Merge pull request #22 from axelparmentier/giom

Clean up docs for JuliaCon

Author: gdalle

.github/workflows/CI.yml

@@ -18,7 +18,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1'
+          - '1.7'
+          - '~1.8.0-0'
         os:
           - ubuntu-latest
         arch:

CITATION.bib

@@ -2,7 +2,7 @@ @misc{InferOpt.jl
 	author  = {Guillaume Dalle, Léo Baty, Louis Bouvier and Axel Parmentier},
 	title   = {InferOpt.jl},
 	url     = {https://github.com/axelparmentier/InferOpt.jl},
-	version = {v0.3.0},
+	version = {v0.3.1},
 	year    = {2022},
 	month   = {7}
 }

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Axel Parmentier, Guillaume Dalle, Léo Baty, Louis Bouvier
+Copyright (c) 2022 Guillaume Dalle, Léo Baty, Louis Bouvier, Axel Parmentier
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Project.toml

@@ -1,7 +1,7 @@
 name = "InferOpt"
 uuid = "4846b161-c94e-4150-8dac-c7ae193c601f"
 authors = ["Guillaume Dalle", "Léo Baty", "Louis Bouvier", "Axel Parmentier"]
-version = "0.3.0"
+version = "0.3.1"
 
 [deps]
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"

README.md

@@ -9,9 +9,8 @@
 
 `InferOpt.jl` is a toolbox for using combinatorial optimization algorithms within machine learning pipelines.
 
-It allows you to differentiate through things that should not be differentiable, such as Mixed Integer Linear Programs or graph algorithms.
-
-> This package is at a very early development stage, so proceed with caution!
+It allows you to create differentiable layers from optimization oracles that do not have meaningful derivatives.
+Typical examples include mixed integer linear programs or graph algorithms.
 
 ## Getting started
 
@@ -26,3 +25,9 @@ To install the development version, run this command instead:
 ```julia
 julia> using Pkg; Pkg.add(url="https://github.com/axelparmentier/InferOpt.jl")
 ```
+
+## Citing us
+
+If you use our package in your research, please cite the following paper:
+
+> [Learning with Combinatorial Optimization Layers: a Probabilistic Approach](https://arxiv.org/abs/2207.13513) - Guillaume Dalle, Léo Baty, Louis Bouvier and Axel Parmentier (2022)

docs/Manifest.toml

@@ -49,15 +49,15 @@ version = "3.5.1+1"
 
 [[deps.ArrayInterface]]
 deps = ["ArrayInterfaceCore", "Compat", "IfElse", "LinearAlgebra", "Static"]
-git-tree-sha1 = "6ccb71b40b04ad69152f1f83d5925de13911417e"
+git-tree-sha1 = "621913bff3923ff489e4268ba2b425bfacbb1759"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "6.0.19"
+version = "6.0.21"
 
 [[deps.ArrayInterfaceCore]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "7d255eb1d2e409335835dc8624c35d97453011eb"
+git-tree-sha1 = "8d9e48436c5589fbd51ae8c8165a299a219188c0"
 uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2"
-version = "0.1.14"
+version = "0.1.15"
 
 [[deps.Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -90,33 +90,33 @@ version = "0.4.2"
 
 [[deps.CUDA]]
 deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "TimerOutputs"]
-git-tree-sha1 = "e4e5ece72fa2f108fb20c3c5538a5fa9ef3d668a"
+git-tree-sha1 = "49549e2c28ffb9cc77b3689dc10e46e6271e9452"
 uuid = "052768ef-5323-5732-b1bb-66c8b64840ba"
-version = "3.11.0"
+version = "3.12.0"
 
 [[deps.ChainRules]]
-deps = ["ChainRulesCore", "Compat", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics"]
-git-tree-sha1 = "b06ed86d99c982cbe9047a45a93ac62d9605a361"
+deps = ["ChainRulesCore", "Compat", "Distributed", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics"]
+git-tree-sha1 = "e762b70af7c1d914f677d9588a1d3b32e5f832af"
 uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2"
-version = "1.36.2"
+version = "1.39.1"
 
