diff --git a/.gitignore b/.gitignore index b5ac9c8..447e0ab 100644 --- a/.gitignore +++ b/.gitignore @@ -3,4 +3,5 @@ *.jl.mem /Manifest.toml /docs/build/ +/docs/src/index.md .vscode/ \ No newline at end of file diff --git a/CITATION.bib b/CITATION.bib index 3d91b39..0d96d1e 100644 --- a/CITATION.bib +++ b/CITATION.bib @@ -1,7 +1,7 @@ @misc{GraphsOptim.jl, author = {Guillaume Dalle, Aurora Rossi and contributors}, title = {GraphsOptim.jl}, - url = {https://github.com/gdalle/GraphsOptim.jl}, + url = {https://github.com/JuliaGraphs/GraphsOptim.jl}, version = {v0.1.0}, year = {2023}, month = {6} diff --git a/README.md b/README.md index 92c5124..e57ab87 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,23 @@ # GraphsOptim - -[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://gdalle.github.io/GraphsOptim.jl/dev) -[![Build Status](https://github.com/gdalle/GraphsOptim.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/gdalle/GraphsOptim.jl/actions/workflows/CI.yml?query=branch%3Amain) -[![Coverage](https://codecov.io/gh/gdalle/GraphsOptim.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/gdalle/GraphsOptim.jl) + +[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliagraphs.org/GraphsOptim.jl/dev) +[![Build Status](https://github.com/JuliaGraphs/GraphsOptim.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaGraphs/GraphsOptim.jl/actions/workflows/CI.yml?query=branch%3Amain) +[![Coverage](https://codecov.io/gh/JuliaGraphs/GraphsOptim.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaGraphs/GraphsOptim.jl) [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle) A package for graph optimization algorithms that rely on mathematical programming. + +## Getting started + +This package is still experimental, which is why it is not yet registered. +To install it, you need to use the GitHub URL: + +```julia +using Pkg; Pkg.add(url="https://github.com/JuliaGraphs/GraphsOptim.jl") +``` + +## Roadmap + +This package only contains a few algorithms, and we would like to add more. +New contributors are always welcome: just pick a problem from [our roadmap issue](https://github.com/JuliaGraphs/GraphsOptim.jl/issues/14), open a pull request following the [guidelines](https://github.com/JuliaGraphs/GraphsOptim.jl/CONTRIBUTING.md), and we will help you get it merged! diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 35a8949..52fdd0c 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,6 +1,6 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.10.0-beta2" manifest_format = "2.0" project_hash = "1660341366c1a9fa8b8e4838eb0fcf4091a1163e" @@ -9,6 +9,21 @@ git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" +[[deps.AbstractTrees]] +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" +version = "0.4.4" + +[[deps.Adapt]] +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "3.6.2" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" + [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" @@ -22,6 +37,12 @@ version = "0.2.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +[[deps.Atomix]] +deps = ["UnsafeAtomics"] +git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" +version = "0.1.0" + [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -37,17 +58,34 @@ git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" +[[deps.CEnum]] +git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" +uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" +version = "0.4.2" + +[[deps.Calculus]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" +uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" +version = "0.5.1" + +[[deps.ChainRulesCore]] +deps = ["Compat", "LinearAlgebra", "SparseArrays"] +git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" +uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" +version = "1.16.0" + [[deps.CodecBzip2]] deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] -git-tree-sha1 = "2e62a725210ce3c3c2e1a3080190e7ca491f18d7" +git-tree-sha1 = "ad41de3795924f7a056243eb3e4161448f0523e6" uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.7.2" +version = "0.8.0" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" +git-tree-sha1 = "02aa26a4cf76381be7f66e020a3eddeb27b0a092" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.1" +version = "0.7.2" [[deps.CommonSubexpressions]] deps = ["MacroTools", "Test"] @@ -57,9 +95,9 @@ version = "0.3.0" [[deps.Compat]] deps = ["UUIDs"] -git-tree-sha1 = "4e88377ae7ebeaf29a047aa1ee40826e0b708a5d" +git-tree-sha1 = "8a62af3e248a8c4bad6b32cbbe663ae02275e32c" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.7.0" +version = "4.10.