diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index c29c1a0b7..7dfd62acd 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,5 +1,6 @@ env: - JULIA_VERSION: "1.5.4" + JULIA_VERSION: "1.6.2" + JULIA_MINOR_VERSION: "1.6" OPENBLAS_NUM_THREADS: 1 GKSwstype: nul @@ -29,7 +30,7 @@ steps: mkdir examples/Lorenz/depot export JULIA_DEPOT_PATH="$$(pwd)/examples/Lorenz/depot:$$JULIA_DEPOT_PATH" - + julia --color=yes --project -e ' println("--- Instantiating Project") using Pkg; @@ -44,7 +45,7 @@ steps: config: cpu queue: central slurm_ntasks: 1 - + - label: "Gaussian Process Emulator" key: "gaussian_process_emulator" command: | @@ -52,21 +53,21 @@ steps: export PYTHONHOME="$$JULIA_DEPOT_PATH/conda/3/bin" export CONDA_JL_HOME="$$JULIA_DEPOT_PATH/conda/3" - mkdir examples/GaussianProcessEmulator/depot - export JULIA_DEPOT_PATH="$$(pwd)/examples/GaussianProcessEmulator/depot:$JULIA_DEPOT_PATH" + mkdir examples/Emulator/GaussianProcess/depot + export JULIA_DEPOT_PATH="$$(pwd)/examples/Emulator/GaussianProcess/depot:$JULIA_DEPOT_PATH" julia --color=yes --project -e ' println("--- Instantiating Project") using Pkg; Pkg.instantiate() - Pkg.activate("examples/GaussianProcessEmulator") + Pkg.activate("examples/Emulator/GaussianProcess") Pkg.instantiate() println("+++ Running Learn Noise") - include("examples/GaussianProcessEmulator/learn_noise.jl") + include("examples/Emulator/GaussianProcess/learn_noise.jl") println("+++ Running PlotGP") - include("examples/GaussianProcessEmulator/plot_GP.jl")' + include("examples/Emulator/GaussianProcess/plot_GP.jl")' artifact_paths: - - "examples/GaussianProcessEmulator/output/*.png" + - "examples/Emulator/GaussianProcess/output/*.png" env: PYTHON: "$$JULIA_DEPOT_PATH/conda/3/bin/python" PYTHONHOME: "$$JULIA_DEPOT_PATH/conda/3/bin" @@ -75,7 +76,7 @@ steps: config: cpu queue: central slurm_ntasks: 1 - + - label: "Cloudy" key: "cloudy" command: | diff --git a/Manifest.toml b/Manifest.toml index c78a0570d..1e69ace69 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,30 +1,19 @@ # This file is machine-generated - editing it directly is not advised -[[AMD]] -deps = ["Libdl", "LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "fc66ffc5cff568936649445f58a55b81eaf9592c" -uuid = "14f7f29c-3bd6-536c-9a0b-7339e30b5a3e" -version = "0.4.0" - -[[AbstractTrees]] -git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" -uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.3.4" - [[Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7" +git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.1" +version = "3.3.3" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "265b06e2b1f6a216e0e8f183d28e4d354eab3220" +git-tree-sha1 = "1ee88c4c76caa995a885dc2f22a5d548dfbbc0ba" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.2.1" +version = "3.2.2" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -32,29 +21,11 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[BenchmarkTools]] -deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "940001114a0147b6e4d10624276d56d531dd9b49" -uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.2.2" - -[[BinaryProvider]] -deps = ["Libdl", "Logging", "SHA"] -git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058" -uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" -version = "0.5.10" - -[[Bzip2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" -uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+0" - [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "4c26b4e9e91ca528ea212927326ece5918a04b47" +git-tree-sha1 = "926870acb6cbcf029396f2f2de030282b6bc1941" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.11.2" +version = "1.11.4" [[ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] @@ -62,18 +33,6 @@ git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" version = "0.1.2" -[[CodecBzip2]] -deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] -git-tree-sha1 = "2e62a725210ce3c3c2e1a3080190e7ca491f18d7" -uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.7.2" - -[[CodecZlib]] -deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" -uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.0" - [[CommonSubexpressions]] deps = ["MacroTools", "Test"] git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" @@ -96,16 +55,10 @@ git-tree-sha1 = "6cdc8832ba11c7695f494c9d9a1c31e90959ce0f" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" version = "1.6.0" -[[Convex]] -deps = ["AbstractTrees", "BenchmarkTools", "LDLFactorizations", "LinearAlgebra", "MathOptInterface", "OrderedCollections", "SparseArrays", "Test"] -git-tree-sha1 = "145c5e0b3ea3c9dd3bba134a58bab4112aa250c8" -uuid = "f65535da-76fb-5f13-bab9-19810c17039a" -version = "0.14.18" - [[Crayons]] -git-tree-sha1 = "3f71217b538d7aaee0b69ab47d9b7724ca8afa0d" +git-tree-sha1 = "b618084b49e78985ffa8422f32b9838e397b9fc2" uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" -version = "4.0.4" +version = "4.1.0" [[DataAPI]] git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" @@ -188,10 +141,8 @@ uuid = "2904ab23-551e-5aed-883f-487f97af5226" version = "0.2.2" [[EnsembleKalmanProcesses]] -deps = ["Convex", "Distributions", "DocStringExtensions", "LinearAlgebra", "Random", "SCS", "SparseArrays", "Statistics", "StatsBase"] -git-tree-sha1 = "8d64c688e053de72dbe24d3ecc2945ee51c8930c" -repo-rev = "main" -repo-url = "https://github.com/CliMA/EnsembleKalmanProcesses.jl" +deps = ["Distributions", "DocStringExtensions", "LinearAlgebra", "Random", "Statistics", "StatsBase"] +git-tree-sha1 = "4a0fb4cd1831d0cb630c63da0c1f1fbf50670bad" uuid = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d" version = "0.1.2" @@ -282,12 +233,6 @@ git-tree-sha1 = "8076680b162ada2a031f707ac7b4953e30667a37" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.2" -[[LDLFactorizations]] -deps = ["AMD", "LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "399bbe845e06e1c2d44ebb241f554d45eaf66788" -uuid = "40e66cde-538c-5869-a4ad-c39174c6795b" -version = "0.8.1" - [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" @@ -336,12 +281,6 @@ version = "0.5.9" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -[[MathOptInterface]] -deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "JSON", "LinearAlgebra", "MutableArithmetics", "OrderedCollections", "Printf", "SparseArrays", "Test", "Unicode"] -git-tree-sha1 = "92b7de61ecb616562fd2501334f729cc9db2a9a6" -uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "0.10.6" - [[MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" @@ -358,12 +297,6 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -[[MutableArithmetics]] -deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "7bb6853d9afec54019c1397c6eb610b9b9a19525" -uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "0.3.1" - [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" @@ -378,10 +311,6 @@ version = "0.3.6" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" -[[OpenBLAS_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] -uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" - [[OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" @@ -394,9 +323,9 @@ version = "0.5.5+0" [[Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "35d435b512fbab1d1a29138b5229279925eba369" +git-tree-sha1 = "916077e0f0f8966eb0dc98a5c39921fdb8f49eb4" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.5.0" +version = "1.6.0" [[OrderedCollections]] git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" @@ -439,9 +368,9 @@ version = "0.2.4" [[Preferences]] deps = ["TOML"] -git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a" +git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.2.2" +version = "1.2.3" [[PrettyTables]] deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] @@ -453,10 +382,6 @@ version = "1.3.1" deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -[[Profile]] -deps = ["Printf"] -uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" - [[ProgressMeter]] deps = ["Distributed", "Printf"] git-tree-sha1 = "afadeba63d90ff223a6a48d2009434ecee2ec9e8" @@ -511,24 +436,6 @@ git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" version = "0.3.0+0" -[[SCS]] -deps = ["BinaryProvider", "Libdl", "LinearAlgebra", "MathOptInterface", "Requires", "SCS_GPU_jll", "SCS_jll", "SparseArrays"] -git-tree-sha1 = "c819d023621358f3c08f08d41bd9354cf1357d35" -uuid = "c946c3f1-0d1f-5ce8-9dea-7daa1f7e2d13" -version = "0.8.1" - -[[SCS_GPU_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"] -git-tree-sha1 = "a96402e3b494a8bbec61b1adb86d4be04112c646" -uuid = "af6e375f-46ec-5fa0-b791-491b0dfa44a4" -version = "2.1.4+0" - -[[SCS_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"] -git-tree-sha1 = "66c07568ecec96260aaac194ee1e5ee8df62f386" -uuid = "f4f2fc5b-1d94-523c-97ea-2ab488bedf4b" -version = "2.1.4+0" - [[SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -578,24 +485,24 @@ version = "0.4.1" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da" +git-tree-sha1 = "88a559da57529581472320892576a486fa2377b9" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.2.13" +version = "1.3.1" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsAPI]] -git-tree-sha1 = "0f2aa8e32d511f758a2ce49208181f7733a0936a" +git-tree-sha1 = "d88665adc9bcf45903013af0982e2fd05ae3d0a6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.1.0" +version = "1.2.0" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "2bb0cb32026a66037360606510fca5984ccc6b75" +git-tree-sha1 = "51383f2d367eb3b444c961d485c565e4c0cf4ba0" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.13" +version = "0.33.14" [[StatsFuns]] deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] @@ -631,12 +538,6 @@ uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -[[TranscodingStreams]] -deps = ["Random", "Test"] -git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" -uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.6" - [[UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" diff --git a/Project.toml b/Project.toml index acbebb50c..340ad244c 100644 --- a/Project.toml +++ b/Project.toml @@ -16,6 +16,9 @@ ScikitLearn = "3646fa90-6ef7-5e7e-9f22-8aca16db6324" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" +[compat] +julia = "~1.6" + [extras] Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" diff --git a/examples/Cloudy/Cloudy_example.jl b/examples/Cloudy/Cloudy_example.jl index c4f7954ef..1cdd5eeb8 100644 --- a/examples/Cloudy/Cloudy_example.jl +++ b/examples/Cloudy/Cloudy_example.jl @@ -18,7 +18,7 @@ using Random # Import Calibrate-Emulate-Sample modules using CalibrateEmulateSample.EnsembleKalmanProcessModule -using CalibrateEmulateSample.GaussianProcessEmulator +using CalibrateEmulateSample.Emulators using CalibrateEmulateSample.MarkovChainMonteCarlo using CalibrateEmulateSample.Observations using CalibrateEmulateSample.Utilities @@ -204,22 +204,31 @@ println(mean(get_u_final(ekiobj), dims=2)) ### Emulate: Gaussian Process Regression ### -gppackage = GaussianProcessEmulator.GPJL() -pred_type = GaussianProcessEmulator.YType() +gppackage = Emulators.GPJL() +pred_type = Emulators.YType() +gauss_proc = GaussianProcess( + gppackage; + kernel=nothing, # use default squared exponential kernel + prediction_type=pred_type, + noise_learn=false +) # Get training points input_output_pairs = Utilities.get_training_points(ekiobj, N_iter) -normalized = true -gpobj = GaussianProcessEmulator.GaussianProcess(input_output_pairs, gppackage; GPkernel=nothing, - obs_noise_cov=Γy, normalized=normalized, - noise_learn=false, prediction_type=pred_type) +emulator = Emulator( + gauss_proc, + input_output_pairs, + obs_noise_cov=Γy, + normalize_inputs=true +) +optimize_hyperparameters!(emulator) # Check how well the Gaussian Process regression predicts on the # true parameters -y_mean, y_var = GaussianProcessEmulator.predict(gpobj, - reshape(transformed_params_true, :, 1), - transform_to_real=true) - +y_mean, y_var = Emulators.predict( + emulator, reshape(transformed_params_true, :, 1); + transform_to_real=true +) println("GP prediction on true parameters: ") println(vec(y_mean)) println("true data: ") @@ -244,7 +253,7 @@ max_iter = 2000 # number of steps before checking acc/rej rate for step size det yt_sample = truth_sample mcmc_test = MarkovChainMonteCarlo.MCMC(yt_sample, Γy, priors, step, u0, max_iter, mcmc_alg, burnin, svdflag=true) -new_step = MarkovChainMonteCarlo.find_mcmc_step!(mcmc_test, gpobj, max_iter=max_iter) +new_step = MarkovChainMonteCarlo.find_mcmc_step!(mcmc_test, emulator, max_iter=max_iter) # Now begin the actual MCMC println("Begin MCMC - with step size ", new_step) @@ -252,7 +261,7 @@ burnin = 1000 max_iter = 100000 mcmc = MarkovChainMonteCarlo.MCMC(yt_sample, Γy, priors, new_step, u0, max_iter, mcmc_alg, burnin, svdflag=true) -MarkovChainMonteCarlo.sample_posterior!(mcmc, gpobj, max_iter) +MarkovChainMonteCarlo.sample_posterior!(mcmc, emulator, max_iter) posterior = MarkovChainMonteCarlo.get_posterior(mcmc) diff --git a/examples/Cloudy/Manifest.toml b/examples/Cloudy/Manifest.toml index 753e209fa..46ec9e740 100644 --- a/examples/Cloudy/Manifest.toml +++ b/examples/Cloudy/Manifest.toml @@ -8,9 +8,12 @@ version = "0.5.0" [[Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "ffcfa2d345aaee0ef3d8346a073d5dd03c983ebe" +git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.2.0" +version = "3.3.3" + +[[ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] @@ -31,10 +34,10 @@ uuid = "68821587-b530-5797-8361-c406ea357684" version = "3.5.0+3" [[ArrayInterface]] -deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "ce17bad65d0842b34a15fffc8879a9f68f08a67f" +deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] +git-tree-sha1 = "1ee88c4c76caa995a885dc2f22a5d548dfbbc0ba" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.6" +version = "3.2.2" [[ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] @@ -43,16 +46,13 @@ uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" version = "0.3.8" [[Artifacts]] -deps = ["Pkg"] -git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744" uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.3.0" [[AxisAlgorithms]] deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] -git-tree-sha1 = "a4d07a1c313392a77042855df46c5f534076fab9" +git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7" uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" -version = "1.0.0" +version = "1.0.1" [[BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] @@ -75,6 +75,12 @@ git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058" uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" version = "0.5.10" +[[BitTwiddlingConvenienceFunctions]] +deps = ["Static"] +git-tree-sha1 = "bc1317f71de8dce26ea67fcdf7eccc0d0693b75b" +uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" +version = "0.1.1" + [[BoundaryValueDiffEq]] deps = ["BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NLsolve", "Reexport", "SparseArrays"] git-tree-sha1 = "fe34902ac0c3a35d016617ab7032742865756d7d" @@ -83,15 +89,27 @@ version = "2.7.1" [[Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e" +git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.6+5" +version = "1.0.8+0" [[CEnum]] git-tree-sha1 = "215a9aa4a1f23fbd05b92769fdd62559488d70e9" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.1" +[[CPUSummary]] +deps = ["Hwloc", "IfElse", "Static"] +git-tree-sha1 = "87b0c9c6ee0124d6c1f4ce8cb035dcaf9f90b803" +uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" +version = "0.1.6" + +[[Cairo_jll]] +deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" +uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" +version = "1.16.1+1" + [[Calculus]] deps = ["LinearAlgebra"] git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" @@ -106,9 +124,21 @@ version = "0.2.4" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "de4f08843c332d355852721adb1592bce7924da3" +git-tree-sha1 = "926870acb6cbcf029396f2f2de030282b6bc1941" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "0.9.29" +version = "1.11.4" + +[[ChangesOfVariables]] +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.2" + +[[CloseOpenIntervals]] +deps = ["ArrayInterface", "Static"] +git-tree-sha1 = "7b8f09d58294dc8aa13d91a8544b37c8a1dcbc06" +uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" +version = "0.1.4" [[Cloudy]] deps = ["Coverage", "DifferentialEquations", "DocStringExtensions", "ForwardDiff", "HCubature", "LinearAlgebra", "Optim", "PyPlot", "SpecialFunctions", "TaylorSeries", "Test"] @@ -123,22 +153,22 @@ uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" version = "0.14.2" [[ColorSchemes]] -deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"] -git-tree-sha1 = "3141757b5832ee7a0386db87997ee5a23ff20f4d" +deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] +git-tree-sha1 = "a851fec56cb73cfdf43762999ec72eff5b86882a" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.10.2" +version = "3.15.0" [[ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "32a2b8af383f11cbb65803883837a149d10dfe8a" +git-tree-sha1 = "024fe24d83e4a5bf5fc80501a314ce0d1aa35597" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.10.12" +version = "0.11.0" [[Colors]] -deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Reexport"] -git-tree-sha1 = "ac5f2213e56ed8a34a3dd2f681f4df1166b34929" +deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] +git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.6" +version = "0.12.8" [[Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -158,27 +188,25 @@ version = "0.3.0" [[Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "919c7f3151e79ff196add81d7f4e45d91bbf420b" +git-tree-sha1 = "44c37b4636bc54afac5c574d2d02b625349d6582" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.25.0" +version = "3.41.0" [[CompilerSupportLibraries_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "8e695f735fca77e9708e795eda62afdb869cbb70" +deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.3.4+0" [[Conda]] -deps = ["JSON", "VersionParsing"] -git-tree-sha1 = "6231e40619c15148bcb80aa19d731e629877d762" +deps = ["Downloads", "JSON", "VersionParsing"] +git-tree-sha1 = "6cdc8832ba11c7695f494c9d9a1c31e90959ce0f" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" -version = "1.5.1" +version = "1.6.0" [[ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "48920211c95a6da1914a06c44ec94be70e84ffff" +git-tree-sha1 = "f74e9d5388b8620b4cee35d4c5a618dd4dc547f4" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.1.0" +version = "1.3.0" [[Contour]] deps = ["StaticArrays"] @@ -188,26 +216,25 @@ version = "0.5.7" [[Coverage]] deps = ["CoverageTools", "HTTP", "JSON", "LibGit2", "MbedTLS"] -git-tree-sha1 = "a485b62b1ce53368e3a1a3a8dc0c39a61b9d3d9c" +git-tree-sha1 = "991f606da16a3ab900d5cad64e90cede27678ab2" uuid = "a2441757-f6aa-5fb2-8edb-039e3f45d037" -version = "1.2.0" +version = "1.4.0" [[CoverageTools]] -deps = ["LibGit2"] -git-tree-sha1 = "08b72d2f2154e33dc2aeb1bfcd4a83cb283abd4f" +git-tree-sha1 = "cc5595feb314d3b226ed765a001a40ca451ad687" uuid = "c36e975a-824b-4404-a568-ef97ca766997" -version = "1.2.2" +version = "1.3.0" [[DataAPI]] -git-tree-sha1 = "dfb3b7e89e395be1e25c2ad6d7690dc29cc53b1d" +git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.6.0" +version = "1.9.0" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677" +git-tree-sha1 = "3daef5523dd2e769dad2365274f760ff5f282c7d" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.9" +version = "0.18.11" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -225,26 +252,26 @@ deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" [[DelayDiffEq]] -deps = ["DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "UnPack"] -git-tree-sha1 = "0c7f367792397f754728a3db960d7ef1eb3d8f09" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "UnPack"] +git-tree-sha1 = "1f4022b5b378c627c44212ea6f19ea36d7f9d3e3" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.29.1" +version = "5.32.4" [[DelimitedFiles]] deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" [[DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "FunctionWrappers", "IterativeSolvers", "LabelledArrays", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "Printf", "RecursiveArrayTools", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "ZygoteRules"] -git-tree-sha1 = "f5d290a67a2105b4cf531b0e3b5178106a661e39" +deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "FastBroadcast", "FunctionWrappers", "IterativeSolvers", "LabelledArrays", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "Printf", "RecursiveArrayTools", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "ZygoteRules"] +git-tree-sha1 = "9d312bb0b7c8ace440a71c64330cf1bea0ade0c8" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.57.9" +version = "6.70.0" [[DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "NLsolve", "OrdinaryDiffEq", "RecipesBase", "RecursiveArrayTools", "StaticArrays"] -git-tree-sha1 = "d4c4a3f442ab749b6b895c514b0be984c75d6d67" +deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "NLsolve", "OrdinaryDiffEq", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArrays"] +git-tree-sha1 = "4fba4f6bc9b8dfa96019ac4b72ac33ba56c07d87" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.16.0" +version = "2.20.0" [[DiffEqDiffTools]] deps = ["LinearAlgebra", "SparseArrays", "StaticArrays"] @@ -259,10 +286,10 @@ uuid = "5a0ffddc-d203-54b0-88ba-2c03c0fc2e67" version = "2.4.0" [[DiffEqJump]] -deps = ["ArrayInterface", "Compat", "DataStructures", "DiffEqBase", "FunctionWrappers", "LinearAlgebra", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "3ec8d5eeb792897b28ef79a851d834ce1415498f" +deps = ["ArrayInterface", "Compat", "DataStructures", "DiffEqBase", "FunctionWrappers", "LightGraphs", "LinearAlgebra", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "StaticArrays", "TreeViews", "UnPack"] +git-tree-sha1 = "9f47b8ae1c6f2b172579ac50397f8314b460fcd9" uuid = "c894b116-72e5-5b58-be3c-e6d8d4ac2b12" -version = "6.13.0" +version = "7.3.1" [[DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "LinearAlgebra", "PoissonRandom", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "StaticArrays", "Statistics"] @@ -283,16 +310,16 @@ uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" version = "1.0.3" [[DiffRules]] -deps = ["NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "214c3fcac57755cfda163d91c58893a8723f93e9" +deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "d529c45b4d95f1ff43640166959360095b1580f8" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.0.2" +version = "1.7.0" [[DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqFinancial", "DiffEqJump", "DiffEqNoiseProcess", "DiffEqPhysics", "DimensionalPlotRecipes", "LinearAlgebra", "MultiScaleArrays", "OrdinaryDiffEq", "ParameterizedFunctions", "Random", "RecursiveArrayTools", "Reexport", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "221b9a427fc8970be5b65171c25f0a6ba0e1f394" +git-tree-sha1 = "ececc535bd2aa55a520131d955639288704e3851" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "6.16.0" +version = "6.18.0" [[DimensionalPlotRecipes]] deps = ["LinearAlgebra", "RecipesBase"] @@ -301,10 +328,10 @@ uuid = "c619ae07-58cd-5f6d-b883-8f17bd6a98f9" version = "1.2.0" [[Distances]] -deps = ["LinearAlgebra", "Statistics"] -git-tree-sha1 = "366715149014943abd71aa647a07a43314158b2d" +deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.2" +version = "0.10.7" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -317,22 +344,26 @@ uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" version = "0.23.8" [[DocStringExtensions]] -deps = ["LibGit2", "Markdown", "Pkg", "Test"] -git-tree-sha1 = "9d4f64f79012636741cf01133158a54b24924c32" +deps = ["LibGit2"] +git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.4" +version = "0.8.6" + +[[Downloads]] +deps = ["ArgTools", "LibCURL", "NetworkOptions"] +uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" [[EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "92d8f9f208637e8d2d28c664051a00569c01493d" +git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d" uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.1.5+1" +version = "2.2.3+0" [[ElasticArrays]] deps = ["Adapt"] -git-tree-sha1 = "395e36b5962bd11bf080f4fe06546cd26a34e0d8" +git-tree-sha1 = "a0fcc1bb3c9ceaf07e1d0529c9806ce94be6adf9" uuid = "fdbdab4c-e67f-52f5-8c3f-e7b388dad3d4" -version = "1.2.6" +version = "1.2.9" [[ElasticPDMats]] deps = ["LinearAlgebra", "MacroTools", "PDMats"] @@ -340,23 +371,29 @@ git-tree-sha1 = "5157c93fe9431a041e4cd84265dfce3d53a52323" uuid = "2904ab23-551e-5aed-883f-487f97af5226" version = "0.2.2" +[[Expat_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "b3bfd02e98aedfa5cf885665493c5598c350cd2f" +uuid = "2e619515-83b5-522b-bb60-26c02a35a201" +version = "2.2.10+0" + [[ExponentialUtilities]] -deps = ["LinearAlgebra", "Printf", "Requires", "SparseArrays"] -git-tree-sha1 = "712cb5af8db62836913970ee035a5fa742986f00" +deps = ["ArrayInterface", "LinearAlgebra", "Printf", "Requires", "SparseArrays"] +git-tree-sha1 = "1b873816d2cfc8c0fcb1edcb08e67fdf630a70b7" uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.8.1" +version = "1.10.2" [[FFMPEG]] -deps = ["FFMPEG_jll", "x264_jll"] -git-tree-sha1 = "9a73ffdc375be61b0e4516d83d880b265366fe1f" +deps = ["FFMPEG_jll"] +git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.0" +version = "0.4.1" [[FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "LibVPX_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "3cc57ad0a213808473eafef4845a74766242e05f" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "d8a578692e3077ac998b50c0217dfd67f21d1e5f" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.3.1+4" +version = "4.4.0+0" [[FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "IntelOpenMP_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Reexport"] @@ -366,9 +403,15 @@ version = "1.3.0" [[FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "5a0d4b6a22a34d17d53543bd124f4b08ed78e8b0" +git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.9+7" +version = "3.3.10+0" + +[[FastBroadcast]] +deps = ["LinearAlgebra", "Polyester", "Static"] +git-tree-sha1 = "0f8ef5dcb040dbb9edd98b1763ac10882ee1ff03" +uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" +version = "0.1.12" [[FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -389,9 +432,9 @@ version = "0.8.14" [[FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "f6f80c8f934efd49a286bb5315360be66956dfc4" +git-tree-sha1 = "8b3c09b56acaf3c0e581c66638b85c8650ee9dca" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.8.0" +version = "2.8.1" [[FixedPointNumbers]] deps = ["Statistics"] @@ -399,6 +442,12 @@ git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.4" +[[Fontconfig_jll]] +deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" +uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" +version = "2.13.93+0" + [[Formatting]] deps = ["Printf"] git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" @@ -406,22 +455,22 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "c68fb7481b71519d313114dca639b35262ff105f" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "2b72a5624e289ee18256111657663721d59c143e" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.17" +version = "0.10.24" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "cbd58c9deb1d304f5a245a0b7eb841a2560cfec6" +git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.10.1+5" +version = "2.10.4+0" [[FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0d20aed5b14dd4c9a2453c1b601d08e1149679cc" +git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.5+6" +version = "1.0.10+0" [[FunctionWrappers]] git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc" @@ -439,10 +488,10 @@ uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" version = "0.52.0" [[GaussianProcesses]] -deps = ["Distances", "Distributions", "ElasticArrays", "ElasticPDMats", "FastGaussQuadrature", "ForwardDiff", "LinearAlgebra", "Optim", "PDMats", "Printf", "ProgressMeter", "Random", "RecipesBase", "ScikitLearnBase", "SpecialFunctions", "StaticArrays", "Statistics", "StatsFuns", "Zygote"] -git-tree-sha1 = "06f890e71136832f1c577aa443d3777ffa9594fa" +deps = ["Distances", "Distributions", "ElasticArrays", "ElasticPDMats", "FastGaussQuadrature", "ForwardDiff", "LinearAlgebra", "Optim", "PDMats", "Printf", "ProgressMeter", "Random", "RecipesBase", "ScikitLearnBase", "SpecialFunctions", "StaticArrays", "Statistics", "StatsFuns"] +git-tree-sha1 = "9cf8ba8037e332b1be14c71e549143e68c42a22d" uuid = "891a1506-143c-57d2-908e-e1f8e92e6de9" -version = "0.12.3" +version = "0.12.4" [[GeneralizedGenerated]] deps = ["CanonicalTraits", "DataStructures", "JuliaVariables", "MLStyle"] @@ -452,20 +501,38 @@ version = "0.2.8" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "c7f81b22b6c255861be4007a16bfdeb60e1c7f9b" +git-tree-sha1 = "4136b8a5668341e58398bb472754bff4ba0456ff" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.3.11" +version = "0.3.12" [[GeometryTypes]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "StaticArrays"] -git-tree-sha1 = "07194161fe4e181c6bf51ef2e329ec4e7d050fc4" +git-tree-sha1 = "d796f7be0383b5416cd403420ce0af083b0f9b28" uuid = "4d00f742-c7ba-57c2-abde-4428a4b178cb" -version = "0.8.4" +version = "0.8.5" + +[[Gettext_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] +git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" +uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" +version = "0.21.0+0" + +[[Glib_jll]] +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" +uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" +version = "2.68.3+2" + +[[Graphite2_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" +uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" +version = "1.3.14+0" [[Grisu]] -git-tree-sha1 = "03d381f65183cb2d0af8b3425fde97263ce9a995" +git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" -version = "1.0.0" +version = "1.0.2" [[HCubature]] deps = ["Combinatorics", "DataStructures", "LinearAlgebra", "QuadGK", "StaticArrays"] @@ -479,16 +546,34 @@ git-tree-sha1 = "c7ec02c4c6a039a98a15f955462cd7aea5df4508" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" version = "0.8.19" -[[IRTools]] -deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "90ee39f9beaaa186e4968417ea2b8ed5673c91c0" -uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.3.3" +[[HarfBuzz_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] +git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" +version = "2.8.1+1" + +[[HostCPUFeatures]] +deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] +git-tree-sha1 = "8f0dc80088981ab55702b04bba38097a44a1a3a9" +uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" +version = "0.1.5" + +[[Hwloc]] +deps = ["Hwloc_jll"] +git-tree-sha1 = "92d99146066c5c6888d5a3abc871e6a214388b91" +uuid = "0e44f5e4-bd66-52a0-8798-143a42290a1d" +version = "2.0.0" + +[[Hwloc_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "3395d4d4aeb3c9d31f5929d32760d8baeee88aaf" +uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" +version = "2.5.0+0" [[IfElse]] -git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef" +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" -version = "0.1.0" +version = "0.1.1" [[Inflate]] git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c" @@ -512,21 +597,32 @@ deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[Interpolations]] -deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "eb1dd6d5b2275faaaa18533e0fc5f9171cec25fa" +deps = ["AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] +git-tree-sha1 = "b15fc0a95c564ca2e0a7ae12c1f095ca848ceb31" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.1" +version = "0.13.5" + +[[InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "a7254c0acd8e62f1ac75ad24d5db43f5f19f3c65" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.2" + +[[IrrationalConstants]] +git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" +version = "0.1.1" [[IterTools]] -git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" +git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.3.0" +version = "1.4.0" [[IterativeSolvers]] deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] -git-tree-sha1 = "6f5ef3206d9dc6510a8b8e2334b96454a2ade590" +git-tree-sha1 = "1169632f425f79429f245113b775a0e3d121457c" uuid = "42fd0dbc-a981-5370-80f2-aaf504508153" -version = "0.9.0" +version = "0.9.2" [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -534,15 +630,16 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[JLLWrappers]] -git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0" +deps = ["Preferences"] +git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.2.0" +version = "1.3.0" [[JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4" +git-tree-sha1 = "8076680b162ada2a031f707ac7b4953e30667a37" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.1" +version = "0.21.2" [[JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -552,26 +649,32 @@ version = "0.2.4" [[KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "09aeec87bdc9c1fa70d0b508dfa94a21acd280d9" +git-tree-sha1 = "591e8dc09ad18386189610acafb970032c519707" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.2" +version = "0.6.3" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "df381151e871f41ee86cee4f5f6fd598b8a68826" +git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.0+3" +version = "3.100.1+0" + +[[LZO_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" +uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" +version = "2.10.1+0" [[LaTeXStrings]] -git-tree-sha1 = "c7f1c695e06c01b95a67f0cd1d34994f3e7db104" +git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.2.1" +version = "1.3.0" [[LabelledArrays]] -deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "StaticArrays"] -git-tree-sha1 = "5e288800819c323de5897fa6d5a002bdad54baf7" +deps = ["ArrayInterface", "ChainRulesCore", "LinearAlgebra", "MacroTools", "StaticArrays"] +git-tree-sha1 = "3609bbf5feba7b22fb35fe7cb207c8c8d2e2fc5b" uuid = "2ee39098-c373-598a-b85f-a56591580800" -version = "1.5.0" +version = "1.6.7" [[Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] @@ -579,19 +682,67 @@ git-tree-sha1 = "864527aa4d14c893fb8c51d48ef314410c88c7b9" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" version = "0.13.5" +[[LayoutPointers]] +deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static"] +git-tree-sha1 = "83b56449c39342a47f3fcdb3bc782bd6d66e1d97" +uuid = "10f19ff3-798f-405d-979b-55457f8fc047" +version = "0.1.4" + +[[LibCURL]] +deps = ["LibCURL_jll", "MozillaCACerts_jll"] +uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" + +[[LibCURL_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] +uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" + [[LibGit2]] -deps = ["Printf"] +deps = ["Base64", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -[[LibVPX_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "85fcc80c3052be96619affa2fe2e6d2da3908e11" -uuid = "dd192d2f-8180-539f-9fb4-cc70b1dcf69a" -version = "1.9.0+1" +[[LibSSH2_jll]] +deps = ["Artifacts", "Libdl", "MbedTLS_jll"] +uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" [[Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" +[[Libffi_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" +uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" +version = "3.2.2+1" + +[[Libgcrypt_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] +git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" +uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" +version = "1.8.7+0" + +[[Libgpg_error_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" +uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" +version = "1.42.0+0" + +[[Libiconv_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778" +uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" +version = "1.16.1+1" + +[[Libmount_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" +uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" +version = "2.35.0+0" + +[[Libuuid_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" +uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" +version = "2.36.0+0" + [[LightGraphs]] deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] git-tree-sha1 = "432428df5f360964040ed60418dd5601ecd240b6" @@ -608,14 +759,20 @@ version = "7.1.1" deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[LogExpFunctions]] +deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "e5718a00af0ab9756305a0392832c8952c7426c1" +uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +version = "0.3.6" + [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -[[METIS_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "2dc1a9fc87e57e32b1fc186db78811157b30c118" -uuid = "d00139f3-1899-568f-a2f0-47f597d42d70" -version = "5.1.0+5" +[[LoopVectorization]] +deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "Requires", "SIMDDualNumbers", "SLEEFPirates", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "9e10579c154f785b911d9ceb96c33fcc1a661171" +uuid = "bdcacae8-1622-11e9-2a5c-532679323890" +version = "0.12.99" [[MKL_jll]] deps = ["IntelOpenMP_jll", "Libdl", "Pkg"] @@ -624,15 +781,20 @@ uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" version = "2020.2.254+0" [[MLStyle]] -git-tree-sha1 = "a667f58636b36ba10145d46a4afe70492850af8c" +git-tree-sha1 = "594e189325f66e23a8818e5beb11c43bb0141bcd" uuid = "d8e11817-5142-5d16-987a-aa16d5891078" -version = "0.4.9" +version = "0.4.10" [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "6a8a2a625ab0dea913aba95c11370589e0239ff0" +git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.6" +version = "0.5.9" + +[[ManualMemory]] +git-tree-sha1 = "9cb207b18148b2199db259adfa923b45593fe08e" +uuid = "d125e4d3-2237-4719-b19c-fa641b8a4667" +version = "0.1.6" [[Markdown]] deps = ["Base64"] @@ -645,10 +807,8 @@ uuid = "739be429-bea8-5141-9913-cc70e7f3736d" version = "1.0.3" [[MbedTLS_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0eef589dd1c26a3ac9d753fe1a8bcad63f956fa6" +deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.16.8+1" [[Measures]] git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f" @@ -657,9 +817,9 @@ version = "0.3.1" [[Missings]] deps = ["DataAPI"] -git-tree-sha1 = "f8c673ccc215eb50fcadb285f522420e29e69e1c" +git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "0.4.5" +version = "1.0.2" [[Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -670,6 +830,9 @@ git-tree-sha1 = "2da0c371ce983b02afd6a957ba3c6b0aa977a3b3" uuid = "961ee093-0014-501f-94e3-6117800e7a78" version = "2.0.0" +[[MozillaCACerts_jll]] +uuid = "14a3606d-f60d-562e-9121-12d972cd8159" + [[MuladdMacro]] git-tree-sha1 = "c6190f9a7fc5d9d5915ab29f2134421b12d24a68" uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" @@ -677,9 +840,9 @@ version = "0.2.2" [[MultiScaleArrays]] deps = ["DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "SparseDiffTools", "Statistics", "StochasticDiffEq", "TreeViews"] -git-tree-sha1 = "258f3be6770fe77be8870727ba9803e236c685b8" +git-tree-sha1 = "03647373a31d9bde3382a31cca11f528b4d6bd5b" uuid = "f9640e96-87f6-5992-9c3b-0743c6a49ffa" -version = "1.8.1" +version = "1.9.0" [[MultivariateStats]] deps = ["Arpack", "LinearAlgebra", "SparseArrays", "Statistics", "StatsBase"] @@ -699,16 +862,10 @@ git-tree-sha1 = "019f12e9a1a7880459d0173c182e6a99365d7ac1" uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" version = "4.5.1" -[[NNlib]] -deps = ["BinaryProvider", "Libdl", "LinearAlgebra", "Requires", "Statistics"] -git-tree-sha1 = "d9f196d911f55aeaff11b11f681b135980783824" -uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.6.6" - [[NaNMath]] -git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" +git-tree-sha1 = "f755f36b19a5116bb580de457cda0c140153f283" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.5" +version = "0.3.6" [[NameResolution]] deps = ["PrettyPrint"] @@ -718,44 +875,45 @@ version = "0.1.5" [[NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "9afd724797039125e8e2cc362098f01dab60bc3a" +git-tree-sha1 = "16baacfdc8758bc374882566c9187e785e85c2f0" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.8" +version = "0.4.9" + +[[NetworkOptions]] +uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" [[NonlinearSolve]] deps = ["ArrayInterface", "FiniteDiff", "ForwardDiff", "IterativeSolvers", "LinearAlgebra", "RecursiveArrayTools", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "UnPack"] -git-tree-sha1 = "ef18e47df4f3917af35be5e5d7f5d97e8a83b0ec" +git-tree-sha1 = "8dc3be3e9edf976a3e79363b3bd2ad776a627c31" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "0.3.8" +version = "0.3.12" [[Observables]] -git-tree-sha1 = "3469ef96607a6b9a1e89e54e6f23401073ed3126" +git-tree-sha1 = "fe29afdef3d0c4a8286128d4e45cc50621b1e43d" uuid = "510215fc-4207-5dde-b226-833fc4488ee2" -version = "0.3.3" +version = "0.4.0" [[OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "b3dfef5f2be7d7eb0e782ba9146a5271ee426e90" +git-tree-sha1 = "043017e0bdeff61cfbb7afeb558ab29536bbb5ed" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.6.2" +version = "1.10.8" [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "a42c0f138b9ebe8b58eba2271c5053773bde52d0" +git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" -version = "1.3.4+2" +version = "1.3.5+1" [[OpenBLAS_jll]] -deps = ["CompilerSupportLibraries_jll", "Libdl", "Pkg"] -git-tree-sha1 = "0c922fd9634e358622e333fc58de61f05a048492" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.9+5" [[OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "71bbbc616a1d710879f5a1021bcba65ffba6ce58" +git-tree-sha1 = "15003dcb7d8db3c6c857fda14891a539a8f2705a" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.1+6" +version = "1.1.10+0" [[Optim]] deps = ["Compat", "FillArrays", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] @@ -765,20 +923,26 @@ version = "0.20.6" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f9d57f4126c39565e05a2b0264df99f497fc6f37" +git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" uuid = "91d4177d-7536-5919-b921-800302f37372" -version = "1.3.1+3" +version = "1.3.2+0" [[OrderedCollections]] -git-tree-sha1 = "4fa2ba51070ec13fcc7517db714445b4ab986bdf" +git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.0" +version = "1.4.1" [[OrdinaryDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "NLsolve", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "d22a75b8ae5b77543c4e1f8eae1ff01ce1f64453" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "NLsolve", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "e9f977a3119e7bfb3bfaeb3daa354f38e9baf76f" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "5.52.2" +version = "5.55.1" + +[[PCRE_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" +uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc" +version = "8.44.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"] @@ -794,18 +958,24 @@ version = "5.6.0" [[Parameters]] deps = ["OrderedCollections", "UnPack"] -git-tree-sha1 = "2276ac65f1e236e0a6ea70baff3f62ad4c625345" +git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" -version = "0.12.2" +version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc" +git-tree-sha1 = "d7fa6237da8004be601e19bd6666083056649918" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "1.1.0" +version = "2.1.3" + +[[Pixman_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" +uuid = "30392449-352a-5448-841d-b1acce4e97dc" +version = "0.40.1+0" [[Pkg]] -deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"] +deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" [[PlotThemes]] @@ -816,9 +986,9 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "ae9a295ac761f64d8c2ec7f9f24d21eb4ffba34d" +git-tree-sha1 = "68604313ed59f0408313228ba09e79252e4b2da8" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.10" +version = "1.1.2" [[Plots]] deps = ["Base64", "Contour", "Dates", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "GeometryTypes", "JSON", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"] @@ -832,12 +1002,30 @@ git-tree-sha1 = "44d018211a56626288b5d3f8c6497d28c26dc850" uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" version = "0.4.0" +[[Polyester]] +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "3c44fc250c04352839cea8d5b9d94bcb7b3de420" +uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" +version = "0.6.2" + +[[PolyesterWeave]] +deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] +git-tree-sha1 = "a3ff99bf561183ee20386aec98ab8f4a12dc724a" +uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" +version = "0.1.2" + [[PositiveFactorizations]] deps = ["LinearAlgebra"] git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" +[[Preferences]] +deps = ["TOML"] +git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af" +uuid = "21216c6a-2e73-6563-6e65-726566657250" +version = "1.2.3" + [[PrettyPrint]] git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" uuid = "8162dcfd-2161-5ef2-ae6c-7681170c5f98" @@ -849,30 +1037,30 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" [[ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "6e9c89cba09f6ef134b00e10625590746ba1e036" +git-tree-sha1 = "afadeba63d90ff223a6a48d2009434ecee2ec9e8" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.5.0" +version = "1.7.1" [[PyCall]] deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"] -git-tree-sha1 = "dd1a970b543bd02efce2984582e996af28cab27f" +git-tree-sha1 = "71fd4022ecd0c6d20180e23ff1b3e05a143959c2" uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" -version = "1.92.2" +version = "1.93.0" [[PyPlot]] deps = ["Colors", "LaTeXStrings", "PyCall", "Sockets", "Test", "VersionParsing"] -git-tree-sha1 = "67dde2482fe1a72ef62ed93f8c239f947638e5a2" +git-tree-sha1 = "14c1b795b9d764e1784713941e787e1384268103" uuid = "d330b81b-6aea-500a-939a-2ce795aea3ee" -version = "2.9.0" +version = "2.10.0" [[QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "12fbe86da16df6679be7521dfb39fbc861e1dc7b" +git-tree-sha1 = "78aadffb3efd2155af139781b8a8df1ef279ea39" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.4.1" +version = "2.4.2" [[REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets"] +deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[Random]] @@ -881,25 +1069,26 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[Random123]] deps = ["Libdl", "Random", "RandomNumbers"] -git-tree-sha1 = "7c6710c8198fd4444b5eb6a3840b7d47bd3593c5" +git-tree-sha1 = "0e8b146557ad1c6deb1367655e052276690e71a3" uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.3.1" +version = "1.4.2" [[RandomNumbers]] deps = ["Random", "Requires"] -git-tree-sha1 = "441e6fc35597524ada7f85e13df1f4e10137d16f" +git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" -version = "1.4.0" +version = "1.5.3" [[Ratios]] -git-tree-sha1 = "37d210f612d70f3f7d57d488cb3b6eff56ad4e41" +deps = ["Requires"] +git-tree-sha1 = "01d341f502250e81f6fec0afe662aa861392a3aa" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.0" +version = "0.4.2" [[RecipesBase]] -git-tree-sha1 = "b3fb709f3c97bfc6e948be68beeecb55a0b340ae" +git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.1.1" +version = "1.2.1" [[RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] @@ -908,16 +1097,16 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.1.13" [[RecursiveArrayTools]] -deps = ["ArrayInterface", "LinearAlgebra", "RecipesBase", "Requires", "StaticArrays", "Statistics", "ZygoteRules"] -git-tree-sha1 = "271a36e18c8806332b7bd0f57e50fcff0d428b11" +deps = ["ArrayInterface", "ChainRulesCore", "DocStringExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArrays", "Statistics", "ZygoteRules"] +git-tree-sha1 = "00bede2eb099dcc1ddc3f9ec02180c326b420ee2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.11.0" +version = "2.17.2" [[RecursiveFactorization]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "6761a5d1f9646affb2a369ff932841fff77934a3" +deps = ["LinearAlgebra", "LoopVectorization"] +git-tree-sha1 = "2e1a88c083ebe8ba69bc0b0084d4b4ba4aa35ae0" uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.1.0" +version = "0.1.13" [[Reexport]] deps = ["Pkg"] @@ -927,31 +1116,48 @@ version = "0.2.0" [[Requires]] deps = ["UUIDs"] -git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621" +git-tree-sha1 = "8f82019e525f4d5c669692772a6f4b0a58b06a6a" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.1.3" +version = "1.2.0" [[ResettableStacks]] deps = ["StaticArrays"] -git-tree-sha1 = "622b3e491fb0a85fbfeed6f17dc320a9f46d8929" +git-tree-sha1 = "256eeeec186fa7f26f2801732774ccf277f05db9" uuid = "ae5879a3-cd67-5da8-be7f-38c6eb64a37b" -version = "1.1.0" +version = "1.1.1" [[Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "86c5647b565873641538d8f812c04e4c9dbeb370" +git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.6.1" +version = "0.7.0" [[Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "1b7bf41258f6c5c9c31df8c1ba34c1fc88674957" +git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.2.2+2" +version = "0.3.0+0" [[SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" +[[SIMDDualNumbers]] +deps = ["ForwardDiff", "IfElse", "SLEEFPirates", "VectorizationBase"] +git-tree-sha1 = "62c2da6eb66de8bb88081d20528647140d4daa0e" +uuid = "3cdde19b-5bb0-4aaf-8931-af3e248e098b" +version = "0.1.0" + +[[SIMDTypes]] +git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" +uuid = "94e857df-77ce-4151-89e5-788b33177be4" +version = "0.1.0" + +[[SLEEFPirates]] +deps = ["IfElse", "Static", "VectorizationBase"] +git-tree-sha1 = "1410aad1c6b35862573c01b96cd1f6dbe3979994" +uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" +version = "0.6.28" + [[SafeTestsets]] deps = ["Test"] git-tree-sha1 = "36ebc5622c82eb9324005cc75e7e2cc51181d181" @@ -959,10 +1165,10 @@ uuid = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" version = "0.0.1" [[SciMLBase]] -deps = ["ArrayInterface", "CommonSolve", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "RecipesBase", "RecursiveArrayTools", "StaticArrays", "Statistics", "Tables", "TreeViews"] -git-tree-sha1 = "9dd06ee4a1238265ddf512851682cb3db326a8a8" +deps = ["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "RecipesBase", "RecursiveArrayTools", "StaticArrays", "Statistics", "Tables", "TreeViews"] +git-tree-sha1 = "c61870a745fb9a468649d9efdd05c18d30e6a6e2" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.8.5" +version = "1.24.0" [[ScikitLearnBase]] deps = ["LinearAlgebra", "Random", "Statistics"] @@ -972,18 +1178,18 @@ version = "0.5.0" [[SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "6ccde405cf0759eba835eb613130723cb8f10ff9" +git-tree-sha1 = "244586bc07462d22aed0113af9c731f2a518c93e" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.2.16" +version = "1.3.10" [[Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" [[Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "Requires"] -git-tree-sha1 = "d5640fc570fb1b6c54512f0bd3853866bd298b3e" +git-tree-sha1 = "fca29e68c5062722b5b4435594c3d1ba557072a3" uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" -version = "0.7.0" +version = "0.7.1" [[SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] @@ -997,18 +1203,18 @@ version = "0.3.2" [[SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] -git-tree-sha1 = "daf7aec3fe3acb2131388f93a4c409b8c7f62226" +git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" -version = "0.9.3" +version = "0.9.4" [[Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[SortingAlgorithms]] -deps = ["DataStructures", "Random", "Test"] -git-tree-sha1 = "03f5898c9959f8115e30bc7226ada7d0df554ddd" +deps = ["DataStructures"] +git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "0.3.1" +version = "1.0.1" [[SparseArrays]] deps = ["LinearAlgebra", "Random"] @@ -1016,9 +1222,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SparseDiffTools]] deps = ["Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "LightGraphs", "LinearAlgebra", "Requires", "SparseArrays", "VertexSafeGraphs"] -git-tree-sha1 = "d05bc362e3fa1b0e2361594a706fc63ffbd140f3" +git-tree-sha1 = "be20320958ccd298c98312137a5ebe75a654ebc8" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "1.13.0" +version = "1.13.2" [[SpecialFunctions]] deps = ["BinDeps", "BinaryProvider", "Libdl"] @@ -1028,9 +1234,9 @@ version = "0.8.0" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "ddec5466a1d2d7e58adf9a427ba69763661aacf6" +git-tree-sha1 = "7f5a513baec6f122401abfc8e9c074fdac54f6c1" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.2.4" +version = "0.4.1" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] @@ -1042,57 +1248,66 @@ version = "0.12.5" deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +[[StatsAPI]] +git-tree-sha1 = "d88665adc9bcf45903013af0982e2fd05ae3d0a6" +uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" +version = "1.2.0" + [[StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"] -git-tree-sha1 = "a83fa3021ac4c5a918582ec4721bc0cf70b495a9" +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "51383f2d367eb3b444c961d485c565e4c0cf4ba0" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.4" +version = "0.33.14" [[StatsFuns]] deps = ["Rmath", "SpecialFunctions"] -git-tree-sha1 = "3b9f665c70712af3264b61c27a7e1d62055dafd1" +git-tree-sha1 = "ced55fd4bae008a8ea12508314e725df61f0ba45" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.6" +version = "0.9.7" [[StatsPlots]] deps = ["Clustering", "DataStructures", "DataValues", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] -git-tree-sha1 = "7c88f73b759ae16a4a1af8bda7a9563471a7baf5" +git-tree-sha1 = "e1e5ed9669d5521d4bbdd4fab9f0945a0ffceba2" uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" -version = "0.14.19" +version = "0.14.30" [[SteadyStateDiffEq]] deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "9b908c7a5933b8ec7c2da44a477f74127baa2ce9" +git-tree-sha1 = "3e057e1f9f12d18cac32011aed9e61eef6c1c0ce" uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" -version = "1.6.1" +version = "1.6.6" [[StochasticDiffEq]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqJump", "DiffEqNoiseProcess", "FillArrays", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "3109ce733c907b941eea4345b0644308e2c6da2d" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqJump", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "45b59a5bd9665fe678c0372d7026321df28769d8" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.33.1" +version = "6.40.0" + +[[StrideArraysCore]] +deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "Requires", "SIMDTypes", "Static", "ThreadingUtilities"] +git-tree-sha1 = "12cf3253ebd8e2a3214ae171fbfe51e7e8d8ad28" +uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" +version = "0.2.9" [[StructArrays]] deps = ["Adapt", "DataAPI", "Tables"] -git-tree-sha1 = "26ea43b4be7e919a2390c3c0f824e7eb4fc19a0a" +git-tree-sha1 = "44b3afd37b17422a62aea25f04c1f7e09ce6b07f" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.5.0" +version = "0.5.1" [[SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[SuiteSparse_jll]] -deps = ["Libdl", "METIS_jll", "OpenBLAS_jll", "Pkg"] -git-tree-sha1 = "4a2295b63d67e6f13a0b539c935ccbf218fa1143" +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.4.0+9" [[Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "28db9e1a8fdd1b8e95cee064a6c2066897cf39c5" +git-tree-sha1 = "a8bbdf8e19058d1cf69c29ebb4514e9bcaa2305f" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.4.1" +version = "4.9.0" [[Sundials_jll]] deps = ["CompilerSupportLibraries_jll", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] @@ -1100,34 +1315,48 @@ git-tree-sha1 = "013ff4504fc1d475aa80c63b455b6b3a58767db2" uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" version = "5.2.0+1" +[[TOML]] +deps = ["Dates"] +uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" + [[TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] -git-tree-sha1 = "a7cf690d0ac3f5b53dd09b5d613540b230233647" +git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1" uuid = "ab02a1b2-a7df-11e8-156e-fb1833f50b87" -version = "1.0.0" +version = "1.2.0" [[TableTraits]] deps = ["IteratorInterfaceExtensions"] -git-tree-sha1 = "b1ad568ba658d8cbb3b892ed5380a6f3e781a81e" +git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" -version = "1.0.0" +version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "a9ff3dfec713c6677af435d6a6d65f9744feef67" +git-tree-sha1 = "bb1064c9a84c52e277f1096cf41434b675cd368b" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.4.1" +version = "1.6.1" + +[[Tar]] +deps = ["ArgTools", "SHA"] +uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" [[TaylorSeries]] deps = ["InteractiveUtils", "LinearAlgebra", "Markdown", "Requires", "SparseArrays"] -git-tree-sha1 = "39523982677336d055907fe734b30b9951b2cadc" +git-tree-sha1 = "66f4d1993bae49eeba21a1634b5f65782585a42c" uuid = "6aa5eb33-94cf-58f4-a9d0-e4b2c4fc25ea" -version = "0.10.11" +version = "0.10.13" [[Test]] -deps = ["Distributed", "InteractiveUtils", "Logging", "Random"] +deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[ThreadingUtilities]] +deps = ["ManualMemory"] +git-tree-sha1 = "884539ba8c4584a3a8173cb4ee7b61049955b79c" +uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" +version = "0.4.7" + [[TreeViews]] deps = ["Test"] git-tree-sha1 = "8d0d7a3fe2f30d6a7f833a5f19f7c7a5b396eae6" @@ -1153,15 +1382,21 @@ version = "1.0.2" uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[Unitful]] -deps = ["ConstructionBase", "LinearAlgebra", "Random"] -git-tree-sha1 = "fdfbea79b5b9a305bf226eb4730321f603281290" +deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"] +git-tree-sha1 = "b95e0b8a8d1b6a6c3e0b3ca393a7a285af47c264" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.6.0" +version = "1.10.1" + +[[VectorizationBase]] +deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "Hwloc", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"] +git-tree-sha1 = "6e261bff5c9f2537776165dea3067df9de4440cf" +uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" +version = "0.21.23" [[VersionParsing]] -git-tree-sha1 = "80229be1f670524750d905f8fc8148e5a8c4537f" +git-tree-sha1 = "e575cf85535c7c3292b4d89d89cc29e8c3098e47" uuid = "81def892-9a0e-5fdd-b105-ffc91e053289" -version = "1.2.0" +version = "1.2.1" [[VertexSafeGraphs]] deps = ["LightGraphs"] @@ -1171,60 +1406,126 @@ version = "0.1.2" [[Widgets]] deps = ["Colors", "Dates", "Observables", "OrderedCollections"] -git-tree-sha1 = "fc0feda91b3fef7fe6948ee09bb628f882b49ca4" +git-tree-sha1 = "80661f59d28714632132c73779f8becc19a113f2" uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62" -version = "0.6.2" +version = "0.6.4" [[WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "59e2ad8fd1591ea019a5259bd012d7aee15f995c" +git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3" uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" -version = "0.5.3" +version = "0.5.5" + +[[XML2_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "1acf5bdf07aa0907e0a37d3718bb88d4b687b74a" +uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" +version = "2.9.12+0" + +[[XSLT_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" +uuid = "aed1982a-8fda-507f-9586-7b0439959a61" +version = "1.1.34+0" + +[[Xorg_libX11_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] +git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" +uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" +version = "1.6.9+4" + +[[Xorg_libXau_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" +uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" +version = "1.0.9+4" -[[Zlib_jll]] +[[Xorg_libXdmcp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "320228915c8debb12cb434c59057290f0834dbf6" -uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.11+18" +git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" +uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" +version = "1.1.3+4" + +[[Xorg_libXext_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] +git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" +uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" +version = "1.3.4+4" + +[[Xorg_libXrender_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] +git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" +version = "0.9.10+4" + +[[Xorg_libpthread_stubs_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" +uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" +version = "0.1.0+3" -[[Zygote]] -deps = ["DiffRules", "FFTW", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NNlib", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "f8329b595c465caf3ca87c4f744e6041a4983e43" -uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.4.8" +[[Xorg_libxcb_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] +git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" +uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" +version = "1.13.0+3" + +[[Xorg_xtrans_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" +uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" +version = "1.4.0+3" + +[[Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" [[ZygoteRules]] deps = ["MacroTools"] -git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" +git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.1" +version = "0.2.2" [[libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "acc685bcf777b2202a904cdcb49ad34c2fa1880c" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.14.0+4" +version = "0.15.1+0" [[libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7a5780a0d9c6864184b3a2eeeb833a0c871f00ab" +git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "0.1.6+4" +version = "2.0.2+0" + +[[libpng_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" +uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" +version = "1.6.38+0" [[libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "fa14ac25af7a4b8a7f61b287a124df7aab601bcd" +git-tree-sha1 = "c45f4e40e7aafe9d086379e5578947ec8b95a8fb" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.6+6" +version = "1.3.7+0" + +[[nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" + +[[p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" [[x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d713c1ce4deac133e3334ee12f4adff07f81778f" +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2020.7.14+2" +version = "2021.5.5+0" [[x265_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "487da2f8f2f0c8ee0e83f39d13037d6bbf0a45ab" +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.0.0+3" +version = "3.5.0+0" diff --git a/examples/Cloudy/Project.toml b/examples/Cloudy/Project.toml index 3b44ceb65..7dc639a81 100644 --- a/examples/Cloudy/Project.toml +++ b/examples/Cloudy/Project.toml @@ -15,4 +15,5 @@ StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" [compat] +julia = "~1.6" FFTW = "= 1.3.0" diff --git a/examples/Emulator/GaussianProcess/Manifest.toml b/examples/Emulator/GaussianProcess/Manifest.toml index 941b6abe4..f0b0040c4 100644 --- a/examples/Emulator/GaussianProcess/Manifest.toml +++ b/examples/Emulator/GaussianProcess/Manifest.toml @@ -2,18 +2,18 @@ [[Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7" +git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.1" +version = "3.3.3" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "e527b258413e0c6d4f66ade574744c94edef81f8" +git-tree-sha1 = "1ee88c4c76caa995a885dc2f22a5d548dfbbc0ba" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.40" +version = "3.2.2" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -29,27 +29,27 @@ version = "1.0.8+0" [[Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "f2202b55d816427cd385a9a4f3ffb226bee80f99" +git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.16.1+0" +version = "1.16.1+1" [[CalibrateEmulateSample]] -deps = ["Conda", "Distributions", "DocStringExtensions", "EnsembleKalmanProcesses", "GaussianProcesses", "JLD2", "LinearAlgebra", "PyCall", "Random", "ScikitLearn", "Statistics", "StatsBase"] -path = "/home/odunbar/Dropbox/Caltech/CESjl/CalibrateEmulateSample.jl/" +deps = ["Conda", "Distributions", "DocStringExtensions", "EnsembleKalmanProcesses", "GaussianProcesses", "LinearAlgebra", "PyCall", "Random", "ScikitLearn", "Statistics", "StatsBase"] +path = "/Users/tsj/Documents/climate/clima/CalibrateEmulateSample.jl" uuid = "95e48a1f-0bec-4818-9538-3db4340308e3" version = "0.1.0" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd" +git-tree-sha1 = "926870acb6cbcf029396f2f2de030282b6bc1941" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.11.1" +version = "1.11.4" [[ChangesOfVariables]] -deps = ["LinearAlgebra", "Test"] -git-tree-sha1 = "9a1d594397670492219635b35a3d830b04730d62" +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.1" +version = "0.1.2" [[CodeTracking]] deps = ["InteractiveUtils", "UUIDs"] @@ -83,19 +83,19 @@ version = "0.3.0" [[Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "dce3e3fea680869eaa0b774b2e8343e9ff442313" +git-tree-sha1 = "44c37b4636bc54afac5c574d2d02b625349d6582" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.40.0" +version = "3.41.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" [[Conda]] -deps = ["JSON", "VersionParsing"] -git-tree-sha1 = "299304989a5e6473d985212c28928899c74e9421" +deps = ["Downloads", "JSON", "VersionParsing"] +git-tree-sha1 = "6cdc8832ba11c7695f494c9d9a1c31e90959ce0f" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" -version = "1.5.2" +version = "1.6.0" [[Contour]] deps = ["StaticArrays"] @@ -104,9 +104,9 @@ uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" version = "0.5.7" [[Crayons]] -git-tree-sha1 = "3f71217b538d7aaee0b69ab47d9b7724ca8afa0d" +git-tree-sha1 = "b618084b49e78985ffa8422f32b9838e397b9fc2" uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" -version = "4.0.4" +version = "4.1.0" [[DataAPI]] git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" @@ -115,15 +115,15 @@ version = "1.9.0" [[DataFrames]] deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "d785f42445b63fc86caa08bb9a9351008be9b765" +git-tree-sha1 = "cfdfef912b7f93e4b848e80b9befdf9e331bc05a" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.2.2" +version = "1.3.1" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "7d9d316f04214f7efdbb6398d545446e246eff02" +git-tree-sha1 = "3daef5523dd2e769dad2365274f760ff5f282c7d" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.10" +version = "0.18.11" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -146,15 +146,15 @@ version = "1.0.3" [[DiffRules]] deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "d8f468c5cd4d94e86816603f7d18ece910b4aaf1" +git-tree-sha1 = "9bc5dac3c8b6706b58ad5ce24cffd9861f07c94f" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.5.0" +version = "1.9.0" [[Distances]] -deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "837c83e5574582e07662bbbba733964ff7c26b9d" +deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.6" +version = "0.10.7" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -196,9 +196,9 @@ version = "0.2.2" [[EnsembleKalmanProcesses]] deps = ["Distributions", "DocStringExtensions", "LinearAlgebra", "Random", "Statistics", "StatsBase"] -git-tree-sha1 = "6e6cff0111d9849c2a2ce253325478a2903b16d0" +git-tree-sha1 = "4a0fb4cd1831d0cb630c63da0c1f1fbf50670bad" uuid = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d" -version = "0.1.1" +version = "0.1.2" [[Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -220,15 +220,9 @@ version = "4.4.0+0" [[FastGaussQuadrature]] deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "5ccd8547615457402a499af9603d55876423eea8" +git-tree-sha1 = "58d83dd5a78a36205bdfddb82b1bb67682e64487" uuid = "442a2c76-b920-505d-bb47-c5924d526838" -version = "0.4.8" - -[[FileIO]] -deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "2db648b6712831ecb333eae76dbfd1c156ca13bb" -uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.11.2" +version = "0.4.9" [[FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -265,9 +259,9 @@ version = "0.4.2" [[ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "6406b5112809c08b1baa5703ad274e1dded0652f" +git-tree-sha1 = "2b72a5624e289ee18256111657663721d59c143e" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.23" +version = "0.10.24" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -293,15 +287,15 @@ version = "3.3.5+1" [[GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "30f2b340c2fff8410d89bfcdc9c0a6dd661ac5f7" +git-tree-sha1 = "b9a93bcdf34618031891ee56aad94cfff0843753" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.62.1" +version = "0.63.0" [[GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "fd75fa3a2080109a2c0ec9864a6e14c60cca3866" +git-tree-sha1 = "f97acd98255568c3c9b416c5a3cf246c1315771b" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.62.0+0" +version = "0.63.0+0" [[GaussianProcesses]] deps = ["Distances", "Distributions", "ElasticArrays", "ElasticPDMats", "FastGaussQuadrature", "ForwardDiff", "LinearAlgebra", "Optim", "PDMats", "Printf", "ProgressMeter", "Random", "RecipesBase", "ScikitLearnBase", "SpecialFunctions", "StaticArrays", "Statistics", "StatsFuns"] @@ -323,9 +317,9 @@ version = "0.21.0+0" [[Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "7bf67e9a481712b3dbe9cb3dac852dc4b1162e02" +git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.68.3+0" +version = "2.68.3+2" [[Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -346,9 +340,9 @@ version = "0.9.17" [[HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] -git-tree-sha1 = "8a954fed8ac097d5be04921d595f741115c1b2ad" +git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "2.8.1+0" +version = "2.8.1+1" [[IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -382,21 +376,15 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.1.1" [[IterTools]] -git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" +git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.3.0" +version = "1.4.0" [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" -[[JLD2]] -deps = ["DataStructures", "FileIO", "MacroTools", "Mmap", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "46b7834ec8165c541b0b5d1c8ba63ec940723ffb" -uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.15" - [[JLLWrappers]] deps = ["Preferences"] git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e" @@ -417,9 +405,9 @@ version = "2.1.0+0" [[JuliaInterpreter]] deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"] -git-tree-sha1 = "e273807f38074f033d94207a201e6e827d8417db" +git-tree-sha1 = "a2366b16704ffe78be1831341e6799ab2f4f07d2" uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a" -version = "0.8.21" +version = "0.9.0" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -523,18 +511,18 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "be9eef9f9d78cecb6f262f3c10da151a6c5ab827" +git-tree-sha1 = "e5718a00af0ab9756305a0392832c8952c7426c1" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.5" +version = "0.3.6" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[LoweredCodeUtils]] deps = ["JuliaInterpreter"] -git-tree-sha1 = "491a883c4fef1103077a7f648961adbf9c8dd933" +git-tree-sha1 = "f46e8f4e38882b32dcc11c8d31c131d556063f39" uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b" -version = "2.1.2" +version = "2.2.0" [[MacroTools]] deps = ["Markdown", "Random"] @@ -580,18 +568,18 @@ uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" version = "7.8.2" [[NaNMath]] -git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" +git-tree-sha1 = "f755f36b19a5116bb580de457cda0c140153f283" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.5" +version = "0.3.6" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7937eda4681660b4d6aeeecc2f7e1c81c8ee4e2f" +git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" -version = "1.3.5+0" +version = "1.3.5+1" [[OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -611,9 +599,9 @@ version = "0.5.5+0" [[Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "35d435b512fbab1d1a29138b5229279925eba369" +git-tree-sha1 = "916077e0f0f8966eb0dc98a5c39921fdb8f49eb4" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.5.0" +version = "1.6.0" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -646,9 +634,9 @@ version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "ae4bbcadb2906ccc085cf52ac286dc1377dceccc" +git-tree-sha1 = "d7fa6237da8004be601e19bd6666083056649918" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.1.2" +version = "2.1.3" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -668,15 +656,15 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "b084324b4af5a438cd63619fd006614b3b20b87b" +git-tree-sha1 = "68604313ed59f0408313228ba09e79252e4b2da8" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.15" +version = "1.1.2" [[Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun"] -git-tree-sha1 = "0d185e8c33401084cab546a756b387b15f76720c" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] +git-tree-sha1 = "71d65e9242935132e71c4fbf084451579491166a" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.23.6" +version = "1.25.4" [[PooledArrays]] deps = ["DataAPI", "Future"] @@ -692,15 +680,15 @@ version = "0.2.4" [[Preferences]] deps = ["TOML"] -git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a" +git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.2.2" +version = "1.2.3" [[PrettyTables]] deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] -git-tree-sha1 = "d940010be611ee9d67064fe559edbb305f8cc0eb" +git-tree-sha1 = "dfb54c4e414caa595a1f2ed759b160f5a3ddcba5" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "1.2.3" +version = "1.3.1" [[Printf]] deps = ["Unicode"] @@ -714,9 +702,9 @@ version = "1.7.1" [[PyCall]] deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"] -git-tree-sha1 = "4ba3651d33ef76e24fef6a598b63ffd1c5e1cd17" +git-tree-sha1 = "71fd4022ecd0c6d20180e23ff1b3e05a143959c2" uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" -version = "1.92.5" +version = "1.93.0" [[PyPlot]] deps = ["Colors", "LaTeXStrings", "PyCall", "Sockets", "Test", "VersionParsing"] @@ -745,9 +733,9 @@ deps = ["Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[RecipesBase]] -git-tree-sha1 = "a4425fe1cde746e278fa895cc69e3113cb2614f6" +git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.2.0" +version = "1.2.1" [[RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] @@ -762,15 +750,15 @@ version = "1.2.2" [[Requires]] deps = ["UUIDs"] -git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621" +git-tree-sha1 = "8f82019e525f4d5c669692772a6f4b0a58b06a6a" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.1.3" +version = "1.2.0" [[Revise]] deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "Requires", "UUIDs", "Unicode"] -git-tree-sha1 = "41deb3df28ecf75307b6e492a738821b031f8425" +git-tree-sha1 = "2f9d4d6679b5f0394c52731db3794166f49d5131" uuid = "295af30f-e4ad-537b-8983-00126c2a3abe" -version = "3.1.20" +version = "3.3.1" [[Rmath]] deps = ["Random", "Rmath_jll"] @@ -839,30 +827,30 @@ version = "1.8.1" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "e7bc80dc93f50857a5d1e3c8121495852f407e6a" +git-tree-sha1 = "7f5a513baec6f122401abfc8e9c074fdac54f6c1" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.4.0" +version = "0.4.1" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da" +git-tree-sha1 = "88a559da57529581472320892576a486fa2377b9" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.2.13" +version = "1.3.1" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsAPI]] -git-tree-sha1 = "0f2aa8e32d511f758a2ce49208181f7733a0936a" +git-tree-sha1 = "d88665adc9bcf45903013af0982e2fd05ae3d0a6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.1.0" +version = "1.2.0" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "2bb0cb32026a66037360606510fca5984ccc6b75" +git-tree-sha1 = "51383f2d367eb3b444c961d485c565e4c0cf4ba0" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.13" +version = "0.33.14" [[StatsFuns]] deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] @@ -892,9 +880,9 @@ version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "fed34d0e71b91734bf0a7e10eb1bb05296ddbcd0" +git-tree-sha1 = "bb1064c9a84c52e277f1096cf41434b675cd368b" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.6.0" +version = "1.6.1" [[Tar]] deps = ["ArgTools", "SHA"] @@ -904,12 +892,6 @@ uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -[[TranscodingStreams]] -deps = ["Random", "Test"] -git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" -uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.6" - [[URIs]] git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" @@ -933,6 +915,11 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[Unzip]] +git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" +uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" +version = "0.1.2" + [[VersionParsing]] git-tree-sha1 = "e575cf85535c7c3292b4d89d89cc29e8c3098e47" uuid = "81def892-9a0e-5fdd-b105-ffc91e053289" diff --git a/examples/Emulator/GaussianProcess/Project.toml b/examples/Emulator/GaussianProcess/Project.toml index 4bb6a44ed..6512fef15 100644 --- a/examples/Emulator/GaussianProcess/Project.toml +++ b/examples/Emulator/GaussianProcess/Project.toml @@ -8,3 +8,6 @@ PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Revise = "295af30f-e4ad-537b-8983-00126c2a3abe" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + +[compat] +julia = "~1.6" diff --git a/examples/Emulator/GaussianProcess/learn_noise.jl b/examples/Emulator/GaussianProcess/learn_noise.jl new file mode 100644 index 000000000..1b1f22e0b --- /dev/null +++ b/examples/Emulator/GaussianProcess/learn_noise.jl @@ -0,0 +1,172 @@ +# Reference the in-tree version of CalibrateEmulateSample on Julias load path +prepend!(LOAD_PATH, [joinpath(@__DIR__, "..", "..")]) + +# Import modules +using Random +using Distributions +using Statistics +using LinearAlgebra +using CalibrateEmulateSample.Emulators +using CalibrateEmulateSample.DataStorage + +############################################################################### +# # +# This examples shows how to fit a Gaussian Process (GP) regression model # +# using GaussianProcessEmulator and demonstrates how the GaussianProcess's built-in Singular # +# Value Decomposition (SVD) decorrelates the training data and maps into # +# a space where the covariance of the observational noise is the identity. # +# # +# When training a GP, the hyperparameters of its kernel (or covariance # +# function) are optimized with respect to the given input-output pairs. # +# When training a separate GP for each output component (as is usually # +# done for multidimensional output, rather than fitting one multi-output # +# model), one assumes that their covariance functions are independent. # +# The SVD transformation ensures that this is a valid assumption. # +# # +# The decorrelation by the SVD is done automatically when instantiating # +# a `GaussianProcess`, but the user can choose to have the `predict` function # +# return its predictions in the original space (by setting # +# transform_to_real=true) # +# # +# Training points: {(x_i, y_i)} (i=1,...,n), where x_i ∈ ℝ ² and y_i ∈ ℝ ² # +# The y_i are assumed to be related to the x_i by: # +# y_i = G(x_i) + η, where G is a map from ℝ ² to ℝ ², and η is noise drawn # +# from a 2D normal distribution with known mean μ and covariance Σ # +# Two Gaussian Process models are fit, one that predicts y_i[1] from x_i # +# and one that predicts y_i[2] from x_i. # +# # +# The GaussianProcessEmulator module can be used as a standalone module to fit # +# Gaussian Process regression models, but it was originally designed as # +# the "Emulate" step of the "Calibrate-Emulate-Sample" framework # +# developed at CliMA. # +# Further reading on Calibrate-Emulate-Sample: # +# Cleary et al., 2020 # +# https://arxiv.org/abs/2001.03689 # +# # +############################################################################### + +rng_seed = 41 +Random.seed!(rng_seed) + +gppackage = GPJL() +prediction_type = YType() +gauss_proc_1 = GaussianProcess( + gppackage; + kernel=nothing, # use default squared exponential kernel + prediction_type=prediction_type, + noise_learn=true +) + +# Generate training data (x-y pairs, where x ∈ ℝ ᵖ, y ∈ ℝ ᵈ) +# x = [x1, x2]: inputs/predictors/features/parameters +# y = [y1, y2]: outputs/predictands/targets/observables +# The observables y are related to the parameters x by: +# y = G(x1, x2) + η, +# where G(x1, x2) := [sin(x1) + cos(x2), sin(x1) - cos(x2)], and η ~ N(0, Σ) +n = 200 # number of training points +p = 2 # input dim +d = 2 # output dim + +X = 2.0 * π * rand(p, n) + +# G(x1, x2) +g1x = sin.(X[1, :]) .+ cos.(X[2, :]) +g2x = sin.(X[1, :]) .- cos.(X[2, :]) +gx = zeros(2,n) +gx[1,:] = g1x +gx[2,:] = g2x +# Add noise η +μ = zeros(d) +Σ = 0.1 * [[0.8, 0.2] [0.2, 0.5]] # d x d +noise_samples = rand(MvNormal(μ, Σ), n) + +# y = G(x) + η +Y = gx .+ noise_samples + +# Fit 2D Gaussian Process regression model +# (To be precise: We fit two models, one that predicts y1 from x1 and x2, and +# one that predicts y2 from x1 and x2) +# Setting GPkernel=nothing leads to the creation of a default squared +# exponential kernel. +# Setting noise_learn=true leads to the addition of white noise to the kernel, +# whose hyperparameter -- the signal variance, or "noise" -- will be learned +# in the training phase via an optimization procedure. +# Because of the SVD transformation applied to the output, we expect the +# learned noise to be close to 1. +iopairs = PairedDataContainer(X,Y,data_are_columns=true) +@assert get_inputs(iopairs) == X +@assert get_outputs(iopairs) == Y + +emulator_1 = Emulator( + gauss_proc_1, + iopairs, + obs_noise_cov=Σ, + normalize_inputs=true +) +println("build GP with ", n, " training points") +#optimize the hyperparameters to best fit the GP. +optimize_hyperparameters!(emulator_1) +println("GP trained") + +# gpobj1 = GaussianProcess(iopairs, gppackage, GPkernel=nothing, obs_noise_cov=Σ, +# normalized=true, noise_learn=true, prediction_type=pred_type) + +println("\n-----------") +println("Results of training Gaussian Process models with noise_learn=true") +println("-----------") + +println("\nKernel of the GP trained to predict y1 from x=(x1, x2):") +println(emulator_1.machine_learning_tool.models[1].kernel) +println("Learned noise parameter, σ_1:") +learned_σ_1 = sqrt(emulator_1.machine_learning_tool.models[1].kernel.kright.σ2) +println("σ_1 = $learned_σ_1") +# Check if the learned noise is approximately 1 +@assert(isapprox(learned_σ_1, 1.0; atol=0.1)) + +println("\nKernel of the GP trained to predict y2 from x=(x1, x2):") +println(emulator_1.machine_learning_tool.models[2].kernel) +println("Learned noise parameter, σ_2:") +learned_σ_2 = sqrt(emulator_1.machine_learning_tool.models[2].kernel.kright.σ2) +println("σ_2 = $learned_σ_2") +# Check if the learned noise is approximately 1 +@assert(isapprox(learned_σ_2, 1.0; atol=0.1)) +println("------------------------------------------------------------------\n") + +# For comparison: When noise_learn is set to false, the observational noise +# is set to 1.0 and is not learned/optimized during the training. But thanks +# to the SVD, 1.0 is the correct value to use. +gauss_proc_2 = GaussianProcess( + gppackage; + kernel=nothing, # use default squared exponential kernel + prediction_type=prediction_type, + noise_learn=false +) +emulator_2 = Emulator( + gauss_proc_2, + iopairs, + obs_noise_cov=Σ, + normalize_inputs=true +) +println("build GP with ", n, " training points") +#optimize the hyperparameters to best fit the GP. +optimize_hyperparameters!(emulator_2) +println("GP trained") + +println("\n-----------") +println("Results of training Gaussian Process models with noise_learn=false") +println("-----------") + +println("\nKernel of the GP trained to predict y1 from x=(x1, x2):") +# Note: In contrast to the kernels of the gpobj1 models, these ones do not +# have a white noise ("Noise") kernel component +println(emulator_2.machine_learning_tool.models[1].kernel) +# logNoise is given as log(sqrt(noise)) +obs_noise_1 = exp(emulator_2.machine_learning_tool.models[1].logNoise.value^2) +println("Observational noise: $obs_noise_1") + +println("\nKernel of the GP trained to predict y1 from x=(x1, x2):") +println(emulator_2.machine_learning_tool.models[2].kernel) +# logNoise is given as log(sqrt(noise)) +obs_noise_2 = exp(emulator_2.machine_learning_tool.models[2].logNoise.value^2) +println("Observational noise: $obs_noise_2") +println("------------------------------------------------------------------") diff --git a/examples/Emulator/GaussianProcess/plot_GP.jl b/examples/Emulator/GaussianProcess/plot_GP.jl index b9eafb466..52d2d52e9 100644 --- a/examples/Emulator/GaussianProcess/plot_GP.jl +++ b/examples/Emulator/GaussianProcess/plot_GP.jl @@ -1,6 +1,6 @@ # Reference the in-tree version of CalibrateEmulateSample on Julias load path prepend!