Update examples and reduce dependencies (#128)

Co-authored-by: Stephen Zhang <[email protected]>

Author: devmotion

examples/basic/Manifest.toml

@@ -132,10 +132,10 @@ deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
-deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "f389cb8974e02d7eaa6ae2ccedbbfb43174cd8e8"
+deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
+git-tree-sha1 = "c2dbc7e0495c3f956e4615b78d03c7aa10091d0c"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.14"
+version = "0.25.15"
 
 [[DocStringExtensions]]
 deps = ["LibGit2"]
@@ -325,6 +325,12 @@ git-tree-sha1 = "d735490ac75c5cb9f1b00d8b5509c11984dc6943"
 uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
 version = "2.1.0+0"
 
+[[Krylov]]
+deps = ["LinearAlgebra", "Printf", "SparseArrays"]
+git-tree-sha1 = "c5b01ca4fa9d09c17da742f67e321386a2557602"
+uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
+version = "0.7.6"
+
 [[LAME_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c"
@@ -586,15 +592,15 @@ version = "2.0.1"
 
 [[PlotUtils]]
 deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"]
-git-tree-sha1 = "c67334c786157d6ef091ce622b365d3d60b1e2c4"
+git-tree-sha1 = "9ff1c70190c1c30aebca35dc489f7411b256cd23"
 uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
-version = "1.0.12"
+version = "1.0.13"
 
 [[Plots]]
 deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"]
-git-tree-sha1 = "0036d433cacff4767ff622be3cb2c281b773a2b4"
+git-tree-sha1 = "9e1a400fb1f27b4146fe35dc1a22de6c793b8f20"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.21.1"
+version = "1.21.2"
 
 [[Preferences]]
 deps = ["TOML"]
@@ -651,9 +657,9 @@ version = "1.1.2"
 
 [[RecipesPipeline]]
 deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"]
-git-tree-sha1 = "e377b29ebe56fadd8b40b04d8eb117c98d0a9960"
+git-tree-sha1 = "d4491becdc53580c6dadb0f6249f90caae888554"
 uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c"
-version = "0.3.6"
+version = "0.4.0"
 
 [[Reexport]]
 git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
@@ -736,15 +742,15 @@ version = "1.0.0"
 
 [[StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "fed1ec1e65749c4d96fc20dd13bea72b55457e62"
+git-tree-sha1 = "8cbbc098554648c84f79a463c9ff0fd277144b6c"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.33.9"
+version = "0.33.10"
 
 [[StatsFuns]]
-deps = ["IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "20d1bb720b9b27636280f751746ba4abb465f19d"
+deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
+git-tree-sha1 = "46d7ccc7104860c38b11966dd1f72ff042f382e4"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.9"
+version = "0.9.10"
 
 [[StructArrays]]
 deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"]
@@ -793,10 +799,10 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.9.6"
 
 [[Tulip]]
-deps = ["CodecBzip2", "CodecZlib", "LDLFactorizations", "LinearAlgebra", "LinearOperators", "Logging", "MathOptInterface", "Printf", "QPSReader", "SparseArrays", "SuiteSparse", "Test", "TimerOutputs"]
-git-tree-sha1 = "e381662f7d351defc05ebbc75c228c38501901f4"
+deps = ["CodecBzip2", "CodecZlib", "Krylov", "LDLFactorizations", "LinearAlgebra", "LinearOperators", "Logging", "MathOptInterface", "Printf", "QPSReader", "SparseArrays", "SuiteSparse", "Test", "TimerOutputs"]
+git-tree-sha1 = "753c5bd161ca2a64da995a21900bcc177bd7d8e4"
 uuid = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa"
-version = "0.7.5"
+version = "0.8.0"
 
