Merge pull request #1097 from SebastianM-C/docs

Fix docs

Author: ChrisRackauckas

.github/workflows/Documentation.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - master
-    tags: '*'
+    tags: "*"
   pull_request:
 
 jobs:
@@ -14,9 +14,11 @@ jobs:
       - uses: actions/checkout@v6
       - uses: julia-actions/setup-julia@latest
         with:
-          version: '1'
+          version: "1"
+      - name: Add the HolyLabRegistry
+        run: julia --project -e 'using Pkg; Pkg.Registry.add(); Pkg.Registry.add(RegistrySpec(url  = "https://github.com/HolyLab/HolyLabRegistry.git"))'
       - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(vcat(PackageSpec(path = pwd()), [PackageSpec(path = joinpath("lib", dir)) for dir in readdir("lib") if (dir !== "OptimizationQuadDIRECT" && dir !== "OptimizationMultistartOptimization")])); Pkg.instantiate()'
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(vcat(PackageSpec(path = pwd()), [PackageSpec(path = joinpath("lib", dir)) for dir in readdir("lib") if (dir !== "OptimizationMultistartOptimization")])); Pkg.instantiate()'
       - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token

docs/Project.toml

@@ -2,6 +2,7 @@
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 AmplNLWriter = "7c4d4715-977e-5154-bfe0-e096adeac482"
 ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
+DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -19,6 +20,7 @@ NLPModels = "a4795742-8479-5a88-8948-cc11e1c8c1a6"
 NLPModelsTest = "7998695d-6960-4d3a-85c4-e1bceb8cd856"
 NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
+OptimizationAuglag = "2ea93f80-9333-43a1-a68d-1f53b957a421"
 OptimizationBBO = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b"
 OptimizationBase = "bca83a33-5cc9-4baa-983d-23429ab6bcbb"
 OptimizationCMAEvolutionStrategy = "bd407f91-200f-4536-9381-e4ba712f53f8"
@@ -27,18 +29,26 @@ OptimizationGCMAES = "6f0a0517-dbc2-4a7a-8a20-99ae7f27e911"
 OptimizationIpopt = "43fad042-7963-4b32-ab19-e2a4f9a67124"
 OptimizationLBFGSB = "22f7324a-a79d-40f2-bebe-3af60c77bd15"
 OptimizationMOI = "fd9f6733-72f4-499f-8506-86b2bdd0dea1"
+OptimizationMadNLP = "5d9c809f-c847-4062-9fba-1793bbfef577"
 OptimizationManopt = "e57b7fff-7ee7-4550-b4f0-90e9476e9fb6"
 OptimizationMetaheuristics = "3aafef2f-86ae-4776-b337-85a36adf0b55"
+OptimizationMultistartOptimization = "e4316d97-8bbb-4fd3-a7d8-3851d2a72823"
 OptimizationNLPModels = "064b21be-54cf-11ef-1646-cdfee32b588f"
 OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
 OptimizationNOMAD = "2cab0595-8222-4775-b714-9828e6a9e01b"
+OptimizationODE = "dfa73e59-e644-4d8a-bf84-188d7ecb34e4"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 OptimizationOptimisers = "42dfb2eb-d2b4-4451-abcd-913932933ac1"
 OptimizationPRIMA = "72f8369c-a2ea-4298-9126-56167ce9cbc2"
 OptimizationPolyalgorithms = "500b13db-7e66-49ce-bda4-eed966be6282"
+OptimizationPyCMA = "fb0822aa-1fe5-41d8-99a6-e7bf6c238d3b"
+OptimizationQuadDIRECT = "842ac81e-713d-465f-80f7-84eddaced298"
+OptimizationSciPy = "cce07bd8-c79b-4b00-aee8-8db9cce22837"
+OptimizationSophia = "892fee11-dca1-40d6-b698-84ba0d87399a"
 OptimizationSpeedMapping = "3d669222-0d7d-4eb9-8a9f-d8528b0d9b91"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+QuadDIRECT = "dae52e8d-d666-5120-a592-9e15c33b8d7a"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
@@ -50,6 +60,7 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [sources]
 Optimization = {path = ".."}
+OptimizationAuglag = {path = "../lib/OptimizationAuglag"}
 OptimizationBBO = {path = "../lib/OptimizationBBO"}
 OptimizationBase = {path = "../lib/OptimizationBase"}
 OptimizationCMAEvolutionStrategy = {path = "../lib/OptimizationCMAEvolutionStrategy"}
@@ -58,15 +69,22 @@ OptimizationGCMAES = {path = "../lib/OptimizationGCMAES"}
 OptimizationIpopt = {path = "../lib/OptimizationIpopt"}
 OptimizationLBFGSB = {path = "../lib/OptimizationLBFGSB"}
 OptimizationMOI = {path = "../lib/OptimizationMOI"}
+OptimizationMadNLP = {path = "../lib/OptimizationMadNLP"}
 OptimizationManopt = {path = "../lib/OptimizationManopt"}
 OptimizationMetaheuristics = {path = "../lib/OptimizationMetaheuristics"}
+OptimizationMultistartOptimization = {path = "../lib/OptimizationMultistartOptimization"}
 OptimizationNLPModels = {path = "../lib/OptimizationNLPModels"}
 OptimizationNLopt = {path = "../lib/OptimizationNLopt"}
 OptimizationNOMAD = {path = "../lib/OptimizationNOMAD"}
+OptimizationODE = {path = "../lib/OptimizationODE"}
 OptimizationOptimJL = {path = "../lib/OptimizationOptimJL"}
 OptimizationOptimisers = {path = "../lib/OptimizationOptimisers"}
 OptimizationPRIMA = {path = "../lib/OptimizationPRIMA"}
 OptimizationPolyalgorithms = {path = "../lib/OptimizationPolyalgorithms"}
+OptimizationPyCMA = {path = "../lib/OptimizationPyCMA"}
+OptimizationQuadDIRECT = {path = "../lib/OptimizationQuadDIRECT"}
+OptimizationSciPy = {path = "../lib/OptimizationSciPy"}
+OptimizationSophia = {path = "../lib/OptimizationSophia"}
 OptimizationSpeedMapping = {path = "../lib/OptimizationSpeedMapping"}
 