(LOAD_PATH, [joinpath(@__DIR__, "..", "..")]) -include(joinpath(@__DIR__, "..", "ci", "linkfig.jl")) +include(joinpath(@__DIR__, "..", "..", "ci", "linkfig.jl")) # Import modules using Random @@ -115,13 +115,13 @@ if plot_flag figpath = joinpath(output_directory, "GP_test_observed_y2nonoise.png") savefig(figpath) - p1 = plot(X[1,:], X[2,:], Y[1,:], st=:surface, camera=(30, 60), c=:cividis, + p3 = plot(X[1,:], X[2,:], Y[1,:], st=:surface, camera=(30, 60), c=:cividis, xlabel="x1", ylabel="x2", zguidefontrotation=90) figpath = joinpath(output_directory, "GP_test_observed_y1.png") savefig(figpath) - p2 = plot(X[1,:], X[2,:], Y[2,:], st=:surface, camera=(30, 60), c=:cividis, + p4 = plot(X[1,:], X[2,:], Y[2,:], st=:surface, camera=(30, 60), c=:cividis, xlabel="x1", ylabel="x2", zguidefontrotation=90) figpath = joinpath(output_directory, "GP_test_observed_y2.png") @@ -182,17 +182,17 @@ for y_i in 1:d mean_grid = reshape(gp_mean[y_i, :], n_pts, n_pts) # 2 x 40000 if plot_flag - p1 = plot(x1, x2, mean_grid, st=:surface, camera=(30, 60), c=:cividis, + p5 = plot(x1, x2, mean_grid, st=:surface, camera=(30, 60), c=:cividis, xlabel="x1", ylabel="x2", zlabel="mean of y"*string(y_i), zguidefontrotation=90) end var_grid = reshape(gp_var[y_i, :], n_pts, n_pts) if plot_flag - p2 = plot(x1, x2, var_grid, st=:surface, camera=(30, 60), c=:cividis, + p6 = plot(x1, x2, var_grid, st=:surface, camera=(30, 60), c=:cividis, xlabel="x1", ylabel="x2", zlabel="var of y"*string(y_i), zguidefontrotation=90) - plot(p1, p2, layout=(1, 2), legend=false) + plot(p5, p6, layout=(1, 2), legend=false) savefig(joinpath(output_directory, "GP_test_y"*string(y_i)*"_predictions.png")) end @@ -202,7 +202,7 @@ end g1_true = sin.(inputs[1,:]) .+ cos.(inputs[2, :]) g1_true_grid = reshape(g1_true, n_pts, n_pts) if plot_flag - p3 = plot(x1, x2, g1_true_grid, st=:surface, camera=(30, 60), c=:cividis, + p7 = plot(x1, x2, g1_true_grid, st=:surface, camera=(30, 60), c=:cividis, xlabel="x1", ylabel="x2", zlabel="sin(x1) + cos(x2)", zguidefontrotation=90) savefig(joinpath(output_directory, "GP_test_true_g1.png")) @@ -211,7 +211,7 @@ end g2_true = sin.(inputs[1, :]) .- cos.(inputs[2, :]) g2_true_grid = reshape(g2_true, n_pts, n_pts) if plot_flag - p4 = plot(x1, x2, g2_true_grid, st=:surface, camera=(30, 60), c=:cividis, + p8 = plot(x1, x2, g2_true_grid, st=:surface, camera=(30, 60), c=:cividis, xlabel="x1", ylabel="x2", zlabel="sin(x1) - cos(x2)", zguidefontrotation=90) g_true_grids = [g1_true_grid, g2_true_grid] @@ -234,7 +234,7 @@ for y_i in 1:d if plot_flag zlabel = "1/var * (true_y"*string(y_i)*" - predicted_y"*string(y_i)*")^2" - p5 = plot(x1, x2, sqrt.(1.0 ./ var_grid .* (g_true_grids[y_i] .- mean_grid).^2), + p9 = plot(x1, x2, sqrt.(1.0 ./ var_grid .* (g_true_grids[y_i] .- mean_grid).^2), st=:surface, camera=(30, 60), c=:magma, zlabel=zlabel, xlabel="x1", ylabel="x2", zguidefontrotation=90) diff --git a/examples/Lorenz/Lorenz_example.jl b/examples/Lorenz/Lorenz_example.jl index 1e4e759f0..26b832e20 100644 --- a/examples/Lorenz/Lorenz_example.jl +++ b/examples/Lorenz/Lorenz_example.jl @@ -15,7 +15,7 @@ using Random using JLD2 # CES -using CalibrateEmulateSample.GaussianProcessEmulator +using CalibrateEmulateSample.Emulators using CalibrateEmulateSample.MarkovChainMonteCarlo using CalibrateEmulateSample.Utilities using CalibrateEmulateSample.EnsembleKalmanProcessModule @@ -208,8 +208,7 @@ else Γy = cov(yt, dims=2) println(Γy) - println(size(Γy)) - println(rank(Γy)) + println(size(Γy), " ", rank(Γy)) end @@ -280,8 +279,14 @@ end standardize = true truncate_svd = 0.95 -gppackage = GaussianProcessEmulator.GPJL() -pred_type = GaussianProcessEmulator.YType() +gppackage = Emulators.GPJL() +pred_type = Emulators.YType() +gauss_proc = GaussianProcess( + gppackage; + kernel=nothing, # use default squared exponential kernel + prediction_type=pred_type, + noise_learn=false +) # Standardize the output data # Use median over all data since all data are the same type @@ -297,24 +302,26 @@ println(norm_factor) N_iter = 5; input_output_pairs = Utilities.get_training_points(ekiobj, N_iter) normalized = true - -# Default kernel -gpobj = GaussianProcessEmulator.GaussianProcess(input_output_pairs, gppackage; - obs_noise_cov=Γy, normalized=normalized, - noise_learn=false, - truncate_svd=truncate_svd, standardize=standardize, - prediction_type=pred_type, - norm_factor=norm_factor) +emulator = Emulator( + gauss_proc, + input_output_pairs; + obs_noise_cov=Γy, + normalize_inputs=normalized, + standardize_outputs=standardize, + standardize_outputs_factors=norm_factor, + truncate_svd=truncate_svd +) +optimize_hyperparameters!(emulator) # Check how well the Gaussian Process regression predicts on the # true parameters #if truncate_svd==1.0 if log_normal==false - y_mean, y_var = GaussianProcessEmulator.predict(gpobj, reshape(params_true, :, 1), - transform_to_real=true) + y_mean, y_var = Emulators.predict(emulator, reshape(params_true, :, 1), + transform_to_real=true) else - y_mean, y_var = GaussianProcessEmulator.predict(gpobj, reshape(log.(params_true), :, 1), - transform_to_real=true) + y_mean, y_var = Emulators.predict(emulator, reshape(log.(params_true), :, 1), + transform_to_real=true) end println("GP prediction on true parameters: ") @@ -322,11 +329,7 @@ gpobj = GaussianProcessEmulator.GaussianProcess(input_output_pairs, gppackage; println(" GP variance") println(diag(y_var[1],0)) println("true data: ") - if standardize - println(truth.mean ./ norm_factor) - else - println(truth.mean) - end + println(truth.mean) # same, regardless of norm_factor println("GP MSE: ") println(mean((truth.mean - vec(y_mean)).^2)) #end @@ -347,11 +350,12 @@ burnin = 0 step = 0.1 # first guess max_iter = 2000 yt_sample = truth_sample -mcmc_test = MarkovChainMonteCarlo.MCMC(yt_sample, Γy, priors, step, u0, max_iter, - mcmc_alg, burnin; - svdflag=svd_flag, standardize=standardize, truncate_svd=truncate_svd, - norm_factor=norm_factor) -new_step = MarkovChainMonteCarlo.find_mcmc_step!(mcmc_test, gpobj, max_iter=max_iter) +mcmc_test = MarkovChainMonteCarlo.MCMC( + yt_sample, Γy, priors, step, u0, max_iter, mcmc_alg, burnin; + svdflag=svd_flag, standardize=standardize, truncate_svd=truncate_svd, + norm_factor=norm_factor +) +new_step = MarkovChainMonteCarlo.find_mcmc_step!(mcmc_test, emulator, max_iter=max_iter) # Now begin the actual MCMC println("Begin MCMC - with step size ", new_step) @@ -360,11 +364,12 @@ println("Begin MCMC - with step size ", new_step) burnin = 2000 max_iter = 100000 -mcmc = MarkovChainMonteCarlo.MCMC(yt_sample, Γy, priors, new_step, u0, max_iter, - mcmc_alg, burnin; - svdflag=svd_flag, standardize=standardize, truncate_svd=truncate_svd, - norm_factor=norm_factor) -MarkovChainMonteCarlo.sample_posterior!(mcmc, gpobj, max_iter) +mcmc = MarkovChainMonteCarlo.MCMC( + yt_sample, Γy, priors, new_step, u0, max_iter, mcmc_alg, burnin; + svdflag=svd_flag, standardize=standardize, truncate_svd=truncate_svd, + norm_factor=norm_factor +) +MarkovChainMonteCarlo.sample_posterior!(mcmc, emulator, max_iter) println("Posterior size") println(size(mcmc.posterior)) diff --git a/examples/Lorenz/Manifest.toml b/examples/Lorenz/Manifest.toml index 73976a39e..a87262e93 100644 --- a/examples/Lorenz/Manifest.toml +++ b/examples/Lorenz/Manifest.toml @@ -8,9 +8,12 @@ version = "0.5.0" [[Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "ffcfa2d345aaee0ef3d8346a073d5dd03c983ebe" +git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.2.0" +version = "3.3.3" + +[[ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[Arpack]] deps = ["Arpack_jll", "Libdl", "LinearAlgebra"] @@ -25,61 +28,46 @@ uuid = "68821587-b530-5797-8361-c406ea357684" version = "3.5.0+3" [[ArrayInterface]] -deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays"] -git-tree-sha1 = "ee07ae00e3cc277dcfa5507ce25be522313ecc3e" +deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] +git-tree-sha1 = "1ee88c4c76caa995a885dc2f22a5d548dfbbc0ba" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.1" - -[[ArrayLayouts]] -deps = ["Compat", "FillArrays", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "a577e27915fdcb3f6b96118b56655b38e3b466f2" -uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "0.4.12" +version = "3.2.2" [[Artifacts]] -deps = ["Pkg"] -git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744" uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.3.0" [[AxisAlgorithms]] deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] -git-tree-sha1 = "a4d07a1c313392a77042855df46c5f534076fab9" +git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7" uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" -version = "1.0.0" +version = "1.0.1" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e" +git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.6+5" +version = "1.0.8+0" [[Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "e2f47f6d8337369411569fd45ae5753ca10394c6" +git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.16.0+6" - -[[CategoricalArrays]] -deps = ["DataAPI", "Future", "JSON", "Missings", "Printf", "Statistics", "StructTypes", "Unicode"] -git-tree-sha1 = "dbfddfafb75fae5356e00529ce67454125935945" -uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" -version = "0.9.3" - -[[ChainRules]] -deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"] -git-tree-sha1 = "e01f521443e3700f40ad3c7c1c6aa3a6940aaea1" -uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "0.7.54" +version = "1.16.1+1" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "de4f08843c332d355852721adb1592bce7924da3" +git-tree-sha1 = "926870acb6cbcf029396f2f2de030282b6bc1941" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "0.9.29" +version = "1.11.4" + +[[ChangesOfVariables]] +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.2" [[Clustering]] deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "SparseArrays", "Statistics", "StatsBase"] @@ -87,29 +75,23 @@ git-tree-sha1 = "75479b7df4167267d75294d14b58244695beb2ac" uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" version = "0.14.2" -[[CodecZlib]] -deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" -uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.0" - [[ColorSchemes]] -deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"] -git-tree-sha1 = "3141757b5832ee7a0386db87997ee5a23ff20f4d" +deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] +git-tree-sha1 = "a851fec56cb73cfdf43762999ec72eff5b86882a" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.10.2" +version = "3.15.0" [[ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "32a2b8af383f11cbb65803883837a149d10dfe8a" +git-tree-sha1 = "024fe24d83e4a5bf5fc80501a314ce0d1aa35597" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.10.12" +version = "0.11.0" [[Colors]] -deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Reexport"] -git-tree-sha1 = "ac5f2213e56ed8a34a3dd2f681f4df1166b34929" +deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] +git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.6" +version = "0.12.8" [[CommonSubexpressions]] deps = ["MacroTools", "Test"] @@ -119,21 +101,19 @@ version = "0.3.0" [[Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "919c7f3151e79ff196add81d7f4e45d91bbf420b" +git-tree-sha1 = "44c37b4636bc54afac5c574d2d02b625349d6582" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.25.0" +version = "3.41.0" [[CompilerSupportLibraries_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "8e695f735fca77e9708e795eda62afdb869cbb70" +deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.3.4+0" [[Conda]] -deps = ["JSON", "VersionParsing"] -git-tree-sha1 = "6231e40619c15148bcb80aa19d731e629877d762" +deps = ["Downloads", "JSON", "VersionParsing"] +git-tree-sha1 = "6cdc8832ba11c7695f494c9d9a1c31e90959ce0f" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" -version = "1.5.1" +version = "1.6.0" [[Contour]] deps = ["StaticArrays"] @@ -141,33 +121,27 @@ git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" version = "0.5.7" -[[CpuId]] -deps = ["Markdown", "Test"] -git-tree-sha1 = "f0464e499ab9973b43c20f8216d088b61fda80c6" -uuid = "adafc99b-e345-5852-983c-f28acb93d879" -version = "0.2.2" - [[Crayons]] -git-tree-sha1 = "3f71217b538d7aaee0b69ab47d9b7724ca8afa0d" +git-tree-sha1 = "b618084b49e78985ffa8422f32b9838e397b9fc2" uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" -version = "4.0.4" +version = "4.1.0" [[DataAPI]] -git-tree-sha1 = "dfb3b7e89e395be1e25c2ad6d7690dc29cc53b1d" +git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.6.0" +version = "1.9.0" [[DataFrames]] -deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "b0db5579803eabb33f1274ca7ca2f472fdfb7f2a" +deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "cfdfef912b7f93e4b848e80b9befdf9e331bc05a" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "0.22.5" +version = "1.3.1" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677" +git-tree-sha1 = "3daef5523dd2e769dad2365274f760ff5f282c7d" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.9" +version = "0.18.11" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -195,16 +169,16 @@ uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" version = "1.0.3" [[DiffRules]] -deps = ["NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "214c3fcac57755cfda163d91c58893a8723f93e9" +deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "9bc5dac3c8b6706b58ad5ce24cffd9861f07c94f" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.0.2" +version = "1.9.0" [[Distances]] -deps = ["LinearAlgebra", "Statistics"] -git-tree-sha1 = "366715149014943abd71aa647a07a43314158b2d" +deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.2" +version = "0.10.7" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -212,27 +186,31 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "e64debe8cd174cc52d7dd617ebc5492c6f8b698c" +git-tree-sha1 = "a837fdf80f333415b69684ba8e8ae6ba76de6aaa" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.24.15" +version = "0.24.18" [[DocStringExtensions]] -deps = ["LibGit2", "Markdown", "Pkg", "Test"] -git-tree-sha1 = "9d4f64f79012636741cf01133158a54b24924c32" +deps = ["LibGit2"] +git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.4" +version = "0.8.6" + +[[Downloads]] +deps = ["ArgTools", "LibCURL", "NetworkOptions"] +uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" [[EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "92d8f9f208637e8d2d28c664051a00569c01493d" +git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d" uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.1.5+1" +version = "2.2.3+0" [[ElasticArrays]] deps = ["Adapt"] -git-tree-sha1 = "395e36b5962bd11bf080f4fe06546cd26a34e0d8" +git-tree-sha1 = "a0fcc1bb3c9ceaf07e1d0529c9806ce94be6adf9" uuid = "fdbdab4c-e67f-52f5-8c3f-e7b388dad3d4" -version = "1.2.6" +version = "1.2.9" [[ElasticPDMats]] deps = ["LinearAlgebra", "MacroTools", "PDMats"] @@ -242,21 +220,21 @@ version = "0.2.2" [[Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "1402e52fcda25064f51c77a9655ce8680b76acf0" +git-tree-sha1 = "b3bfd02e98aedfa5cf885665493c5598c350cd2f" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.2.7+6" +version = "2.2.10+0" [[FFMPEG]] -deps = ["FFMPEG_jll", "x264_jll"] -git-tree-sha1 = "9a73ffdc375be61b0e4516d83d880b265366fe1f" +deps = ["FFMPEG_jll"] +git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.0" +version = "0.4.1" [[FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "LibVPX_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "3cc57ad0a213808473eafef4845a74766242e05f" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "d8a578692e3077ac998b50c0217dfd67f21d1e5f" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.3.1+4" +version = "4.4.0+0" [[FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "IntelOpenMP_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Reexport"] @@ -266,27 +244,33 @@ version = "1.3.0" [[FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "5a0d4b6a22a34d17d53543bd124f4b08ed78e8b0" +git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.9+7" +version = "3.3.10+0" [[FastGaussQuadrature]] deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "5829b25887e53fb6730a9df2ff89ed24baa6abf6" +git-tree-sha1 = "58d83dd5a78a36205bdfddb82b1bb67682e64487" uuid = "442a2c76-b920-505d-bb47-c5924d526838" -version = "0.4.7" +version = "0.4.9" + +[[FileIO]] +deps = ["Pkg", "Requires", "UUIDs"] +git-tree-sha1 = "67551df041955cc6ee2ed098718c8fcd7fc7aebe" +uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" +version = "1.12.0" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "ff537e5a3cba92fb48f30fec46723510450f2c0e" +git-tree-sha1 = "693210145367e7685d8604aee33d9bfb85db8b31" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.10.2" +version = "0.11.9" [[FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "f6f80c8f934efd49a286bb5315360be66956dfc4" +git-tree-sha1 = "8b3c09b56acaf3c0e581c66638b85c8650ee9dca" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.8.0" +version = "2.8.1" [[FixedPointNumbers]] deps = ["Statistics"] @@ -296,9 +280,9 @@ version = "0.8.4" [[Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "35895cf184ceaab11fd778b4590144034a167a2f" +git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.1+14" +version = "2.13.93+0" [[Formatting]] deps = ["Printf"] @@ -307,22 +291,22 