~cgeoga/GPMaxlik.jl

42e561f9af823bf56afe72a641a877e9e7c5e31d — Chris Geoga a month ago b37afcf master
Add wrapper layer to the `gnll` function so that the coordinate
derivative functions work.
M example/Manifest.toml => example/Manifest.toml +88 -60
@@ 1,7 1,8 @@
# This file is machine-generated - editing it directly is not advised

julia_version = "1.7.1"
julia_version = "1.8.2"
manifest_format = "2.0"
project_hash = "d72f18d88061ccb59f25a65e6e393c6da6e25291"

[[deps.ASL_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]


@@ 11,6 12,7 @@ version = "0.1.3+0"

[[deps.ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
version = "1.1.1"

[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"


@@ 20,9 22,9 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[deps.BenchmarkTools]]
deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"]
git-tree-sha1 = "4c10eee4af024676200bc7752e536f858c6b8f93"
git-tree-sha1 = "d9a9701b899b30332bbcb3e1679c41cce81fb0e8"
uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
version = "1.3.1"
version = "1.3.2"

[[deps.Bzip2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]


@@ 32,15 34,15 @@ version = "1.0.8+0"

[[deps.ChainRulesCore]]
deps = ["Compat", "LinearAlgebra", "SparseArrays"]
git-tree-sha1 = "9950387274246d08af38f6eef8cb5480862a435f"
git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb"
uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
version = "1.14.0"
version = "1.15.6"

[[deps.ChangesOfVariables]]
deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
git-tree-sha1 = "1e315e3f4b0b7ce40feded39c73049692126cf53"
git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8"
uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
version = "0.1.3"
version = "0.1.4"

[[deps.CodecBzip2]]
deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"]


@@ 61,60 63,63 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950"
version = "0.3.0"

[[deps.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 = "b153278a25dd42c65abbf4e62344f9d22e59191b"
deps = ["Dates", "LinearAlgebra", "UUIDs"]
git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
version = "3.43.0"
version = "4.5.0"

[[deps.CompilerSupportLibraries_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "0.5.2+0"

[[deps.DataStructures]]
deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0"
uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
version = "0.18.13"

[[deps.Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"

[[deps.DelimitedFiles]]
deps = ["Mmap"]
uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"

[[deps.DiffResults]]
deps = ["StaticArrays"]
git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805"
deps = ["StaticArraysCore"]
git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621"
uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
version = "1.0.3"
version = "1.1.0"

[[deps.DiffRules]]
deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"]
git-tree-sha1 = "28d605d9a0ac17118fe2c5e9ce0fbb76c3ceb120"
git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494"
uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
version = "1.11.0"

[[deps.Distributed]]
deps = ["Random", "Serialization", "Sockets"]
uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
version = "1.12.2"

[[deps.DocStringExtensions]]
deps = ["LibGit2"]
git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b"
git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
version = "0.8.6"
version = "0.9.3"

[[deps.Downloads]]
deps = ["ArgTools", "LibCURL", "NetworkOptions"]
deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
version = "1.6.0"

[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"

[[deps.ForwardDiff]]
deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"]
git-tree-sha1 = "7a380de46b0a1db85c59ebbce5788412a39e4cb7"
git-tree-sha1 = "a69dd6db8a809f78846ff259298678f0d6212180"
uuid = "f6369f11-7733-5829-9624-2563aa707210"
version = "0.10.28"
version = "0.10.34"

[[deps.GPMaxlik]]
deps = ["ForwardDiff", "LinearAlgebra", "Statistics"]
deps = ["ForwardDiff", "LinearAlgebra", "StaticArrays", "Statistics"]
path = "/home/cg/Personal/Repos/GPMaxlik.jl/"
uuid = "988d40dc-a58a-4803-bd2c-6d7438fe27fe"
version = "0.14.0"
version = "0.14.2"

[[deps.InteractiveUtils]]
deps = ["Markdown"]


