From 13c62d9a79d18e368759563254acbb4be60ceee1 Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 11:50:40 +0100 Subject: [PATCH 01/26] add benchmark workflow --- .github/workflows/benchmark-EpiAware.yaml | 28 +++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 .github/workflows/benchmark-EpiAware.yaml diff --git a/.github/workflows/benchmark-EpiAware.yaml b/.github/workflows/benchmark-EpiAware.yaml new file mode 100644 index 000000000..ad849703f --- /dev/null +++ b/.github/workflows/benchmark-EpiAware.yaml @@ -0,0 +1,28 @@ +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: Run benchmarks + run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge()' + - name: Post results + run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.postjudge()' + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} From a8a149a157420ce0fcd4f2fe3dcd8f9e195eb03e Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 11:56:13 +0100 Subject: [PATCH 02/26] make sure to install benchmark deps --- .github/workflows/benchmark-EpiAware.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/benchmark-EpiAware.yaml b/.github/workflows/benchmark-EpiAware.yaml index ad849703f..b91b239de 100644 --- a/.github/workflows/benchmark-EpiAware.yaml +++ b/.github/workflows/benchmark-EpiAware.yaml @@ -20,6 +20,8 @@ jobs: - 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.instantiate()' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge()' - name: Post results From 143243f2e6b43ae41b1ebafb52b31f12f276142b Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 12:02:01 +0100 Subject: [PATCH 03/26] add benchmark folder --- .github/workflows/benchmark-EpiAware.yaml | 2 +- EpiAware/.gitignore | 4 ++++ EpiAware/benchmark/Project.toml | 5 +++++ 3 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 EpiAware/benchmark/Project.toml diff --git a/.github/workflows/benchmark-EpiAware.yaml b/.github/workflows/benchmark-EpiAware.yaml index b91b239de..75692bdd1 100644 --- a/.github/workflows/benchmark-EpiAware.yaml +++ b/.github/workflows/benchmark-EpiAware.yaml @@ -23,7 +23,7 @@ jobs: - name: Setup benchmark environment run: julia --project=benchmark -e 'using Pkg; Pkg.instantiate()' - name: Run benchmarks - run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge()' + 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: diff --git a/EpiAware/.gitignore b/EpiAware/.gitignore index 352da8fa0..bc49b4cee 100644 --- a/EpiAware/.gitignore +++ b/EpiAware/.gitignore @@ -42,3 +42,7 @@ docs/build *.zip .DS_Store + +# benchmark ignore +/.benchmarkci +/benchmark/*.json diff --git a/EpiAware/benchmark/Project.toml b/EpiAware/benchmark/Project.toml new file mode 100644 index 000000000..37b4c1e33 --- /dev/null +++ b/EpiAware/benchmark/Project.toml @@ -0,0 +1,5 @@ +[deps] +BenchmarkCI = "20533458-34a3-403d-a444-e18f38190b5b" +BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" +EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855" +PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d" From 3ebcdcea31caba9939696ec5f1880cb3d82287d4 Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 12:10:53 +0100 Subject: [PATCH 04/26] add infracstructure to run benchmarks --- EpiAware/benchmark/benchmarks.jl | 7 +++++++ EpiAware/benchmark/runbenchmarks.jl | 11 +++++++++++ 2 files changed, 18 insertions(+) create mode 100644 EpiAware/benchmark/benchmarks.jl create mode 100644 EpiAware/benchmark/runbenchmarks.jl diff --git a/EpiAware/benchmark/benchmarks.jl b/EpiAware/benchmark/benchmarks.jl new file mode 100644 index 000000000..d980f8832 --- /dev/null +++ b/EpiAware/benchmark/benchmarks.jl @@ -0,0 +1,7 @@ +using BenchmarkTools +SUITE = BenchmarkGroup() +for file in readdir(joinpath(@__DIR__, "bench")) + if endswith(file, ".jl") + SUITE[basename(file, ".jl")] = include(joinpath(@__DIR__, "bench", file)) + end +end diff --git a/EpiAware/benchmark/runbenchmarks.jl b/EpiAware/benchmark/runbenchmarks.jl new file mode 100644 index 