Rename SVGP to SparseVariationalApproximation (#70)

* Rename `SVGP` to `StochasticVariationalApproximation` * Stochastic -> sparse * Formatting Co-authored-by: st-- <[email protected]> * Add SVGP deprecation * Patch bump and change author * Update test, docs & examples Projects and Manifests Co-authored-by: st-- <[email protected]>
JuliaGaussianProcesses · Nov 5, 2021 · 4d207c5 · 4d207c5 · rossviljoen · Nov 5, 2021
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diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "ApproximateGPs"
 uuid = "298c2ebc-0411-48ad-af38-99e88101b606"
-authors = ["Ross Viljoen <[email protected]>"]
-version = "0.1.2"
+authors = ["JuliaGaussianProcesses Team"]
+version = "0.2.0"
 
 [deps]
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"

diff --git a/docs/Manifest.toml b/docs/Manifest.toml
@@ -7,15 +7,15 @@ version = "0.0.1"
 
 [[AbstractGPs]]
 deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"]
-git-tree-sha1 = "80b6c9734d00ae7518e65a0e1063772a050d04a0"
+git-tree-sha1 = "e2af18922f65ea8cee7b8cd97a1668691f76f4b2"
 uuid = "99985d1d-32ba-4be9-9821-2ec096f28918"
-version = "0.5.1"
+version = "0.5.3"
 
 [[ApproximateGPs]]
-deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"]
+deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"]
 path = ".."
 uuid = "298c2ebc-0411-48ad-af38-99e88101b606"
-version = "0.1.0"
+version = "0.2.0"
 
 [[ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
@@ -28,15 +28,21 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "4ce9393e871aca86cc457d9f66976c3da6902ea7"
+git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.4.0"
+version = "1.11.1"
+
+[[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 = "4866e381721b30fac8dda4c8cb1d9db45c8d2994"
+git-tree-sha1 = "dce3e3fea680869eaa0b774b2e8343e9ff442313"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "3.37.0"
+version = "3.40.0"
 
 [[CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -48,9 +54,9 @@ uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b"
 version = "0.1.1"
 
 [[DataAPI]]
-git-tree-sha1 = "bec2532f8adb82005476c141ec23e921fc20971b"
+git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
-version = "1.8.0"
+version = "1.9.0"
 
 [[DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -66,33 +72,45 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 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 = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"]
+git-tree-sha1 = "3287dacf67c3652d3fed09f4c12c187ae4dbb89a"
+uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
+version = "1.4.0"
+
 [[Distances]]
 deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
-git-tree-sha1 = "9f46deb4d4ee4494ffb5a40a27a2aced67bdd838"
+git-tree-sha1 = "837c83e5574582e07662bbbba733964ff7c26b9d"
 uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
-version = "0.10.4"
+version = "0.10.6"
 
 [[Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
 deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "f4efaa4b5157e0cdb8283ae0b5428bc9208436ed"
+git-tree-sha1 = "72dcda9e19f88d09bf21b5f9507a0bb430bce2aa"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.16"
+version = "0.25.24"
 
 [[DocStringExtensions]]
 deps = ["LibGit2"]
-git-tree-sha1 = "a32185f5428d3986f47c2ab78b1f216d5e6cc96f"
+git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-version = "0.8.5"
+version = "0.8.6"
 
 [[Documenter]]
 deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "fe0bc46b27cd3413df55859152fd70e50744025f"
+git-tree-sha1 = "f425293f7e0acaf9144de6d731772de156676233"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.27.6"
+version = "0.27.10"
 
 [[Downloads]]
 deps = ["ArgTools", "LibCURL", "NetworkOptions"]
@@ -106,20 +124,26 @@ version = "0.4.7"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"]
-git-tree-sha1 = "caf289224e622f518c9dbfe832cdafa17d7c80a6"
+git-tree-sha1 = "8756f9935b7ccc9064c6eef0bff0ad643df733a3"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.12.4"
+version = "0.12.7"
+
+[[ForwardDiff]]
+deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"]
+git-tree-sha1 = "ef3fec65f9db26fa2cf8f4133c697c5b7ce63c1d"
+uuid = "f6369f11-7733-5829-9624-2563aa707210"
+version = "0.10.22"
 
 [[Functors]]
-git-tree-sha1 = "e2727f02325451f6b24445cd83bfa9aaac19cbe7"
+git-tree-sha1 = "e4768c3b7f597d5a352afa09874d16e3c3f6ead2"
 uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
-version = "0.2.5"
+version = "0.2.7"
 