@@ 122,15 127,15 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[deps.InverseFunctions]]
deps = ["Test"]
git-tree-sha1 = "336cc738f03e069ef2cac55a104eb823455dca75"
git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f"
uuid = "3587e190-3f89-42d0-90ee-14403ec27112"
version = "0.1.4"
version = "0.1.8"

[[deps.Ipopt]]
deps = ["Ipopt_jll", "MathOptInterface"]
git-tree-sha1 = "8b7b5fdbc71d8f88171865faa11d1c6669e96e32"
git-tree-sha1 = "14a305ededd75330246aaa0380130561d8924120"
uuid = "b6b21f68-93f8-5de0-b562-5493be1d77c9"
version = "1.0.2"
version = "1.1.0"

[[deps.Ipopt_jll]]
deps = ["ASL_jll", "Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "MUMPS_seq_jll", "OpenBLAS32_jll", "Pkg"]


@@ 158,10 163,12 @@ version = "0.21.3"
[[deps.LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
version = "0.6.3"

[[deps.LibCURL_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
version = "7.84.0+0"

[[deps.LibGit2]]
deps = ["Base64", "NetworkOptions", "Printf", "SHA"]


@@ 170,6 177,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
[[deps.LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
version = "1.10.2+0"

[[deps.Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"


@@ 180,18 188,18 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[[deps.LogExpFunctions]]
deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
git-tree-sha1 = "09e4b894ce6a976c354a69041a04748180d43637"
git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239"
uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
version = "0.3.15"
version = "0.3.19"

[[deps.Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

[[deps.METIS_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "1d31872bb9c5e7ec1f618e8c4a56c8b0d9bddc7e"
git-tree-sha1 = "1fd0a97409e418b78c53fac671cf4622efdf0f21"
uuid = "d00139f3-1899-568f-a2f0-47f597d42d70"
version = "5.1.1+0"
version = "5.1.2+0"

[[deps.MUMPS_seq_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "METIS_jll", "OpenBLAS32_jll", "Pkg"]


@@ 201,43 209,47 @@ version = "5.4.1+0"

[[deps.MacroTools]]
deps = ["Markdown", "Random"]
git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf"
git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2"
uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
version = "0.5.9"
version = "0.5.10"

[[deps.Markdown]]
deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"

[[deps.MathOptInterface]]
deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "JSON", "LinearAlgebra", "MutableArithmetics", "OrderedCollections", "Printf", "SparseArrays", "Test", "Unicode"]
git-tree-sha1 = "23c99cadd752cc0b70d4c74c969a679948b1bb6a"
deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"]
git-tree-sha1 = "34bc4ea9d1b1ee5da976bc88e5546df98872c56f"
uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
version = "1.2.0"
version = "1.11.1"

[[deps.MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
version = "2.28.0+0"

[[deps.Mmap]]
uuid = "a63ad114-7e13-5084-954f-fe012c677804"

[[deps.MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
version = "2022.2.1"

[[deps.MutableArithmetics]]
deps = ["LinearAlgebra", "SparseArrays", "Test"]
git-tree-sha1 = "ba8c0f8732a24facba709388c74ba99dcbfdda1e"
git-tree-sha1 = "aa532179d4a643d4bd9f328589ca01fa20a0d197"
uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0"
version = "1.0.0"
version = "1.1.0"

[[deps.NaNMath]]
git-tree-sha1 = "737a5957f387b17e74d4ad2f440eb330b39a62c5"
deps = ["OpenLibm_jll"]
git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211"
uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
version = "1.0.0"
version = "1.0.1"

[[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
version = "1.2.0"

[[deps.OpenBLAS32_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]


@@ 248,10 260,12 @@ version = "0.3.17+0"
[[deps.OpenBLAS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
version = "0.3.20+0"

[[deps.OpenLibm_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
version = "0.8.1+0"

[[deps.OpenSpecFun_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]


@@ 265,14 279,15 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.4.1"