000000000..3041bdb2d --- /dev/null +++ b/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") +) From 11feb0eb0732ef9f479ca281448da7186f2c3985 Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 12:28:40 +0100 Subject: [PATCH 05/26] add a proposed structure for future benchmarks --- EpiAware/benchmark/Project.toml | 1 + .../benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl | 10 ++++++++++ EpiAware/benchmark/bench/EpiAwareUtils/censored_pmf.jl | 5 +++++ EpiAware/benchmark/benchmarks.jl | 10 +++++++--- 4 files changed, 23 insertions(+), 3 deletions(-) create mode 100644 EpiAware/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl create mode 100644 EpiAware/benchmark/bench/EpiAwareUtils/censored_pmf.jl diff --git a/EpiAware/benchmark/Project.toml b/EpiAware/benchmark/Project.toml index 37b4c1e33..1a606ac46 100644 --- a/EpiAware/benchmark/Project.toml +++ b/EpiAware/benchmark/Project.toml @@ -1,5 +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" diff --git a/EpiAware/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl b/EpiAware/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl new file mode 100644 index 000000000..c0a80834b --- /dev/null +++ b/EpiAware/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl @@ -0,0 +1,10 @@ +module BenchEpiAwareUtils + +using BenchmarkTools, EpiAware + +suite = BenchmarkGroup() + +include("censored_pmf.jl") + +end +BenchEpiAwareUtils.suite diff --git a/EpiAware/benchmark/bench/EpiAwareUtils/censored_pmf.jl b/EpiAware/benchmark/bench/EpiAwareUtils/censored_pmf.jl new file mode 100644 index 000000000..15c3d7db7 --- /dev/null +++ b/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 diff --git a/EpiAware/benchmark/benchmarks.jl b/EpiAware/benchmark/benchmarks.jl index d980f8832..d87c1a7fa 100644 --- a/EpiAware/benchmark/benchmarks.jl +++ b/EpiAware/benchmark/benchmarks.jl @@ -1,7 +1,11 @@ using BenchmarkTools SUITE = BenchmarkGroup() -for file in readdir(joinpath(@__DIR__, "bench")) - if endswith(file, ".jl") - SUITE[basename(file, ".jl")] = include(joinpath(@__DIR__, "bench", file)) +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 From a0c6aed468ee5bcb7e1fe4ef3bf5de7ef43ea153 Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 12:38:28 +0100 Subject: [PATCH 06/26] fix action indexing --- .github/workflows/benchmark-EpiAware.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/benchmark-EpiAware.yaml b/.github/workflows/benchmark-EpiAware.yaml index 75692bdd1..b3374cbf7 100644 --- a/.github/workflows/benchmark-EpiAware.yaml +++ b/.github/workflows/benchmark-EpiAware.yaml @@ -4,9 +4,10 @@ on: pull_request: merge_group: - concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: Benchmark: runs-on: ubuntu-latest From 7488991731a83f0552cd9389e87b6f2c42b8f51f Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 12:44:04 +0100 Subject: [PATCH 07/26] tweak action for detection of local EpiAware --- .github/workflows/benchmark-EpiAware.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark-EpiAware.yaml b/.github/workflows/benchmark-EpiAware.yaml index b3374cbf7..f049efe50 100644 --- a/.github/workflows/benchmark-EpiAware.yaml +++ b/.github/workflows/benchmark-EpiAware.yaml @@ -22,7 +22,7 @@ jobs: - uses: julia-actions/cache@v1 - uses: julia-actions/julia-buildpkg@v1 - name: Setup benchmark environment - run: julia --project=benchmark -e 'using Pkg; Pkg.instantiate()' + run: julia --project=benchmark -e 'using Pkg; Pkg.activate(shared = TRUE)' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(baseline = "origin/main")' - name: Post results From 0e54c944424655ba34c8bb3fdd82b846fdd8979e Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 12:45:12 +0100 Subject: [PATCH 08/26] tweak action for detection of local EpiAware --- .github/workflows/benchmark-EpiAware.