Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,11 @@

language: julia
julia:
- 1.5
- 1.6

# run these in parallel
env:
- GEN_EXAMPLE=rws_mnist JULIA_NUM_THREADS=2 OPENBLAS_NUM_THREADS=1
- GEN_EXAMPLE=gp_structure GKS_ENCODING="utf8" GKSwstype="100"
- GEN_EXAMPLE=regression
- GEN_EXAMPLE=involutive_mcmc
Expand Down
2 changes: 2 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -26,3 +26,5 @@ NOTE: These examples take substantially longer to run than Gen's unit tests.
- Minimal example of maximum likelihood estimation: `mle/`

- Reversible jump MCMC in change point model: `coal/`

- Learning a deep generative model of binarized MNIST digits using [reweighted wake sleep](https://arxiv.org/abs/1406.2751): `rws_mnist/`
194 changes: 132 additions & 62 deletions mle/Manifest.toml
Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
# This file is machine-generated - editing it directly is not advised

[[ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"

[[Artifacts]]
deps = ["Pkg"]
git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
version = "1.3.0"

[[Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[ChainRulesCore]]
deps = ["Compat", "LinearAlgebra", "SparseArrays"]
git-tree-sha1 = "de4f08843c332d355852721adb1592bce7924da3"
git-tree-sha1 = "b391f22252b8754f4440de1f37ece49d8a7314bb"
uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
version = "0.9.29"
version = "0.9.44"

[[CommonSubexpressions]]
deps = ["MacroTools", "Test"]
Expand All @@ -23,20 +23,18 @@ version = "0.3.0"

[[Compat]]
deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
git-tree-sha1 = "919c7f3151e79ff196add81d7f4e45d91bbf420b"
git-tree-sha1 = "e4e2b39db08f967cc1360951f01e8a75ec441cab"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
version = "3.25.0"
version = "3.30.0"

[[CompilerSupportLibraries_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "8e695f735fca77e9708e795eda62afdb869cbb70"
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "0.3.4+0"

[[DataAPI]]
git-tree-sha1 = "8ab70b4de35bb3b8cc19654f6b893cf5164f8ee8"
git-tree-sha1 = "dfb3b7e89e395be1e25c2ad6d7690dc29cc53b1d"
uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
version = "1.5.1"
version = "1.6.0"

[[DataStructures]]
deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
Expand Down Expand Up @@ -70,26 +68,36 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"

[[Distributions]]
deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
git-tree-sha1 = "f0e06a5b5ccda38e2fb8f59d91316e657b67047d"
git-tree-sha1 = "a837fdf80f333415b69684ba8e8ae6ba76de6aaa"
uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
version = "0.24.12"
version = "0.24.18"

[[DocStringExtensions]]
deps = ["LibGit2", "Markdown", "Pkg", "Test"]
git-tree-sha1 = "9d4f64f79012636741cf01133158a54b24924c32"
uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
version = "0.8.4"

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

[[FillArrays]]
deps = ["LinearAlgebra", "Random", "SparseArrays"]
git-tree-sha1 = "e384d3cff80ac79c7a541a817192841836e46331"
git-tree-sha1 = "31939159aeb8ffad1d4d8ee44d07f8558273120a"
uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
version = "0.11.2"
version = "0.11.7"

[[ForwardDiff]]
deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"]
git-tree-sha1 = "d48a40c0f54f29a5c8748cfb3225719accc72b77"
deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Printf", "Random", "SpecialFunctions", "StaticArrays"]
git-tree-sha1 = "e2af66012e08966366a43251e1fd421522908be6"
uuid = "f6369f11-7733-5829-9624-2563aa707210"
version = "0.10.16"
version = "0.10.18"

[[FunctionWrappers]]
git-tree-sha1 = "e4813d187be8c7b993cb7f85cbf2b7bfbaadc694"
git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc"
uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
version = "1.1.1"
version = "1.1.2"

[[FunctionalCollections]]
deps = ["Test"]
Expand All @@ -98,37 +106,58 @@ uuid = "de31a74c-ac4f-5751-b3fd-e18cd04993ca"
version = "0.5.0"

[[Gen]]
deps = ["DataStructures", "Distributions", "ForwardDiff", "FunctionalCollections", "JSON", "LinearAlgebra", "MacroTools", "Parameters", "Random", "ReverseDiff", "SpecialFunctions"]
git-tree-sha1 = "00b42c1484d658ed9fd74ffe93ddc5259d0d010e"
deps = ["Compat", "DataStructures", "Distributions", "ForwardDiff", "FunctionalCollections", "JSON", "LinearAlgebra", "MacroTools", "Parameters", "Random", "ReverseDiff", "SpecialFunctions"]
git-tree-sha1 = "b6cd202d1dc5020e5c9a300338413010e3aed5c9"
repo-rev = "20210512-marcoct-gradopts"
repo-url = "https://github.com/probcomp/Gen.jl.git"
uuid = "ea4f424c-a589-11e8-07c0-fd5c91b9da4a"
version = "0.4.1"
version = "0.4.3"

[[InteractiveUtils]]
deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[JLLWrappers]]
git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0"
deps = ["Preferences"]
git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e"
uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
version = "1.2.0"
version = "1.3.0"

[[JSON]]
deps = ["Dates", "Mmap", "Parsers", "Unicode"]
git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4"
uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
version = "0.21.1"

[[LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"