 [[deps.ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "2dd813e5f2f7eec2d1268c57cf2373d3ee91fcea"
+git-tree-sha1 = "80ca332f6dcb2508adba68f22f551adb2d00a624"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.15.1"
+version = "1.15.3"
 
 [[deps.ChangesOfVariables]]
 deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
-git-tree-sha1 = "1e315e3f4b0b7ce40feded39c73049692126cf53"
+git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8"
 uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
-version = "0.1.3"
+version = "0.1.4"
 
 [[deps.CodeTracking]]
 deps = ["InteractiveUtils", "UUIDs"]
-git-tree-sha1 = "6d4fa04343a7fc9f9cb9cff9558929f3d2752717"
+git-tree-sha1 = "bfae3e59e3e20c0655e963c7f06362dce07c98d6"
 uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
-version = "1.0.9"
+version = "1.0.10"
 
 [[deps.CodecBzip2]]
 deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"]
@@ -177,9 +177,9 @@ uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 version = "1.4.0"
 
 [[deps.Contour]]
-git-tree-sha1 = "a599cfb8b1909b0f97c5e1b923ab92e1c0406076"
+git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781"
 uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
-version = "0.6.1"
+version = "0.6.2"
 
 [[deps.Crayons]]
 git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
@@ -228,15 +228,15 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[deps.DocStringExtensions]]
 deps = ["LibGit2"]
-git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b"
+git-tree-sha1 = "5158c2b41018c5f7eb1470d558127ac274eca0c9"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-version = "0.8.6"
+version = "0.9.1"
 
 [[deps.Documenter]]
 deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "f7809f532671564e48cd81627ddcfb1ba670f87d"
+git-tree-sha1 = "ee945ed10767de73cf8b610951b98228cb65af80"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.27.19"
+version = "0.27.22"
 
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
@@ -281,9 +281,9 @@ version = "0.8.4"
 
 [[deps.Flux]]
 deps = ["Adapt", "ArrayInterface", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "Optimisers", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Test", "Zygote"]
-git-tree-sha1 = "62350a872545e1369b1d8f11358a21681aa73929"
+git-tree-sha1 = "96dc065bf4a998e8adeebc0ff1302902b6e59362"
 uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c"
-version = "0.13.3"
+version = "0.13.4"
 
 [[deps.ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"]
@@ -293,9 +293,9 @@ version = "0.10.30"
 
 [[deps.FrankWolfe]]
 deps = ["Arpack", "GenericSchur", "Hungarian", "LinearAlgebra", "MathOptInterface", "Printf", "ProgressMeter", "Random", "Setfield", "SparseArrays", "TimerOutputs"]
-git-tree-sha1 = "87622f91e2256920debd418da506a9490f5c3efc"
+git-tree-sha1 = "5ca2f722d3cb24f834fcd578a90c3e1d265b7b12"
 uuid = "f55ce6ea-fdc5-4628-88c5-0087fe54bd30"
-version = "0.2.1"
+version = "0.2.6"
 
 [[deps.FreeType]]
 deps = ["CEnum", "FreeType2_jll"]
@@ -311,9 +311,9 @@ version = "2.10.4+0"
 
 [[deps.FreeTypeAbstraction]]
 deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"]
-git-tree-sha1 = "b5c7fe9cea653443736d264b85466bad8c574f4a"
+git-tree-sha1 = "38a92e40157100e796690421e34a11c107205c86"
 uuid = "663a7486-cb36-511b-a19d-713bb74d65c9"
-version = "0.9.9"
+version = "0.10.0"
 
 [[deps.Functors]]
 git-tree-sha1 = "223fffa49ca0ff9ce4f875be001ffe173b2b7de4"
@@ -326,21 +326,21 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[deps.GPUArrays]]
 deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"]
-git-tree-sha1 = "73a4c9447419ce058df716925893e452ba5528ad"
+git-tree-sha1 = "73145f1d724b5ee0e90098aec39a65e9697429a6"
 uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-version = "8.4.0"
+version = "8.4.2"
 
