From 3f643a7c528fdac3fa4e7af11661c952cf20fe0c Mon Sep 17 00:00:00 2001
From: ST John <st--@users.noreply.github.com>
Date: Mon, 19 Jul 2021 14:53:11 +0300
Subject: [PATCH 1/8] move to KernelFunctions style literate.jl

---
 .github/workflows/docs.yml                    |    3 +-
 docs/Manifest.toml                            |  799 -----------
 docs/Project.toml                             |   20 -
 docs/literate.jl                              |   53 +
 docs/make.jl                                  |   92 +-
 examples/README.md                            |   52 +
 examples/regression-1d/Manifest.toml          | 1164 +++++++++++++++++
 examples/regression-1d/Project.toml           |   28 +
 .../script.jl}                                |    0
 9 files changed, 1360 insertions(+), 851 deletions(-)
 create mode 100644 docs/literate.jl
 create mode 100644 examples/README.md
 create mode 100644 examples/regression-1d/Manifest.toml
 create mode 100644 examples/regression-1d/Project.toml
 rename examples/{regression_1d.jl => regression-1d/script.jl} (100%)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 75960473..2b57c0c9 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -19,7 +19,8 @@ jobs:
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy
         env:
-          GKSwstype: nul # Remove GR error messages
+          GKSwstype: nul # turn off GR's interactive plotting for notebooks
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          JULIA_DEBUG: Documenter # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955)
         run: julia --project=docs/ docs/make.jl
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
index b8157517..a0a3b326 100644
--- a/docs/Manifest.toml
+++ b/docs/Manifest.toml
@@ -6,108 +6,21 @@ path = ".."
 uuid = "99985d1d-32ba-4be9-9821-2ec096f28918"
 version = "0.3.5"
 
-[[AbstractMCMC]]
-deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"]
-git-tree-sha1 = "21279159f6be4b2fd00e1a4a1f736893100408fc"
-uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
-version = "3.2.0"
-
-[[AbstractTrees]]
-git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5"
-uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
-version = "0.3.4"
-
-[[Adapt]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7"
-uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "3.3.1"
-
-[[AdvancedHMC]]
-deps = ["ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "Parameters", "ProgressMeter", "Random", "Requires", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "7e85ed4917716873423f8d47da8c1275f739e0b7"
-uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.2.27"
-
-[[ArgCheck]]
-git-tree-sha1 = "dedbbb2ddb876f899585c4ec4433265e3017215a"
-uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197"
-version = "2.1.0"
-
 [[ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
 
-[[ArrayInterface]]
-deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"]
-git-tree-sha1 = "045ff5e1bc8c6fb1ecb28694abba0a0d55b5f4f5"
-uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "3.1.17"
-
 [[Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 
-[[BangBang]]
-deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"]
-git-tree-sha1 = "d53b1eaefd48e233545d21f5b764c8ee54df4a09"
-uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66"
-version = "0.3.30"
-
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
-[[Baselet]]
-git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e"
-uuid = "9718e550-a3fa-408a-8086-8db961cd8217"
-version = "0.1.1"
-
-[[BenchmarkTools]]
-deps = ["JSON", "Logging", "Printf", "Statistics", "UUIDs"]
-git-tree-sha1 = "068fda9b756e41e6c75da7b771e6f89fa8a43d15"
-uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-version = "0.7.0"
-
-[[Bzip2_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e"
-uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
-version = "1.0.6+5"
-
-[[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"
-uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
-version = "1.16.0+6"
-
 [[ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
 git-tree-sha1 = "8b31cc69cbc38c5c826aaa1c890c694be3622d99"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 version = "0.10.3"
 
-[[ColorSchemes]]
-deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"]
-git-tree-sha1 = "c8fd01e4b736013bc61b704871d20503b33ea402"
-uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
-version = "3.12.1"
-
-[[ColorTypes]]
-deps = ["FixedPointNumbers", "Random"]
-git-tree-sha1 = "024fe24d83e4a5bf5fc80501a314ce0d1aa35597"
-uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
-version = "0.11.0"
-
-[[Colors]]
-deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
-git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40"
-uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.12.8"
-
-[[CommonSubexpressions]]
-deps = ["MacroTools", "Test"]
-git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7"
-uuid = "bbf7d656-a473-5ed7-a52c-81e309532950"
-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 = "e4e2b39db08f967cc1360951f01e8a75ec441cab"
@@ -123,24 +36,6 @@ git-tree-sha1 = "f3955eb38944e5dd0fabf8ca1e267d94941d34a5"
 uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b"
 version = "0.1.0"
 
-[[ConsoleProgressMonitor]]
-deps = ["Logging", "ProgressMeter"]
-git-tree-sha1 = "3ab7b2136722890b9af903859afcf457fa3059e8"
-uuid = "88cd18e8-d9cc-4ea6-8889-5259c0d15c8b"
-version = "0.1.2"
-
-[[ConstructionBase]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "1dc43957fb9a1574fa1b7a449e101bd1fd3a9fb7"
-uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
-version = "1.2.1"
-
-[[Contour]]
-deps = ["StaticArrays"]
-git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7"
-uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
-version = "0.5.7"
-
 [[DataAPI]]
 git-tree-sha1 = "dfb3b7e89e395be1e25c2ad6d7690dc29cc53b1d"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
@@ -152,36 +47,14 @@ git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 version = "0.18.9"
 