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark-EpiAware.yaml b/.github/workflows/benchmark-EpiAware.yaml index f049efe50..419600335 100644 --- a/.github/workflows/benchmark-EpiAware.yaml +++ b/.github/workflows/benchmark-EpiAware.yaml @@ -22,7 +22,7 @@ jobs: - uses: julia-actions/cache@v1 - uses: julia-actions/julia-buildpkg@v1 - name: Setup benchmark environment - run: julia --project=benchmark -e 'using Pkg; Pkg.activate(shared = TRUE)' + run: julia --project=benchmark -e 'using Pkg; Pkg.activate(shared = true)' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(baseline = "origin/main")' - name: Post results From 8be1faf48c8a38fe9cddd2463b31912296fcb4b0 Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 12:52:25 +0100 Subject: [PATCH 09/26] add benchmark run --- .github/workflows/benchmark-EpiAware.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark-EpiAware.yaml b/.github/workflows/benchmark-EpiAware.yaml index 419600335..a0aff65c4 100644 --- a/.github/workflows/benchmark-EpiAware.yaml +++ b/.github/workflows/benchmark-EpiAware.yaml @@ -22,7 +22,7 @@ jobs: - uses: julia-actions/cache@v1 - uses: julia-actions/julia-buildpkg@v1 - name: Setup benchmark environment - run: julia --project=benchmark -e 'using Pkg; Pkg.activate(shared = true)' + 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 From 3a835e46d38f03a50bb18edef146f55dacc97028 Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 15:22:57 +0100 Subject: [PATCH 10/26] move benchmarks to the top level and wrap everything in a utility package --- .../{benchmark-EpiAware.yaml => benchmark.yaml} | 15 ++++++--------- .gitignore | 4 ++++ Project.toml | 8 ++++++++ {EpiAware/benchmark => benchmark}/Project.toml | 2 ++ .../bench/EpiAwareUtils/EpiAwareUtils.jl | 0 .../bench/EpiAwareUtils/censored_pmf.jl | 0 {EpiAware/benchmark => benchmark}/benchmarks.jl | 0 .../benchmark => benchmark}/runbenchmarks.jl | 0 src/Rtwithoutrenewal.jl | 3 +++ 9 files changed, 23 insertions(+), 9 deletions(-) rename .github/workflows/{benchmark-EpiAware.yaml => benchmark.yaml} (62%) create mode 100644 Project.toml rename {EpiAware/benchmark => benchmark}/Project.toml (70%) rename {EpiAware/benchmark => benchmark}/bench/EpiAwareUtils/EpiAwareUtils.jl (100%) rename {EpiAware/benchmark => benchmark}/bench/EpiAwareUtils/censored_pmf.jl (100%) rename {EpiAware/benchmark => benchmark}/benchmarks.jl (100%) rename {EpiAware/benchmark => benchmark}/runbenchmarks.jl (100%) create mode 100644 src/Rtwithoutrenewal.jl diff --git a/.github/workflows/benchmark-EpiAware.yaml b/.github/workflows/benchmark.yaml similarity index 62% rename from .github/workflows/benchmark-EpiAware.yaml rename to .github/workflows/benchmark.yaml index a0aff65c4..d07322dce 100644 --- a/.github/workflows/benchmark-EpiAware.yaml +++ b/.github/workflows/benchmark.yaml @@ -1,8 +1,12 @@ -name: Run EpiAware benchmarks +name: Run benchmarks on: pull_request: + paths: + - 'EpiAware/**' merge_group: + paths: + - 'EpiAware/**' concurrency: group: ${{ github.workflow }}-${{ github.ref }} @@ -13,18 +17,11 @@ jobs: 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")' + 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: diff --git a/.gitignore b/.gitignore index 759bf3179..34c9b96bc 100644 --- a/.gitignore +++ b/.gitignore @@ -385,3 +385,7 @@ docs/site/ #Ignore generated Pluto notebooks EpiAware/docs/src/examples/*.md + +# benchmark ignore +/.benchmarkci +/benchmark/*.json diff --git a/Project.toml b/Project.toml new file mode 100644 index 000000000..cad82ab95 --- /dev/null +++ b/Project.toml @@ -0,0 +1,8 @@ +name = "Rtwithoutrenewal" +uuid = "5f18122a-2e46-11ef-2c26-2d57cbc8fe48" +authors = ["Samuel Abbott ", "Samuel Brand ", "Zachary Susswein "] +version = "0.1.0-DEV" + +[deps] +EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855" +EpiAwarePipeline = "66314692-3678-4cbb-b3ac-6fcb54505317" diff --git a/EpiAware/benchmark/Project.toml b/benchmark/Project.toml similarity index 70% rename from EpiAware/benchmark/Project.toml rename to benchmark/Project.toml index 1a606ac46..de0addb96 100644 --- a/EpiAware/benchmark/Project.toml +++ b/benchmark/Project.toml @@ -3,4 +3,6 @@ BenchmarkCI = "20533458-34a3-403d-a444-e18f38190b5b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855" +EpiAwarePipeline = "66314692-3678-4cbb-b3ac-6fcb54505317" PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d" +Rtwithoutrenewal = "5f18122a-2e46-11ef-2c26-2d57cbc8fe48" diff --git a/EpiAware/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl b/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl similarity index 100% rename from EpiAware/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl rename to benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl diff --git a/EpiAware/benchmark/bench/EpiAwareUtils/censored_pmf.jl b/benchmark/bench/EpiAwareUtils/censored_pmf.jl similarity index 100% rename from EpiAware/benchmark/bench/EpiAwareUtils/censored_pmf.jl rename to benchmark/bench/EpiAwareUtils/censored_pmf.jl diff --git a/EpiAware/benchmark/benchmarks.jl b/benchmark/benchmarks.jl similarity index 100% rename from EpiAware/benchmark/benchmarks.jl rename to benchmark/benchmarks.jl diff --git a/EpiAware/benchmark/runbenchmarks.jl b/benchmark/runbenchmarks.jl similarity index 100% rename from EpiAware/benchmark/runbenchmarks.jl rename to benchmark/runbenchmarks.jl diff --git a/src/Rtwithoutrenewal.jl b/src/Rtwithoutrenewal.jl new file mode 100644 index 000000000..bbeebe0e0 --- /dev/null +++ b/src/Rtwithoutrenewal.jl @@ -0,0 +1,3 @@ +module Rtwithoutrenewal + +end From 80b423a9ff8e553bb7e9de9b0abb4fc89da840de Mon Sep 17 00:00:00 2001 From: Sam Date: Wed, 19 Jun 2024 15:28:35 +0100 Subject: [PATCH 11/26] add in subdirectory builds --- .github/workflows/benchmark.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index d07322dce..e88874294 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -19,6 +19,10 @@ jobs: - uses: actions/checkout@v4 - uses: julia-actions/setup-julia@v1 - uses: julia-actions/cache@v1 + - name: Build EpiAware + run: julia --project=EpiAware -e 'using Pkg; Pkg.build()' + - name: Build EpiAwarePipeline + run: julia --project=EpiAwarePipeline -e 'using Pkg; Pkg.build()' - uses: julia-actions/julia-buildpkg@v1 - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' From bfbf9fcb0b897fec08d581a542f0a8493da7d826 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Wed, 19 Jun 2024 16:31:43 +0100 Subject: [PATCH 12/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index e88874294..91cd24763 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -19,11 +19,6 @@ jobs: - uses: actions/checkout@v4 - uses: julia-actions/setup-julia@v1 - uses: julia-actions/cache@v1 - - name: Build EpiAware - run: julia --project=EpiAware -e 'using Pkg; Pkg.build()' - - name: Build EpiAwarePipeline - run: julia --project=EpiAwarePipeline -e 'using Pkg; Pkg.build()' - - uses: julia-actions/julia-buildpkg@v1 - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' - name: Post results From 68c13cbb4bc5c008bbf99993625888751fc882cd Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Wed, 19 Jun 2024 16:33:55 +0100 Subject: [PATCH 13/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index 91cd24763..d11a5bb27 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -19,6 +19,8 @@ jobs: - uses: actions/checkout@v4 - uses: julia-actions/setup-julia@v1 - uses: julia-actions/cache@v1 + - name: Instal dependencies + run: julia --project=benchmark -e 'using Pkg; Pkg.instantiate()' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' - name: Post results From 0e31d2c5ea79bf4d1d8e0e3a2b608c26e1473264 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Wed, 19 Jun 2024 16:43:43 +0100 Subject: [PATCH 14/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index d11a5bb27..137f069a1 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -20,7 +20,13 @@ jobs: - uses: julia-actions/setup-julia@v1 - uses: julia-actions/cache@v1 - name: Instal dependencies - run: julia --project=benchmark -e 'using Pkg; Pkg.instantiate()' + run: | + julia --project=benchmark -e ' + using Pkg; + Pkg.develop("../Rt-without-renewal"); + Pkg.develop("./EpiAware"); + Pkg.develop("./pipeline"); + Pkg.instantiate()' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' - name: Post results From 110b36e167693b1156bc23b240a298de598696e2 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Wed, 19 Jun 2024 16:45:31 +0100 Subject: [PATCH 15/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index 137f069a1..38eff63ca 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -23,9 +23,9 @@ jobs: run: | julia --project=benchmark -e ' using Pkg; - Pkg.develop("../Rt-without-renewal"); - Pkg.develop("./EpiAware"); - Pkg.develop("./pipeline"); + Pkg.develop(path = "../Rt-without-renewal"); + Pkg.develop(path = "./EpiAware"); + Pkg.develop(path = "./pipeline"); Pkg.instantiate()' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' From ac136d58241251946289077206d3d3834f553a66 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Wed, 19 Jun 2024 16:47:15 +0100 Subject: [PATCH 16/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index 38eff63ca..6979c64b8 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -23,9 +23,9 @@ jobs: run: | julia --project=benchmark -e ' using Pkg; - Pkg.develop(path = "../Rt-without-renewal"); Pkg.develop(path = "./EpiAware"); Pkg.develop(path = "./pipeline"); + Pkg.develop(path = "../Rt-without-renewal"); Pkg.instantiate()' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' From 623a759f102cbb2f7a23c64f166c7ae212b22fb8 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Wed, 19 Jun 2024 16:48:58 +0100 Subject: [PATCH 17/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index 6979c64b8..6e6eb0a0f 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -23,8 +23,8 @@ jobs: run: | julia --project=benchmark -e ' using Pkg; - Pkg.develop(path = "./EpiAware"); - Pkg.develop(path = "./pipeline"); + Pkg.develop("./EpiAware"); + Pkg.develop("./EpiAwarePipeline"); Pkg.develop(path = "../Rt-without-renewal"); Pkg.instantiate()' - name: Run benchmarks From c267c85547be5365245d9527756cfdb4a3f2c0a2 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Wed, 19 Jun 2024 16:50:30 +0100 Subject: [PATCH 18/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index 6e6eb0a0f..74409079b 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -19,13 +19,13 @@ jobs: - uses: actions/checkout@v4 - uses: julia-actions/setup-julia@v1 - uses: julia-actions/cache@v1 - - name: Instal dependencies + - name: Install dependencies run: | julia --project=benchmark -e ' using Pkg; - Pkg.develop("./EpiAware"); - Pkg.develop("./EpiAwarePipeline"); - Pkg.develop(path = "../Rt-without-renewal"); + Pkg.develop("EpiAware"); + Pkg.develop("EpiAwarePipeline"); + Pkg.develop("Rtwithoutrenewal"); Pkg.instantiate()' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' From 4e2ca1b7682e1cb7b3867ea73e727817b470b339 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Thu, 20 Jun 2024 12:20:33 +0100 Subject: [PATCH 19/26] Update Rtwithoutrenewal.jl --- src/Rtwithoutrenewal.jl | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/Rtwithoutrenewal.jl b/src/Rtwithoutrenewal.jl index bbeebe0e0..225d6b2ca 100644 --- a/src/Rtwithoutrenewal.jl +++ b/src/Rtwithoutrenewal.jl @@ -1,3 +1,6 @@ module Rtwithoutrenewal +using EpiAware +using EpiAwarePipeline + end From 56c3d852879e4c62b8d449c567c29c4a52cfd9fd Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Thu, 20 Jun 2024 12:21:14 +0100 Subject: [PATCH 20/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index 74409079b..fb2e00c86 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -20,13 +20,7 @@ jobs: - uses: julia-actions/setup-julia@v1 - uses: julia-actions/cache@v1 - name: Install dependencies - run: | - julia --project=benchmark -e ' - using Pkg; - Pkg.develop("EpiAware"); - Pkg.develop("EpiAwarePipeline"); - Pkg.develop("Rtwithoutrenewal"); - Pkg.instantiate()' + run: julia --project=benchmark -e 