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -68,13 +106,18 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.5+0" +version = "1.0.5+1" + +[[deps.DataAPI]] +git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" +uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" +version = "1.15.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "cf25ccb972fec4e4817764d01c82386ae94f77b4" +git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.14" +version = "0.18.15" [[deps.Dates]] deps = ["Printf"] @@ -92,10 +135,34 @@ git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" +[[deps.Distances]] +deps = ["LinearAlgebra", "Statistics", "StatsAPI"] +git-tree-sha1 = "b6def76ffad15143924a2199f72a5cd883a2e8a9" +uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" +version = "0.10.9" +weakdeps = ["SparseArrays"] + + [deps.Distances.extensions] + DistancesSparseArraysExt = "SparseArrays" + [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" +[[deps.Distributions]] +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "938fe2981db009f531b6332e31c58e9584a2f9bd" +uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" +version = "0.25.100" + + [deps.Distributions.extensions] + DistributionsChainRulesCoreExt = "ChainRulesCore" + DistributionsDensityInterfaceExt = "DensityInterface" + + [deps.Distributions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" + [[deps.DocStringExtensions]] deps = ["LibGit2"] git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" @@ -103,16 +170,28 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" [[deps.Documenter]] -deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "39fd748a73dce4c05a9655475e437170d8fb1b67" +deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "Dates", "DocStringExtensions", "Downloads", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "Test", "Unicode"] +git-tree-sha1 = "f1a7eaf2b5ac7a4feb27973a09d25daf80dc56db" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.25" +version = "1.0.1" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" +[[deps.DualNumbers]] +deps = ["Calculus", "NaNMath", "SpecialFunctions"] +git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" +uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" +version = "0.6.8" + +[[deps.ExactOptimalTransport]] +deps = ["Distances", "Distributions", "FillArrays", "LinearAlgebra", "MathOptInterface", "PDMats", "QuadGK", "SparseArrays", "StatsBase"] +git-tree-sha1 = "aca11e5cbf419be6778707f4ddc90d486bc79e92" +uuid = "24df6009-d856-477c-ac5c-91f668376b31" +version = "0.2.5" + [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -124,14 +203,20 @@ version = "0.13.11" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" +git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.35" +version = "0.10.36" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] ForwardDiffStaticArraysExt = "StaticArrays" +[[deps.GPUArraysCore]] +deps = ["Adapt"] +git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" +uuid = "46192b85-c4d5-4398-a991-12ede77f4527" +version = "0.1.5" + [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" @@ -139,16 +224,16 @@ uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" version = "1.8.0" [[deps.GraphsOptim]] -deps = ["FillArrays", "Graphs", "HiGHS", "JuMP", "LinearAlgebra", "MathOptInterface", "SparseArrays"] +deps = ["FillArrays", "Graphs", "HiGHS", "JuMP", "LinearAlgebra", "MathOptInterface", "OptimalTransport", "SparseArrays"] path = ".." uuid = "e79ef3ae-79c8-4b97-b165-63f338db30c2" version = "0.1.0" [[deps.HiGHS]] deps = ["HiGHS_jll", "MathOptInterface", "PrecompileTools", "SparseArrays"] -git-tree-sha1 = "bbd4ab443dfac4c9d5c5b40dd45f598dfad2e26a" +git-tree-sha1 = "c8801de1b535a44540792be039d7d87f87584b1f" uuid = "87dc4568-4c63-4d18-b0c0-bb2238e4078b" -version = "1.5.2" +version = "1.6.0" [[deps.HiGHS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -156,6 +241,12 @@ git-tree-sha1 = "216e7198aeb256e7c7921ef2937d7e1e589ba6fd" uuid = "8fd58aa0-07eb-5a78-9b36-339c94fd15ea" version = "1.5.3+0" +[[deps.HypergeometricFunctions]] +deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" +uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" +version = "0.3.23" + [[deps.IOCapture]] deps = ["Logging", "Random"] git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6" @@ -176,11 +267,17 @@ git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.2.2" +[[deps.IterativeSolvers]] +deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] +git-tree-sha1 = "1169632f425f79429f245113b775a0e3d121457c" +uuid = "42fd0dbc-a981-5370-80f2-aaf504508153" +version = "0.9.2" + [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", 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[[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" -version = "0.6.3" +version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "7.84.0+0" +version = "8.0.1+1" [[deps.LibGit2]] deps = ["Base64", "NetworkOptions", "Printf", "SHA"] @@ -211,7 +347,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" -version = "1.10.2+0" +version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -222,9 +358,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -241,37 +377,61 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[deps.MarkdownAST]] +deps = ["AbstractTrees", "Markdown"] +git-tree-sha1 = "e8513266815200c0c8f522d6d44ffb5e9b366ae4" +uuid = "d0879d2d-cac2-40c8-9cee-1863dc0c7391" +version = "0.1.1" + [[deps.MathOptInterface]] deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] -git-tree-sha1 = "5c5cd501ae1d76d3ccd7c7e6b4325a15dde7f31c" +git-tree-sha1 = "5c9f1e635e8d491297e596b56fec1c95eafb95a3" uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.18.0" +version = "1.20.1" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.2+1" + +[[deps.Missings]] +deps = ["DataAPI"] +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" +uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" +version = "1.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2023.1.10" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "964cb1a7069723727025ae295408747a0b36a854" +git-tree-sha1 = "6985021d02ab8c509c841bb8b2becd3145a7b490" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.3.0" +version = "1.3.3" + +[[deps.NNlib]] +deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] +git-tree-sha1 = "72240e3f5ca031937bd536182cb2c031da5f46dd" +uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" +version = "0.8.21" + + [deps.NNlib.extensions] + NNlibAMDGPUExt = "AMDGPU" + + [deps.NNlib.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" [[deps.NaNMath]] deps = ["OpenLibm_jll"] @@ -286,12 +446,12 @@ version = "1.2.0" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.21+4" +version = "0.3.23+2" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+0" +version = "0.8.1+2" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -299,33 +459,45 @@ git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" +[[deps.OptimalTransport]] +deps = ["ExactOptimalTransport", "IterativeSolvers", "LinearAlgebra", "LogExpFunctions", "NNlib", "Reexport"] +git-tree-sha1 = "79ba1dab46dfc7b677278ebe892a431788da86a9" +uuid = "7e02d93a-ae51-4f58-b602-d97af76e3b33" +version = "0.3.19" + [[deps.OrderedCollections]] -git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282" +git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.0" +version = "1.6.2" + +[[deps.PDMats]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "bf6085e8bd7735e68c210c6e5d81f9a6fe192060" +uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" +version = "0.11.19" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29" +git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.7.1" +version = "2.7.2" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.9.2" +version = "1.10.0" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" +git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.0" +version = "1.4.1" [[deps.Printf]] deps = ["Unicode"] @@ -335,14 +507,55 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" deps = ["Printf"] uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" +[[deps.QuadGK]] +deps = ["DataStructures", "LinearAlgebra"] +git-tree-sha1 = "9ebcd48c498668c7fa0e97a9cae873fbee7bfee1" +uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" +version = "2.9.1" + [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[deps.Random]] -deps = ["SHA", "Serialization"] +deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +[[deps.RecipesBase]] +deps = ["PrecompileTools"] +git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" +uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" +version = "1.3.4" + +[[deps.Reexport]] +git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" +uuid = "189a3867-3050-52da-a836-e630ba90ab69" +version = "1.2.2" + +[[deps.RegistryInstances]] +deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"] +git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51" +uuid = "2792f1a3-b283-48e8-9a74-f99dce5104f3" +version = "0.1.0" + +[[deps.Requires]] +deps = ["UUIDs"] +git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" +uuid = "ae029012-a4dd-5104-9daa-d747884805df" +version = "1.3.0" + +[[deps.Rmath]] +deps = ["Random", "Rmath_jll"] +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" +version = "0.7.1" + +[[deps.Rmath_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" +uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" +version = "0.4.0+0" + [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" @@ -369,46 +582,81 @@ version = "1.0.3" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" +[[deps.SortingAlgorithms]] +deps = ["DataStructures"] +git-tree-sha1 = "c60ec5c62180f27efea3ba2908480f8055e17cee" +uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" +version = "1.1.1" + [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +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 = "0da7e6b70d1bb40b1ace3b576da9ea2992f76318" +git-tree-sha1 = "d5fb407ec3179063214bc6277712928ba78459e2" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.0" +version = "1.6.4" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" +git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.0" +version = "1.4.2" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" version = "1.9.0" +[[deps.StatsAPI]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" +uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" +version = "1.7.0" + +[[deps.StatsBase]] +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "75ebe04c5bed70b91614d684259b661c9e6274a4" +uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" +version = "0.34.0" + +[[deps.StatsFuns]] +deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" +uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" +version = "1.3.0" + + [deps.StatsFuns.extensions] + StatsFunsChainRulesCoreExt = "ChainRulesCore" + StatsFunsInverseFunctionsExt = "InverseFunctions" + + [deps.StatsFuns.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" + +[[deps.SuiteSparse]] +deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] +uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" + [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+6" +version = "7.2.0+1" [[deps.TOML]] deps = ["Dates"] @@ -437,22 +685,33 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" +[[deps.UnsafeAtomics]] +git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" +uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" +version = "0.2.1" + +[[deps.UnsafeAtomicsLLVM]] +deps = ["LLVM", "UnsafeAtomics"] +git-tree-sha1 = "323e3d0acf5e78a56dfae7bd8928c989b4f3083e" +uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" +version = "0.1.3" + [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.13+1" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+0" +version = "5.8.0+1" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" diff --git a/docs/Project.toml b/docs/Project.toml index d3c0ab6..ce6a40f 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,3 +1,6 @@ [deps] Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" GraphsOptim = "e79ef3ae-79c8-4b97-b165-63f338db30c2" + +[compat] +Documenter = "1.0" \ No newline at end of file diff --git a/docs/make.jl b/docs/make.jl index 240147b..e0a68aa 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -3,18 +3,38 @@ using Documenter DocMeta.setdocmeta!(GraphsOptim, :DocTestSetup, :(using GraphsOptim); recursive=true) +generated_path = joinpath(@__DIR__, "src") +base_url = "https://github.com/JuliaGraphs/GraphsOptim.jl/blob/main/" +isdir(generated_path) || mkdir(generated_path) + +open(joinpath(generated_path, "index.md"), "w") do io + # Point to source license file + println( + io, + """ + ```@meta + EditURL = "$(base_url)README.md" + ``` + """, + ) + # Write the contents out below the meta block + for line in eachline(joinpath(dirname(@__DIR__), "README.md")) + println(io, line) + end +end + makedocs(; modules=[GraphsOptim], - authors="Guillaume Dalle <22795598+gdalle@users.noreply.github.com> and contributors", - repo="https://github.com/gdalle/GraphsOptim.jl/blob/{commit}{path}#{line}", + authors="Guillaume Dalle, Aurora Rossi and contributors", sitename="GraphsOptim.jl", format=Documenter.HTML(; + repolink="https://github.com/JuliaGraphs/GraphsOptim.jl/", prettyurls=get(ENV, "CI", "false") == "true", - canonical="https://gdalle.github.io/GraphsOptim.jl", + canonical="https://JuliaGraphs.github.io/GraphsOptim.jl", assets=String[], edit_link=:commit, ), pages=["Home" => "index.md", "Algorithms" => "algorithms.md"], ) -deploydocs(; repo="github.com/gdalle/GraphsOptim.jl", devbranch="main") +deploydocs(; repo="github.com/JuliaGraphs/GraphsOptim.jl", devbranch="main") diff --git a/docs/src/algorithms.md b/docs/src/algorithms.md index 5fd73ca..15335df 100644 --- a/docs/src/algorithms.md +++ b/docs/src/algorithms.md @@ -1,5 +1,9 @@ # Algorithms +```@docs +GraphsOptim +``` + ## Flow ```@docs @@ -55,6 +59,7 @@ GraphsOptim.min_cost_assignment! ```@docs graph_matching +GraphsOptim.graph_matching_step_size ``` ## Utils diff --git a/docs/src/index.md b/docs/src/index.md deleted file mode 100644 index 64f83aa..0000000 --- a/docs/src/index.md +++ /dev/null @@ -1,16 +0,0 @@ -```@meta -CurrentModule = GraphsOptim -``` - -# GraphsOptim - -Documentation for [GraphsOptim](https://github.com/gdalle/GraphsOptim.jl). - -```@docs -GraphsOptim -``` - -## Index - -```@index -```