 [[URIs]]
 git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355"

examples/basic/Project.toml

@@ -14,5 +14,5 @@ Literate = "2.9"
 OptimalTransport = "0.3"
 Plots = "1"
 PythonOT = "0.1"
-Tulip = "0.7"
+Tulip = "0.8"
 julia = "1"

examples/variational/Manifest.toml

@@ -11,9 +11,9 @@ uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
 
 [[ArrayInterface]]
 deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"]
-git-tree-sha1 = "b6dec2ed4f10840e2cf836508525656450d4d289"
+git-tree-sha1 = "2cc636ec3015631b1c6ae1ccabb459fd9407997b"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "3.1.26"
+version = "3.1.29"
 
 [[Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -144,10 +144,10 @@ deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
-deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "f389cb8974e02d7eaa6ae2ccedbbfb43174cd8e8"
+deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
+git-tree-sha1 = "c2dbc7e0495c3f956e4615b78d03c7aa10091d0c"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.14"
+version = "0.25.15"
 
 [[DocStringExtensions]]
 deps = ["LibGit2"]
@@ -231,11 +231,6 @@ git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91"
 uuid = "559328eb-81f9-559d-9380-de523a88c83c"
 version = "1.0.10+0"
 
-[[FunctionWrappers]]
-git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc"
-uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
-version = "1.1.2"
-
 [[GLFW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"]
 git-tree-sha1 = "dba1e8614e98949abfa60480b13653813d8f0157"
@@ -622,15 +617,15 @@ version = "2.0.1"
 
 [[PlotUtils]]
 deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"]
-git-tree-sha1 = "c67334c786157d6ef091ce622b365d3d60b1e2c4"
+git-tree-sha1 = "9ff1c70190c1c30aebca35dc489f7411b256cd23"
 uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
-version = "1.0.12"
+version = "1.0.13"
 
 [[Plots]]
 deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"]
-git-tree-sha1 = "0036d433cacff4767ff622be3cb2c281b773a2b4"
+git-tree-sha1 = "9e1a400fb1f27b4146fe35dc1a22de6c793b8f20"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.21.1"
+version = "1.21.2"
 
 [[PositiveFactorizations]]
 deps = ["LinearAlgebra"]
@@ -675,9 +670,9 @@ version = "1.1.2"
 
 [[RecipesPipeline]]
 deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"]
-git-tree-sha1 = "e377b29ebe56fadd8b40b04d8eb117c98d0a9960"
+git-tree-sha1 = "d4491becdc53580c6dadb0f6249f90caae888554"
 uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c"
-version = "0.3.6"
+version = "0.4.0"
 
 [[Reexport]]
 git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
@@ -690,12 +685,6 @@ git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621"
 uuid = "ae029012-a4dd-5104-9daa-d747884805df"
 version = "1.1.3"
 
-[[ReverseDiff]]
-deps = ["DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"]
-git-tree-sha1 = "63ee24ea0689157a1113dbdab10c6cb011d519c4"
-uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
-version = "1.9.0"
-
 [[Rmath]]
 deps = ["Random", "Rmath_jll"]
 git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f"
@@ -751,9 +740,9 @@ version = "1.6.1"
 
 [[Static]]
 deps = ["IfElse"]
-git-tree-sha1 = "62701892d172a2fa41a1f829f66d2b0db94a9a63"
+git-tree-sha1 = "854b024a4a81b05c0792a4b45293b85db228bd27"
 uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
-version = "0.3.0"
+version = "0.3.1"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
@@ -772,15 +761,15 @@ version = "1.0.0"
 
 [[StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "fed1ec1e65749c4d96fc20dd13bea72b55457e62"
+git-tree-sha1 = "8cbbc098554648c84f79a463c9ff0fd277144b6c"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.33.9"
+version = "0.33.10"
 
 [[StatsFuns]]
-deps = ["IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "20d1bb720b9b27636280f751746ba4abb465f19d"
+deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
+git-tree-sha1 = "46d7ccc7104860c38b11966dd1f72ff042f382e4"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.9"
+version = "0.9.10"
 