 [[GPLikelihoods]]
 deps = ["Distributions", "Functors", "LinearAlgebra", "Random", "StatsFuns"]
-git-tree-sha1 = "e07acc5ca79ead40c8cf0338c9357fc7fb90eea1"
+git-tree-sha1 = "bdfe8a65b3ca3aa92812d74138264570f33aa66e"
 uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40"
-version = "0.2.0"
+version = "0.2.4"
 
 [[IOCapture]]
 deps = ["Logging", "Random"]
@@ -131,10 +155,16 @@ version = "0.2.2"
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
+[[InverseFunctions]]
+deps = ["Test"]
+git-tree-sha1 = "f0c6489b12d28fb4c2103073ec7452f3423bd308"
+uuid = "3587e190-3f89-42d0-90ee-14403ec27112"
+version = "0.1.1"
+
 [[IrrationalConstants]]
-git-tree-sha1 = "f76424439413893a832026ca355fe273e93bce94"
+git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151"
 uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
-version = "0.1.0"
+version = "0.1.1"
 
 [[JLLWrappers]]
 deps = ["Preferences"]
@@ -156,9 +186,9 @@ version = "0.2.1"
 
 [[KernelFunctions]]
 deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Random", "Requires", "SpecialFunctions", "StatsBase", "TensorCore", "Test", "ZygoteRules"]
-git-tree-sha1 = "3b7fceeab37b650c280eb072ffe2b868b03a5423"
+git-tree-sha1 = "9c3d38dafc02feae68a4747813b8b0205fd03da5"
 uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392"
-version = "0.10.17"
+version = "0.10.26"
 
 [[LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
@@ -184,19 +214,19 @@ deps = ["Libdl"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[LogExpFunctions]]
-deps = ["ChainRulesCore", "DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "34dc30f868e368f8a17b728a1238f3fcda43931a"
+deps = ["ChainRulesCore", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
+git-tree-sha1 = "6193c3815f13ba1b78a51ce391db8be016ae9214"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.3"
+version = "0.3.4"
 
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[MacroTools]]
 deps = ["Markdown", "Random"]
-git-tree-sha1 = "5a5bc6bf062f0f95e62d0fe0a2d99699fed82dd9"
+git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf"
 uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-version = "0.5.8"
+version = "0.5.9"
 
 [[Markdown]]
 deps = ["Base64"]
@@ -218,9 +248,18 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 [[MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 
+[[NaNMath]]
+git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb"
+uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
+version = "0.3.5"
+
 [[NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 
+[[OpenLibm_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
+
 [[OpenSpecFun_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1"
@@ -234,15 +273,15 @@ version = "1.4.1"
 
 [[PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "4dd403333bcf0909341cfe57ec115152f937d7d8"
+git-tree-sha1 = "c8b8775b2f242c80ea85c83714c64ecfa3c53355"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.11.1"
+version = "0.11.3"
 
 [[Parsers]]
 deps = ["Dates"]
-git-tree-sha1 = "438d35d2d95ae2c5e8780b330592b6de8494e779"
+git-tree-sha1 = "ae4bbcadb2906ccc085cf52ac286dc1377dceccc"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.0.3"
+version = "2.1.2"
 
 [[Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
@@ -260,9 +299,9 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [[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", "Unicode"]
@@ -324,16 +363,16 @@ deps = ["LinearAlgebra", "Random"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
-deps = ["ChainRulesCore", "LogExpFunctions", "OpenSpecFun_jll"]
-git-tree-sha1 = "a322a9493e49c5f3a10b50df3aedaf1cdb3244b7"
+deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
+git-tree-sha1 = "f0bccf98e16759818ffc5d97ac3ebf87eb950150"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "1.6.1"
+version = "1.8.1"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "3240808c6d463ac46f1c1cd7638375cd22abbccb"
+git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.2.12"
+version = "1.2.13"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -345,16 +384,16 @@ uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
 version = "1.0.0"
 
 [[StatsBase]]
-deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "8cbbc098554648c84f79a463c9ff0fd277144b6c"
+deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
+git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.33.10"
+version = "0.33.12"
 
 [[StatsFuns]]
 deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "46d7ccc7104860c38b11966dd1f72ff042f382e4"
+git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.10"
+version = "0.9.12"
 
 [[SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
@@ -391,9 +430,9 @@ 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"
 
 [[nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -3,5 +3,5 @@ ApproximateGPs = "298c2ebc-0411-48ad-af38-99e88101b606"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 
 [compat]
-ApproximateGPs = "0.1"
+ApproximateGPs = "0.2"
 Documenter = "0.27"