 [[deps.GPUArraysCore]]
 deps = ["Adapt"]
-git-tree-sha1 = "4078d3557ab15dd9fe6a0cf6f65e3d4937e98427"
+git-tree-sha1 = "d88b17a38322e153c519f5a9ed8d91e9baa03d8f"
 uuid = "46192b85-c4d5-4398-a991-12ede77f4527"
-version = "0.1.0"
+version = "0.1.1"
 
 [[deps.GPUCompiler]]
 deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"]
-git-tree-sha1 = "47f63159f7cb5d0e5e0cfd2f20454adea429bec9"
+git-tree-sha1 = "1067cd05184719ba86f19cf1d49d57f0bcbabbf6"
 uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
-version = "0.16.1"
+version = "0.16.2"
 
 [[deps.GenericSchur]]
 deps = ["LinearAlgebra", "Printf"]
@@ -393,7 +393,7 @@ version = "0.1.1"
 deps = ["ChainRulesCore", "FrankWolfe", "Krylov", "LinearAlgebra", "LinearOperators", "Random", "SimpleTraits", "SparseArrays", "Statistics", "StatsBase", "Test"]
 path = ".."
 uuid = "4846b161-c94e-4150-8dac-c7ae193c601f"
-version = "0.2.0"
+version = "0.3.1"
 
 [[deps.Inflate]]
 git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c"
@@ -439,15 +439,15 @@ version = "0.21.3"
 
 [[deps.JuliaInterpreter]]
 deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"]
-git-tree-sha1 = "52617c41d2761cc05ed81fe779804d3b7f14fff7"
+git-tree-sha1 = "1101d9e5a062963612e8d2bd5bd653d73ae033f4"
 uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a"
-version = "0.9.13"
+version = "0.9.14"
 
 [[deps.Krylov]]
 deps = ["LinearAlgebra", "Printf", "SparseArrays"]
-git-tree-sha1 = "7f0a89bd74c30aa7ff96c4bf1bc884c39663a621"
+git-tree-sha1 = "a2327039e1c84615e22d662adb3df113caf44b70"
 uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
-version = "0.8.2"
+version = "0.8.3"
 
 [[deps.LDLFactorizations]]
 deps = ["AMD", "LinearAlgebra", "SparseArrays", "Test"]
@@ -513,9 +513,9 @@ version = "2.13.4"
 
 [[deps.LogExpFunctions]]
 deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "09e4b894ce6a976c354a69041a04748180d43637"
+git-tree-sha1 = "7c88f63f9f0eb5929f15695af9a4d7d3ed278a91"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.15"
+version = "0.3.16"
 
 [[deps.Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
@@ -550,9 +550,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[deps.MathOptInterface]]
 deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"]
-git-tree-sha1 = "10d26d62dab815306bbd2c46eb52460e98f01e46"
+git-tree-sha1 = "e652a21eb0b38849ad84843a50dcbab93313e537"
 uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
-version = "1.6.0"
+version = "1.6.1"
 
 [[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -578,20 +578,21 @@ version = "1.0.4"
 
 [[deps.NNlib]]
 deps = ["Adapt", "ChainRulesCore", "LinearAlgebra", "Pkg", "Requires", "Statistics"]
-git-tree-sha1 = "1a80840bcdb73de345230328d49767ab115be6f2"
+git-tree-sha1 = "415108fd88d6f55cedf7ee940c7d4b01fad85421"
 uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
-version = "0.8.8"
+version = "0.8.9"
 
 [[deps.NNlibCUDA]]
-deps = ["CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"]
-git-tree-sha1 = "e161b835c6aa9e2339c1e72c3d4e39891eac7a4f"
+deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"]
+git-tree-sha1 = "4429261364c5ea5b7308aecaa10e803ace101631"
 uuid = "a00861dc-f156-4864-bf3c-e6376f28a68d"
-version = "0.2.3"
+version = "0.2.4"
 
 [[deps.NaNMath]]
-git-tree-sha1 = "737a5957f387b17e74d4ad2f440eb330b39a62c5"
+deps = ["OpenLibm_jll"]
+git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
-version = "1.0.0"
+version = "1.0.1"
 
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
@@ -612,9 +613,9 @@ version = "0.5.5+0"
 