'Pkg; Pkg.instantiate()' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' - name: Post results From 6d02b23fdb04f8355f2684df58e5d6e24f18f9a3 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Thu, 20 Jun 2024 12:22:13 +0100 Subject: [PATCH 21/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index fb2e00c86..45f83231e 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -20,7 +20,7 @@ jobs: - uses: julia-actions/setup-julia@v1 - uses: julia-actions/cache@v1 - name: Install dependencies - run: julia --project=benchmark -e 'Pkg; Pkg.instantiate()' + run: julia --project=benchmark -e 'using Pkg; Pkg.instantiate()' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' - name: Post results From 07ea3c86f30d1728c6b99a7bb1be759a7ccab2b9 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Fri, 21 Jun 2024 12:36:55 +0100 Subject: [PATCH 22/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index 45f83231e..1c9781cec 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -20,7 +20,13 @@ jobs: - uses: julia-actions/setup-julia@v1 - uses: julia-actions/cache@v1 - name: Install dependencies - run: julia --project=benchmark -e 'using Pkg; Pkg.instantiate()' + run: | + julia --project=benchmark -e 'using Pkg; + Pkg.remove("EpiAware"); + Pkg.remove("EpiAwarePipeline"); + Pkg.develop("./EpiAware"); + Pkg.develop("./pipeline"); + Pkg.instantiate()' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' - name: Post results From f595f5c4b6dd68869e28f4922e53cf3802c69215 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Fri, 21 Jun 2024 12:38:07 +0100 Subject: [PATCH 23/26] Update Project.toml --- benchmark/Project.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/benchmark/Project.toml b/benchmark/Project.toml index de0addb96..c8b3a4241 100644 --- a/benchmark/Project.toml +++ b/benchmark/Project.toml @@ -5,4 +5,3 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855" EpiAwarePipeline = "66314692-3678-4cbb-b3ac-6fcb54505317" PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d" -Rtwithoutrenewal = "5f18122a-2e46-11ef-2c26-2d57cbc8fe48" From 927a36ecd6f03e822c2847914bd200142a207910 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Fri, 21 Jun 2024 12:40:58 +0100 Subject: [PATCH 24/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index 1c9781cec..ef7913ffc 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -22,11 +22,11 @@ jobs: - name: Install dependencies run: | julia --project=benchmark -e 'using Pkg; - Pkg.remove("EpiAware"); - Pkg.remove("EpiAwarePipeline"); + Pkg.rm("EpiAware"); + Pkg.rm("EpiAwarePipeline"); + Pkg.instantiate(); Pkg.develop("./EpiAware"); - Pkg.develop("./pipeline"); - Pkg.instantiate()' + Pkg.develop("./pipeline")' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' - name: Post results From e18c555db5e05e1827dd0c1248e5a4f355d93af6 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Fri, 21 Jun 2024 12:42:20 +0100 Subject: [PATCH 25/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index ef7913ffc..20df56b04 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -24,6 +24,7 @@ jobs: julia --project=benchmark -e 'using Pkg; Pkg.rm("EpiAware"); Pkg.rm("EpiAwarePipeline"); + Pkg.resolve(); Pkg.instantiate(); Pkg.develop("./EpiAware"); Pkg.develop("./pipeline")' From df9120a9ad13a6085473963d5bfd512800bab0a6 Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Fri, 21 Jun 2024 12:43:57 +0100 Subject: [PATCH 26/26] Update benchmark.yaml --- .github/workflows/benchmark.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/benchmark.yaml b/.github/workflows/benchmark.yaml index 20df56b04..098af0cf3 100644 --- a/.github/workflows/benchmark.yaml +++ b/.github/workflows/benchmark.yaml @@ -26,8 +26,8 @@ jobs: Pkg.rm("EpiAwarePipeline"); Pkg.resolve(); Pkg.instantiate(); - Pkg.develop("./EpiAware"); - Pkg.develop("./pipeline")' + Pkg.develop(path = "./EpiAware"); + Pkg.develop(path = "./pipeline")' - name: Run benchmarks run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")' - name: Post results