-[[DataValueInterfaces]]
-git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
-uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
-version = "1.0.0"
-
 [[Dates]]
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
-[[DefineSingletons]]
-git-tree-sha1 = "77b4ca280084423b728662fe040e5ff8819347c5"
-uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52"
-version = "0.1.1"
-
 [[DelimitedFiles]]
 deps = ["Mmap"]
 uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 
-[[DiffResults]]
-deps = ["StaticArrays"]
-git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805"
-uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
-version = "1.0.3"
-
-[[DiffRules]]
-deps = ["NaNMath", "Random", "SpecialFunctions"]
-git-tree-sha1 = "214c3fcac57755cfda163d91c58893a8723f93e9"
-uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
-version = "1.0.2"
-
 [[Distances]]
 deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
 git-tree-sha1 = "abe4ad222b26af3337262b8afb28fab8d215e9f8"
@@ -214,189 +87,28 @@ version = "0.27.0"
 deps = ["ArgTools", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 
-[[DynamicHMC]]
-deps = ["ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "Parameters", "ProgressMeter", "Random", "Statistics"]
-git-tree-sha1 = "b60dcde7440787fb21cd8347edc5623cb89aace8"
-uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb"
-version = "3.1.0"
-
-[[EarCut_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "92d8f9f208637e8d2d28c664051a00569c01493d"
-uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5"
-version = "2.1.5+1"
-
-[[EllipticalSliceSampling]]
-deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"]
-git-tree-sha1 = "764cddab41cd15f127767855722f1bf54b49c64a"
-uuid = "cad2338a-1db2-11e9-3401-43bc07c9ede2"
-version = "0.4.3"
-
-[[Expat_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "b3bfd02e98aedfa5cf885665493c5598c350cd2f"
-uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
-version = "2.2.10+0"
-
-[[FFMPEG]]
-deps = ["FFMPEG_jll"]
-git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8"
-uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
-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"
-uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
-version = "4.3.1+4"
-
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
 git-tree-sha1 = "31939159aeb8ffad1d4d8ee44d07f8558273120a"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
 version = "0.11.7"
 
-[[FiniteDiff]]
-deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"]
-git-tree-sha1 = "f6f80c8f934efd49a286bb5315360be66956dfc4"
-uuid = "6a86dc24-6348-571c-b903-95158fe2bd41"
-version = "2.8.0"
-
-[[FixedPointNumbers]]
-deps = ["Statistics"]
-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 = "35895cf184ceaab11fd778b4590144034a167a2f"
-uuid = "a3f928ae-7b40-5064-980b-68af3947d34b"
-version = "2.13.1+14"
-
-[[Formatting]]
-deps = ["Printf"]
-git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8"
-uuid = "59287772-0a20-5a39-b81b-1366585eb4c0"
-version = "0.4.2"
-
-[[ForwardDiff]]
-deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Printf", "Random", "SpecialFunctions", "StaticArrays"]
-git-tree-sha1 = "e2af66012e08966366a43251e1fd421522908be6"
-uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "0.10.18"
-
-[[FreeType2_jll]]
-deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "cbd58c9deb1d304f5a245a0b7eb841a2560cfec6"
-uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7"
-version = "2.10.1+5"
-
-[[FriBidi_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91"
-uuid = "559328eb-81f9-559d-9380-de523a88c83c"
-version = "1.0.10+0"
-
 [[Functors]]
 deps = ["MacroTools"]
 git-tree-sha1 = "a7bb2af991c43dcf5c3455d276dd83976799634f"
 uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
 version = "0.2.1"
 
-[[Future]]
-deps = ["Random"]
-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 = "dba1e8614e98949abfa60480b13653813d8f0157"
-uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89"
-version = "3.3.5+0"
-
-[[GR]]
-deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"]
-git-tree-sha1 = "b83e3125048a9c3158cbb7ca423790c7b1b57bea"
-uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
-version = "0.57.5"
-
-[[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 = "e14907859a1d3aee73a019e7b3c98e9e7b8b5b3e"
-uuid = "d2c73de3-f751-5644-a686-071e5b155ba9"
-version = "0.57.3+0"
-
-[[GeometryBasics]]
-deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
-git-tree-sha1 = "4136b8a5668341e58398bb472754bff4ba0456ff"
-uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
-version = "0.3.12"
-
-[[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 = "47ce50b742921377301e15005c96e979574e130b"
-uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
-version = "2.68.1+0"
-
-[[Grisu]]
-git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
-uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe"
-version = "1.0.2"
-
-[[HTTP]]
-deps = ["Base64", "Dates", "IniFile", "MbedTLS", "NetworkOptions", "Sockets", "URIs"]
-git-tree-sha1 = "86ed84701fbfd1142c9786f8e53c595ff5a4def9"
-uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "0.9.10"
-
 [[IOCapture]]
 deps = ["Logging"]
 git-tree-sha1 = "1868e4e7ad2f93d8de0904d89368c527b46aa6a1"
 uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
 version = "0.2.1"
 
-[[IfElse]]
-git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef"
-uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
-version = "0.1.0"
-
-[[IniFile]]
-deps = ["Test"]
-git-tree-sha1 = "098e4d2c533924c921f9f9847274f2ad89e018b8"
-uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f"
-version = "0.5.0"
-
-[[InitialValues]]
-git-tree-sha1 = "26c8832afd63ac558b98a823265856670d898b6c"
-uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c"
-version = "0.2.10"
-
-[[InplaceOps]]
-deps = ["LinearAlgebra", "Test"]
-git-tree-sha1 = "50b41d59e7164ab6fda65e71049fee9d890731ff"
-uuid = "505f98c9-085e-5b2c-8e89-488be7bf1f34"
-version = "0.3.0"
-
 [[InteractiveUtils]]
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
-[[IterTools]]
-git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18"
-uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
-version = "1.3.0"
-
-[[IteratorInterfaceExtensions]]
-git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
-uuid = "82899510-4779-5014-852e-03e436cf321d"
-version = "1.0.0"
-
 [[JLLWrappers]]
 deps = ["Preferences"]
 git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e"
@@ -409,47 +121,12 @@ git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.1"
 
-[[JpegTurbo_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "d735490ac75c5cb9f1b00d8b5509c11984dc6943"
-uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
-version = "2.1.0+0"
-
 [[KernelFunctions]]
 deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"]
 git-tree-sha1 = "c7b25bc625ca2ee217021d29e3ddf031967bf0ff"
 uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392"
 version = "0.10.5"
 