 [compat]
@@ -89,22 +107,29 @@ NLPModels = "0.21"
 NLPModelsTest = "0.10"
 NLopt = "0.6, 1"
 Optimization = "5"
+OptimizationAuglag = "1"
 OptimizationBBO = "0.4"
 OptimizationBase = "4"
 OptimizationCMAEvolutionStrategy = "0.3"
 OptimizationEvolutionary = "0.4"
 OptimizationGCMAES = "0.3"
 OptimizationIpopt = "0.2"
 OptimizationMOI = "0.5"
+OptimizationMadNLP = "0.3"
 OptimizationManopt = "1"
 OptimizationMetaheuristics = "0.3"
+OptimizationMultistartOptimization = "0.3"
 OptimizationNLPModels = "0.0.2, 1"
 OptimizationNLopt = "0.3"
 OptimizationNOMAD = "0.3"
+OptimizationODE = "0.1"
 OptimizationOptimJL = "0.4"
 OptimizationOptimisers = "0.3"
 OptimizationPRIMA = "0.3"
 OptimizationPolyalgorithms = "0.3"
+OptimizationQuadDIRECT = "0.3"
+OptimizationSciPy = "0.4"
+OptimizationSophia = "1"
 OptimizationSpeedMapping = "0.2"
 OrdinaryDiffEq = "6"
 Plots = "1"

docs/make.jl

@@ -1,16 +1,15 @@
 using Documenter, Optimization
-using FiniteDiff, ForwardDiff, ModelingToolkit, ReverseDiff, Tracker, Zygote
-using ADTypes
+using OptimizationLBFGSB, OptimizationSophia
 
-cp("./docs/Manifest.toml", "./docs/src/assets/Manifest.toml", force = true)
-cp("./docs/Project.toml", "./docs/src/assets/Project.toml", force = true)
+cp(joinpath(@__DIR__, "Manifest.toml"), joinpath(@__DIR__, "src/assets/Manifest.toml"), force = true)
+cp(joinpath(@__DIR__, "Project.toml"), joinpath(@__DIR__, "src/assets/Project.toml"), force = true)
 
 include("pages.jl")
 
 makedocs(sitename = "Optimization.jl",
     authors = "Chris Rackauckas, Vaibhav Kumar Dixit et al.",
-    modules = [Optimization, Optimization.SciMLBase, Optimization.OptimizationBase,
-        FiniteDiff, ForwardDiff, ModelingToolkit, ReverseDiff, Tracker, Zygote, ADTypes],
+    modules = [Optimization, Optimization.SciMLBase, Optimization.OptimizationBase, Optimization.ADTypes,
+        OptimizationLBFGSB, OptimizationSophia],
     clean = true, doctest = false, linkcheck = true,
     warnonly = [:missing_docs, :cross_references],
     format = Documenter.HTML(assets = ["assets/favicon.ico"],

docs/src/API/ad.md

@@ -13,15 +13,15 @@ The choices for the auto-AD fill-ins with quick descriptions are:
 
