diff --git a/Project.toml b/Project.toml index f3655fc..6c97f64 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "ProfileLikelihood" uuid = "3fca794e-44fa-49a6-b6a0-8cd45572ba0a" authors = ["Daniel VandenHeuvel "] -version = "0.3.2" +version = "0.3.3" [deps] ChunkSplitters = "ae650224-84b6-46f8-82ea-d812ca08434e" @@ -36,7 +36,7 @@ OffsetArrays = "1.12" PolygonInbounds = "0.2" PreallocationTools = "0.4" Requires = "1.3" -SciMLBase = "1.77, 1.91, 1.94" +SciMLBase = "=2.9.1" SimpleNonlinearSolve = "0.1" StatsFuns = "1.1, 1.3" julia = "1" diff --git a/docs/src/figures/linear_exponential_example.png b/docs/src/figures/linear_exponential_example.png index e15fa7e..85b8178 100644 Binary files a/docs/src/figures/linear_exponential_example.png and b/docs/src/figures/linear_exponential_example.png differ diff --git a/docs/src/figures/logistic_example.png b/docs/src/figures/logistic_example.png index 403555a..af7e29d 100644 Binary files a/docs/src/figures/logistic_example.png and b/docs/src/figures/logistic_example.png differ diff --git a/docs/src/figures/logistic_example_prediction.png b/docs/src/figures/logistic_example_prediction.png index b388b2a..d409811 100644 Binary files a/docs/src/figures/logistic_example_prediction.png and b/docs/src/figures/logistic_example_prediction.png differ diff --git a/docs/src/figures/lokta_example_bivariate_predictions.png b/docs/src/figures/lokta_example_bivariate_predictions.png index 51be105..c1cbab8 100644 Binary files a/docs/src/figures/lokta_example_bivariate_predictions.png and b/docs/src/figures/lokta_example_bivariate_predictions.png differ diff --git a/docs/src/figures/lokta_example_bivariate_profiles_low_quality.png b/docs/src/figures/lokta_example_bivariate_profiles_low_quality.png index cea0d00..9b6e252 100644 Binary files a/docs/src/figures/lokta_example_bivariate_profiles_low_quality.png and b/docs/src/figures/lokta_example_bivariate_profiles_low_quality.png differ diff --git a/docs/src/figures/lokta_example_bivariate_profiles_smoothed_quality.png b/docs/src/figures/lokta_example_bivariate_profiles_smoothed_quality.png index 0d14e21..518d6ea 100644 Binary files a/docs/src/figures/lokta_example_bivariate_profiles_smoothed_quality.png and b/docs/src/figures/lokta_example_bivariate_profiles_smoothed_quality.png differ diff --git a/docs/src/figures/lokta_example_profiles.png b/docs/src/figures/lokta_example_profiles.png index a737233..259d216 100644 Binary files a/docs/src/figures/lokta_example_profiles.png and b/docs/src/figures/lokta_example_profiles.png differ diff --git a/docs/src/figures/lokta_example_univariate_predictions.png b/docs/src/figures/lokta_example_univariate_predictions.png index e9cc2d1..0554cf5 100644 Binary files a/docs/src/figures/lokta_example_univariate_predictions.png and b/docs/src/figures/lokta_example_univariate_predictions.png differ diff --git a/docs/src/figures/noisy_pde_data.png b/docs/src/figures/noisy_pde_data.png index 63748ff..56548bb 100644 Binary files a/docs/src/figures/noisy_pde_data.png and b/docs/src/figures/noisy_pde_data.png differ diff --git a/docs/src/figures/pde_prediction_intervals.png b/docs/src/figures/pde_prediction_intervals.png index 5a347b0..3a0158c 100644 Binary files a/docs/src/figures/pde_prediction_intervals.png and b/docs/src/figures/pde_prediction_intervals.png differ diff --git a/docs/src/figures/pde_profiles.png b/docs/src/figures/pde_profiles.png index 8bce357..a774421 100644 Binary files a/docs/src/figures/pde_profiles.png and b/docs/src/figures/pde_profiles.png differ diff --git a/docs/src/figures/regression_profiles.png b/docs/src/figures/regression_profiles.png index c5d828e..f5e0a47 100644 Binary files a/docs/src/figures/regression_profiles.png and b/docs/src/figures/regression_profiles.png differ diff --git a/docs/src/heat.md b/docs/src/heat.md index f62b7cb..bcc5406 100644 --- a/docs/src/heat.md +++ b/docs/src/heat.md @@ -244,7 +244,7 @@ using CairoMakie, LaTeXStrings fig = plot_profiles(prof; nrow=1, ncol=3, latex_names=[L"k", L"c", L"u_0"], true_vals=[k[1], c, u₀], - fig_kwargs=(fontsize=38, resolution=(2109.644f0, 444.242f0)), + fig_kwargs=(fontsize=38, size=(2109.644f0, 444.242f0)), axis_kwargs=(width=600, height=300)) scatter!(fig.content[1], get_parameter_values(prof, :k), get_profile_values(prof, :k), color=:black, markersize=9) scatter!(fig.content[2], get_parameter_values(prof, :c), get_profile_values(prof, :c), color=:black, markersize=9) @@ -358,7 +358,7 @@ The confidence intervals contain the true values. We can now visualise. fig = plot_profiles(prof; nrow=1, ncol=3, latex_names=[L"k", L"u_0"], true_vals=[k[1], u₀], - fig_kwargs=(fontsize=38, resolution=(1441.9216f0, 470.17322f0)), + fig_kwargs=(fontsize=38, size=(1441.9216f0, 470.17322f0)), axis_kwargs=(width=600, height=300)) scatter!(fig.content[1], get_parameter_values(prof, :k), get_profile_values(prof, :k), color=:black, markersize=9) scatter!(fig.content[2], get_parameter_values(prof, :u₀), get_profile_values(prof, :u₀), color=:black, markersize=9) @@ -452,7 +452,7 @@ Now we can visualise the curves. We will also show the mass curve from the exact ```julia exact_soln = compute_mass_function([k[1], u₀], prediction_data) mle_soln = compute_mass_function(get_mle(mle_sol), prediction_data) -fig = Figure(fontsize=38, resolution=(1360.512f0, 848.64404f0)) +fig = Figure(fontsize=38, size=(1360.512f0, 848.64404f0)) alp = join('a':'z') latex_names = [L"k", L"u_0"] for i in 1:2 @@ -619,7 +619,7 @@ using CairoMakie, LaTeXStrings fig = plot_profiles(prof; nrow=1, ncol=3, latex_names=[L"k", L"c", L"u_0"], true_vals=[k[1], c, u₀], - fig_kwargs=(fontsize=38, resolution=(2109.644f0, 444.242f0)), + fig_kwargs=(fontsize=38, size=(2109.644f0, 444.242f0)), axis_kwargs=(width=600, height=300)) scatter!(fig.content[1], get_parameter_values(prof, :k), get_profile_values(prof, :k), color=:black, markersize=9) scatter!(fig.content[2], get_parameter_values(prof, :c), get_profile_values(prof, :c), color=:black, markersize=9) @@ -674,7 +674,7 @@ prof = profile(likprob_2, mle_sol; ftol_abs=1e-4, ftol_rel=1e-4, xtol_abs=1e-4, fig = plot_profiles(prof; nrow=1, ncol=3, latex_names=[L"k", L"u_0"], true_vals=[k[1], u₀], - fig_kwargs=(fontsize=38, resolution=(1441.9216f0, 470.17322f0)), + fig_kwargs=(fontsize=38, size=(1441.9216f0, 470.17322f0)), axis_kwargs=(width=600, height=300)) scatter!(fig.content[1], get_parameter_values(prof, :k), get_profile_values(prof, :k), color=:black, markersize=9) scatter!(fig.content[2], get_parameter_values(prof, :u₀), get_profile_values(prof, :u₀), color=:black, markersize=9) @@ -705,7 +705,7 @@ parameter_wise, union_intervals, all_curves, param_range = exact_soln = compute_mass_function([k[1], u₀], prediction_data) mle_soln = compute_mass_function(get_mle(mle_sol), prediction_data) -fig = Figure(fontsize=38, resolution=(1360.512f0, 848.64404f0)) +fig = Figure(fontsize=38, size=(1360.512f0, 848.64404f0)) alp = join('a':'z') latex_names = [L"k", L"u_0"] for i in 1:2 diff --git a/docs/src/logistic.md b/docs/src/logistic.md index 73e01ed..c57579e 100644 --- a/docs/src/logistic.md +++ b/docs/src/logistic.md @@ -69,6 +69,7 @@ prob = LikelihoodProblem( data=(uᵒ, σ), ode_parameters=[1.0, 1.0], # temp values for [λ, K] ode_kwargs=(verbose=false, saveat=t), + f_kwargs=(adtype=Optimization.AutoFiniteDiff(),), prob_kwargs=(lb=lb, ub=ub), ode_alg=Rosenbrock23() ) diff --git a/docs/src/lotka.md b/docs/src/lotka.md index 33e44c5..9a05f2c 100644 --- a/docs/src/lotka.md +++ b/docs/src/lotka.md @@ -200,7 +200,7 @@ fig_2 = plot_profiles(prof_2, param_pairs; # param_pairs not needed, but this en true_vals=[α, β, a₀, b₀], xlim_tuples=[(0.5, 1.5), (0.5, 1.5), (0.5, 1.5), (0.7, 1.3), (0.7, 1.3), (0.5, 1.1)], ylim_tuples=[(0.5, 1.5), (0.5, 1.05), (0.1, 0.5), (0.5, 1.05), (0.1, 0.5), (0.1, 0.5)], - fig_kwargs=(fontsize=24,)) + fig_kwargs=(fontsize=17,)) ``` ```@raw html @@ -226,7 +226,7 @@ fig_3 = plot_profiles(prof_2, param_pairs; interpolation=true, xlim_tuples=[(0.5, 1.5), (0.5, 1.5), (0.5, 1.5), (0.7, 1.3), (0.7, 1.3), (0.5, 1.1)], ylim_tuples=[(0.5, 1.5), (0.5, 1.05), (0.1, 0.5), (0.5, 1.05), (0.1, 0.5), (0.1, 0.5)], - fig_kwargs=(fontsize=24,)) + fig_kwargs=(fontsize=17,)) ``` ```@raw html @@ -269,7 +269,7 @@ prediction_function!