-[[LAME_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c"
-uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d"
-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"
-uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
-version = "1.2.1"
-
-[[Latexify]]
-deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"]
-git-tree-sha1 = "a4b12a1bd2ebade87891ab7e36fdbce582301a92"
-uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
-version = "0.15.6"
-
-[[LeftChildRightSiblingTrees]]
-deps = ["AbstractTrees"]
-git-tree-sha1 = "71be1eb5ad19cb4f61fa8c73395c0338fd092ae0"
-uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e"
-version = "0.1.2"
-
 [[LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
 uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
@@ -466,85 +143,13 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
 uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 
-[[LibVPX_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "12ee7e23fa4d18361e7c2cde8f8337d4c3101bc7"
-uuid = "dd192d2f-8180-539f-9fb4-cc70b1dcf69a"
-version = "1.10.0+0"
-
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[Libffi_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "761a393aeccd6aa92ec3515e428c26bf99575b3b"
-uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490"
-version = "3.2.2+0"
-
-[[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"
-
-[[Libglvnd_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"]
-git-tree-sha1 = "7739f837d6447403596a75d19ed01fd08d6f56bf"
-uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29"
-version = "1.3.0+3"
-
-[[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 = "8d22e127ea9a0917bc98ebd3755c8bd31989381e"
-uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
-version = "1.16.1+0"
-
-[[Libmount_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73"
-uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9"
-version = "2.35.0+0"
-
-[[Libtiff_jll]]
-deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "340e257aada13f95f98ee352d316c3bed37c8ab9"
-uuid = "89763e89-9b03-5906-acba-b20f662cd828"
-version = "4.3.0+0"
-
-[[Libuuid_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066"
-uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
-version = "2.36.0+0"
-
-[[LineSearches]]
-deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"]
-git-tree-sha1 = "f27132e551e959b3667d8c93eae90973225032dd"
-uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
-version = "7.1.1"
-
 [[LinearAlgebra]]
 deps = ["Libdl"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
-[[Literate]]
-deps = ["Base64", "IOCapture", "JSON", "REPL"]
-git-tree-sha1 = "501a1a74a0c825037860d36d87d703e987d39dbc"
-uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
-version = "2.8.1"
-
-[[LogDensityProblems]]
-deps = ["ArgCheck", "BenchmarkTools", "DiffResults", "DocStringExtensions", "Random", "Requires", "TransformVariables", "UnPack"]
-git-tree-sha1 = "e3600cd2468d2b5356c240a5d27e0ef48fd451a3"
-uuid = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
-version = "0.10.5"
-
 [[LogExpFunctions]]
 deps = ["DocStringExtensions", "LinearAlgebra"]
 git-tree-sha1 = "1ba664552f1ef15325e68dc4c05c3ef8c2d5d885"
@@ -554,12 +159,6 @@ version = "0.2.4"
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
-[[LoggingExtras]]
-deps = ["Dates", "Logging"]
-git-tree-sha1 = "59b45fd91b743dff047313bb7af0f84167aef80d"
-uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
-version = "0.4.6"
-
 [[MacroTools]]
 deps = ["Markdown", "Random"]
 git-tree-sha1 = "6a8a2a625ab0dea913aba95c11370589e0239ff0"
@@ -570,27 +169,10 @@ version = "0.5.6"
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
-[[MbedTLS]]
-deps = ["Dates", "MbedTLS_jll", "Random", "Sockets"]
-git-tree-sha1 = "1c38e51c3d08ef2278062ebceade0e46cefc96fe"
-uuid = "739be429-bea8-5141-9913-cc70e7f3736d"
-version = "1.0.3"
-
 [[MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
-[[Measures]]
-git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f"
-uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
-version = "0.3.1"
-
-[[MicroCollections]]
-deps = ["BangBang", "Setfield"]
-git-tree-sha1 = "e991b6a9d38091c4a0d7cd051fcb57c05f98ac03"
-uuid = "128add7d-3638-4c79-886c-908ea0c25c34"
-version = "0.1.0"
-
 [[Missings]]
 deps = ["DataAPI"]
 git-tree-sha1 = "4ea90bd5d3985ae1f9a908bd4500ae88921c5ce7"
@@ -603,113 +185,36 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 [[MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 
-[[NLSolversBase]]
-deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"]
-git-tree-sha1 = "50608f411a1e178e0129eab4110bd56efd08816f"
-uuid = "d41bc354-129a-5804-8e4c-c37616107c6c"
-version = "7.8.0"
-
-[[NaNMath]]
-git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb"
-uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
-version = "0.3.5"
-
 [[NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 
-[[Ogg_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "7937eda4681660b4d6aeeecc2f7e1c81c8ee4e2f"
-uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051"
-version = "1.3.5+0"
-
-[[OpenSSL_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "15003dcb7d8db3c6c857fda14891a539a8f2705a"
-uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "1.1.10+0"
-
 [[OpenSpecFun_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1"
 uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
 version = "0.5.5+0"
 
-[[Optim]]
-deps = ["Compat", "FillArrays", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"]
-git-tree-sha1 = "d34366a3abc25c41f88820762ef7dfdfe9306711"
-uuid = "429524aa-4258-5aef-a3af-852621145aeb"
-version = "1.3.0"
-
-[[Opus_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720"
-uuid = "91d4177d-7536-5919-b921-800302f37372"
-version = "1.3.2+0"
-
 [[OrderedCollections]]
 git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.4.1"
 
-[[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"]
 git-tree-sha1 = "f82a0e71f222199de8e9eb9a09977bd0767d52a0"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
 version = "0.11.0"
 
-[[Parameters]]
-deps = ["OrderedCollections", "UnPack"]
-git-tree-sha1 = "2276ac65f1e236e0a6ea70baff3f62ad4c625345"
-uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a"
-version = "0.12.2"
-
 [[Parsers]]
 deps = ["Dates"]
 git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 version = "1.1.0"
 