 [[deps.Optimisers]]
 deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "afb2b39a354025a6db6decd68f2ef5353e8ff1ae"
+git-tree-sha1 = "62844c5525c3f13b3107aa2c25a06208ecadde88"
 uuid = "3bd65402-5787-11e9-1adc-39752487f4e2"
-version = "0.2.7"
+version = "0.2.8"
 
 [[deps.OrderedCollections]]
 git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c"
@@ -696,9 +697,9 @@ version = "1.3.0"
 
 [[deps.Revise]]
 deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "Requires", "UUIDs", "Unicode"]
-git-tree-sha1 = "4d4239e93531ac3e7ca7e339f15978d0b5149d03"
+git-tree-sha1 = "c73149ff75d4efb19b6d77411d293ae8fb55c58e"
 uuid = "295af30f-e4ad-537b-8983-00126c2a3abe"
-version = "3.3.3"
+version = "3.3.4"
 
 [[deps.SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
@@ -748,15 +749,15 @@ version = "2.1.7"
 
 [[deps.Static]]
 deps = ["IfElse"]
-git-tree-sha1 = "46638763d3a25ad7818a15d441e0c3446a10742d"
+git-tree-sha1 = "f94f9d627ba3f91e41a815b9f9f977d729e2e06f"
 uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
-version = "0.7.5"
+version = "0.7.6"
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "9f8a5dc5944dc7fbbe6eb4180660935653b0a9d9"
+git-tree-sha1 = "23368a3313d12a2326ad0035f0db0c0966f438ef"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.5.0"
+version = "1.5.2"
 
 [[deps.StaticArraysCore]]
 git-tree-sha1 = "66fe9eb253f910fe8cf161953880cfdaef01cdf0"
@@ -775,9 +776,9 @@ version = "1.4.0"
 
 [[deps.StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "48598584bacbebf7d30e20880438ed1d24b7c7d6"
+git-tree-sha1 = "0005d75f43ff23688914536c5e9d5ac94f8077f7"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.33.18"
+version = "0.33.20"
 
 [[deps.StructArrays]]
 deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"]
@@ -840,9 +841,9 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[deps.UnicodePlots]]
 deps = ["ColorSchemes", "ColorTypes", "Contour", "Crayons", "Dates", "FileIO", "FreeTypeAbstraction", "LazyModules", "LinearAlgebra", "MarchingCubes", "NaNMath", "Printf", "SparseArrays", "StaticArrays", "StatsBase", "Unitful"]
-git-tree-sha1 = "e8192bf70f28cf0e79ae9c215008e2f1464edbd6"
+git-tree-sha1 = "a2a83d67213fceb792b5f265b939e0049a26c76d"
 uuid = "b8865327-cd53-5732-bb35-84acbb429228"
-version = "3.0.3"
+version = "3.0.4"
 
 [[deps.Unitful]]
 deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"]

docs/make.jl

@@ -29,7 +29,7 @@ Literate.markdown(tuto_jl_file, tuto_md_dir; documenter=true, execute=false)
 
 makedocs(;
     modules=[InferOpt],
-    authors="Axel Parmentier, Guillaume Dalle, Léo Baty, Louis Bouvier",
+    authors="Guillaume Dalle, Léo Baty, Louis Bouvier, Axel Parmentier",
     repo="https://github.com/axelparmentier/InferOpt.jl/blob/{commit}{path}#{line}",
     sitename="InferOpt.jl",
     format=Documenter.HTML(;
@@ -40,10 +40,14 @@ makedocs(;
     pages=[
         "Home" => "index.md",
         "Tutorial" => "tutorial.md",
-        "Mathematical background" => "math.md",
-        "Implementation" => "implementation.md",
+        "Background" => "background.md",
         "Algorithms & API" => "algorithms.md",
     ],
 )
 
+for file in
+    [joinpath(@__DIR__, "src", "index.md"), joinpath(@__DIR__, "src", "tutorial.md")]
+    rm(file)
+end
+
 deploydocs(; repo="github.com/axelparmentier/InferOpt.jl", devbranch="main")