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "c68fb7481b71519d313114dca639b35262ff105f" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "2b72a5624e289ee18256111657663721d59c143e" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.17" +version = "0.10.24" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "cbd58c9deb1d304f5a245a0b7eb841a2560cfec6" +git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.10.1+5" +version = "2.10.4+0" [[FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0d20aed5b14dd4c9a2453c1b601d08e1149679cc" +git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.5+6" +version = "1.0.10+0" [[Future]] deps = ["Random"] @@ -330,50 +314,56 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "bd1dbf065d7a4a0bdf7e74dd26cf932dda22b929" +git-tree-sha1 = "0c603255764a1fa0b61752d2bec14cfbd18f7fe8" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.3+0" +version = "3.3.5+1" [[GR]] -deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "12d971c928b7ecf19b748a2c7df6a365690dbf2c" +deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] +git-tree-sha1 = "b9a93bcdf34618031891ee56aad94cfff0843753" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.55.0" +version = "0.63.0" [[GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "8aee6fa096b0cbdb05e71750c978b96a08c78951" +deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "f97acd98255568c3c9b416c5a3cf246c1315771b" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.53.0+0" +version = "0.63.0+0" [[GaussianProcesses]] -deps = ["Distances", "Distributions", "ElasticArrays", "ElasticPDMats", "FastGaussQuadrature", "ForwardDiff", "LinearAlgebra", "Optim", "PDMats", "Printf", "ProgressMeter", "Random", "RecipesBase", "ScikitLearnBase", "SpecialFunctions", "StaticArrays", "Statistics", "StatsFuns", "Zygote"] -git-tree-sha1 = "06f890e71136832f1c577aa443d3777ffa9594fa" +deps = ["Distances", "Distributions", "ElasticArrays", "ElasticPDMats", "FastGaussQuadrature", "ForwardDiff", "LinearAlgebra", "Optim", "PDMats", "Printf", "ProgressMeter", "Random", "RecipesBase", "ScikitLearnBase", "SpecialFunctions", "StaticArrays", "Statistics", "StatsFuns"] +git-tree-sha1 = "9cf8ba8037e332b1be14c71e549143e68c42a22d" uuid = "891a1506-143c-57d2-908e-e1f8e92e6de9" -version = "0.12.3" +version = "0.12.4" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "c7f81b22b6c255861be4007a16bfdeb60e1c7f9b" +git-tree-sha1 = "58bcdf5ebc057b085e58d95c138725628dd7453c" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.3.11" +version = "0.4.1" [[Gettext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "8c14294a079216000a0bdca5ec5a447f073ddc9d" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] +git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" -version = "0.20.1+7" +version = "0.21.0+0" [[Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "04690cc5008b38ecbdfede949220bc7d9ba26397" +git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.59.0+4" +version = "2.68.3+2" + +[[Graphite2_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" +uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" +version = "1.3.14+0" [[Grisu]] -git-tree-sha1 = "03d381f65183cb2d0af8b3425fde97263ce9a995" +git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" -version = "1.0.0" +version = "1.0.2" [[HTTP]] deps = ["Base64", "Dates", "IniFile", "MbedTLS", "Sockets"] @@ -381,16 +371,16 @@ git-tree-sha1 = "c7ec02c4c6a039a98a15f955462cd7aea5df4508" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" version = "0.8.19" -[[IRTools]] -deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "c67e7515a11f726f44083e74f218d134396d6510" -uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.2" +[[HarfBuzz_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] +git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" +version = "2.8.1+1" [[IfElse]] -git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef" +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" -version = "0.1.0" +version = "0.1.1" [[IniFile]] deps = ["Test"] @@ -409,21 +399,31 @@ deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[Interpolations]] -deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "eb1dd6d5b2275faaaa18533e0fc5f9171cec25fa" +deps = ["AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] +git-tree-sha1 = "b15fc0a95c564ca2e0a7ae12c1f095ca848ceb31" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.1" +version = "0.13.5" -[[InvertedIndices]] +[[InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "15732c475062348b0165684ffe28e85ea8396afc" +git-tree-sha1 = "a7254c0acd8e62f1ac75ad24d5db43f5f19f3c65" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.2" + +[[InvertedIndices]] +git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.0.0" +version = "1.1.0" + +[[IrrationalConstants]] +git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" +version = "0.1.1" [[IterTools]] -git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" +git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.3.0" +version = "1.4.0" [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -431,81 +431,88 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[JLD2]] -deps = ["CodecZlib", "DataStructures", "MacroTools", "Mmap", "Pkg", "Printf", "Requires", "UUIDs"] -git-tree-sha1 = "9f2f2f24e60305feb6ae293a617ddf06f429efc3" +deps = ["DataStructures", "FileIO", "MacroTools", "Mmap", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "09ef0c32a26f80b465d808a1ba1e85775a282c97" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.3" +version = "0.4.17" [[JLLWrappers]] -git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0" +deps = ["Preferences"] +git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.2.0" +version = "1.3.0" [[JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4" +git-tree-sha1 = "8076680b162ada2a031f707ac7b4953e30667a37" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.1" +version = "0.21.2" [[JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9aff0587d9603ea0de2c6f6300d9f9492bbefbd3" +git-tree-sha1 = "d735490ac75c5cb9f1b00d8b5509c11984dc6943" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.0.1+3" +version = "2.1.0+0" [[KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "09aeec87bdc9c1fa70d0b508dfa94a21acd280d9" +git-tree-sha1 = "591e8dc09ad18386189610acafb970032c519707" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.2" +version = "0.6.3" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "df381151e871f41ee86cee4f5f6fd598b8a68826" +git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.0+3" +version = "3.100.1+0" [[LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f128cd6cd05ffd6d3df0523ed99b90ff6f9b349a" +git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.0+3" +version = "2.10.1+0" [[LaTeXStrings]] -git-tree-sha1 = "c7f1c695e06c01b95a67f0cd1d34994f3e7db104" +git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.2.1" +version = "1.3.0" [[Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "fbc08b5a78e264ba3d19da90b36ce1789ca67a40" +git-tree-sha1 = "a8f4f279b6fa3c3c4f1adadd78a621b13a506bce" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.14.11" +version = "0.15.9" + +[[LibCURL]] +deps = ["LibCURL_jll", "MozillaCACerts_jll"] +uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" + +[[LibCURL_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] +uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" [[LibGit2]] -deps = ["Printf"] +deps = ["Base64", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -[[LibVPX_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "85fcc80c3052be96619affa2fe2e6d2da3908e11" -uuid = "dd192d2f-8180-539f-9fb4-cc70b1dcf69a" -version = "1.9.0+1" +[[LibSSH2_jll]] +deps = ["Artifacts", "Libdl", "MbedTLS_jll"] +uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" [[Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" [[Libffi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "a2cd088a88c0d37eef7d209fd3d8712febce0d90" +git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" -version = "3.2.1+4" +version = "3.2.2+1" [[Libgcrypt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] -git-tree-sha1 = "b391a18ab1170a2e568f9fb8d83bc7c780cb9999" +git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.5+4" +version = "1.8.7+0" [[Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -515,33 +522,33 @@ version = "1.3.0+3" [[Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ec7f2e8ad5c9fa99fc773376cdbc86d9a5a23cb7" +git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.36.0+3" +version = "1.42.0+0" [[Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "8e924324b2e9275a51407a4e06deb3455b1e359f" +git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.0+7" +version = "1.16.1+1" [[Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "51ad0c01c94c1ce48d5cad629425035ad030bfd5" +git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.34.0+3" +version = "2.35.0+0" [[Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "291dd857901f94d683973cdf679984cdf73b56d0" +git-tree-sha1 = "340e257aada13f95f98ee352d316c3bed37c8ab9" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.1.0+2" +version = "4.3.0+0" [[Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f879ae9edbaa2c74c922e8b85bb83cc84ea1450b" +git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.34.0+7" +version = "2.36.0+0" [[LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] @@ -553,15 +560,15 @@ version = "7.1.1" deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[LogExpFunctions]] +deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "e5718a00af0ab9756305a0392832c8952c7426c1" +uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +version = "0.3.6" + [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -[[LoopVectorization]] -deps = ["DocStringExtensions", "LinearAlgebra", "OffsetArrays", "SIMDPirates", "SLEEFPirates", "UnPack", "VectorizationBase"] -git-tree-sha1 = "3242a8f411e19eda9adc49d0b877681975c11375" -uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.8.26" - [[MKL_jll]] deps = ["IntelOpenMP_jll", "Libdl", "Pkg"] git-tree-sha1 = "eb540ede3aabb8284cb482aa41d00d6ca850b1f8" @@ -570,9 +577,9 @@ version = "2020.2.254+0" [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "6a8a2a625ab0dea913aba95c11370589e0239ff0" +git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.6" +version = "0.5.9" [[Markdown]] deps = ["Base64"] @@ -585,10 +592,8 @@ uuid = "739be429-bea8-5141-9913-cc70e7f3736d" version = "1.0.3" [[MbedTLS_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0eef589dd1c26a3ac9d753fe1a8bcad63f956fa6" +deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.16.8+1" [[Measures]] git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f" @@ -597,13 +602,16 @@ version = "0.3.1" [[Missings]] deps = ["DataAPI"] -git-tree-sha1 = "f8c673ccc215eb50fcadb285f522420e29e69e1c" +git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "0.4.5" +version = "1.0.2" [[Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" +[[MozillaCACerts_jll]] +uuid = "14a3606d-f60d-562e-9121-12d972cd8159" + [[MultivariateStats]] deps = ["Arpack", "LinearAlgebra", "SparseArrays", "Statistics", "StatsBase"] git-tree-sha1 = "8d958ff1854b166003238fe191ec34b9d592860a" @@ -612,84 +620,83 @@ version = "0.8.0" [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "50608f411a1e178e0129eab4110bd56efd08816f" +git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.0" - -[[NNlib]] -deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "ab1d43fead2ecb9aa5ae460d3d547c2cf8d89461" -uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.7.17" +version = "7.8.2" [[NaNMath]] -git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" +git-tree-sha1 = "f755f36b19a5116bb580de457cda0c140153f283" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.5" +version = "0.3.6" [[NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "9afd724797039125e8e2cc362098f01dab60bc3a" +git-tree-sha1 = "16baacfdc8758bc374882566c9187e785e85c2f0" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.8" +version = "0.4.9" + +[[NetworkOptions]] +uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" [[Observables]] -git-tree-sha1 = "3469ef96607a6b9a1e89e54e6f23401073ed3126" +git-tree-sha1 = "fe29afdef3d0c4a8286128d4e45cc50621b1e43d" uuid = "510215fc-4207-5dde-b226-833fc4488ee2" -version = "0.3.3" +version = "0.4.0" [[OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "b3dfef5f2be7d7eb0e782ba9146a5271ee426e90" +git-tree-sha1 = "043017e0bdeff61cfbb7afeb558ab29536bbb5ed" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.6.2" +version = "1.10.8" [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "a42c0f138b9ebe8b58eba2271c5053773bde52d0" +git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" -version = "1.3.4+2" +version = "1.3.5+1" [[OpenBLAS_jll]] -deps = ["CompilerSupportLibraries_jll", "Libdl", "Pkg"] -git-tree-sha1 = "0c922fd9634e358622e333fc58de61f05a048492" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.9+5" + +[[OpenLibm_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "05823500-19ac-5b8b-9628-191a04bc5112" [[OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "71bbbc616a1d710879f5a1021bcba65ffba6ce58" +git-tree-sha1 = "15003dcb7d8db3c6c857fda14891a539a8f2705a" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.1+6" +version = "1.1.10+0" [[OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9db77584158d0ab52307f8c04f8e7c08ca76b5b3" +git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" -version = "0.5.3+4" +version = "0.5.5+0" [[Optim]] -deps = ["Compat", "FillArrays", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "d34366a3abc25c41f88820762ef7dfdfe9306711" +deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] +git-tree-sha1 = "916077e0f0f8966eb0dc98a5c39921fdb8f49eb4" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.3.0" +version = "1.6.0" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f9d57f4126c39565e05a2b0264df99f497fc6f37" +git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" uuid = "91d4177d-7536-5919-b921-800302f37372" -version = "1.3.1+3" +version = "1.3.2+0" [[OrderedCollections]] -git-tree-sha1 = "4fa2ba51070ec13fcc7517db714445b4ab986bdf" +git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.0" +version = "1.4.1" [[PCRE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "1b556ad51dceefdbf30e86ffa8f528b73c7df2bb" +git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc" -version = "8.42.0+4" +version = "8.44.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"] @@ -699,24 +706,24 @@ version = "0.10.1" [[Parameters]] deps = ["OrderedCollections", "UnPack"] -git-tree-sha1 = "2276ac65f1e236e0a6ea70baff3f62ad4c625345" +git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" -version = "0.12.2" +version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc" +git-tree-sha1 = "d7fa6237da8004be601e19bd6666083056649918" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "1.1.0" +version = "2.1.3" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6a20a83c1ae86416f0a5de605eaea08a552844a3" +git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.40.0+0" +version = "0.40.1+0" [[Pkg]] -deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"] +deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" [[PlotThemes]] @@ -727,21 +734,21 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "ae9a295ac761f64d8c2ec7f9f24d21eb4ffba34d" +git-tree-sha1 = "68604313ed59f0408313228ba09e79252e4b2da8" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.10" +version = "1.1.2" [[Plots]] -deps = ["Base64", "Contour", "Dates", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"] -git-tree-sha1 = "40031283dbb5ae602aa132f423daedfc18c82069" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] +git-tree-sha1 = "71d65e9242935132e71c4fbf084451579491166a" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.11.0" +version = "1.25.4" [[PooledArrays]] deps = ["DataAPI", "Future"] -git-tree-sha1 = "cde4ce9d6f33219465b55162811d8de8139c0414" +git-tree-sha1 = "db3a23166af8aebf4db5ef87ac5b00d36eb771e2" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" -version = "1.2.1" +version = "1.4.0" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -749,11 +756,17 @@ git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" +[[Preferences]] +deps = ["TOML"] +git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af" +uuid = "21216c6a-2e73-6563-6e65-726566657250" +version = "1.2.3" + [[PrettyTables]] deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] -git-tree-sha1 = "574a6b3ea95f04e8757c0280bb9c29f1a5e35138" +git-tree-sha1 = "dfb54c4e414caa595a1f2ed759b160f5a3ddcba5" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "0.11.1" +version = "1.3.1" [[Printf]] deps = ["Unicode"] @@ -761,30 +774,30 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" [[ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "6e9c89cba09f6ef134b00e10625590746ba1e036" +git-tree-sha1 = "afadeba63d90ff223a6a48d2009434ecee2ec9e8" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.5.0" +version = "1.7.1" [[PyCall]] deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"] -git-tree-sha1 = "dd1a970b543bd02efce2984582e996af28cab27f" +git-tree-sha1 = "71fd4022ecd0c6d20180e23ff1b3e05a143959c2" uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" -version = "1.92.2" +version = "1.93.0" -[[Qt_jll]] +[[Qt5Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] -git-tree-sha1 = "588b799506f0b956a7e6e18f767dfa03cf333f26" -uuid = "ede63266-ebff-546c-83e0-1c6fb6d0efc8" -version = "5.15.2+2" +git-tree-sha1 = "ad368663a5e20dbb8d6dc2fddeefe4dae0781ae8" +uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" +version = "5.15.3+0" [[QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "12fbe86da16df6679be7521dfb39fbc861e1dc7b" +git-tree-sha1 = "78aadffb3efd2155af139781b8a8df1ef279ea39" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.4.1" +version = "2.4.2" [[REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets"] +deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[Random]] @@ -792,64 +805,53 @@ deps = ["Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[Ratios]] -git-tree-sha1 = "37d210f612d70f3f7d57d488cb3b6eff56ad4e41" +deps = ["Requires"] +git-tree-sha1 = "01d341f502250e81f6fec0afe662aa861392a3aa" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.0" +version = "0.4.2" [[RecipesBase]] -git-tree-sha1 = "b3fb709f3c97bfc6e948be68beeecb55a0b340ae" +git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.1.1" +version = "1.2.1" [[RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] -git-tree-sha1 = "c4d54a78e287de7ec73bbc928ce5eb3c60f80b24" +git-tree-sha1 = "7ad0dfa8d03b7bcf8c597f59f5292801730c55b8" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.3.1" +version = "0.4.1" [[Reexport]] -git-tree-sha1 = "57d8440b0c7d98fc4f889e478e80f268d534c9d5" +git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" -version = "1.0.0" +version = "1.2.2" [[Requires]] deps = ["UUIDs"] -git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621" +git-tree-sha1 = "8f82019e525f4d5c669692772a6f4b0a58b06a6a" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.1.3" +version = "1.2.0" [[Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "86c5647b565873641538d8f812c04e4c9dbeb370" +git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.6.1" +version = "0.7.0" [[Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "1b7bf41258f6c5c9c31df8c1ba34c1fc88674957" +git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.2.2+2" +version = "0.3.0+0" [[SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" -[[SIMDPirates]] -deps = ["VectorizationBase"] -git-tree-sha1 = "a1b418634d6478bf2163920eae3b536dcc768626" -uuid = "21efa798-c60a-11e8-04d3-e1a92915a26a" -version = "0.8.26" - -[[SLEEFPirates]] -deps = ["Libdl", "SIMDPirates", "VectorizationBase"] -git-tree-sha1 = "67ae90a18aa8c22bf159318300e765fbd89ddf6e" -uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.5.5" - [[ScikitLearn]] deps = ["Compat", "Conda", "DataFrames", "Distributed", "IterTools", "LinearAlgebra", "MacroTools", "Parameters", "Printf", "PyCall", "Random", "ScikitLearnBase", "SparseArrays", "StatsBase", "VersionParsing"] -git-tree-sha1 = "bf4c558a0d0f1129b23e80f1ca772a9db457df4d" +git-tree-sha1 = "ccb822ff4222fcf6ff43bbdbd7b80332690f168e" uuid = "3646fa90-6ef7-5e7e-9f22-8aca16db6324" -version = "0.6.3" +version = "0.6.4" [[ScikitLearnBase]] deps = ["LinearAlgebra", "Random", "Statistics"] @@ -859,15 +861,15 @@ version = "0.5.0" [[Scratch]] deps = ["Dates"] -git-tree-sha1 = "ad4b278adb62d185bbcb6864dc24959ab0627bf6" +git-tree-sha1 = "0b4b7f1393cff97c33891da2a0bf69c6ed241fda" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.0.3" +version = "1.1.0" [[SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "6ccde405cf0759eba835eb613130723cb8f10ff9" +git-tree-sha1 = "244586bc07462d22aed0113af9c731f2a518c93e" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.2.16" +version = "1.3.10" [[Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -878,100 +880,113 @@ uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" [[Showoff]] deps = ["Dates", "Grisu"] -git-tree-sha1 = "ee010d8f103468309b8afac4abb9be2e18ff1182" +git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" -version = "0.3.2" +version = "1.0.3" [[Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[SortingAlgorithms]] -deps = ["DataStructures", "Random", "Test"] -git-tree-sha1 = "03f5898c9959f8115e30bc7226ada7d0df554ddd" +deps = ["DataStructures"] +git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "0.3.1" +version = "1.0.1" [[SparseArrays]] deps = ["LinearAlgebra", "Random"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SpecialFunctions]] -deps = ["ChainRulesCore", "OpenSpecFun_jll"] -git-tree-sha1 = "5919936c0e92cff40e57d0ddf0ceb667d42e5902" +deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "f0bccf98e16759818ffc5d97ac3ebf87eb950150" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "1.3.0" +version = "1.8.1" + +[[Static]] +deps = ["IfElse"] +git-tree-sha1 = "7f5a513baec6f122401abfc8e9c074fdac54f6c1" +uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" +version = "0.4.1" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "9da72ed50e94dbff92036da395275ed114e04d49" +git-tree-sha1 = "88a559da57529581472320892576a486fa2377b9" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.0.1" +version = "1.3.1" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +[[StatsAPI]] +git-tree-sha1 = "d88665adc9bcf45903013af0982e2fd05ae3d0a6" +uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" +version = "1.2.0" + [[StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"] -git-tree-sha1 = "a83fa3021ac4c5a918582ec4721bc0cf70b495a9" +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "51383f2d367eb3b444c961d485c565e4c0cf4ba0" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.4" +version = "0.33.14" [[StatsFuns]] -deps = ["Rmath", "SpecialFunctions"] -git-tree-sha1 = "3b9f665c70712af3264b61c27a7e1d62055dafd1" +deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "bedb3e17cc1d94ce0e6e66d3afa47157978ba404" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.6" +version = "0.9.14" [[StatsPlots]] deps = ["Clustering", "DataStructures", "DataValues", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] -git-tree-sha1 = "7c88f73b759ae16a4a1af8bda7a9563471a7baf5" +git-tree-sha1 = "e1e5ed9669d5521d4bbdd4fab9f0945a0ffceba2" uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" -version = "0.14.19" +version = "0.14.30" [[StructArrays]] -deps = ["Adapt", "DataAPI", "Tables"] -git-tree-sha1 = "26ea43b4be7e919a2390c3c0f824e7eb4fc19a0a" +deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] +git-tree-sha1 = "2ce41e0d042c60ecd131e9fb7154a3bfadbf50d3" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.5.0" - -[[StructTypes]] -deps = ["Dates", "UUIDs"] -git-tree-sha1 = "89b390141d2fb2ef3ac2dc32e336f7a5c4810751" -uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" -version = "1.5.0" +version = "0.6.3" [[SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" +[[TOML]] +deps = ["Dates"] +uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" + [[TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] -git-tree-sha1 = "a7cf690d0ac3f5b53dd09b5d613540b230233647" +git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1" uuid = "ab02a1b2-a7df-11e8-156e-fb1833f50b87" -version = "1.0.0" +version = "1.2.0" [[TableTraits]] deps = ["IteratorInterfaceExtensions"] -git-tree-sha1 = "b1ad568ba658d8cbb3b892ed5380a6f3e781a81e" +git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" -version = "1.0.0" +version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "a9ff3dfec713c6677af435d6a6d65f9744feef67" +git-tree-sha1 = "bb1064c9a84c52e277f1096cf41434b675cd368b" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.4.1" +version = "1.6.1" + +[[Tar]] +deps = ["ArgTools", "SHA"] +uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" [[Test]] -deps = ["Distributed", "InteractiveUtils", "Logging", "Random"] +deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c" +git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.5" +version = "0.9.6" [[UUIDs]] deps = ["Random", "SHA"] @@ -985,52 +1000,57 @@ version = "1.0.2" [[Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -[[VectorizationBase]] -deps = ["CpuId", "Libdl", "LinearAlgebra"] -git-tree-sha1 = "03e2fbb479a1ea350398195b6fbf439bae0f8260" -uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.12.33" +[[UnicodeFun]] +deps = ["REPL"] +git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" +uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" +version = "0.4.1" + +[[Unzip]] +git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" +uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" +version = "0.1.2" [[VersionParsing]] -git-tree-sha1 = "80229be1f670524750d905f8fc8148e5a8c4537f" +git-tree-sha1 = "e575cf85535c7c3292b4d89d89cc29e8c3098e47" uuid = "81def892-9a0e-5fdd-b105-ffc91e053289" -version = "1.2.0" +version = "1.2.1" [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "dc643a9b774da1c2781413fd7b6dcd2c56bb8056" +git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.17.0+4" +version = "1.19.0+0" [[Wayland_protocols_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll"] -git-tree-sha1 = "2839f1c1296940218e35df0bbb220f2a79686670" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "66d72dc6fcc86352f01676e8f0f698562e60510f" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.18.0+4" +version = "1.23.0+0" [[Widgets]] deps = ["Colors", "Dates", "Observables", "OrderedCollections"] -git-tree-sha1 = "fc0feda91b3fef7fe6948ee09bb628f882b49ca4" +git-tree-sha1 = "80661f59d28714632132c73779f8becc19a113f2" uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62" -version = "0.6.2" +version = "0.6.4" [[WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "59e2ad8fd1591ea019a5259bd012d7aee15f995c" +git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3" uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" -version = "0.5.3" +version = "0.5.5" [[XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "be0db24f70aae7e2b89f2f3092e93b8606d659a6" +git-tree-sha1 = "1acf5bdf07aa0907e0a37d3718bb88d4b687b74a" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.9.10+3" +version = "2.9.12+0" [[XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "2b3eac39df218762d2d005702d601cd44c997497" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.33+4" +version = "1.1.34+0" [[Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] @@ -1159,64 +1179,58 @@ uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" version = "1.4.0+3" [[Zlib_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "320228915c8debb12cb434c59057290f0834dbf6" +deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.11+18" [[Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "2c1332c54931e83f8f94d310fa447fd743e8d600" +git-tree-sha1 = "cc4bf3fdde8b7e3e9fa0351bdeedba1cf3b7f6e6" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.4.8+0" - -[[Zygote]] -deps = ["AbstractFFTs", "ArrayLayouts", "ChainRules", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "LoopVectorization", "MacroTools", "NNlib", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "18f758f28ca2c236e449be64e366e201965129a7" -uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.5.17" - -[[ZygoteRules]] -deps = ["MacroTools"] -git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.1" +version = "1.5.0+0" [[libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "acc685bcf777b2202a904cdcb49ad34c2fa1880c" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.14.0+4" +version = "0.15.1+0" [[libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7a5780a0d9c6864184b3a2eeeb833a0c871f00ab" +git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "0.1.6+4" +version = "2.0.2+0" [[libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "6abbc424248097d69c0c87ba50fcb0753f93e0ee" +git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.37+6" +version = "1.6.38+0" [[libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "fa14ac25af7a4b8a7f61b287a124df7aab601bcd" +git-tree-sha1 = "c45f4e40e7aafe9d086379e5578947ec8b95a8fb" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.6+6" +version = "1.3.7+0" + +[[nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" + +[[p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" [[x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d713c1ce4deac133e3334ee12f4adff07f81778f" +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2020.7.14+2" +version = "2021.5.5+0" [[x265_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "487da2f8f2f0c8ee0e83f39d13037d6bbf0a45ab" +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.0.0+3" +version = "3.5.0+0" [[xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] diff --git a/examples/Lorenz/Project.toml b/examples/Lorenz/Project.toml index f79d7ed84..3fa5d84f9 100644 --- a/examples/Lorenz/Project.toml +++ b/examples/Lorenz/Project.toml @@ -12,4 +12,5 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" [compat] +julia = "~1.6" FFTW = "= 1.3.0" diff --git a/src/Emulator.jl b/src/Emulator.jl index fd82462b4..44b9676bb 100644 --- a/src/Emulator.jl +++ b/src/Emulator.jl @@ -93,7 +93,7 @@ function Emulator( # For Consistency checks input_dim, output_dim = size(input_output_pairs, 1) - if obs_noise_cov != nothing + if obs_noise_cov !== nothing err2 = "obs_noise_cov must be of size ($output_dim, $output_dim), got $(size(obs_noise_cov))" size(obs_noise_cov) == (output_dim, output_dim) || throw(ArgumentError(err2)) end @@ -184,15 +184,14 @@ function predict(emulator::Emulator{FT}, new_inputs; transform_to_real=false) wh ds_outputs, ds_output_var = predict(emulator.machine_learning_tool, normalized_new_inputs) # [3.] transform back to real coordinates or remain in decorrelated coordinates - if transform_to_real && emulator.decomposition == nothing + if transform_to_real && emulator.decomposition === nothing throw(ArgumentError("""Need SVD decomposition to transform back to original space, but GaussianProcess.decomposition == nothing. Try setting transform_to_real=false""")) - elseif transform_to_real && emulator.decomposition != nothing + elseif transform_to_real && emulator.decomposition !== nothing #transform back to real coords - cov becomes dense s_outputs, s_output_cov = svd_reverse_transform_mean_cov( ds_outputs, ds_output_var, emulator.decomposition) - if output_dim == 1 s_output_cov = [s_output_cov[i][1] for i in 1:N_samples] end @@ -259,7 +258,7 @@ reverse a previous standardization with the stored vector of factors (size equal """ function reverse_standardize(emulator::Emulator{FT}, outputs, output_cov) where {FT} if emulator.standardize_outputs - return standardize(outputs, output_cov, 1. / emulator.standardize_output_factors) + return standardize(outputs, output_cov, 1.0 ./ emulator.standardize_outputs_factors) else return outputs, output_cov end @@ -286,10 +285,10 @@ function svd_transform( obs_noise_cov; truncate_svd::FT=1.0) where {FT} - if obs_noise_cov != nothing + if obs_noise_cov !== nothing @assert ndims(obs_noise_cov) == 2 end - if obs_noise_cov != nothing + if obs_noise_cov !== nothing # Truncate the SVD as a form of regularization if truncate_svd<1.0 # this variable needs to be provided to this function # Perform SVD @@ -336,10 +335,10 @@ function svd_transform( truncate_svd::FT=1.0) where {FT} - if obs_noise_cov != nothing + if obs_noise_cov !== nothing @assert ndims(obs_noise_cov) == 2 end - if obs_noise_cov != nothing + if obs_noise_cov !== nothing # Truncate the SVD as a form of regularization if truncate_svd<1.0 # this variable needs to be provided to this function # Perform SVD diff --git a/src/GaussianProcess.jl b/src/GaussianProcess.jl index 3f5d7cdce..c2915e6e0 100644 --- a/src/GaussianProcess.jl +++ b/src/GaussianProcess.jl @@ -110,7 +110,7 @@ function build_models!( # Use a default kernel unless a kernel was supplied to GaussianProcess - if gp.kernel==nothing + if gp.kernel === nothing println("Using default squared exponential kernel, learning length scale and variance parameters") # Construct kernel: # Note that the kernels take the signal standard deviations on a @@ -179,8 +179,9 @@ optimize Gaussian Process hyperparameters using in-build package method function optimize_hyperparameters!(gp::GaussianProcess{GPJL}) N_models = length(gp.models) for i = 1:N_models - #noise_learn == true means we do it explicitly (thus don't need it here) - optimize!(gp.models[i], noise=!gp.noise_learn) + # always regress with noise_learn=false; if gp was created with noise_learn=true + # we've already explicitly added noise to the kernel + optimize!(gp.models[i], noise=false) println("optimized hyperparameters of GP: ", i) println(gp.models[i].kernel) end @@ -240,7 +241,7 @@ function build_models!( models = gp.models N_models = size(output_values,1); #size(transformed_data)[1] - if gp.kernel==nothing + if gp.kernel === nothing println("Using default squared exponential kernel, learning length scale and variance parameters") # Create default squared exponential kernel const_value = 1.0