Issue 274: Add continuous benchmark structure

.github/workflows/benchmark-EpiAware.yaml

@@ -0,0 +1,31 @@
+name: Run EpiAware benchmarks
+
+on:
+  pull_request:
+  merge_group:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  Benchmark:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: EpiAware
+          sparse-checkout-cone-mode: false
+      - name: Move EpiAware to root
+        run: mv EpiAware/* .
+      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: Setup benchmark environment
+        run: julia --project=benchmark -e 'using Pkg; Pkg.activate("benchmark-run"; shared = true)'
+      - name: Run benchmarks
+        run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(baseline = "origin/main")'
+      - name: Post results
+        run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.postjudge()'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

EpiAware/.gitignore

@@ -42,3 +42,7 @@ docs/build
 *.zip
 
 .DS_Store
+
+# benchmark ignore
+/.benchmarkci
+/benchmark/*.json

EpiAware/benchmark/Project.toml

@@ -0,0 +1,6 @@
+[deps]
+BenchmarkCI = "20533458-34a3-403d-a444-e18f38190b5b"
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855"
+PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d"

EpiAware/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl

@@ -0,0 +1,10 @@
+module BenchEpiAwareUtils
+
+using BenchmarkTools, EpiAware
+
+suite = BenchmarkGroup()
+
+include("censored_pmf.jl")
+
+end
+BenchEpiAwareUtils.suite

EpiAware/benchmark/bench/EpiAwareUtils/censored_pmf.jl

@@ -0,0 +1,5 @@
+let
+    using Distributions
+    dist = Exponential(1.0)
+    suite["censored_pmf"] = @benchmarkable(censored_pmf($dist, Δd = 1.0, D = 3.0))
+end

EpiAware/benchmark/benchmarks.jl

@@ -0,0 +1,11 @@
+using BenchmarkTools
+SUITE = BenchmarkGroup()
+for folder in readdir(joinpath(@__DIR__, "bench"))
+    if isdir(joinpath(@__DIR__, "bench", folder))
+        suite_name = basename(folder)
+        suite_file = joinpath(@__DIR__, "bench", folder, "$suite_name.jl")
+        if isfile(suite_file)
+            SUITE[suite_name] = include(suite_file)
+        end
+    end
+end

EpiAware/benchmark/runbenchmarks.jl

@@ -0,0 +1,11 @@
+using PkgBenchmark
+benchmarkpkg(
+    dirname(@__DIR__),
+    BenchmarkConfig(
+        env = Dict(
+        "JULIA_NUM_THREADS" => "1",
+        "OMP_NUM_THREADS" => "1"
+    ),
+    ),
+    resultfile = joinpath(@__DIR__, "result.json")
+)