Skip to content

Commit

Permalink
Update examples and reduce dependencies (#128)
Browse files Browse the repository at this point in the history 
Co-authored-by: Stephen Zhang <[email protected]>
  • Loading branch information
@devmotion @zsteve
devmotion and zsteve authored Aug 31, 2021
1 parent 59ff422 commit ab9bc76
Show file tree
Hide file tree
Showing 5 changed files with 66 additions and 80 deletions.
40 changes: 23 additions & 17 deletions examples/basic/Manifest.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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"]
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"]
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"]
Expand Down Expand Up @@ -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"
Expand Down
2 changes: 1 addition & 1 deletion examples/basic/Project.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,5 +14,5 @@ Literate = "2.9"
OptimalTransport = "0.3"
Plots = "1"
PythonOT = "0.1"
Tulip = "0.7"
Tulip = "0.8"
julia = "1"
52 changes: 18 additions & 34 deletions examples/variational/Manifest.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down Expand Up @@ -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"]
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"]
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand Down Expand Up @@ -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"]
Expand All @@ -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"]
Expand All @@ -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"
Expand Down
7 changes: 1 addition & 6 deletions examples/variational/Project.toml
View file
Original file line number Diff line number Diff line change
@@ -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"
45 changes: 23 additions & 22 deletions examples/variational/script.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand Down Expand Up @@ -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,
)
Expand All @@ -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,
)

3 comments on commit ab9bc76

@zsteve
Copy link
Member

@zsteve zsteve commented on ab9bc76 Aug 31, 2021 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@devmotion time for new version? what do you think

@zsteve
Copy link
Member

@zsteve zsteve commented on ab9bc76 Aug 31, 2021

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@JuliaRegistrator register

@JuliaRegistrator
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Registration pull request created: JuliaRegistries/General/43905

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.3.15 -m "<description of version>" ab9bc76a13c106f451ef58126cab07758f905f3f
git push origin v0.3.15

Please sign in to comment.