[[deps.Parsers]]
deps = ["Dates"]
git-tree-sha1 = "1285416549ccfcdf0c50d4997a94331e88d68413"
deps = ["Dates", "SnoopPrecompile"]
git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559"
uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
version = "2.3.1"
version = "2.5.2"

[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
version = "1.8.0"

[[deps.Preferences]]
deps = ["TOML"]


@@ 298,13 313,15 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

[[deps.SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"

[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

[[deps.SharedArrays]]
deps = ["Distributed", "Mmap", "Random", "Serialization"]
uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
[[deps.SnoopPrecompile]]
git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85"
uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c"
version = "1.0.1"

[[deps.Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"


@@ 315,9 332,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[[deps.SpecialFunctions]]
deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
git-tree-sha1 = "5ba658aeecaaf96923dce0da9e703bd1fe7666f9"
git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d"
uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
version = "2.1.4"
version = "2.1.7"

[[deps.StableRNGs]]
deps = ["Random", "Test"]


@@ 326,10 343,15 @@ uuid = "860ef19b-820b-49d6-a774-d7a799459cd3"
version = "1.0.0"

[[deps.StaticArrays]]
deps = ["LinearAlgebra", "Random", "Statistics"]
git-tree-sha1 = "cd56bf18ed715e8b09f06ef8c6b781e6cdc49911"
deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"]
git-tree-sha1 = "ffc098086f35909741f71ce21d03dadf0d2bfa76"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.4.4"
version = "1.5.11"

[[deps.StaticArraysCore]]
git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a"
uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
version = "1.4.0"

[[deps.Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]


@@ 338,10 360,12 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
version = "1.0.0"

[[deps.Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.1"

[[deps.Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]


@@ 349,9 373,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[deps.TranscodingStreams]]
deps = ["Random", "Test"]
git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c"
git-tree-sha1 = "e4bdc63f5c6d62e80eb1c0043fcc0360d5950ff7"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.9.6"
version = "0.9.10"

[[deps.UUIDs]]
deps = ["Random", "SHA"]


@@ 363,15 387,19 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.12+3"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.1.1+0"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.48.0+0"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+0"

M example/Project.toml => example/Project.toml +1 -0
@@ 6,3 6,4 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"

M example/simulate_data.jl => example/simulate_data.jl +2 -2
@@ 1,6 1,6 @@

# Set the seed so this script gives the same output each time.
using Random, LinearAlgebra, ForwardDiff, GPMaxlik, StableRNGs
using Random, LinearAlgebra, ForwardDiff, GPMaxlik, StableRNGs, StaticArrays

# Choose a covariance function and derivatives. Derivatives here show off a lazy
# option: use AD! 


@@ 25,7 25,7 @@ prof_kd1(x,y,p) = ForwardDiff.gradient(pr->prof_kfn(x,y,pr), p)[1]
# Simulate some data using that function.
seed = StableRNG(100)
const pr     = [5.0, 2.0]
const pts    = vec(collect.(Iterators.product(1:32, 1:32)))
const pts    = SVector{2,Float64}.(vec(collect.(Iterators.product(1:32, 1:32))))
const covm   = Symmetric([kfn(ptj, ptk, pr) for ptj in pts, ptk in pts])
const covch  = cholesky!(covm)
const simul  = covch.L*randn(seed, length(pts))

M src/nll.jl => src/nll.jl +9 -0
@@ 328,6 328,15 @@ various optimization software suites.
function gnll(pts, datav, kfn, dfns, pr; saa, nll, grad, fish, pscale=false, 
              profile=false, vrb=false, K=nothing, Kdv=DerivativeCovarianceMatrix[],
              store=nothing)
  p = SVector{length(pr), eltype(pr)}(pr...)
  _gnll(pts, datav, kfn, dfns, p; saa=saa, nll=nll, grad=grad, fish=fish, pscale=pscale,
        profile=profile, vrb=vrb, K=K, Kdv=Kdv, store=store)
end


function _gnll(pts, datav, kfn, dfns, pr; saa, nll, grad, fish, pscale=false, 
               profile=false, vrb=false, K=nothing, Kdv=DerivativeCovarianceMatrix[],
               store=nothing)
  # Check if there is just one sample provided as a simple vector. If so, modify
  # the call accordingly:
  if (datav isa Vector{T} where{T<:Number})