 ## Automatic Differentiation Choice API
 
-The following sections describe the Auto-AD choices in detail.
+The following sections describe the Auto-AD choices in detail. These types are defined in the [ADTypes.jl](https://github.com/SciML/ADTypes.jl) package.
 
 ```@docs
-OptimizationBase.AutoForwardDiff
-OptimizationBase.AutoFiniteDiff
-OptimizationBase.AutoReverseDiff
-OptimizationBase.AutoZygote
-OptimizationBase.AutoTracker
-OptimizationBase.AutoSymbolics
-OptimizationBase.AutoEnzyme
+ADTypes.AutoForwardDiff
+ADTypes.AutoFiniteDiff
+ADTypes.AutoReverseDiff
+ADTypes.AutoZygote
+ADTypes.AutoTracker
+ADTypes.AutoSymbolics
+ADTypes.AutoEnzyme
 ADTypes.AutoMooncake
 ```

docs/src/API/optimization_state.md

@@ -1,5 +1,5 @@
 # [OptimizationState](@id optstate)
 
 ```@docs
-Optimization.OptimizationState
+OptimizationBase.OptimizationState
 ```

docs/src/examples/rosenbrock.md

@@ -41,15 +41,16 @@ An optimization problem can now be defined and solved to estimate the values for
 
 ```@example rosenbrock
 # Define the problem to solve
-using Optimization, ForwardDiff, Zygote
+using SciMLBase, OptimizationBase
+using ADTypes, ForwardDiff, Zygote
 
 rosenbrock(x, p) = (p[1] - x[1])^2 + p[2] * (x[2] - x[1]^2)^2
 x0 = zeros(2)
 _p = [1.0, 100.0]
 
-f = OptimizationFunction(rosenbrock, Optimization.AutoForwardDiff())
+f = SciMLBase.OptimizationFunction(rosenbrock, ADTypes.AutoForwardDiff())
 l1 = rosenbrock(x0, _p)
-prob = OptimizationProblem(f, x0, _p)
+prob = SciMLBase.OptimizationProblem(f, x0, _p)
 ```
 
 ## Optim.jl Solvers
@@ -59,19 +60,19 @@ prob = OptimizationProblem(f, x0, _p)
 ```@example rosenbrock
 using OptimizationOptimJL
 sol = solve(prob, SimulatedAnnealing())
-prob = OptimizationProblem(f, x0, _p, lb = [-1.0, -1.0], ub = [0.8, 0.8])
+prob = SciMLBase.OptimizationProblem(f, x0, _p, lb = [-1.0, -1.0], ub = [0.8, 0.8])
 sol = solve(prob, SAMIN())
 
 l1 = rosenbrock(x0, _p)
-prob = OptimizationProblem(rosenbrock, x0, _p)
+prob = SciMLBase.OptimizationProblem(rosenbrock, x0, _p)
 sol = solve(prob, NelderMead())
 ```
 
 ### Now a gradient-based optimizer with forward-mode automatic differentiation
 
 ```@example rosenbrock
-optf = OptimizationFunction(rosenbrock, Optimization.AutoForwardDiff())
-prob = OptimizationProblem(optf, x0, _p)
+optf = SciMLBase.OptimizationFunction(rosenbrock, ADTypes.AutoForwardDiff())
+prob = SciMLBase.OptimizationProblem(optf, x0, _p)
 sol = solve(prob, BFGS())
 ```
 
