Shorter benchmarks

.github/workflows/benchmark.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   Benchmark:
     runs-on: ubuntu-latest
-    if: contains(github.event.pull_request.labels.*.name, 'run-benchmark')
+    if: contains(github.event.pull_request.labels.*.name, 'run benchmark')
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest

benchmark/HMMBenchmark/src/HMMBenchmark.jl

@@ -7,6 +7,8 @@ using Distributions: Normal, DiagNormal, PDiagMat
 using HiddenMarkovModels
 using HiddenMarkovModels:
     LightDiagNormal,
+    rand_prob_vec,
+    rand_trans_mat,
     initialize_viterbi,
     viterbi!,
     initialize_forward,

benchmark/Manifest.toml

@@ -4,11 +4,6 @@ julia_version = "1.9.4"
 manifest_format = "2.0"
 project_hash = "30d194898a132aa612114340054b3f9c8df83b1c"
 
-[[deps.ArgCheck]]
-git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4"
-uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197"
-version = "2.3.0"
-
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
 version = "1.1.1"
@@ -37,11 +32,15 @@ git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad"
 uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 version = "0.5.1"
 
-[[deps.Clustering]]
-deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"]
-git-tree-sha1 = "7ebbd653f74504447f1c33b91cd706a69a1b189f"
-uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
-version = "0.14.4"
+[[deps.ChainRulesCore]]
+deps = ["Compat", "LinearAlgebra"]
+git-tree-sha1 = "e0af648f0692ec1691b5d094b8724ba1346281cf"
+uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+version = "1.18.0"
+weakdeps = ["SparseArrays"]
+
+    [deps.ChainRulesCore.extensions]
+    ChainRulesCoreSparseArraysExt = "SparseArrays"
 
 [[deps.CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
@@ -101,36 +100,18 @@ git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b"
 uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
 version = "0.4.0"
 
-[[deps.Distances]]
-deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
-git-tree-sha1 = "5225c965635d8c21168e32a12954675e7bea1151"
-uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
-version = "0.10.10"
-
-    [deps.Distances.extensions]
-    DistancesChainRulesCoreExt = "ChainRulesCore"
-    DistancesSparseArraysExt = "SparseArrays"
-
-    [deps.Distances.weakdeps]
-    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-
 [[deps.Distributions]]
 deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
 git-tree-sha1 = "a6c00f894f24460379cb7136633cef54ac9f6f4a"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
 version = "0.25.103"
+weakdeps = ["ChainRulesCore", "DensityInterface", "Test"]
 
     [deps.Distributions.extensions]
     DistributionsChainRulesCoreExt = "ChainRulesCore"
     DistributionsDensityInterfaceExt = "DensityInterface"
     DistributionsTestExt = "Test"
 
-    [deps.Distributions.weakdeps]
-    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-    DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
-    Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
 [[deps.DocStringExtensions]]
 deps = ["LibGit2"]
 git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
@@ -172,12 +153,6 @@ weakdeps = ["SparseArrays", "Statistics"]
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
-[[deps.HMMBase]]
-deps = ["ArgCheck", "Clustering", "Distributions", "Hungarian", "LinearAlgebra", "Random"]
-git-tree-sha1 = "47d95dcc06cafd4a1c100bfad64da3ab06ad38c7"
-uuid = "b2b3ca75-8444-5ffa-85e6-af70e2b64fe7"
-version = "1.0.7"
-
 [[deps.HMMBenchmark]]
 deps = ["BenchmarkTools", "CSV", "DataFrames", "Distributions", "HiddenMarkovModels", "LinearAlgebra", "Pkg", "Random", "SimpleUnPack", "SparseArrays"]
 path = "HMMBenchmark"
@@ -194,27 +169,19 @@ version = "0.1.0"
     PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 
 [[deps.HiddenMarkovModels]]
-deps = ["DensityInterface", "DocStringExtensions", "LinearAlgebra", "PrecompileTools", "Random", "Requires", "SimpleUnPack", "SparseArrays", "StatsAPI"]
+deps = ["ChainRulesCore", "DensityInterface", "DocStringExtensions", "LinearAlgebra", "PrecompileTools", "Random", "Requires", "SimpleUnPack", "SparseArrays", "StatsAPI"]
 path = ".."
 uuid = "84ca31d5-effc-45e0-bfda-5a68cd981f47"
 version = "0.4.0"
 