M test/Manifest.toml => test/Manifest.toml +63 -49
@@ 1,10 1,12 @@
# This file is machine-generated - editing it directly is not advised

julia_version = "1.7.1"
julia_version = "1.8.2"
manifest_format = "2.0"
project_hash = "215b169b9ee3f85dd8ec533535c8b7794cd2387e"

[[deps.ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
version = "1.1.1"

[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"


@@ 14,15 16,15 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[deps.ChainRulesCore]]
deps = ["Compat", "LinearAlgebra", "SparseArrays"]
git-tree-sha1 = "c9a6160317d1abe9c44b3beb367fd448117679ca"
git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb"
uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
version = "1.13.0"
version = "1.15.6"

[[deps.ChangesOfVariables]]
deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1"
git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8"
uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
version = "0.1.2"
version = "0.1.4"

[[deps.CommonSubexpressions]]
deps = ["MacroTools", "Test"]


@@ 31,60 33,57 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950"
version = "0.3.0"

[[deps.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 = "44c37b4636bc54afac5c574d2d02b625349d6582"
deps = ["Dates", "LinearAlgebra", "UUIDs"]
git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
version = "3.41.0"
version = "4.5.0"

[[deps.CompilerSupportLibraries_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "0.5.2+0"

[[deps.Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"

[[deps.DelimitedFiles]]
deps = ["Mmap"]
uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"

[[deps.DiffResults]]
deps = ["StaticArrays"]
git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805"
deps = ["StaticArraysCore"]
git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621"
uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
version = "1.0.3"
version = "1.1.0"

[[deps.DiffRules]]
deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"]
git-tree-sha1 = "dd933c4ef7b4c270aacd4eb88fa64c147492acf0"
git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494"
uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
version = "1.10.0"

[[deps.Distributed]]
deps = ["Random", "Serialization", "Sockets"]
uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
version = "1.12.2"

[[deps.DocStringExtensions]]
deps = ["LibGit2"]
git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b"
git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
version = "0.8.6"
version = "0.9.3"

[[deps.Downloads]]
deps = ["ArgTools", "LibCURL", "NetworkOptions"]
deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
version = "1.6.0"

[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"

[[deps.FiniteDifferences]]
deps = ["ChainRulesCore", "LinearAlgebra", "Printf", "Random", "Richardson", "SparseArrays", "StaticArrays"]
git-tree-sha1 = "0ee1275eb003b6fc7325cb14301665d1072abda1"
git-tree-sha1 = "9788a26511ad46afd12197955c2b984d5faf83c8"
uuid = "26cc04aa-876d-5657-8c51-4c34ba976000"
version = "0.12.24"
version = "0.12.25"

[[deps.ForwardDiff]]
deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"]
git-tree-sha1 = "1bd6fc0c344fc0cbee1f42f8d2e7ec8253dda2d2"
git-tree-sha1 = "a69dd6db8a809f78846ff259298678f0d6212180"
uuid = "f6369f11-7733-5829-9624-2563aa707210"
version = "0.10.25"
version = "0.10.34"

[[deps.InteractiveUtils]]
deps = ["Markdown"]


@@ 92,9 91,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[deps.InverseFunctions]]
deps = ["Test"]
git-tree-sha1 = "a7254c0acd8e62f1ac75ad24d5db43f5f19f3c65"
git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f"
uuid = "3587e190-3f89-42d0-90ee-14403ec27112"
version = "0.1.2"
version = "0.1.8"