@@ -91,19 +92,19 @@ sol = solve(prob, Optim.KrylovTrustRegion())
 
 ```@example rosenbrock
 cons = (res, x, p) -> res .= [x[1]^2 + x[2]^2]
-optf = OptimizationFunction(rosenbrock, Optimization.AutoForwardDiff(); cons = cons)
+optf = SciMLBase.OptimizationFunction(rosenbrock, ADTypes.AutoForwardDiff(); cons = cons)
 
-prob = OptimizationProblem(optf, x0, _p, lcons = [-Inf], ucons = [Inf])
+prob = SciMLBase.OptimizationProblem(optf, x0, _p, lcons = [-Inf], ucons = [Inf])
 sol = solve(prob, IPNewton()) # Note that -Inf < x[1]^2 + x[2]^2 < Inf is always true
 
-prob = OptimizationProblem(optf, x0, _p, lcons = [-5.0], ucons = [10.0])
+prob = SciMLBase.OptimizationProblem(optf, x0, _p, lcons = [-5.0], ucons = [10.0])
 sol = solve(prob, IPNewton()) # Again, -5.0 < x[1]^2 + x[2]^2 < 10.0
 
-prob = OptimizationProblem(optf, x0, _p, lcons = [-Inf], ucons = [Inf],
+prob = SciMLBase.OptimizationProblem(optf, x0, _p, lcons = [-Inf], ucons = [Inf],
     lb = [-500.0, -500.0], ub = [50.0, 50.0])
 sol = solve(prob, IPNewton())
 
-prob = OptimizationProblem(optf, x0, _p, lcons = [0.5], ucons = [0.5],
+prob = SciMLBase.OptimizationProblem(optf, x0, _p, lcons = [0.5], ucons = [0.5],
     lb = [-500.0, -500.0], ub = [50.0, 50.0])
 sol = solve(prob, IPNewton())
 
@@ -118,8 +119,8 @@ function con_c(res, x, p)
     res .= [x[1]^2 + x[2]^2]
 end
 
-optf = OptimizationFunction(rosenbrock, Optimization.AutoForwardDiff(); cons = con_c)
-prob = OptimizationProblem(optf, x0, _p, lcons = [-Inf], ucons = [0.25^2])
+optf = SciMLBase.OptimizationFunction(rosenbrock, ADTypes.AutoForwardDiff(); cons = con_c)
+prob = SciMLBase.OptimizationProblem(optf, x0, _p, lcons = [-Inf], ucons = [0.25^2])
 sol = solve(prob, IPNewton()) # -Inf < cons_circ(sol.u, _p) = 0.25^2
 ```
 
@@ -139,17 +140,17 @@ function con2_c(res, x, p)
     res .= [x[1]^2 + x[2]^2, x[2] * sin(x[1]) - x[1]]
 end
 
-optf = OptimizationFunction(rosenbrock, Optimization.AutoZygote(); cons = con2_c)
-prob = OptimizationProblem(optf, x0, _p, lcons = [-Inf, -Inf], ucons = [100.0, 100.0])
+optf = SciMLBase.OptimizationFunction(rosenbrock, ADTypes.AutoZygote(); cons = con2_c)
+prob = SciMLBase.OptimizationProblem(optf, x0, _p, lcons = [-Inf, -Inf], ucons = [100.0, 100.0])
 sol = solve(prob, Ipopt.Optimizer())
 ```
 
 ## Now let's switch over to OptimizationOptimisers with reverse-mode AD
 
 ```@example rosenbrock
 import OptimizationOptimisers
-optf = OptimizationFunction(rosenbrock, Optimization.AutoZygote())
-prob = OptimizationProblem(optf, x0, _p)
+optf = SciMLBase.OptimizationFunction(rosenbrock, ADTypes.AutoZygote())
+prob = SciMLBase.OptimizationProblem(optf, x0, _p)
 sol = solve(prob, OptimizationOptimisers.Adam(0.05), maxiters = 1000, progress = false)
 ```
 
@@ -164,8 +165,8 @@ sol = solve(prob, CMAEvolutionStrategyOpt())
 
 ```@example rosenbrock
 using OptimizationNLopt, ModelingToolkit
-optf = OptimizationFunction(rosenbrock, Optimization.AutoSymbolics())
-prob = OptimizationProblem(optf, x0, _p)
+optf = SciMLBase.OptimizationFunction(rosenbrock, ADTypes.AutoSymbolics())
+prob = SciMLBase.OptimizationProblem(optf, x0, _p)
 
 sol = solve(prob, Opt(:LN_BOBYQA, 2))
 sol = solve(prob, Opt(:LD_LBFGS, 2))
@@ -174,7 +175,7 @@ sol = solve(prob, Opt(:LD_LBFGS, 2))
 ### Add some box constraints and solve with a few NLopt.jl methods
 
 ```@example rosenbrock
-prob = OptimizationProblem(optf, x0, _p, lb = [-1.0, -1.0], ub = [0.8, 0.8])
+prob = SciMLBase.OptimizationProblem(optf, x0, _p, lb = [-1.0, -1.0], ub = [0.8, 0.8])
 sol = solve(prob, Opt(:LD_LBFGS, 2))
 sol = solve(prob, Opt(:G_MLSL_LDS, 2), local_method = Opt(:LD_LBFGS, 2), maxiters = 10000) #a global optimizer with random starts of local optimization
 ```
@@ -183,7 +184,7 @@ sol = solve(prob, Opt(:G_MLSL_LDS, 2), local_method = Opt(:LD_LBFGS, 2), maxiter
 
 ```@example rosenbrock
 using OptimizationBBO
-prob = Optimization.OptimizationProblem(rosenbrock, [0.0, 0.3], _p, lb = [-1.0, 0.2],
+prob = SciMLBase.OptimizationProblem(rosenbrock, [0.0, 0.3], _p, lb = [-1.0, 0.2],
     ub = [0.8, 0.43])
 sol = solve(prob, BBO_adaptive_de_rand_1_bin()) # -1.0 ≤ x[1] ≤ 0.8, 0.2 ≤ x[2] ≤ 0.43
 ```