 [[StructArrays]]
 deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"]
@@ -792,11 +781,6 @@ version = "0.6.1"
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 
-[[Suppressor]]
-git-tree-sha1 = "a819d77f31f83e5792a76081eee1ea6342ab8787"
-uuid = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
-version = "0.2.0"
-
 [[TOML]]
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"

examples/variational/Project.toml

@@ -1,25 +1,20 @@
 [deps]
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
-LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 OptimalTransport = "7e02d93a-ae51-4f58-b602-d97af76e3b33"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
 
 [compat]
 Distances = "0.10"
-LaTeXStrings = "1.2"
 Literate = "2.9"
 LogExpFunctions = "0.3"
 Optim = "1.4"
 OptimalTransport = "0.3"
 Plots = "1"
-ReverseDiff = "1.9"
 StatsBase = "0.33"
-Suppressor = "0.2"
 julia = "1"

examples/variational/script.jl

@@ -59,12 +59,14 @@
 # ## Problem setup
 #
 using OptimalTransport
-using StatsBase, Distances
-using ReverseDiff, Optim, LinearAlgebra
-using Plots
+using Distances
 using LogExpFunctions
-using LaTeXStrings
-using Suppressor
+using Optim
+using Plots
+using StatsBase
+
+using LinearAlgebra
+using Logging
 
 # Here, we set up the computational domain that we work on - we discretize the interval $[-1, 1]$. 
 # The natural boundary conditions to use will be Neumann (zero flux), see e.g. [^Santam2017]
@@ -119,29 +121,30 @@ end;
 
 # `step` solves the implicit step problem to produce $\rho_{t + \tau}$ from $\rho_t$. 
 function step(ρ0, τ, ε, C, G)
-    opt = optimize(
-        u -> G(softmax(u), ρ0, τ, ε, C),
-        ones(size(ρ0)),
-        LBFGS(),
-        Optim.Options(; iterations=50, g_tol=1e-6);
-        autodiff=:forward,
-    )
+    ## only print error messages
+    opt = with_logger(SimpleLogger(stderr, Logging.Error)) do
+        optimize(
+            u -> G(softmax(u), ρ0, τ, ε, C),
+            ones(size(ρ0)),
+            LBFGS(),
+            Optim.Options(; iterations=50, g_tol=1e-6);
+            autodiff=:forward,
+        )
+    end
     return softmax(Optim.minimizer(opt))
 end
 # Now we simulate `N = 10` iterates of the gradient flow and plot the result. 
 N = 10
 ρ = similar(ρ0, size(ρ0, 1), N)
 ρ[:, 1] = ρ0
-@suppress begin
-    for i in 2:N
-        ρ[:, i] = step(ρ[:, i - 1], τ, ε, C, G_fpe)
-    end
+for i in 2:N
+    ρ[:, i] = step(ρ[:, i - 1], τ, ε, C, G_fpe)
 end
 colors = range(colorant"red"; stop=colorant"blue", length=N)
 plot(
     support,
     ρ;
-    title=L"F(\rho) = \langle \psi, \rho \rangle + \langle \rho, \log(\rho) \rangle",
+    title=raw"$F(\rho) = \langle \psi, \rho \rangle + \langle \rho, \log(\rho) \rangle$",
     palette=colors,
     legend=nothing,
 )
@@ -164,15 +167,13 @@ end;
 N = 10
 ρ = similar(ρ0, size(ρ0, 1), N)
 ρ[:, 1] = ρ0
-@suppress begin
-    for i in 2:N
-        ρ[:, i] = step(ρ[:, i - 1], τ, ε, C, G_pme)
-    end
+for i in 2:N
+    ρ[:, i] = step(ρ[:, i - 1], τ, ε, C, G_pme)
 end
 plot(
     support,
     ρ;
-    title=L"F(\rho) = \langle \psi, \rho \rangle + \langle \rho, \rho - 1\rangle",
+    title=raw"$F(\rho) = \langle \psi, \rho \rangle + \langle \rho, \rho - 1\rangle$",
     palette=colors,
     legend=nothing,
 )