(exact_soln, [α, β, a₀, b₀], pred_data) prediction_function!(mle_soln, get_mle(sol), pred_data) # Plot the parameter-wise intervals -fig = Figure(fontsize=38, resolution=(2935.488f0, 1392.64404f0)) +fig = Figure(fontsize=38, size=(2935.488f0, 1392.64404f0)) alp = [['a', 'b', 'e', 'f'], ['c', 'd', 'g', 'h']] latex_names = [L"\alpha", L"\beta", L"a_0", L"b_0"] for (k, idx) in enumerate((a_idx, b_idx)) @@ -338,7 +338,7 @@ individual_intervals, union_intervals, q_vals, param_ranges = q_prototype) # Plot the intervals -fig = Figure(fontsize=38, resolution=(2935.488f0, 1854.64404f0)) +fig = Figure(fontsize=38, size=(2935.488f0, 1854.64404f0)) integer_param_pairs = ProfileLikelihood.convert_symbol_tuples(param_pairs, prof_2) # converts to the integer representation alp = [['a', 'b', 'e', 'f', 'i', 'j'], ['c', 'd', 'g', 'h', 'k', 'l']] for (k, idx) in enumerate((a_idx, b_idx)) diff --git a/src/problem_updates.jl b/src/problem_updates.jl index 51119eb..ee4bd40 100644 --- a/src/problem_updates.jl +++ b/src/problem_updates.jl @@ -2,17 +2,40 @@ update_initial_estimate(prob::OptimizationProblem, θ) = remake(prob; u0=θ) update_initial_estimate(prob::OptimizationProblem, sol::SciMLBase.OptimizationSolution) = update_initial_estimate(prob, sol.u) # replace obj with a new obj -function replace_objective_function(prob::OptimizationProblem{iip,FF,uType,P,B,LC,UC,Sns,K}, obj::F) where {F,iip,AD,G,H,HV,C,CJ,CH,LH,HP,CJP,CHP,LHP,S,S2,O,HCV,CJCV,CHCV,LHCV,EX,CEX,SYS,FF2,FF<:OptimizationFunction{iip,AD,FF2,G,H,HV,C,CJ,CH,LH,HP,CJP,CHP,LHP,S,S2,O,HCV,CJCV,CHCV,LHCV,EX,CEX,SYS},uType,P,B,LC,UC,Sns,K} - f = OptimizationFunction{iip,AD,F,G,H,HV,C,CJ,CH,LH,HP,CJP,CHP,LHP,S,S2,O,HCV,CJCV,CHCV,LHCV,EX,CEX,SYS - }(obj, - prob.f.adtype, prob.f.grad, - prob.f.hess, prob.f.hv, - prob.f.cons, prob.f.cons_j, prob.f.cons_h, prob.f.lag_h, - prob.f.hess_prototype, prob.f.cons_jac_prototype, prob.f.cons_hess_prototype, prob.f.lag_hess_prototype, - prob.f.syms, prob.f.paramsyms, prob.f.observed, - prob.f.hess_colorvec, prob.f.cons_jac_colorvec, prob.f.cons_hess_colorvec, prob.f.lag_hess_colorvec, - prob.f.expr, prob.f.cons_expr, prob.f.sys) - return remake(prob; f=f) +@inline function replace_objective_function(f::OF, new_f::FF) where {iip,AD,F,G,H,HV,C,CJ,CH,HP,CJP,CHP,S,S2,O,EX,CEX,SYS,LH,LHP,HCV,CJCV,CHCV,LHCV,OF<:OptimizationFunction{iip,AD,F,G,H,HV,C,CJ,CH,HP,CJP,CHP,S,S2,O,EX,CEX,SYS,LH,LHP,HCV,CJCV,CHCV,LHCV},FF} + # scimlbase needs to add a constructorof method for OptimizationFunction before we can just do @set with accessors.jl. + # g = @set f.f = new_f + # return g + return OptimizationFunction{iip,AD,FF,G,H,HV,C,CJ,CH,HP,CJP,CHP,S,S2,O,EX,CEX,SYS,LH,LHP,HCV,CJCV,CHCV,LHCV}( + new_f, + f.adtype, + f.grad, + f.hess, + f.hv, + f.cons, + f.cons_j, + f.cons_h, + f.hess_prototype, + f.cons_jac_prototype, + f.cons_hess_prototype, + f.syms, + f.paramsyms, + f.observed, + f.expr, + f.cons_expr, + f.sys, + f.lag_h, + f.lag_hess_prototype, + f.hess_colorvec, + f.cons_jac_colorvec, + f.cons_hess_colorvec, + f.lag_hess_colorvec, + ) +end + +@inline function replace_objective_function(prob::F, obj::FF) where {F<:OptimizationProblem,FF} + g = replace_objective_function(prob.f, obj) + return remake(prob; f=g) end # fix the objective function's nth parameter at θₙ diff --git a/test/Manifest.toml b/test/Manifest.toml index e4fc590..d0a9d64 100644 --- a/test/Manifest.toml +++ b/test/Manifest.toml @@ -1,19 +1,19 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.10.0-rc2" manifest_format = "2.0" project_hash = "40117e3c9c4592f6a041cc79b3e1d123b5f6edfb" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "332e5d7baeff8497b923b730b994fa480601efc7" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.5" [[deps.AbbreviatedStackTraces]] deps = ["Distributed", "REPL"] -git-tree-sha1 = "c1c7c9671073f2241ae90b937032494152b83c1e" +git-tree-sha1 = "304f6b497d4a46312c1dd9a25d8cf47271632835" uuid = "ac637c84-cc71-43bf-9c33-c1b4316be3d4" -version = "0.1.12" +version = "0.2.3" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -27,20 +27,39 @@ weakdeps = ["ChainRulesCore", "Test"] AbstractFFTsTestExt = "Test" [[deps.AbstractLattices]] -git-tree-sha1 = "f35684b7349da49fcc8a9e520e30e45dbb077166" +git-tree-sha1 = "222ee9e50b98f51b5d78feb93dd928880df35f06" uuid = "398f06c4-4d28-53ec-89ca-5b2656b7603d" -version = "0.2.1" +version = "0.3.0" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.4" +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Test"] +git-tree-sha1 = "a7055b939deae2455aa8a67491e034f735dd08d3" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.33" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" +git-tree-sha1 = "02f731463748db57cc2ebfbd9fbc9ce8280d3433" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.6.2" +version = "3.7.1" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -64,9 +83,9 @@ version = "0.2.0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "f83ec24f76d4c8f525099b2ac475fc098138ec31" +git-tree-sha1 = "247efbccf92448be332d154d6ca56b9fcdd93c31" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.4.11" +version = "7.6.1" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" @@ -84,20 +103,14 @@ version = "7.4.11" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -[[deps.ArrayInterfaceCore]] -deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" -uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.29" - [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[deps.Automa]] -deps = ["ScanByte", "TranscodingStreams"] -git-tree-sha1 = "48e54446df62fdf9ef76959c32dc33f3cff659ee" +deps = ["PrecompileTools", "TranscodingStreams"] +git-tree-sha1 = "0da671c730d79b8f9a88a391556ec695ea921040" uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" -version = "0.8.3" +version = "1.0.2" [[deps.AxisAlgorithms]] deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] @@ -116,14 +129,14 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[deps.BenchmarkTools]] deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "d9a9701b899b30332bbcb3e1679c41cce81fb0e8" +git-tree-sha1 = "f1f03a9fa24271160ed7e73051fba3c1a759b53f" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.3.2" +version = "1.4.0" [[deps.BitFlags]] -git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.7" +version = "0.1.8" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] @@ -150,9 +163,9 @@ version = "0.4.2" [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] -git-tree-sha1 = "89e0654ed8c7aebad6d5ad235d6242c2d737a928" +git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.3" +version = "0.2.4" [[deps.CPUTime]] git-tree-sha1 = "2dcc50ea6a0a1ef6440d6eecd0fe3813e5671f45" @@ -181,10 +194,10 @@ uuid = "159f3aea-2a34-519c-b102-8c37f9878175" version = "1.0.5" [[deps.CairoMakie]] -deps = ["Base64", "Cairo", "Colors", "FFTW", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools", "SHA"] -git-tree-sha1 = "e041782fed7614b1726fa250f2bf24fd5c789689" +deps = ["CRC32c", "Cairo", "Colors", "FFTW", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] +git-tree-sha1 = "fdbad23ab5b44ecd1aa77c84e110becfddf2d789" uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" -version = "0.10.7" +version = "0.11.2" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] @@ -199,16 +212,20 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRulesCore]] -deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" +deps = ["Compat", "LinearAlgebra"] +git-tree-sha1 = "e0af648f0692ec1691b5d094b8724ba1346281cf" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.16.0" +version = "1.18.0" +weakdeps = ["SparseArrays"] + + [deps.ChainRulesCore.extensions] + ChainRulesCoreSparseArraysExt = "SparseArrays" [[deps.ChunkSplitters]] deps = ["TestItems"] -git-tree-sha1 = "47952f11225e834eb3125184eeea4f6b8c8d934b" +git-tree-sha1 = "a0d0d0372dbc00735bce1976928094acedfdbf8e" uuid = "ae650224-84b6-46f8-82ea-d812ca08434e" -version = "1.0.0" +version = "2.0.3" [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] @@ -218,15 +235,15 @@ version = "0.1.12" [[deps.CodecBzip2]] deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] -git-tree-sha1 = "2e62a725210ce3c3c2e1a3080190e7ca491f18d7" +git-tree-sha1 = "c0ae2a86b162fb5d7acc65269b469ff5b8a73594" uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.7.2" +version = "0.8.1" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "02aa26a4cf76381be7f66e020a3eddeb27b0a092" +git-tree-sha1 = "cd67fc487743b2f0fd4380d4cbd3a24660d0eec8" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.2" +version = "0.7.3" [[deps.ColorBrewer]] deps = ["Colors", "JSON", "Test"] @@ -236,9 +253,9 @@ version = "0.4.0" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "dd3000d954d483c1aad05fe1eb9e6a715c97013e" +git-tree-sha1 = "67c1f244b991cad9b0aa4b7540fb758c2488b129" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.22.0" +version = "3.24.