-[[Pixman_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29"
-uuid = "30392449-352a-5448-841d-b1acce4e97dc"
-version = "0.40.1+0"
-
 [[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"
 
-[[PlotThemes]]
-deps = ["PlotUtils", "Requires", "Statistics"]
-git-tree-sha1 = "a3a964ce9dc7898193536002a6dd892b1b5a6f1d"
-uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a"
-version = "2.0.1"
-
-[[PlotUtils]]
-deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"]
-git-tree-sha1 = "ae9a295ac761f64d8c2ec7f9f24d21eb4ffba34d"
-uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
-version = "1.0.10"
-
-[[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 = "e995fa1821b6daff8b107a8eafbec234ae2263d0"
-uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.16.5"
-
-[[PositiveFactorizations]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20"
-uuid = "85a6dd25-e78a-55b7-8502-1745935b8125"
-version = "0.2.4"
-
 [[Preferences]]
 deps = ["TOML"]
 git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a"
@@ -720,24 +225,6 @@ version = "1.2.2"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[ProgressLogging]]
-deps = ["Logging", "SHA", "UUIDs"]
-git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539"
-uuid = "33c8b6b6-d38a-422a-b730-caa89a2f386c"
-version = "0.1.4"
-
-[[ProgressMeter]]
-deps = ["Distributed", "Printf"]
-git-tree-sha1 = "afadeba63d90ff223a6a48d2009434ecee2ec9e8"
-uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
-version = "1.7.1"
-
-[[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 = "ad368663a5e20dbb8d6dc2fddeefe4dae0781ae8"
-uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1"
-version = "5.15.3+0"
-
 [[QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
 git-tree-sha1 = "12fbe86da16df6679be7521dfb39fbc861e1dc7b"
@@ -757,12 +244,6 @@ git-tree-sha1 = "b3fb709f3c97bfc6e948be68beeecb55a0b340ae"
 uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 version = "1.1.1"
 
-[[RecipesPipeline]]
-deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"]
-git-tree-sha1 = "7a5026a6741c14147d1cb6daf2528a77ca28eb51"
-uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c"
-version = "0.3.2"
-
 [[Reexport]]
 git-tree-sha1 = "5f6c21241f0f655da3952fd60aa18477cf96c220"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
@@ -789,31 +270,13 @@ version = "0.3.0+0"
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
-[[Scratch]]
-deps = ["Dates"]
-git-tree-sha1 = "0b4b7f1393cff97c33891da2a0bf69c6ed241fda"
-uuid = "6c6a2e73-6563-6170-7368-637461726353"
-version = "1.1.0"
-
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
-[[Setfield]]
-deps = ["ConstructionBase", "Future", "MacroTools", "Requires"]
-git-tree-sha1 = "d5640fc570fb1b6c54512f0bd3853866bd298b3e"
-uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46"
-version = "0.7.0"
-
 [[SharedArrays]]
 deps = ["Distributed", "Mmap", "Random", "Serialization"]
 uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
 
-[[Showoff]]
-deps = ["Dates", "Grisu"]
-git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de"
-uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f"
-version = "1.0.3"
-
 [[Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
@@ -833,24 +296,6 @@ git-tree-sha1 = "a50550fa3164a8c46747e62063b4d774ac1bcf49"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
 version = "1.5.1"
 
-[[SplittablesBase]]
-deps = ["Setfield", "Test"]
-git-tree-sha1 = "edef25a158db82f4940720ebada14a60ef6c4232"
-uuid = "171d559e-b47b-412a-8079-5efa626c420e"
-version = "0.1.13"
-
-[[Static]]
-deps = ["IfElse"]
-git-tree-sha1 = "2740ea27b66a41f9d213561a04573da5d3823d4b"
-uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
-version = "0.2.5"
-
-[[StaticArrays]]
-deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "42378d3bab8b4f57aa1ca443821b752850592668"
-uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.2.2"
-
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -872,12 +317,6 @@ git-tree-sha1 = "30cd8c360c54081f806b1ee14d2eecbef3c04c49"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 version = "0.9.8"
 
-[[StructArrays]]
-deps = ["Adapt", "DataAPI", "Tables"]
-git-tree-sha1 = "44b3afd37b17422a62aea25f04c1f7e09ce6b07f"
-uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
-version = "0.5.1"
-
 [[SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
@@ -886,18 +325,6 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 
-[[TableTraits]]
-deps = ["IteratorInterfaceExtensions"]
-git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
-uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
-version = "1.0.1"
-
-[[Tables]]
-deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
-git-tree-sha1 = "aa30f8bb63f9ff3f8303a06c604c8500a69aa791"
-uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "1.4.3"
-
 [[Tar]]
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
@@ -908,235 +335,27 @@ git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6"
 uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50"
 version = "0.1.1"
 