[[deps.IrrationalConstants]]
git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151"


@@ 110,10 109,12 @@ version = "1.4.1"
[[deps.LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
version = "0.6.3"

[[deps.LibCURL_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
version = "7.84.0+0"

[[deps.LibGit2]]
deps = ["Base64", "NetworkOptions", "Printf", "SHA"]


@@ 122,6 123,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
[[deps.LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
version = "1.10.2+0"

[[deps.Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"


@@ 132,18 134,18 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[[deps.LogExpFunctions]]
deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
git-tree-sha1 = "e5718a00af0ab9756305a0392832c8952c7426c1"
git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239"
uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
version = "0.3.6"
version = "0.3.19"

[[deps.Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

[[deps.MacroTools]]
deps = ["Markdown", "Random"]
git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf"
git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2"
uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
version = "0.5.9"
version = "0.5.10"

[[deps.Markdown]]
deps = ["Base64"]


@@ 152,28 154,31 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
[[deps.MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"

[[deps.Mmap]]
uuid = "a63ad114-7e13-5084-954f-fe012c677804"
version = "2.28.0+0"

[[deps.MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
version = "2022.2.1"

[[deps.NaNMath]]
git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe"
deps = ["OpenLibm_jll"]
git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211"
uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
version = "0.3.7"
version = "1.0.1"

[[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
version = "1.2.0"

[[deps.OpenBLAS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
version = "0.3.20+0"

[[deps.OpenLibm_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
version = "0.8.1+0"

[[deps.OpenSpecFun_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]


@@ 184,12 189,13 @@ version = "0.5.5+0"
[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
version = "1.8.0"

[[deps.Preferences]]
deps = ["TOML"]
git-tree-sha1 = "de893592a221142f3db370f48290e3a2ef39998f"
git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d"
uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.2.4"
version = "1.3.0"

[[deps.Printf]]
deps = ["Unicode"]


@@ 211,14 217,11 @@ version = "1.4.0"

[[deps.SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"

[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

[[deps.SharedArrays]]
deps = ["Distributed", "Mmap", "Random", "Serialization"]
uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"

[[deps.Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"



@@ 228,9 231,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[[deps.SpecialFunctions]]
deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
git-tree-sha1 = "5ba658aeecaaf96923dce0da9e703bd1fe7666f9"
git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d"
uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
version = "2.1.4"
version = "2.1.7"

[[deps.StableRNGs]]
deps = ["Random", "Test"]


@@ 239,9 242,14 @@ uuid = "860ef19b-820b-49d6-a774-d7a799459cd3"
version = "1.0.0"

[[deps.StaticArrays]]
deps = ["LinearAlgebra", "Random", "Statistics"]
git-tree-sha1 = "6354dfaf95d398a1a70e0b28238321d5d17b2530"
deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"]
git-tree-sha1 = "ffc098086f35909741f71ce21d03dadf0d2bfa76"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.5.11"

[[deps.StaticArraysCore]]
git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a"
uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
version = "1.4.0"

[[deps.Statistics]]


@@ 251,10 259,12 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
version = "1.0.0"

[[deps.Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.1"

[[deps.Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]


@@ 270,15 280,19 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.12+3"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.1.1+0"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.48.0+0"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+0"

M test/Project.toml => test/Project.toml +1 -0
@@ 4,4 4,5 @@ ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

M test/runtests.jl => test/runtests.jl +2 -2
@@ 9,7 9,8 @@ function naive_nll(p)
end

# Basic expected fisher.
function efish(p)
function efish(vec_p)
  p   = @SVector [vec_p[1], vec_p[2]]
  out = zeros(2,2)
  K   = cholesky!(Symmetric([kfn(x,y,p) for x in pts, y in pts]))
  Kd1 = Symmetric([kd1(x,y,p) for x in pts, y in pts])


@@ 50,4 51,3 @@ end
                 ForwardDiff.hessian(naive_nll,  [3.0, 3.0]))
end