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -276,9 +293,9 @@ version = "0.3.0" [[deps.Compat]] deps = ["UUIDs"] -git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7" +git-tree-sha1 = "886826d76ea9e72b35fcd000e535588f7b60f21d" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.9.0" +version = "4.10.1" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -287,13 +304,27 @@ 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.CompositionsBase]] +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + +[[deps.ConcreteStructs]] +git-tree-sha1 = "f749037478283d372048690eb3b5f92a79432b34" +uuid = "2569d6c7-a4a2-43d3-a901-331e8e4be471" +version = "0.2.3" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "5372dbbf8f0bdb8c700db5367132925c0771ef7e" +git-tree-sha1 = "8cfa272e8bdedfa88b6aefbbca7c19f1befac519" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.2.1" +version = "2.3.0" [[deps.ConsoleProgressMonitor]] deps = ["Logging", "ProgressMeter"] @@ -303,9 +334,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -334,10 +365,10 @@ uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.15.0" [[deps.DataInterpolations]] -deps = ["LinearAlgebra", "RecipesBase", "RecursiveArrayTools", "Reexport", "Requires"] -git-tree-sha1 = "e52a7c2388471ca6e7e6dcd68c98073f378b8967" +deps = ["LinearAlgebra", "PrettyTables", "RecipesBase", "RecursiveArrayTools", "Reexport", "Requires"] +git-tree-sha1 = "97b5c6115165fc9f99908cbdd2ea4c0efda0843e" uuid = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" -version = "4.0.1" +version = "4.5.0" [deps.DataInterpolations.extensions] DataInterpolationsChainRulesCoreExt = "ChainRulesCore" @@ -373,22 +404,26 @@ version = "1.2.0" [[deps.DelaunayTriangulation]] deps = ["DataStructures", "EnumX", "ExactPredicates", "Random", "SimpleGraphs"] -git-tree-sha1 = "a1d8532de83f8ce964235eff1edeff9581144d02" +git-tree-sha1 = "26eb8e2331b55735c3d305d949aabd7363f07ba7" uuid = "927a84f5-c5f4-47a5-9785-b46e178433df" -version = "0.7.2" -weakdeps = ["MakieCore"] +version = "0.8.11" - [deps.DelaunayTriangulation.extensions] - DelaunayTriangulationMakieCoreExt = "MakieCore" +[[deps.DelimitedFiles]] +deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" +uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +version = "1.9.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "ed586656058844e48660c6d6fdb384e83afc50db" +deps = ["ArrayInterface", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] +git-tree-sha1 = "309efb205c30d43b595466283bbecf2769283e22" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.128.0" +version = "6.141.0" [deps.DiffEqBase.extensions] + DiffEqBaseChainRulesCoreExt = "ChainRulesCore" DiffEqBaseDistributionsExt = "Distributions" + DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" DiffEqBaseMPIExt = "MPI" DiffEqBaseMeasurementsExt = "Measurements" @@ -396,10 +431,11 @@ version = "6.128.0" DiffEqBaseReverseDiffExt = "ReverseDiff" DiffEqBaseTrackerExt = "Tracker" DiffEqBaseUnitfulExt = "Unitful" - DiffEqBaseZygoteExt = "Zygote" [deps.DiffEqBase.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" @@ -407,7 +443,6 @@ version = "6.128.0" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -423,12 +458,13 @@ version = "1.15.1" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "b6def76ffad15143924a2199f72a5cd883a2e8a9" +git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.9" -weakdeps = ["SparseArrays"] +version = "0.10.11" +weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] + DistancesChainRulesCoreExt = "ChainRulesCore" DistancesSparseArraysExt = "SparseArrays" [[deps.Distributed]] @@ -436,18 +472,20 @@ 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 = "27a18994a5991b1d2e2af7833c4f8ecf9af6b9ea" +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "a6c00f894f24460379cb7136633cef54ac9f6f4a" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.99" +version = "0.25.103" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" DistributionsDensityInterfaceExt = "DensityInterface" + DistributionsTestExt = "Test" [deps.Distributions.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -477,16 +515,22 @@ git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" +[[deps.EnzymeCore]] +deps = ["Adapt"] +git-tree-sha1 = "2efe862de93cd87f620ad6ac9c9e3f83f1b2841b" +uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" +version = "0.6.4" + [[deps.ErrorfreeArithmetic]] git-tree-sha1 = "d6863c556f1142a061532e79f611aa46be201686" uuid = "90fa49ef-747e-5e6f-a989-263ba693cf1a" version = "0.5.2" [[deps.ExactPredicates]] -deps = ["IntervalArithmetic", "Random", "StaticArraysCore", "Test"] -git-tree-sha1 = "276e83bc8b21589b79303b9985c321024ffdf59c" +deps = ["IntervalArithmetic", "Random", "StaticArraysCore"] +git-tree-sha1 = "499b1ca78f6180c8f8bdf1cabde2d39120229e5c" uuid = "429591f6-91af-11e9-00e2-59fbe8cec110" -version = "2.2.5" +version = "2.2.6" [[deps.ExceptionUnwrapping]] deps = ["Test"] @@ -501,10 +545,10 @@ uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.5.0+0" [[deps.ExponentialUtilities]] -deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "Printf", "SnoopPrecompile", "SparseArrays", "libblastrampoline_jll"] -git-tree-sha1 = "fb7dbef7d2631e2d02c49e2750f7447648b0ec9b" +deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] +git-tree-sha1 = "602e4585bcbd5a25bc06f514724593d13ff9e862" uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.24.0" +version = "1.25.0" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" @@ -512,21 +556,15 @@ uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" [[deps.Extents]] -git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" +git-tree-sha1 = "2140cd04483da90b2da7f99b2add0750504fc39c" uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" -version = "0.1.1" - -[[deps.FFMPEG]] -deps = ["FFMPEG_jll"] -git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" -uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.1" +version = "0.1.2" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "b8660105ccaff705c70894c5f1e24f5c18974220" +git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.4+0" +version = "4.4.4+1" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -542,9 +580,9 @@ version = "3.3.10+0" [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "aa9925a229d45fe3018715238956766fa21804d1" +git-tree-sha1 = "a6e756a880fc419c8b41592010aebe6a5ce09136" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.2.6" +version = "0.2.8" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -569,14 +607,32 @@ git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" version = "1.16.1" +[[deps.FilePaths]] +deps = ["FilePathsBase", "MacroTools", "Reexport", "Requires"] +git-tree-sha1 = "919d9412dbf53a2e6fe74af62a73ceed0bce0629" +uuid = "8fc22ac5-c921-52a6-82fd-178b2807b824" +version = "0.8.3" + +[[deps.FilePathsBase]] +deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] +git-tree-sha1 = "9f00e42f8d99fdde64d40c8ea5d14269a2e2c1aa" +uuid = "48062228-2e41-5def-b9a4-89aafe57970f" +version = "0.9.21" + [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "01dba5dbad6b2766e2ddd7b9d64af0e6d68d95cd" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.9.1" +weakdeps = ["PDMats", "SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysPDMatsExt = "PDMats" + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] @@ -595,10 +651,10 @@ version = "2.21.1" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FiniteVolumeMethod]] -deps = ["ChunkSplitters", "DelaunayTriangulation", "DiffEqBase", "FunctionWrappersWrappers", "LinearAlgebra", "MuladdMacro", "PreallocationTools", "SciMLBase", "SparseArrays"] -git-tree-sha1 = "5956b736dae61ad3a67e9eef26718fb1df847f94" +deps = ["ChunkSplitters", "CommonSolve", "DelaunayTriangulation", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "SciMLBase", "SparseArrays"] +git-tree-sha1 = "4a000442e807c67821f7ef07afed9e447e71b2c7" uuid = "d4f04ab7-4f65-4d72-8a28-7087bc7f46f4" -version = "0.4.7" +version = "1.1.2" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -620,9 +676,9 @@ version = "0.4.2" [[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] @@ -630,15 +686,15 @@ weakdeps = ["StaticArrays"] [[deps.FreeType]] deps = ["CEnum", "FreeType2_jll"] -git-tree-sha1 = "cabd77ab6a6fdff49bfd24af2ebe76e6e018a2b4" +git-tree-sha1 = "50351f83f95282cf903e968d7c6e8d44a5f83d0b" uuid = "b38be410-82b0-50bf-ab77-7b57e271db43" -version = "4.0.0" +version = "4.1.0" [[deps.FreeType2_jll]] -deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" +deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.10.4+0" +version = "2.13.1+0" [[deps.FreeTypeAbstraction]] deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] @@ -681,9 +737,9 @@ version = "0.5.3" [[deps.GeoInterface]] deps = ["Extents"] -git-tree-sha1 = "bb198ff907228523f3dee1070ceee63b9359b6ab" +git-tree-sha1 = "d53480c0793b13341c40199190f92c611aa2e93c" uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" -version = "1.3.1" +version = "1.3.2" [[deps.GeometryBasics]] deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -698,10 +754,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] @@ -717,15 +773,15 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" +git-tree-sha1 = "899050ace26649433ef1af25bc17a815b3db52b7" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.8.0" +version = "1.9.0" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] -git-tree-sha1 = "678d136003ed5bceaab05cf64519e3f956ffa4ba" +git-tree-sha1 = "af13a277efd8a6e716d79ef635d5342ccb75be61" uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" -version = "0.9.1" +version = "0.10.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -734,9 +790,9 @@ version = "1.0.2" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "cb56ccdd481c0dd7f975ad2b3b62d9eda088f7e2" +git-tree-sha1 = "abbbb9ec3afd783a7cbd82ef01dcd088ea051398" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.9.14" +version = "1.10.1" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -746,9 +802,9 @@ version = "2.8.1+1" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "d38bd0d9759e3c6cfa19bdccc314eccf8ce596cc" +git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.15" +version = "0.1.16" [[deps.HypergeometricFunctions]] deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] @@ -803,9 +859,9 @@ uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" version = "1.0.0" [[deps.Inflate]] -git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" +git-tree-sha1 = "ea8031dea4aff6bd41f1df8f2fdfb25b33626381" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.3" +version = "0.1.4" [[deps.IntegerMathUtils]] git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" @@ -813,10 +869,10 @@ uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" version = "0.1.2" [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0cb9352ef2e01574eeebdb102948a58740dcaf83" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "31d6adb719886d4e32e38197aae466e98881320b" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2023.1.0+0" +version = "2024.0.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -829,21 +885,27 @@ uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" version = "0.14.7" [[deps.IntervalArithmetic]] -deps = ["CRlibm", "FastRounding", "LinearAlgebra", "Markdown", "Random", "RecipesBase", "RoundingEmulator", "SetRounding", "StaticArrays"] -git-tree-sha1 = "5ab7744289be503d76a944784bac3f2df7b809af" +deps = ["CRlibm", "EnumX", "FastRounding", "LinearAlgebra", "Markdown", "Random", "RecipesBase", "RoundingEmulator", "SetRounding", "StaticArrays"] +git-tree-sha1 = "f59e639916283c1d2e106d2b00910b50f4dab76c" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.20.9" +version = "0.21.2" [[deps.IntervalSets]] deps = ["Dates", "Random"] -git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6" +git-tree-sha1 = "3d8866c029dd6b16e69e0d4a939c4dfcb98fac47" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.7" +version = "0.7.8" weakdeps = ["Statistics"] [deps.IntervalSets.extensions] IntervalSetsStatisticsExt = "Statistics" +[[deps.InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "68772f49f54b479fa88ace904f6127f0a3bb2e46" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.12" + [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" @@ -871,10 +933,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[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", "Parsers", "Unicode"] @@ -884,9 +946,9 @@ version = "0.21.4" [[deps.JpegTurbo]] deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"] -git-tree-sha1 = "327713faef2a3e5c80f96bf38d1fa26f7a6ae29e" +git-tree-sha1 = "d65930fa2bc96b07d7691c652d701dcbe7d9cf0b" uuid = "b835a17e-a41a-41e7-81f0-2f016b05efe0" -version = "0.1.3" +version = "0.1.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -896,9 +958,9 @@ version = "2.1.91+0" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "764164ed65c30738750965d55652db9c94c59bfe" +git-tree-sha1 = "884c2968c2e8e7e6bf5956af88cb46aa745c854b" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.4.0" +version = "0.4.1" [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] @@ -908,9 +970,9 @@ version = "0.6.7" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "6dc4ad9cd74ad4ca0a8e219e945dbd22039f2125" +git-tree-sha1 = "17e462054b42dcdda73e9a9ba0c67754170c88ae" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.2" +version = "0.9.4" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -931,9 +993,9 @@ uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" version = "2.10.1+0" [[deps.LaTeXStrings]] -git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" +git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.0" +version = "1.3.1" [[deps.LatinHypercubeSampling]] deps = ["Random", "StableRNGs", "StatsBase", "Test"] @@ -941,11 +1003,17 @@ git-tree-sha1 = "825289d43c753c7f1bf9bed334c253e9913997f8" uuid = "a5e1c1ea-c99a-51d3-a14d-a9a37257b02d" version = "1.9.0" +[[deps.LatticeRules]] +deps = ["Random"] +git-tree-sha1 = "7f5b02258a3ca0221a6a9710b0a0a2e8fb4957fe" +uuid = "73f95e8e-ec14-4e6a-8b18-0d2e271c4e55" +version = "0.0.1" + [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "88b8f66b604da079a627b6fb2860d3704a6729a1" +git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.14" +version = "0.1.15" [[deps.Lazy]] deps = ["MacroTools"] @@ -971,21 +1039,26 @@ version = "0.2.0" [[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 = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[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" @@ -1009,10 +1082,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1028,9 +1101,9 @@ version = "2.36.0+0" [[deps.LightXML]] deps = ["Libdl", "XML2_jll"] -git-tree-sha1 = "e129d9391168c677cd4800f5c0abb1ed8cb3794f" +git-tree-sha1 = "3a994404d3f6709610701c7dabfc03fed87a81f8" uuid = "9c8b4983-aa76-5018-a973-4c85ecc9e179" -version = "0.9.0" +version = "0.9.1" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] @@ -1044,35 +1117,49 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearAlgebraX]] deps = ["LinearAlgebra", "Mods", "Permutations", "Primes", "SimplePolynomials"] -git-tree-sha1 = "558a338f1eeabe933f9c2d4052aa7c2c707c3d52" +git-tree-sha1 = "89ed93300377e0742ae8a7423f7543c8f5eb73a4" uuid = "9b3f67b0-2d00-526e-9884-9e4938f8fb88" -version = "0.1.12" +version = "0.2.5" [[deps.LinearSolve]] -deps = ["ArrayInterface", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LinearAlgebra", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] -git-tree-sha1 = "d2605a42d5453f510ca0fe37eff8aa0bfc5a3c80" +deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "EnzymeCore", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "UnPack"] +git-tree-sha1 = "051943b8b8e81c548e9d099d6eb3d3ed23093c35" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.4.2" +version = "2.20.0" [deps.LinearSolve.extensions] + LinearSolveBandedMatricesExt = "BandedMatrices" + LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" + LinearSolveEnzymeExt = "Enzyme" + LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" + LinearSolveKernelAbstractionsExt = "KernelAbstractions" LinearSolveKrylovKitExt = "KrylovKit" + LinearSolveMetalExt = "Metal" LinearSolvePardisoExt = "Pardiso" + LinearSolveRecursiveArrayToolsExt = "RecursiveArrayTools" [deps.LinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" + KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" + RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" [[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" @@ -1089,15 +1176,15 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.3" [[deps.LoopVectorization]] -deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "c88a4afe1703d731b1c4fdf4e3c7e77e3b176ea2" +deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "0f5648fbae0d015e3abe5867bca2b362f67a5894" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.165" +version = "0.12.166" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] @@ -1106,27 +1193,27 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "154d7aaa82d24db6d8f7e4ffcfe596f40bff214b" +git-tree-sha1 = "eb006abbd7041c28e0d16260e50a24f8f9104913" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2023.1.0+0" +version = "2023.2.0+0" [[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.Makie]] -deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Setfield", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "StableHashTraits", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"] -git-tree-sha1 = "729640354756782c89adba8857085a69e19be7ab" +deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Setfield", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "StableHashTraits", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"] +git-tree-sha1 = "db14b5ba682d431317435c866734995a89302c3c" uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" -version = "0.19.7" +version = "0.20.2" [[deps.MakieCore]] -deps = ["Observables"] -git-tree-sha1 = "87a85ff81583bd392642869557cb633532989517" +deps = ["Observables", "REPL"] +git-tree-sha1 = "e81e6f1e8a0e96bf2bf267e4bf7f94608bf09b5c" uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" -version = "0.6.4" +version = "0.7.1" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1142,16 +1229,11 @@ version = "0.4.2" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -[[deps.Match]] -git-tree-sha1 = "1d9bc5c1a6e7ee24effb93f175c9342f9154d97f" -uuid = "7eb4fadd-790c-5f42-8a69-bfa0b872bfbf" -version = "1.2.0" - [[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 = "362ae34a5291a79e16b8eb87b5738532c5e799ff" uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.18.0" +version = "1.23.0" [[deps.MathProgBase]] deps = ["LinearAlgebra", "SparseArrays"] @@ -1160,21 +1242,21 @@ uuid = "fdba3010-5040-5b88-9595-932c9decdf73" version = "0.7.8" [[deps.MathTeXEngine]] -deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "Test", "UnicodeFun"] -git-tree-sha1 = "8f52dbaa1351ce4cb847d95568cb29e62a307d93" +deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"] +git-tree-sha1 = "96ca8a313eb6437db5ffe946c457a401bbb8ce1d" uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" -version = "0.5.6" +version = "0.5.7" [[deps.MbedTLS]] -deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] -git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" +deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] +git-tree-sha1 = "c067a280ddc25f196b5e7df3877c6b226d390aaf" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.1.7" +version = "1.1.9" [[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"] @@ -1186,9 +1268,9 @@ version = "1.1.0" uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.Mods]] -git-tree-sha1 = "61be59e4daffff43a8cec04b5e0dc773cbb5db3a" +git-tree-sha1 = "c703557e9194fce2417b6afc3e1f0318213c401a" uuid = "7475f97c-0381-53b1-977b-4c60186c8d62" -version = "1.3.3" +version = "2.1.0" [[deps.MosaicViews]] deps = ["MappedArrays", "OffsetArrays", "PaddedViews", "StackViews"] @@ -1198,13 +1280,13 @@ version = "0.3.4" [[deps.MovingBoundaryProblems1D]] deps = ["CommonSolve", "SciMLBase", "SparseArrays"] -git-tree-sha1 = "c732ef1f7af2616c7ccfe2adba1ad0939a45b323" +git-tree-sha1 = "deed93ca6b9d64e4c5ff07bab653a5c8d83268af" uuid = "a903a81a-d576-4eaa-89dc-ab2b94f0d51c" -version = "1.0.2" +version = "1.0.3" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2023.1.10" [[deps.MuladdMacro]] git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" @@ -1218,9 +1300,9 @@ version = "0.4.4" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "964cb1a7069723727025ae295408747a0b36a854" +git-tree-sha1 = "806eea990fb41f9b36f1253e5697aa645bf6a9f8" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.3.0" +version = "1.4.0" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1263,15 +1345,25 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "23dabe80f8ebec9a68b0db4cd02f2d2cdbc4f653" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LineSearches", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "6166ccd8f79c93c636ca61ab4cd18f555932563d" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "1.9.0" +version = "2.8.2" + + [deps.NonlinearSolve.extensions] + NonlinearSolveBandedMatricesExt = "BandedMatrices" + NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" + NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" + + [deps.NonlinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" + LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" [[deps.Observables]] -git-tree-sha1 = "6862738f9796b3edc1c09d0890afce4eca9e7e93" +git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" uuid = "510215fc-4207-5dde-b226-833fc4488ee2" -version = "0.5.4" +version = "0.5.5" [[deps.OffsetArrays]] deps = ["Adapt"] @@ -1288,7 +1380,7 @@ version = "1.3.5+1" [[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.OpenEXR]] deps = ["Colors", "FileIO", "OpenEXR_jll"] @@ -1305,7 +1397,7 @@ version = "3.1.4+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+0" +version = "0.8.1+2" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] @@ -1315,9 +1407,9 @@ version = "1.4.1" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e78db7bd5c26fc5a6911b50a47ee302219157ea8" +git-tree-sha1 = "cc6e1927ac521b659af340e0ca45828a3ffc748f" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.10+0" +version = "3.0.12+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1327,22 +1419,23 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "e3a6546c1577bfd701771b477b794a52949e7594" +git-tree-sha1 = "01f85d9269b13fedc61e63cc72ee2213565f7a72" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.6" +version = "1.7.8" [[deps.Optimization]] deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LinearAlgebra", "Logging", "LoggingExtras", "Pkg", "Printf", "ProgressLogging", "Reexport", "Requires", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "80005bc7d96d4d00e56b8a58c5240a35bd638d4a" +git-tree-sha1 = "1aa7ffea6e171167e9cae620d749e16d5874414a" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "3.15.2" +version = "3.19.3" [deps.Optimization.extensions] OptimizationEnzymeExt = "Enzyme" - OptimizationFinitediffExt = "FiniteDiff" - OptimizationForwarddiffExt = "ForwardDiff" + OptimizationFiniteDiffExt = "FiniteDiff" + OptimizationForwardDiffExt = "ForwardDiff" OptimizationMTKExt = "ModelingToolkit" - OptimizationReversediffExt = "ReverseDiff" + OptimizationReverseDiffExt = "ReverseDiff" + OptimizationSparseDiffExt = ["SparseDiffTools", "Symbolics", "ReverseDiff"] OptimizationTrackerExt = "Tracker" OptimizationZygoteExt = "Zygote" @@ -1352,26 +1445,28 @@ version = "3.15.2" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.OptimizationBBO]] deps = ["BlackBoxOptim", "Optimization", "Reexport"] -git-tree-sha1 = "5f653f29459f2aba3c1961dff265b727bd1ed5be" +git-tree-sha1 = "939b19f2c213901aa544d1fd50e5f0065e66127c" uuid = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b" -version = "0.1.4" +version = "0.1.5" [[deps.OptimizationNLopt]] deps = ["NLopt", "Optimization", "Reexport"] -git-tree-sha1 = "e957c68dabb518cb4c7d3d3697968850e86789ef" +git-tree-sha1 = "dc1b76eae7c47ae77560803587911d4d219af531" uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" -version = "0.1.7" +version = "0.1.8" [[deps.OptimizationOptimJL]] deps = ["Optim", "Optimization", "Reexport", "SparseArrays"] -git-tree-sha1 = "76a57a8484370bb26ae82a0a330abfff96d561aa" +git-tree-sha1 = "bea24fb320d58cb639e3cbc63f8eedde6c667bd3" uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" -version = "0.1.9" +version = "0.1.14" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1380,37 +1475,37 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.2+0" [[deps.OrderedCollections]] -git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3" +git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.2" +version = "1.6.3" [[deps.OrdinaryDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "47c560dcb059570bdbd9f887a6b8958190e498a4" +git-tree-sha1 = "5f9e7ce227d0e447c3803cc05ef5d8f75f84b9ea" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.53.4" +version = "6.59.3" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.42.0+0" +version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" +git-tree-sha1 = "4e5be6bb265d33669f98eb55d2a57addd1eeb72c" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.17" +version = "0.11.30" [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] -git-tree-sha1 = "9b02b27ac477cad98114584ff964e3052f656a0f" +git-tree-sha1 = "eed372b0fa15624273a9cdb188b1b88476e6a233" uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883" -version = "0.4.0" +version = "0.4.2" [[deps.PackageExtensionCompat]] -git-tree-sha1 = "32f3d52212a8d1c5d589a58851b1f04c97339110" +git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" -version = "1.0.0" +version = "1.0.2" weakdeps = ["Requires", "TOML"] [[deps.Packing]] @@ -1426,10 +1521,10 @@ uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" version = "0.5.12" [[deps.Pango_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "84a314e3926ba9ec66ac097e3635e270986b0f10" +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "4745216e94f71cb768d58330b059c9b76f32cb66" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.50.9+0" +version = "1.50.14+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -1439,15 +1534,15 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851" +git-tree-sha1 = "a935806434c9d4c506ba941871b327b96d41f2bf" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.7.2" +version = "2.8.0" [[deps.Permutations]] deps = ["Combinatorics", "LinearAlgebra", "Random"] -git-tree-sha1 = "6e6cab1c54ae2382bcc48866b91cf949cea703a1" +git-tree-sha1 = "c7745750b8a829bc6039b7f1f0981bcda526a946" uuid = "2ae35dd2-176d-5d53-8349-f30d82d94d4f" -version = "0.4.16" +version = "0.4.19" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] @@ -1458,13 +1553,13 @@ version = "0.42.2+0" [[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.PkgVersion]] deps = ["Pkg"] -git-tree-sha1 = "f6cf8e7944e50901594838951729a1861e668cb8" +git-tree-sha1 = "f9501cc0430a26bc3d156ae1b5b0c1b47af4d6da" uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" -version = "0.3.2" +version = "0.3.3" [[deps.PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] @@ -1474,9 +1569,9 @@ version = "1.3.5" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "3d811babe092a6e7b130beee84998fe7663348b6" +git-tree-sha1 = "fca25670784a1ae44546bcb17288218310af2778" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.5" +version = "0.7.9" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] @@ -1495,14 +1590,15 @@ uuid = "647866c9-e3ac-4575-94e7-e3d426903924" version = "0.1.2" [[deps.Polynomials]] -deps = ["LinearAlgebra", "RecipesBase"] -git-tree-sha1 = "3aa2bb4982e575acd7583f01531f241af077b163" +deps = ["LinearAlgebra", "RecipesBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "a9c7a523d5ed375be3983db190f6a5874ae9286d" uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45" -version = "3.2.13" -weakdeps = ["ChainRulesCore", "MakieCore", "MutableArithmetics"] +version = "4.0.6" +weakdeps = ["ChainRulesCore", "FFTW", "MakieCore", "MutableArithmetics"] [deps.Polynomials.extensions] PolynomialsChainRulesCoreExt = "ChainRulesCore" + PolynomialsFFTWExt = "FFTW" PolynomialsMakieCoreExt = "MakieCore" PolynomialsMutableArithmeticsExt = "MutableArithmetics" @@ -1526,21 +1622,27 @@ version = "0.4.12" [[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.PrettyTables]] +deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] +git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" +uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" +version = "2.3.1" [[deps.Primes]] deps = ["IntegerMathUtils"] -git-tree-sha1 = "4c9f306e5d6603ae203c2000dd460d81a5251489" +git-tree-sha1 = "1d05623b5952aed1307bf8b43bec8b8d1ef94b6e" uuid = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae" -version = "0.5.4" +version = "0.5.5" [[deps.Printf]] deps = ["Unicode"] @@ -1558,9 +1660,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "00099623ffee15972c16111bcf84c58a0051257c" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.9.0" [[deps.QOI]] deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] @@ -1570,16 +1672,26 @@ version = "1.0.0" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "6ec7ac8412e83d57e313393220879ede1740f9ee" +git-tree-sha1 = "9ebcd48c498668c7fa0e97a9cae873fbee7bfee1" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.8.2" +version = "2.9.1" + +[[deps.QuasiMonteCarlo]] +deps = ["Accessors", "ConcreteStructs", "LatticeRules", "LinearAlgebra", "Primes", "Random", "Requires", "Sobol", "StatsBase"] +git-tree-sha1 = "cc086f8485bce77b6187141e1413c3b55f9a4341" +uuid = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b" +version = "0.3.3" +weakdeps = ["Distributions"] + + [deps.QuasiMonteCarlo.extensions] + QuasiMonteCarloDistributionsExt = "Distributions" [[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.RangeArrays]] @@ -1605,25 +1717,27 @@ version = "1.3.4" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "d7087c013e8a496ff396bae843b1e16d9a30ede8" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.10" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" + RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" [deps.RecursiveArrayTools.weakdeps] Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "PrecompileTools", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "34fd98298dc3fcfc657d65559491b18ab3f7f28c" +git-tree-sha1 = "8bc86c78c7d8e2a5fe559e3721c0f9c9e303b2ed" uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.19" +version = "0.2.21" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1638,9 +1752,9 @@ version = "0.10.2" [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] -git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" +git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864" uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" -version = "1.0.0" +version = "1.0.1" [[deps.Requires]] deps = ["UUIDs"] @@ -1650,9 +1764,9 @@ version = "1.3.0" [[deps.RingLists]] deps = ["Random"] -git-tree-sha1 = "9712ebc42e91850f35272b48eb840e60c0270ec0" +git-tree-sha1 = "f39da63aa6d2d88e0c1bd20ed6a3ff9ea7171ada" uuid = "286e9d63-9694-5540-9e3c-4e6708fa07b2" -version = "0.2.7" +version = "0.2.8" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1673,20 +1787,14 @@ version = "0.2.1" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "237edc1563bbf078629b4f8d194bd334e97907cf" +git-tree-sha1 = "6aacc5eefe8415f47b3e34214c1d79d2674a0ba2" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.11" +version = "0.5.12" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" -[[deps.SIMD]] -deps = ["PrecompileTools"] -git-tree-sha1 = "0e270732477b9e551d884e6b07e23bb2ec947790" -uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.4.5" - [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" uuid = "94e857df-77ce-4151-89e5-788b33177be4" @@ -1694,44 +1802,55 @@ version = "0.1.0" [[deps.SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "4b8586aece42bee682399c4c4aee95446aa5cd19" +git-tree-sha1 = "3aac6d68c5e57449f5b9b865c9ba50ac2970c4cf" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.39" +version = "0.6.42" [[deps.SafeTestsets]] git-tree-sha1 = "81ec49d645af090901120a1542e67ecbbe044db3" uuid = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" version = "0.1.0" -[[deps.ScanByte]] -deps = ["Libdl", "SIMD"] -git-tree-sha1 = "d49e35f413186528f1d7cc675e67d0ed16fd7800" -uuid = "7b38b023-a4d7-4c5e-8d43-3f3097f304eb" -version = "0.4.0" - [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "QuasiMonteCarlo", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] +git-tree-sha1 = "d432b4c4cc922fb7b21b555c138aa87f9fb7beb8" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "2.9.1" + + [deps.SciMLBase.extensions] + SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBasePartialFunctionsExt = "PartialFunctions" + SciMLBasePyCallExt = "PyCall" + SciMLBasePythonCallExt = "PythonCall" + SciMLBaseRCallExt = "RCall" + SciMLBaseZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" + PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" + PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" + RCall = "6f49c342-dc21-5d91-9882-a32aef131414" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLNLSolve]] deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "9dfc8e9e3d58c0c74f1a821c762b5349da13eccf" +git-tree-sha1 = "765b788339abd7d983618c09cfc0192e2b6b15fd" uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.8" +version = "0.1.9" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] -git-tree-sha1 = "65c2e6ced6f62ea796af251eb292a0e131a3613b" +git-tree-sha1 = "51ae235ff058a64815e0a2c34b1db7578a06813d" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.6" +version = "0.3.7" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" +git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.2.0" +version = "1.2.1" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1749,9 +1868,9 @@ version = "1.1.1" [[deps.ShaderAbstractions]] deps = ["ColorTypes", "FixedPointNumbers", "GeometryBasics", "LinearAlgebra", "Observables", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "0d15c3e7b2003f4451714f08ffec2b77badc2dc4" +git-tree-sha1 = "db0219befe4507878b1a90e07820fed3e62c289d" uuid = "65257c39-d410-5151-9873-9b3e5be5013e" -version = "0.3.0" +version = "0.4.0" [[deps.SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] @@ -1776,15 +1895,15 @@ version = "1.1.0" [[deps.SimpleGraphs]] deps = ["AbstractLattices", "Combinatorics", "DataStructures", "IterTools", "LightXML", "LinearAlgebra", "LinearAlgebraX", "Optim", "Primes", "Random", "RingLists", "SimplePartitions", "SimplePolynomials", "SimpleRandom", "SparseArrays", "Statistics"] -git-tree-sha1 = "b608903049d11cc557c45e03b3a53e9260579c19" +git-tree-sha1 = "f65caa24a622f985cc341de81d3f9744435d0d0f" uuid = "55797a34-41de-5266-9ec1-32ac4eb504d3" -version = "0.8.4" +version = "0.8.6" [[deps.SimpleNonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PackageExtensionCompat", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "20aa9831d654bab67ed561e78917047143ecb9bf" +deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "69b1a53374dd14d7c165d98cb646aeb5f36f8d07" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "0.1.19" +version = "0.1.25" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveNNlibExt = "NNlib" @@ -1794,15 +1913,15 @@ version = "0.1.19" [[deps.SimplePartitions]] deps = ["AbstractLattices", "DataStructures", "Permutations"] -git-tree-sha1 = "dcc02923a53f316ab97da8ef3136e80b4543dbf1" +git-tree-sha1 = "e9330391d04241eafdc358713b48396619c83bcb" uuid = "ec83eff0-a5b5-5643-ae32-5cbf6eedec9d" -version = "0.3.0" +version = "0.3.1" [[deps.SimplePolynomials]] deps = ["Mods", "Multisets", "Polynomials", "Primes"] -git-tree-sha1 = "ac7b9bd0d2d2ee86e9c7016fb76ff7c1037838e9" +git-tree-sha1 = "7063828369cafa93f3187b3d0159f05582011405" uuid = "cc47b68c-3164-5771-a705-2bc0097375a0" -version = "0.2.12" +version = "0.2.17" [[deps.SimpleRandom]] deps = ["Distributions", "LinearAlgebra", "Random"] @@ -1827,35 +1946,40 @@ git-tree-sha1 = "2da10356e31327c7096832eb9cd86307a50b1eb6" uuid = "45858cf5-a6b0-47a3-bbea-62219f50df47" version = "0.1.3" -[[deps.SnoopPrecompile]] -deps = ["Preferences"] -git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" -uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.3" +[[deps.Sobol]] +deps = ["DelimitedFiles", "Random"] +git-tree-sha1 = "5a74ac22a9daef23705f010f72c81d6925b19df8" +uuid = "ed01d8cd-4d21-5b2a-85b4-cc3bdc58bad4" +version = "1.5.0" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "c60ec5c62180f27efea3ba2908480f8055e17cee" +git-tree-sha1 = "5165dfb9fd131cf0c6957a3a7605dede376e7b63" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.1.1" +version = "1.2.0" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Reexport", "Requires", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "VertexSafeGraphs"] -git-tree-sha1 = "4c1a57bcbc0b795fbfdc2009e70f9c2fd2815bfe" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "07272c80c278947baca092df0a01da4a10622ad5" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.4.1" +version = "2.13.0" [deps.SparseDiffTools.extensions] + SparseDiffToolsEnzymeExt = "Enzyme" + SparseDiffToolsSymbolicsExt = "Symbolics" SparseDiffToolsZygoteExt = "Zygote" [deps.SparseDiffTools.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.Sparspak]] @@ -1865,25 +1989,25 @@ uuid = "e56a9233-b9d6-4f03-8d0f-1825330902ac" version = "0.3.9" [[deps.SpatialIndexing]] -git-tree-sha1 = "bacf5065cd7c0d6449b8bba6fa8e75b3087356b0" +git-tree-sha1 = "84efe17c77e1f2156a7a0d8a7c163c1e1c7bdaed" uuid = "d4ead438-fe20-5cc5-a293-4fd39a41b74c" -version = "0.1.5" +version = "0.1.6" [[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.StableHashTraits]] -deps = ["CRC32c", "Compat", "Dates", "SHA", "Tables", "TupleTools", "UUIDs"] -git-tree-sha1 = "0b8b801b8f03a329a4e86b44c5e8a7d7f4fe10a3" +deps = ["Compat", "SHA", "Tables", "TupleTools"] +git-tree-sha1 = "d29023a76780bb8a3f2273b29153fd00828cb73f" uuid = "c5dd0088-6c3f-4803-b00e-f31a60c170fa" -version = "0.3.1" +version = "1.1.1" [[deps.StableRNGs]] deps = ["Random", "Test"] @@ -1904,10 +2028,10 @@ uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" version = "0.8.8" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "33040351d2403b84afce74dae2e22d3f5b18edcb" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] +git-tree-sha1 = "03fec6800a986d191f64f5c0996b59ed526eda25" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.4.0" +version = "1.4.1" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -1915,10 +2039,10 @@ weakdeps = ["OffsetArrays", "StaticArrays"] StaticArrayInterfaceStaticArraysExt = "StaticArrays" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] +git-tree-sha1 = "5ef59aea6f18c25168842bded46b16662141ab87" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.7.0" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1932,13 +2056,13 @@ version = "1.4.2" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.9.0" +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1951,26 +2075,29 @@ deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Re git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" version = "1.3.0" +weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] StatsFunsChainRulesCoreExt = "ChainRulesCore" StatsFunsInverseFunctionsExt = "InverseFunctions" - [deps.StatsFuns.