-[[TerminalLoggers]]
-deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"]
-git-tree-sha1 = "e185a19bb9172f0cf5bc71233fab92a46f7ae154"
-uuid = "5d786b92-1e48-4d6f-9151-6b4477ca9bed"
-version = "0.1.3"
-
 [[Test]]
 deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
-[[Transducers]]
-deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"]
-git-tree-sha1 = "34f27ac221cb53317ab6df196f9ed145077231ff"
-uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999"
-version = "0.4.65"
-
-[[TransformVariables]]
-deps = ["ArgCheck", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "Pkg", "Random", "UnPack"]
-git-tree-sha1 = "1ea54f326e7d8f0abd74eeae8df2eaf8d584660b"
-uuid = "84d833dd-6860-57f9-a1a7-6da5db126cff"
-version = "0.4.0"
-
-[[URIs]]
-git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355"
-uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
-version = "1.3.0"
-
 [[UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
-[[UnPack]]
-git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b"
-uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
-version = "1.0.2"
-
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
-[[Wayland_jll]]
-deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"]
-git-tree-sha1 = "dc643a9b774da1c2781413fd7b6dcd2c56bb8056"
-uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89"
-version = "1.17.0+4"
-
-[[Wayland_protocols_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll"]
-git-tree-sha1 = "2839f1c1296940218e35df0bbb220f2a79686670"
-uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91"
-version = "1.18.0+4"
-
-[[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"
-
-[[Xorg_libXcursor_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"]
-git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd"
-uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724"
-version = "1.2.0+4"
-
-[[Xorg_libXdmcp_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-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_libXfixes_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"]
-git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4"
-uuid = "d091e8ba-531a-589c-9de9-94069b037ed8"
-version = "5.0.3+4"
-
-[[Xorg_libXi_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"]
-git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246"
-uuid = "a51aa0fd-4e3c-5386-b890-e753decda492"
-version = "1.7.10+4"
-
-[[Xorg_libXinerama_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"]
-git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123"
-uuid = "d1454406-59df-5ea1-beac-c340f2130bc3"
-version = "1.1.4+4"
-
-[[Xorg_libXrandr_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"]
-git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631"
-uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484"
-version = "1.5.2+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"
-
-[[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_libxkbfile_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"]
-git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2"
-uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a"
-version = "1.1.0+4"
-
-[[Xorg_xcb_util_image_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
-git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97"
-uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b"
-version = "0.4.0+1"
-
-[[Xorg_xcb_util_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"]
-git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1"
-uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5"
-version = "0.4.0+1"
-
-[[Xorg_xcb_util_keysyms_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
-git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00"
-uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7"
-version = "0.4.0+1"
-
-[[Xorg_xcb_util_renderutil_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
-git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e"
-uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e"
-version = "0.3.9+1"
-
-[[Xorg_xcb_util_wm_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
-git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67"
-uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361"
-version = "0.4.1+1"
-
-[[Xorg_xkbcomp_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"]
-git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b"
-uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4"
-version = "1.4.2+4"
-
-[[Xorg_xkeyboard_config_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"]
-git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d"
-uuid = "33bec58e-1273-512f-9401-5d533626f822"
-version = "2.27.0+4"
-
-[[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"
 
-[[Zstd_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "cc4bf3fdde8b7e3e9fa0351bdeedba1cf3b7f6e6"
-uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
-version = "1.5.0+0"
-
 [[ZygoteRules]]
 deps = ["MacroTools"]
 git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7"
 uuid = "700de1a5-db45-46bc-99cf-38207098b444"
 version = "0.2.1"
 
-[[libass_jll]]
-deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "acc685bcf777b2202a904cdcb49ad34c2fa1880c"
-uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0"
-version = "0.14.0+4"
-
-[[libfdk_aac_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "7a5780a0d9c6864184b3a2eeeb833a0c871f00ab"
-uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280"
-version = "0.1.6+4"
-
-[[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 = "c45f4e40e7aafe9d086379e5578947ec8b95a8fb"
-uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
-version = "1.3.7+0"
-
 [[nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
@@ -1144,21 +363,3 @@ 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"
-uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a"
-version = "2020.7.14+2"
-
-[[x265_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "487da2f8f2f0c8ee0e83f39d13037d6bbf0a45ab"
-uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76"
-version = "3.0.0+3"
-
-[[xkbcommon_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"]
-git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6"
-uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd"
-version = "0.9.1+5"
diff --git a/docs/Project.toml b/docs/Project.toml
index a3d978d4..e24ca49b 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -1,28 +1,8 @@
 [deps]
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"
-AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
-EllipticalSliceSampling = "cad2338a-1db2-11e9-3401-43bc07c9ede2"
-ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
-Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
-LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
-Optim = "429524aa-4258-5aef-a3af-852621145aeb"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 
 [compat]
 AbstractGPs = "0.3"
-AdvancedHMC = "0.2"
-Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
 Documenter = "0.27"
-DynamicHMC = "2.2, 3.1"
-EllipticalSliceSampling = "0.3, 0.4"
-ForwardDiff = "0.10"
-Literate = "2.5"
-LogDensityProblems = "0.10"
-Optim = "0.21, 0.22, 1.0"
-Plots = "1"
-StatsFuns = "0.9"
diff --git a/docs/literate.jl b/docs/literate.jl
new file mode 100644
index 00000000..304d236b
--- /dev/null
+++ b/docs/literate.jl
@@ -0,0 +1,53 @@
+# Retrieve name of example and output directory
+if length(ARGS) != 2
+    error("please specify the name of the example and the output directory")
+end
+const EXAMPLE = ARGS[1]
+const OUTDIR = ARGS[2]
+
+# Activate environment
+# Note that each example's Project.toml must include Literate as a dependency
+using Pkg: Pkg
+const EXAMPLEPATH = joinpath(@__DIR__, "..", "examples", EXAMPLE)
+Pkg.activate(EXAMPLEPATH)
+Pkg.instantiate()
+using Literate: Literate
+
+function preprocess(content)
+    # Add link to nbviewer below the first heading of level 1
+    sub = SubstitutionString(
+        """
+#md # ```@meta
+#md # EditURL = "@__REPO_ROOT_URL__/examples/@__NAME__/script.jl"
+#md # ```
+#md #
+\\0
+#
+#md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/examples/@__NAME__.ipynb)
+#md #
+# *You are seeing the
+#md # HTML output generated by [Documenter.jl](https://github.com/JuliaDocs/Documenter.jl) and
+#nb # notebook output generated by
+# [Literate.jl](https://github.com/fredrikekre/Literate.jl) from the
+# [Julia source file](@__REPO_ROOT_URL__/examples/@__NAME__/script.jl).
+#md # The corresponding notebook can be viewed in [nbviewer](@__NBVIEWER_ROOT_URL__/examples/@__NAME__.ipynb).*
+#nb # The rendered HTML can be viewed [in the docs](https://juliagaussianprocesses.github.io/AbstractGPs.jl/dev/examples/@__NAME__/).*
+#
+        """,
+    )
+    content = replace(content, r"^# # [^\n]*"m => sub; count=1)
+
+    # remove VSCode `##` block delimiter lines
+    content = replace(content, r"^##$."ms => "")
+
+    return content
+end
+
+# Convert to markdown and notebook
+const SCRIPTJL = joinpath(EXAMPLEPATH, "script.jl")
+Literate.markdown(
+    SCRIPTJL, OUTDIR; name=EXAMPLE, documenter=false, execute=true, preprocess=preprocess
+)
+Literate.notebook(
+    SCRIPTJL, OUTDIR; name=EXAMPLE, documenter=false, execute=true, preprocess=preprocess
+)
diff --git a/docs/make.jl b/docs/make.jl
index 94747d49..14094e97 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -1,51 +1,81 @@
-using Documenter
+### Process examples
+# Always rerun examples
+const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples")
+ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true)
+mkpath(EXAMPLES_OUT)
 
-# Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955)
-if haskey(ENV, "GITHUB_ACTIONS")
-    ENV["JULIA_DEBUG"] = "Documenter"
+# Install and precompile all packages
+# Workaround for https://github.com/JuliaLang/Pkg.jl/issues/2219
+examples = filter!(isdir, readdir(joinpath(@__DIR__, "..", "examples"); join=true))
+let script = "using Pkg; Pkg.activate(ARGS[1]); Pkg.instantiate()"
+    for example in examples
+        if !success(`$(Base.julia_cmd()) -e $script $example`)
+            error(
+                "project environment of example ",
+                basename(example),
+                " could not be instantiated",
+            )
+        end
+    end
+end
+# Run examples asynchronously
+processes = let literatejl = joinpath(@__DIR__, "literate.jl")
+    map(examples) do example
+        return run(
+            pipeline(
+                `$(Base.julia_cmd()) $literatejl $(basename(example)) $EXAMPLES_OUT`;
+                stdin=devnull,
+                stdout=devnull,
+                stderr=stderr,
+            );
+            wait=false,
+        )::Base.Process
+    end
 end
 
-using Literate, AbstractGPs
-
-EXAMPLES = joinpath(@__DIR__, "..", "examples")
-OUTPUT = joinpath(@__DIR__, "src", "examples")
-
-ispath(OUTPUT) && rm(OUTPUT; recursive=true)
+# Check that all examples were run successfully
+isempty(processes) || success(processes) || error("some examples were not run successfully")
 
-# add links to binder and nbviewer below the first heading of level 1
-function preprocess(content)
-    sub = s"""
-\0
-#
-# [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/examples/@__NAME__.ipynb)
-"""
-    return replace(content, r"^# # .*$"m => sub; count=1)
-end
+### Build documentation
+using Documenter
 
-for file in readdir(EXAMPLES; join=true)
-    endswith(file, ".jl") || continue
-    Literate.markdown(file, OUTPUT; documenter=true, preprocess=preprocess)
-    Literate.notebook(file, OUTPUT; documenter=true)
-end
+using AbstractGPs
+# If any features of AbstractGPs depend on optional packages (e.g. via @require),
+# make sure to load them here in order to generate the full API documentation.
 
+# Doctest setup
 DocMeta.setdocmeta!(
-    AbstractGPs, :DocTestSetup, :(using AbstractGPs, LinearAlgebra, Random); recursive=true
+    AbstractGPs,
+    :DocTestSetup,
+    quote
+        using AbstractGPs
+        using LinearAlgebra
+        using Random
+    end;  # we have to load all packages used (implicitly) within jldoctest blocks in the API docstrings
+    recursive=true,
 )
 
 makedocs(;
-    modules=[AbstractGPs],
-    format=Documenter.HTML(),
-    repo="https://github.com/JuliaGaussianProcesses/AbstractGPs.jl/blob/{commit}{path}#L{line}",
     sitename="AbstractGPs.jl",
+    repo="https://github.com/JuliaGaussianProcesses/AbstractGPs.jl/blob/{commit}{path}#L{line}",
+    format=Documenter.HTML(),
+    modules=[AbstractGPs],
     pages=[
         "Home" => "index.md",
         "The Main APIs" => "api.md",
         "Concrete Features" => "concrete_features.md",
         "Examples" =>
-            joinpath.("examples", filter(x -> endswith(x, ".md"), readdir(OUTPUT))),
+            map(filter!(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT))) do x
+                return joinpath("examples", x)
+            end,
+    ],
+    strict=true,
+    checkdocs=:exports,
+    doctestfilters=[
+        r"{([a-zA-Z0-9]+,\s?)+[a-zA-Z0-9]+}",
+        r"(Array{[a-zA-Z0-9]+,\s?1}|Vector{[a-zA-Z0-9]+})",
+        r"(Array{[a-zA-Z0-9]+,\s?2}|Matrix{[a-zA-Z0-9]+})",
     ],
-    # strict=true,
-    # checkdocs=:exports,
 )
 