docs/src/getting_started.md

@@ -14,15 +14,15 @@ The simplest copy-pasteable code using a quasi-Newton method (LBFGS) to solve th
 
 ```@example intro
 # Import the package and define the problem to optimize
-using Optimization, OptimizationLBFGSB, Zygote
+using OptimizationBase, OptimizationLBFGSB, ADTypes, Zygote
 rosenbrock(u, p) = (p[1] - u[1])^2 + p[2] * (u[2] - u[1]^2)^2
 u0 = zeros(2)
 p = [1.0, 100.0]
 
-optf = OptimizationFunction(rosenbrock, AutoZygote())
+optf = OptimizationFunction(rosenbrock, ADTypes.AutoZygote())
 prob = OptimizationProblem(optf, u0, p)
 
-sol = solve(prob, OptimizationLBFGSB.LBFGS())
+sol = solve(prob, OptimizationLBFGSB.LBFGSB())
 ```
 
 ```@example intro
@@ -131,8 +131,8 @@ automatically construct the derivative functions using ForwardDiff.jl. This
 looks like:
 
 ```@example intro
-using ForwardDiff
-optf = OptimizationFunction(rosenbrock, Optimization.AutoForwardDiff())
+using ForwardDiff, ADTypes
+optf = OptimizationFunction(rosenbrock, ADTypes.AutoForwardDiff())
 prob = OptimizationProblem(optf, u0, p)
 sol = solve(prob, OptimizationOptimJL.BFGS())
 ```
@@ -155,7 +155,7 @@ We can demonstrate this via:
 
 ```@example intro
 using Zygote
-optf = OptimizationFunction(rosenbrock, Optimization.AutoZygote())
+optf = OptimizationFunction(rosenbrock, ADTypes.AutoZygote())
 prob = OptimizationProblem(optf, u0, p)
 sol = solve(prob, OptimizationOptimJL.BFGS())
 ```

docs/src/optimization_packages/blackboxoptim.md

@@ -63,7 +63,7 @@ rosenbrock(x, p) = (p[1] - x[1])^2 + p[2] * (x[2] - x[1]^2)^2
 x0 = zeros(2)
 p = [1.0, 100.0]
 f = OptimizationFunction(rosenbrock)
-prob = Optimization.OptimizationProblem(f, x0, p, lb = [-1.0, -1.0], ub = [1.0, 1.0])
+prob = SciMLBase.OptimizationProblem(f, x0, p, lb = [-1.0, -1.0], ub = [1.0, 1.0])
 sol = solve(prob, BBO_adaptive_de_rand_1_bin_radiuslimited(), maxiters = 100000,
     maxtime = 1000.0)
 ```

docs/src/optimization_packages/cmaevolutionstrategy.md

@@ -30,6 +30,6 @@ rosenbrock(x, p) = (p[1] - x[1])^2 + p[2] * (x[2] - x[1]^2)^2
 x0 = zeros(2)
 p = [1.0, 100.0]
 f = OptimizationFunction(rosenbrock)
-prob = Optimization.OptimizationProblem(f, x0, p, lb = [-1.0, -1.0], ub = [1.0, 1.0])
+prob = SciMLBase.OptimizationProblem(f, x0, p, lb = [-1.0, -1.0], ub = [1.0, 1.0])
 sol = solve(prob, CMAEvolutionStrategyOpt())
 ```

docs/src/optimization_packages/evolutionary.md

@@ -38,6 +38,6 @@ rosenbrock(x, p) = (p[1] - x[1])^2 + p[2] * (x[2] - x[1]^2)^2
 x0 = zeros(2)
 p = [1.0, 100.0]
 f = OptimizationFunction(rosenbrock)
-prob = Optimization.OptimizationProblem(f, x0, p, lb = [-1.0, -1.0], ub = [1.0, 1.0])
+prob = SciMLBase.OptimizationProblem(f, x0, p, lb = [-1.0, -1.0], ub = [1.0, 1.0])
 sol = solve(prob, Evolutionary.CMAES(μ = 40, λ = 100))
 ```