     [deps.HiddenMarkovModels.extensions]
-    HiddenMarkovModelsChainRulesCoreExt = "ChainRulesCore"
     HiddenMarkovModelsDistributionsExt = "Distributions"
     HiddenMarkovModelsHMMBaseExt = "HMMBase"
 
     [deps.HiddenMarkovModels.weakdeps]
-    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
     HMMBase = "b2b3ca75-8444-5ffa-85e6-af70e2b64fe7"
 
-[[deps.Hungarian]]
-deps = ["LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "371a7df7a6cce5909d6c576f234a2da2e3fa0c98"
-uuid = "e91730f6-4275-51fb-a7a0-7064cfbd3b39"
-version = "0.6.0"
-
 [[deps.HypergeometricFunctions]]
 deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
 git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685"
@@ -342,12 +309,6 @@ git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 version = "1.0.2"
 
-[[deps.NearestNeighbors]]
-deps = ["Distances", "StaticArrays"]
-git-tree-sha1 = "2c3726ceb3388917602169bed973dbc97f1b51a8"
-uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
-version = "0.4.13"
-
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 version = "1.2.0"
@@ -495,28 +456,11 @@ deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_j
 git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
 version = "2.3.1"
+weakdeps = ["ChainRulesCore"]
 
     [deps.SpecialFunctions.extensions]
     SpecialFunctionsChainRulesCoreExt = "ChainRulesCore"
 
-    [deps.SpecialFunctions.weakdeps]
-    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-
-[[deps.StaticArrays]]
-deps = ["LinearAlgebra", "Random", "StaticArraysCore"]
-git-tree-sha1 = "0adf069a2a490c47273727e029371b31d44b72b2"
-uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.6.5"
-weakdeps = ["Statistics"]
-
-    [deps.StaticArrays.extensions]
-    StaticArraysStatisticsExt = "Statistics"
-
-[[deps.StaticArraysCore]]
-git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d"
-uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
-version = "1.4.2"
-
 [[deps.Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -539,15 +483,12 @@ deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Re
 git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 version = "1.3.0"
+weakdeps = ["ChainRulesCore", "InverseFunctions"]
 
     [deps.StatsFuns.extensions]
     StatsFunsChainRulesCoreExt = "ChainRulesCore"
     StatsFunsInverseFunctionsExt = "InverseFunctions"
 
-    [deps.StatsFuns.weakdeps]
-    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-    InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
-
 [[deps.StringManipulation]]
 deps = ["PrecompileTools"]
 git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5"

benchmark/benchmarks.jl

@@ -4,11 +4,11 @@ using BenchmarkTools
 implems = ("HiddenMarkovModels.jl",)
 algos = ("rand", "logdensity", "viterbi", "forward_backward", "baum_welch")
 configurations = []
-for sparse in (false, true), nb_states in (4, 16)
+for sparse in (false, true), nb_states in (4, 16, 64)
     push!(
         configurations,
         Configuration(;
-            sparse, nb_states, obs_dim=1, seq_length=1000, nb_seqs=100, bw_iter=10
+            sparse, nb_states, obs_dim=1, seq_length=100, nb_seqs=100, bw_iter=1
         ),
     )
 end

benchmark/run.jl

@@ -1,4 +1,4 @@
 include("benchmarks.jl")
 
-results = run(SUITE; verbose=true, samples=10)
+results = run(SUITE; verbose=true, samples=5)
 data = parse_results(minimum(results); path=joinpath(@__DIR__, "results.csv"))