 deploydocs(; repo="github.com/JuliaGaussianProcesses/AbstractGPs.jl.git", push_preview=true)
diff --git a/examples/README.md b/examples/README.md
new file mode 100644
index 00000000..aa69ec5e
--- /dev/null
+++ b/examples/README.md
@@ -0,0 +1,52 @@
+# Example notebooks
+
+The examples in this directory are stored in [Literate.jl](https://github.com/fredrikekre/Literate.jl) format.
+
+To run them locally, navigate to the directory with the example that you want to run and
+start the Julia REPL and activate the project environment of the example:
+```julia
+julia> ] activate .
+```
+Alternatively, you can start Julia with `julia --project=.`. Then install all required
+packages with
+```julia
+julia> ] instantiate
+```
+Afterwards simply run
+```julia
+julia> include("script.jl")
+```
+In particular when editing an example, it can be convenient to (re-)run only some parts of
+an example.
+Many editors with Julia support such as VSCode, Juno, and Emacs support the evaluation of individual lines or code chunks.
+
+You can convert a notebook to markdown and Jupyter notebook formats, respectively, by executing
+```julia
+julia> using Literate
+julia> Literate.markdown("script.jl", "output_directory")
+julia> Literate.notebook("script.jl", "output_directory")
+```
+(see the [Literate.jl docs](https://fredrikekre.github.io/Literate.jl/v2/) for additional options) or run
+```shell
+julia docs/literate.jl myexample output_directory
+```
+which also executes the code and generates embedded plots etc. in the same way as in building the AbstractGPs documentation.
+
+## Add a new example
+
+Create a new subdirectory in here, and put your code in a file called `script.jl` so that it will get picked up by the automatic docs build.
+
+Every example uses a separate project environment. Therefore you should also create a new
+project environment in the directory of the example that contains all packages required by your script.
+Note that the dependencies of your example *must* include the `Literate` package.
+
+From a Julia REPL started in your example script's directory, you can run
+```julia
+julia> ] activate .
+julia> ] add Literate
+julia> ] add AbstractGPs
+julia> # add any other example-specific dependencies
+```
+to generate the project files.
+
+Make sure to commit both the `Project.toml` and the `Manifest.toml` file when you want to contribute your example in a pull request.
diff --git a/examples/regression-1d/Manifest.toml b/examples/regression-1d/Manifest.toml
new file mode 100644
index 00000000..b8157517
--- /dev/null
+++ b/examples/regression-1d/Manifest.toml
@@ -0,0 +1,1164 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[AbstractGPs]]
+deps = ["ChainRulesCore", "Distributions", "FillArrays", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase"]
+path = ".."
+uuid = "99985d1d-32ba-4be9-9821-2ec096f28918"
+version = "0.3.5"
+
+[[AbstractMCMC]]
+deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"]
+git-tree-sha1 = "21279159f6be4b2fd00e1a4a1f736893100408fc"
+uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
+version = "3.2.0"
+
+[[AbstractTrees]]
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+uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+version = "0.3.4"
+
+[[Adapt]]
+deps = ["LinearAlgebra"]
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+uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
+version = "3.3.1"
+
+[[AdvancedHMC]]
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diff --git a/examples/regression-1d/Project.toml b/examples/regression-1d/Project.toml
new file mode 100644
index 00000000..a3d978d4
--- /dev/null
+++ b/examples/regression-1d/Project.toml
@@ -0,0 +1,28 @@
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+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
+EllipticalSliceSampling = "cad2338a-1db2-11e9-3401-43bc07c9ede2"
+ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
+Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
+
+[compat]
+AbstractGPs = "0.3"
+AdvancedHMC = "0.2"
+Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
+Documenter = "0.27"
+DynamicHMC = "2.2, 3.1"
+EllipticalSliceSampling = "0.3, 0.4"
+ForwardDiff = "0.10"
+Literate = "2.5"
+LogDensityProblems = "0.10"
+Optim = "0.21, 0.22, 1.0"
+Plots = "1"
+StatsFuns = "0.9"
diff --git a/examples/regression_1d.jl b/examples/regression-1d/script.jl
similarity index 100%
rename from examples/regression_1d.jl
rename to examples/regression-1d/script.jl

From 16f6c0b2311d3b24044baa8244ffd653cdb103df Mon Sep 17 00:00:00 2001
From: ST John <st--@users.noreply.github.com>
Date: Mon, 19 Jul 2021 14:57:56 +0300
Subject: [PATCH 2/8] remove Documenter from example dependencies

---
 examples/regression-1d/Manifest.toml | 6 ------
 examples/regression-1d/Project.toml  | 2 --
 2 files changed, 8 deletions(-)

diff --git a/examples/regression-1d/Manifest.toml b/examples/regression-1d/Manifest.toml
index b8157517..253233a9 100644
--- a/examples/regression-1d/Manifest.toml
+++ b/examples/regression-1d/Manifest.toml
@@ -204,12 +204,6 @@ git-tree-sha1 = "a32185f5428d3986f47c2ab78b1f216d5e6cc96f"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 version = "0.8.5"
 
-[[Documenter]]
-deps = ["Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "5acbebf1be22db43589bc5aa1bb5fcc378b17780"
-uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.27.0"
-
 [[Downloads]]
 deps = ["ArgTools", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
diff --git a/examples/regression-1d/Project.toml b/examples/regression-1d/Project.toml
index a3d978d4..77c8eda6 100644
--- a/examples/regression-1d/Project.toml
+++ b/examples/regression-1d/Project.toml
@@ -2,7 +2,6 @@
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"
 AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
 EllipticalSliceSampling = "cad2338a-1db2-11e9-3401-43bc07c9ede2"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -17,7 +16,6 @@ StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 AbstractGPs = "0.3"
 AdvancedHMC = "0.2"
 Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
-Documenter = "0.27"
 DynamicHMC = "2.2, 3.1"
 EllipticalSliceSampling = "0.3, 0.4"
 ForwardDiff = "0.10"

From 8bfdfe2bda0a250c05e5b598e17b683cdf28186b Mon Sep 17 00:00:00 2001
From: ST John <st--@users.noreply.github.com>
Date: Mon, 19 Jul 2021 15:35:54 +0300
Subject: [PATCH 3/8] depend on AbstractGPs explicit hash rather than .. for
 example

---
 examples/regression-1d/Manifest.toml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/examples/regression-1d/Manifest.toml b/examples/regression-1d/Manifest.toml
index 253233a9..fef14320 100644
--- a/examples/regression-1d/Manifest.toml
+++ b/examples/regression-1d/Manifest.toml
@@ -2,9 +2,9 @@
 
 [[AbstractGPs]]
 deps = ["ChainRulesCore", "Distributions", "FillArrays", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase"]
-path = ".."
+git-tree-sha1 = "d8b6584ff1d523dd1304671f2c8a557dad26e214"
 uuid = "99985d1d-32ba-4be9-9821-2ec096f28918"
-version = "0.3.5"
+version = "0.3.6"
 