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

[[LibGit2]]
deps = ["Printf"]
deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"

[[LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"

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

[[LinearAlgebra]]
deps = ["Libdl"]
uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[[LogExpFunctions]]
deps = ["DocStringExtensions", "LinearAlgebra"]
git-tree-sha1 = "1ba664552f1ef15325e68dc4c05c3ef8c2d5d885"
uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
version = "0.2.4"

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

Expand All @@ -142,36 +171,46 @@ version = "0.5.6"
deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"

[[MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"

[[Missings]]
deps = ["DataAPI"]
git-tree-sha1 = "f8c673ccc215eb50fcadb285f522420e29e69e1c"
git-tree-sha1 = "4ea90bd5d3985ae1f9a908bd4500ae88921c5ce7"
uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
version = "0.4.5"
version = "1.0.0"

[[Mmap]]
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"

[[OpenSpecFun_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "9db77584158d0ab52307f8c04f8e7c08ca76b5b3"
git-tree-sha1 = "b9b8b8ed236998f91143938a760c2112dceeb2b4"
uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
version = "0.5.3+4"
version = "0.5.4+0"

[[OrderedCollections]]
git-tree-sha1 = "d45739abcfc03b51f6a42712894a593f74c80a23"
git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.3.3"
version = "1.4.1"

[[PDMats]]
deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"]
git-tree-sha1 = "95a4038d1011dfdbde7cecd2ad0ac411e53ab1bc"
deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
git-tree-sha1 = "f82a0e71f222199de8e9eb9a09977bd0767d52a0"
uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
version = "0.10.1"
version = "0.11.0"

[[Parameters]]
deps = ["OrderedCollections", "UnPack"]
Expand All @@ -181,14 +220,20 @@ version = "0.12.2"

[[Parsers]]
deps = ["Dates"]
git-tree-sha1 = "50c9a9ed8c714945e01cd53a21007ed3865ed714"
git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc"
uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
version = "1.0.15"
version = "1.1.0"

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

[[Preferences]]
deps = ["TOML"]
git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a"
uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.2.2"

[[Printf]]
deps = ["Unicode"]
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
Expand All @@ -200,7 +245,7 @@ uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
version = "2.4.1"

[[REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets"]
deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[Random]]
Expand All @@ -209,21 +254,21 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

[[ReverseDiff]]
deps = ["DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"]
git-tree-sha1 = "ca062d55a167a81909772a325932e72c389f9724"
git-tree-sha1 = "63ee24ea0689157a1113dbdab10c6cb011d519c4"
uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
version = "1.5.0"
version = "1.9.0"

[[Rmath]]
deps = ["Random", "Rmath_jll"]
git-tree-sha1 = "86c5647b565873641538d8f812c04e4c9dbeb370"
git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f"
uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa"
version = "0.6.1"
version = "0.7.0"

[[Rmath_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "d76185aa1f421306dec73c057aa384bad74188f0"
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7"
uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f"
version = "0.2.2+1"
version = "0.3.0+0"

[[SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
Expand All @@ -239,49 +284,62 @@ uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"

[[SortingAlgorithms]]
deps = ["DataStructures", "Random", "Test"]
git-tree-sha1 = "03f5898c9959f8115e30bc7226ada7d0df554ddd"
deps = ["DataStructures"]
git-tree-sha1 = "2ec1962eba973f383239da22e75218565c390a96"
uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
version = "0.3.1"
version = "1.0.0"

[[SparseArrays]]
deps = ["LinearAlgebra", "Random"]
uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[[SpecialFunctions]]
deps = ["ChainRulesCore", "OpenSpecFun_jll"]
git-tree-sha1 = "75394dbe2bd346beeed750fb02baa6445487b862"
deps = ["ChainRulesCore", "LogExpFunctions", "OpenSpecFun_jll"]
git-tree-sha1 = "9146da51b38e9705b9f5ccfadc3ab10a482cae36"
uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
version = "1.2.1"
version = "1.4.0"

[[StaticArrays]]
deps = ["LinearAlgebra", "Random", "Statistics"]
git-tree-sha1 = "9da72ed50e94dbff92036da395275ed114e04d49"
git-tree-sha1 = "c635017268fd51ed944ec429bcc4ad010bcea900"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.0.1"
version = "1.2.0"

[[Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[[StatsAPI]]
git-tree-sha1 = "1958272568dc176a1d881acb797beb909c785510"
uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
version = "1.0.0"

[[StatsBase]]
deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"]
git-tree-sha1 = "7bab7d4eb46b225b35179632852b595a3162cb61"
deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
git-tree-sha1 = "2f6792d523d7448bbe2fec99eca9218f06cc746d"
uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
version = "0.33.2"
version = "0.33.8"

[[StatsFuns]]
deps = ["Rmath", "SpecialFunctions"]
git-tree-sha1 = "3b9f665c70712af3264b61c27a7e1d62055dafd1"
deps = ["LogExpFunctions", "Rmath", "SpecialFunctions"]
git-tree-sha1 = "30cd8c360c54081f806b1ee14d2eecbef3c04c49"
uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
version = "0.9.6"
version = "0.9.8"

[[SuiteSparse]]
deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"

[[TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"

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

[[Test]]
deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[UUIDs]]
Expand All @@ -295,3 +353,15 @@ version = "1.0.2"

[[Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"

[[nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"

[[p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
Loading