_" *
+           string(inference_config["T"])
+end
+
+"""
+This is an internal method that generates the part of the prefix for the inference
+    results file name from the pipeline.
+"""
+_prefix_from_pipeline(pipeline::AbstractEpiAwarePipeline) = "observables"
+_prefix_from_pipeline(pipeline::SmoothOutbreakPipeline) = "smooth_outbreak"
+_prefix_from_pipeline(pipeline::MeasuresOutbreakPipeline) = "measures_outbreak"
+_prefix_from_pipeline(pipeline::SmoothEndemicPipeline) = "smooth_endemic"
+_prefix_from_pipeline(pipeline::RoughEndemicPipeline) = "rough_endemic"
+
 """
 This is an internal method that generates the prefix for the inference results file name.
 """
@@ -24,31 +47,12 @@ function _inference_prefix(
            string(inference_config["gi_mean"])
 end
 
-function _inference_prefix(truthdata, inference_config, pipeline::SmoothOutbreakPipeline)
-    return "smooth_outbreak" * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
-           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
-           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
-           string(inference_config["gi_mean"])
-end
-
-function _inference_prefix(truthdata, inference_config, pipeline::MeasuresOutbreakPipeline)
-    return "measures_outbreak" * "_igp_" * string(inference_config["igp"]) *
-           "_latentmodel_" *
-           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
-           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
-           string(inference_config["gi_mean"])
-end
-
-function _inference_prefix(truthdata, inference_config, pipeline::SmoothEndemicPipeline)
-    return "smooth_endemic" * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
-           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
-           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
-           string(inference_config["gi_mean"])
-end
-
-function _inference_prefix(truthdata, inference_config, pipeline::RoughEndemicPipeline)
-    return "rough_endemic" * "_igp_" * string(inference_config["igp"]) * "_latentmodel_" *
-           inference_config["latent_namemodels"].first * "_truth_gi_mean_" *
-           string(truthdata["truth_gi_mean"]) * "_used_gi_mean_" *
-           string(inference_config["gi_mean"])
+"""
+This is an internal method that generates the prefix for the inference results file name for
+    `pipeline` objects of type `AbstractRtwithoutRenewalPipeline`.
+"""
+function _inference_prefix(
+        truthdata, inference_config, pipeline::AbstractRtwithoutRenewalPipeline)
+    return _prefix_from_pipeline(pipeline) *
+           _prefix_from_config(truthdata, inference_config)
 end

pipeline/src/pipeline/do_pipeline.jl

@@ -22,7 +22,7 @@ Perform the pipeline for each `AbstractEpiAwarePipeline` in the given vector `pi
 """
 function do_pipeline(pipelines::Vector{<:AbstractEpiAwarePipeline})
     map(pipelines) do pipeline
-        Dagger.@spawn do_pipeline(pipeline)
+        do_pipeline(pipeline)
     end
     return nothing
 end

pipeline/test/pipeline/test_pipelinefunctions.jl

@@ -37,13 +37,3 @@ end
     res = do_pipeline(pipelines)
     @test isnothing(res)
 end
-
-@testset "do_pipeline test: main scenarios" begin
-    using EpiAwarePipeline
-    pipelines = [SmoothOutbreakPipeline(ndraws = 20, nchains = 1),
-        MeasuresOutbreakPipeline(ndraws = 20, nchains = 1),
-        SmoothEndemicPipeline(ndraws = 20, nchains = 1),
-        RoughEndemicPipeline(ndraws = 20, nchains = 1)]
-    res = do_pipeline(pipelines)
-    @test isnothing(res)
-end