 [[AbstractMCMC]]
 deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"]
@@ -495,9 +495,9 @@ version = "1.42.0+0"
 
 [[Libiconv_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "8d22e127ea9a0917bc98ebd3755c8bd31989381e"
+git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778"
 uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
-version = "1.16.1+0"
+version = "1.16.1+1"
 
 [[Libmount_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]

From 7832f10392c27170aa80cccfd3a06d90b75556d1 Mon Sep 17 00:00:00 2001
From: ST John <st--@users.noreply.github.com>
Date: Mon, 19 Jul 2021 15:37:56 +0300
Subject: [PATCH 4/8] update CompatHelper workflow from KernelFunctions.jl

---
 .github/workflows/CompatHelper.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
index bd3dfde5..c13c749e 100644
--- a/.github/workflows/CompatHelper.yml
+++ b/.github/workflows/CompatHelper.yml
@@ -9,6 +9,7 @@ jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
+      - uses: actions/checkout@v2
       - name: "Install CompatHelper"
         run: |
           import Pkg
@@ -20,7 +21,14 @@ jobs:
       - name: "Run CompatHelper"
         run: |
           import CompatHelper
-          CompatHelper.main(; subdirs=["", "test", "test/ppl", "docs"])
+          subdirs = ["", "test", "docs"]
+          for f in readdir("examples"; join=true)
+              if isdir(f)
+                  push!(subdirs, joinpath("examples", basename(f)))
+              end
+          end
+          @info "CompatHelper directories" subdirs
+          CompatHelper.main(; subdirs=subdirs)
         shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

From 694eab3568dcaa07a91ba648f599852f2a2ed854 Mon Sep 17 00:00:00 2001
From: ST John <st--@users.noreply.github.com>
Date: Mon, 19 Jul 2021 15:47:25 +0300
Subject: [PATCH 5/8] add jitter to VI example

---
 examples/regression-1d/script.jl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/examples/regression-1d/script.jl b/examples/regression-1d/script.jl
index 7257131e..21e2f3ea 100644
--- a/examples/regression-1d/script.jl
+++ b/examples/regression-1d/script.jl
@@ -392,7 +392,9 @@ function objective_function(x, y)
             softplus(params[1]) * (Matern52Kernel() ∘ ScaleTransform(softplus(params[2])))
         f = GP(kernel)
         fx = f(x, 0.1)
-        return -elbo(fx, y, f(logistic.(params[3:end])))
+        z = logistic.(params[3:end])
+        fz = f(z, 1e-6)  # "observing" the latent process with some (small) amount of jitter improves numerical stability
+        return -elbo(fx, y, fz)
     end
     return negative_elbo
 end

From abc88d0e33b583a7712d8d777fe0746c12f59501 Mon Sep 17 00:00:00 2001
From: st-- <st--@users.noreply.github.com>
Date: Mon, 19 Jul 2021 22:57:59 +0300
Subject: [PATCH 6/8] Update docs/make.jl

---
 docs/make.jl | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docs/make.jl b/docs/make.jl
index 14094e97..72d77ef3 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -57,7 +57,6 @@ DocMeta.setdocmeta!(
 
 makedocs(;
     sitename="AbstractGPs.jl",
-    repo="https://github.com/JuliaGaussianProcesses/AbstractGPs.jl/blob/{commit}{path}#L{line}",
     format=Documenter.HTML(),
     modules=[AbstractGPs],
     pages=[

From 681942eb9fa9abc28822054fb077d90b25b026ed Mon Sep 17 00:00:00 2001
From: ST John <st--@users.noreply.github.com>
Date: Tue, 20 Jul 2021 11:22:11 +0300
Subject: [PATCH 7/8] move to dev ../.. for AbstractGPs dependencies in
 examples

---
 examples/README.md                   | 3 ++-
 examples/regression-1d/Manifest.toml | 6 +++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/examples/README.md b/examples/README.md
index aa69ec5e..7eb486cc 100644
--- a/examples/README.md
+++ b/examples/README.md
@@ -44,7 +44,8 @@ From a Julia REPL started in your example script's directory, you can run
 ```julia
 julia> ] activate .
 julia> ] add Literate
-julia> ] add AbstractGPs
+julia> # the following line adds an AbstractGPs dependency that is based on the local directories, not a hash:
+julia> ] dev ../..
 julia> # add any other example-specific dependencies
 ```
 to generate the project files.
diff --git a/examples/regression-1d/Manifest.toml b/examples/regression-1d/Manifest.toml
index fef14320..006d505c 100644
--- a/examples/regression-1d/Manifest.toml
+++ b/examples/regression-1d/Manifest.toml
@@ -1,10 +1,10 @@
 # This file is machine-generated - editing it directly is not advised
 
 [[AbstractGPs]]
-deps = ["ChainRulesCore", "Distributions", "FillArrays", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase"]
-git-tree-sha1 = "d8b6584ff1d523dd1304671f2c8a557dad26e214"
+deps = ["ChainRulesCore", "Distributions", "FillArrays", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"]
+path = "../.."
 uuid = "99985d1d-32ba-4be9-9821-2ec096f28918"
-version = "0.3.6"
+version = "0.3.7"
 
 [[AbstractMCMC]]
 deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"]

From bff43cb44b8d800d175aad792078d5e45a8ac87a Mon Sep 17 00:00:00 2001
From: ST John <st--@users.noreply.github.com>
Date: Tue, 20 Jul 2021 11:31:38 +0300
Subject: [PATCH 8/8] cannot makedocs with strict=true as there are exported
 docstrings not included in the docs

---
 docs/make.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/make.jl b/docs/make.jl
index 14094e97..10eac3d4 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -69,7 +69,7 @@ makedocs(;
                 return joinpath("examples", x)
             end,
     ],
-    strict=true,
+    #strict=true,
     checkdocs=:exports,
     doctestfilters=[
         r"{([a-zA-Z0-9]+,\s?)+[a-zA-Z0-9]+}",