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Put HMMTest and HMMBenchmarks into libs/
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gdalle committed Dec 11, 2023
1 parent 24385f7 commit 5f13f80
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3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,8 @@
/Manifest.toml
/docs/build/
/docs/Manifest.toml
/benchmark/HMMBenchmark/Manifest.toml
/test/Manifest.toml
/libs/**/Manifest.toml

scratchpad.jl

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43 changes: 2 additions & 41 deletions Project.toml
Original file line number Diff line number Diff line change
Expand Up @@ -13,18 +13,17 @@ PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Requires = "ae029012-a4dd-5104-9daa-d747884805df"
SimpleUnPack = "ce78b400-467f-4804-87d8-8f486da07d0a"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
StatsAPI = "82ae8749-77ed-4fe6-ae5f-f523153014b0"

[weakdeps]
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
HMMBase = "b2b3ca75-8444-5ffa-85e6-af70e2b64fe7"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[extensions]
HiddenMarkovModelsDistributionsExt = "Distributions"
HiddenMarkovModelsHMMBaseExt = "HMMBase"
HiddenMarkovModelsTestExt = "Test"
HiddenMarkovModelsSparseArraysExt = "SparseArrays"

[compat]
ChainRulesCore = "1.16"
Expand All @@ -40,43 +39,5 @@ Requires = "1.3"
SimpleUnPack = "1.1"
SparseArrays = "1"
StatsAPI = "1.6"
Test = "1"
julia = "1.6"

[extras]
Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
HMMBase = "b2b3ca75-8444-5ffa-85e6-af70e2b64fe7"
JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
SimpleUnPack = "ce78b400-467f-4804-87d8-8f486da07d0a"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"

[targets]
test = [
"Aqua",
"ComponentArrays",
"Distributions",
"Documenter",
"Enzyme",
"ForwardDiff",
"HMMBase",
"JET",
"JuliaFormatter",
"LinearAlgebra",
"Random",
"SimpleUnPack",
"SparseArrays",
"Statistics",
"Test",
"Zygote",
]
36 changes: 19 additions & 17 deletions benchmark/Manifest.toml
Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,9 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[deps.BenchmarkTools]]
deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"]
git-tree-sha1 = "d9a9701b899b30332bbcb3e1679c41cce81fb0e8"
git-tree-sha1 = "f1f03a9fa24271160ed7e73051fba3c1a759b53f"
uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
version = "1.3.2"
version = "1.4.0"

[[deps.CSV]]
deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"]
Expand Down Expand Up @@ -102,9 +102,9 @@ version = "0.4.0"

[[deps.Distributions]]
deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
git-tree-sha1 = "a6c00f894f24460379cb7136633cef54ac9f6f4a"
git-tree-sha1 = "9242eec9b7e2e14f9952e8ea1c7e31a50501d587"
uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
version = "0.25.103"
version = "0.25.104"
weakdeps = ["ChainRulesCore", "DensityInterface", "Test"]

[deps.Distributions.extensions]
Expand Down Expand Up @@ -155,7 +155,7 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"

[[deps.HMMBenchmark]]
deps = ["BenchmarkTools", "CSV", "DataFrames", "Distributions", "HiddenMarkovModels", "LinearAlgebra", "Pkg", "Random", "SimpleUnPack", "SparseArrays"]
path = "HMMBenchmark"
path = "../libs/HMMBenchmark"
uuid = "557005d5-2e4a-43f9-8aa7-ba8df2d03179"
version = "0.1.0"

Expand All @@ -169,18 +169,20 @@ version = "0.1.0"
PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"

[[deps.HiddenMarkovModels]]
deps = ["ChainRulesCore", "DensityInterface", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PrecompileTools", "Random", "Requires", "SimpleUnPack", "SparseArrays", "StatsAPI"]
deps = ["ChainRulesCore", "DensityInterface", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PrecompileTools", "Random", "Requires", "SimpleUnPack", "StatsAPI"]
path = ".."
uuid = "84ca31d5-effc-45e0-bfda-5a68cd981f47"
version = "0.4.0"

[deps.HiddenMarkovModels.extensions]
HiddenMarkovModelsDistributionsExt = "Distributions"
HiddenMarkovModelsHMMBaseExt = "HMMBase"
HiddenMarkovModelsSparseArraysExt = "SparseArrays"

[deps.HiddenMarkovModels.weakdeps]
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
HMMBase = "b2b3ca75-8444-5ffa-85e6-af70e2b64fe7"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[[deps.HypergeometricFunctions]]
deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
Expand Down Expand Up @@ -330,21 +332,21 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
version = "0.5.5+0"

[[deps.OrderedCollections]]
git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3"
git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.6.2"
version = "1.6.3"

[[deps.PDMats]]
deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
git-tree-sha1 = "66b2fcd977db5329aa35cac121e5b94dd6472198"
git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65"
uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
version = "0.11.28"
version = "0.11.31"

[[deps.Parsers]]
deps = ["Dates", "PrecompileTools", "UUIDs"]
git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
git-tree-sha1 = "a935806434c9d4c506ba941871b327b96d41f2bf"
uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
version = "2.7.2"
version = "2.8.0"

[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
Expand All @@ -370,10 +372,10 @@ uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.4.1"

[[deps.PrettyTables]]
deps = ["Crayons", "LaTeXStrings", "Markdown", "Printf", "Reexport", "StringManipulation", "Tables"]
git-tree-sha1 = "6842ce83a836fbbc0cfeca0b5a4de1a4dcbdb8d1"
deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"]
git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660"
uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
version = "2.2.8"
version = "2.3.1"

[[deps.Printf]]
deps = ["Unicode"]
Expand Down Expand Up @@ -474,9 +476,9 @@ version = "1.7.0"

[[deps.StatsBase]]
deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916"
git-tree-sha1 = "1d77abd07f617c4868c33d4f5b9e1dbb2643c9cf"
uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
version = "0.33.21"
version = "0.34.2"

[[deps.StatsFuns]]
deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
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4 changes: 2 additions & 2 deletions benchmark/benchmarks.jl
Original file line number Diff line number Diff line change
Expand Up @@ -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, 64)
for nb_states in (4, 16, 64)
push!(
configurations,
Configuration(;
sparse, nb_states, obs_dim=1, seq_length=100, nb_seqs=100, bw_iter=1
sparse=false, nb_states, obs_dim=1, seq_length=100, nb_seqs=100, bw_iter=1
),
)
end
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2 changes: 1 addition & 1 deletion benchmark/tune.json
Original file line number Diff line number Diff line change
@@ -1 +1 @@
[{"Julia":"1.9.4","BenchmarkTools":"1.0.0"},[["BenchmarkGroup",{"data":{"HiddenMarkovModels.jl":["BenchmarkGroup",{"data":{"(1, 16, 1, 100, 100, 1)":["BenchmarkGroup",{"data":{"viterbi_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"logdensity":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"rand":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"viterbi!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"(0, 16, 1, 100, 100, 1)":["BenchmarkGroup",{"data":{"viterbi_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"logdensity":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"rand":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"viterbi!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"(1, 4, 1, 100, 100, 1)":["BenchmarkGroup",{"data":{"viterbi_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"logdensity":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"rand":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"viterbi!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"(0, 4, 1, 100, 100, 1)":["BenchmarkGroup",{"data":{"viterbi_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"logdensity":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"rand":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"viterbi!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"(1, 64, 1, 100, 100, 1)":["BenchmarkGroup",{"data":{"viterbi_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"logdensity":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"baum_welch!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"forward_backward_init":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"rand":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"viterbi!":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"(0, 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