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "f02eb61eb5c97b48c153861c72fbbfdddc607e06" +git-tree-sha1 = "d6415f66f3d89c615929af907fdc6a3e17af0d8c" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.4.17" +version = "0.5.2" + +[[deps.StringManipulation]] +deps = ["PrecompileTools"] +git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" +uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" +version = "0.3.4" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1979,7 +2106,7 @@ 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 = "7.2.1+1" [[deps.SymbolicIndexingInterface]] deps = ["DocStringExtensions"] @@ -1999,10 +2126,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.1" +version = "1.11.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -2038,26 +2165,29 @@ version = "0.5.2" [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"] -git-tree-sha1 = "8621f5c499a8aa4aa970b1ae381aae0ef1576966" +git-tree-sha1 = "34cc045dd0aaa59b8bbe86c644679bc57f1d5bd0" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.6.4" +version = "0.6.8" [[deps.TranscodingStreams]] -deps = ["Random", "Test"] -git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" +git-tree-sha1 = "1fbeaaca45801b4ba17c251dd8603ef24801dd84" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.13" +version = "0.10.2" +weakdeps = ["Random", "Test"] + + [deps.TranscodingStreams.extensions] + TestExt = ["Test", "Random"] [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "31eedbc0b6d07c08a700e26d31298ac27ef330eb" +git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.19" +version = "0.1.20" [[deps.Tricks]] -git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" +git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.7" +version = "0.1.8" [[deps.TriplotBase]] git-tree-sha1 = "4d4ed7f294cda19382ff7de4c137d24d16adc89b" @@ -2071,14 +2201,14 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.TupleTools]] -git-tree-sha1 = "3c712976c47707ff893cf6ba4354aa14db1d8938" +git-tree-sha1 = "155515ed4c4236db30049ac1495e2969cc06be9d" uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" -version = "1.3.0" +version = "1.4.3" [[deps.URIs]] -git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" +git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.4.2" +version = "1.5.1" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -2100,9 +2230,9 @@ version = "0.4.1" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "b182207d4af54ac64cbc71797765068fdeff475d" +git-tree-sha1 = "7209df901e6ed7489fe9b7aa3e46fb788e15db85" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.64" +version = "0.21.65" [[deps.VertexSafeGraphs]] deps = ["Graphs"] @@ -2112,15 +2242,15 @@ version = "0.2.0" [[deps.WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3" +git-tree-sha1 = "5f24e158cf4cee437052371455fe361f526da062" uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" -version = "0.5.5" +version = "0.5.6" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "da69178aacc095066bad1f69d2f59a60a1dd8ad1" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.12.0+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -2185,13 +2315,7 @@ version = "1.5.0+0" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" - -[[deps.ZygoteRules]] -deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.3" +version = "1.2.13+1" [[deps.isoband_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2214,7 +2338,7 @@ version = "0.15.1+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+0" +version = "5.8.0+1" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2243,12 +2367,12 @@ version = "1.3.7+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" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/test/figures/regression_profiles_a.png b/test/figures/regression_profiles_a.png index 2610466..8aaa6d6 100644 Binary files a/test/figures/regression_profiles_a.png and b/test/figures/regression_profiles_a.png differ diff --git a/test/figures/regression_profiles_b.png b/test/figures/regression_profiles_b.png index 32260c2..7d56c94 100644 Binary files a/test/figures/regression_profiles_b.png and b/test/figures/regression_profiles_b.png differ diff --git a/test/figures/regression_profiles_c.png b/test/figures/regression_profiles_c.png index 6e855c0..52ec79c 100644 Binary files a/test/figures/regression_profiles_c.png and b/test/figures/regression_profiles_c.png differ diff --git a/test/figures/regression_profiles_d.png b/test/figures/regression_profiles_d.png index c890b63..f06e37e 100644 Binary files a/test/figures/regression_profiles_d.png and b/test/figures/regression_profiles_d.png differ diff --git a/test/lotka_volterra_example.jl b/test/lotka_volterra_example.jl index e7dcb39..ed5714c 100644 --- a/test/lotka_volterra_example.jl +++ b/test/lotka_volterra_example.jl @@ -126,7 +126,7 @@ fig_2 = plot_profiles(prof_2, param_pairs; # param_pairs not needed, but this en true_vals=[α, β, a₀, b₀], xlim_tuples=[(0.5, 1.5), (0.5, 1.5), (0.5, 1.5), (0.7, 1.3), (0.7, 1.3), (0.5, 1.1)], ylim_tuples=[(0.5, 1.5), (0.5, 1.05), (0.1, 0.5), (0.5, 1.05), (0.1, 0.5), (0.1, 0.5)], - fig_kwargs=(fontsize=24,)) + fig_kwargs=(fontsize=17,)) @test_reference joinpath(fig_path, "lokta_example_bivariate_profiles_low_quality.png") fig_2 fig_3 = plot_profiles(prof_2, param_pairs; @@ -138,7 +138,7 @@ fig_3 = plot_profiles(prof_2, param_pairs; interpolation=true, xlim_tuples=[(0.5, 1.5), (0.5, 1.5), (0.5, 1.5), (0.7, 1.3), (0.7, 1.3), (0.5, 1.1)], ylim_tuples=[(0.5, 1.5), (0.5, 1.05), (0.1, 0.5), (0.5, 1.05), (0.1, 0.5), (0.1, 0.5)], - fig_kwargs=(fontsize=24,)) + fig_kwargs=(fontsize=17,)) @test_reference joinpath(fig_path, "lokta_example_bivariate_profiles_smoothed_quality.png") fig_3 ## Step 7: Get prediction intervals @@ -167,7 +167,7 @@ prediction_function!(exact_soln, [α, β, a₀, b₀], pred_data) prediction_function!(mle_soln, get_mle(sol), pred_data) # Plot the parameter-wise intervals -fig = Figure(fontsize=38, resolution=(2935.488f0, 1392.64404f0)) +fig = Figure(fontsize=38, size=(2935.488f0, 1392.64404f0)) alp = [['a', 'b', 'e', 'f'], ['c', 'd', 'g', 'h']] latex_names = [L"\alpha", L"\beta", L"a_0", L"b_0"] for (k, idx) in enumerate((a_idx, b_idx)) @@ -225,7 +225,7 @@ individual_intervals, union_intervals, q_vals, param_ranges = q_prototype) # Plot the intervals -fig = Figure(fontsize=38, resolution=(2935.488f0, 1854.64404f0)) +fig = Figure(fontsize=38, size=(2935.488f0, 1854.64404f0)) integer_param_pairs = ProfileLikelihood.convert_symbol_tuples(param_pairs, prof_2) # converts to the integer representation alp = [['a', 'b', 'e', 'f', 'i', 'j'], ['c', 'd', 'g', 'h', 'k', 'l']] for (k, idx) in enumerate((a_idx, b_idx)) diff --git a/test/pde_example.jl b/test/pde_example.jl index 962e612..4fa6258 100644 --- a/test/pde_example.jl +++ b/test/pde_example.jl @@ -106,7 +106,6 @@ function mb_loglik(θ, data, integrator) Lᵢ = integrator.sol.u[i][end] ℓ = ℓ - 0.5log(2π * σL^2) - 0.5(L[i] - Lᵢ)^2 / σL^2 end - @show ℓ return ℓ end lb = [0.2, 0.5, 0.1, 10.0] @@ -198,4 +197,4 @@ vlines!(ax, [20.0], color=:purple, linestyle=:dash, linewidth=2) resize_to_layout!(fig) fig -@test_reference joinpath(fig_path, "pde_prediction_intervals.png") fig +@test_reference joinpath(fig_path, "pde_prediction_intervals.png") fig by=psnr_equality(18) diff --git a/test/runtests.jl b/test/runtests.jl index 00355af..a1e4fd0 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -48,7 +48,9 @@ using SafeTestsets @safetestset "Evample IV: Lotka-Volterra ODE" begin include("lotka_volterra_example.jl") end - #@safetestset "Example V: Fisher-Stefan PDE" begin - # include("pde_example.jl") - #end + if !(get(ENV, "CI", "false") == "true") + @safetestset "Example V: Fisher-Stefan PDE" begin + include("pde_example.jl") + end + end end \ No newline at end of file