diff --git a/.travis.yml b/.travis.yml index c4265aafe..027ba815b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,9 +15,7 @@ jobs: env: STAGE=test script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + - julia --check-bounds=yes -e 'using Pkg; Pkg.test("Turing"; coverage=true)' - stage: test os: linux @@ -25,9 +23,7 @@ jobs: env: STAGE=test script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + - julia --check-bounds=yes -e 'using Pkg; Pkg.test("Turing"; coverage=true)' - stage: numerical allow_failures: true @@ -36,9 +32,7 @@ jobs: env: STAGE=numerical script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + - julia --check-bounds=yes -e 'using Pkg; Pkg.test("Turing"; coverage=true)' - stage: numerical allow_failures: true @@ -48,8 +42,7 @@ jobs: script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + Pkg.add("Turing"); Pkg.test("Turing"; coverage=true)' - stage: test julia: 1.0 @@ -58,9 +51,7 @@ jobs: env: STAGE=test script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + - julia --check-bounds=yes -e 'using Pkg; Pkg.test("Turing"; coverage=true)' - stage: test julia: 1.1 @@ -69,9 +60,7 @@ jobs: env: STAGE=test script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + - julia --check-bounds=yes -e 'using Pkg; Pkg.test("Turing"; coverage=true)' - stage: stan allow_failures: true @@ -80,9 +69,7 @@ jobs: env: STAGE=stan script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + - julia --check-bounds=yes -e 'using Pkg; Pkg.test("Turing"; coverage=true)' - stage: stan allow_failures: true @@ -91,9 +78,7 @@ jobs: env: STAGE=stan script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + - julia --check-bounds=yes -e 'using Pkg; Pkg.test("Turing"; coverage=true)' - stage: dynamichmc allow_failures: true @@ -102,9 +87,7 @@ jobs: env: STAGE=dynamichmc script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + - julia --check-bounds=yes -e 'using Pkg; Pkg.test("Turing"; coverage=true)' - stage: dynamichmc allow_failures: true @@ -113,9 +96,7 @@ jobs: env: STAGE=dynamichmc script: - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --check-bounds=yes -e 'using Pkg;Pkg.update(); - Pkg.clone(pwd(), "Turing"); - Pkg.build("Turing"); + - julia --check-bounds=yes -e 'using Pkg; Pkg.test("Turing"; coverage=true)' - stage: documentation julia: 1.1 @@ -123,7 +104,7 @@ jobs: if: branch = master env: STAGE=documentation script: - - julia -e 'using Pkg; Pkg.update(); Pkg.clone(pwd(), "Turing"); Pkg.build("Turing");' + - julia -e 'using Pkg; Pkg.update();' - julia -e 'using Pkg; Pkg.add("Documenter"), Pkg.add("DocumenterMarkdown"), Pkg.add("DynamicHMC")' - julia -e 'using Pkg, Turing; cd(joinpath(dirname(pathof(Turing)), "..")); diff --git a/Manifest.toml b/Manifest.toml new file mode 100644 index 000000000..9a4d04489 --- /dev/null +++ b/Manifest.toml @@ -0,0 +1,592 @@ +# This file is machine-generated - editing it directly is not advised + +[[AbstractFFTs]] +deps = ["LinearAlgebra", "Test"] +git-tree-sha1 = "dfaf23dba016254bb0eed6de326510caea2889bf" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "0.4.0" + +[[AbstractTrees]] +deps = ["Markdown", "Test"] +git-tree-sha1 = "6621d9645702c1c4e6970cc6a3eae440c768000b" +uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" +version = "0.2.1" + +[[Adapt]] +deps = ["LinearAlgebra", "Test"] +git-tree-sha1 = "53d8fec4f662088c1202530e338a11a919407f3b" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "0.4.2" + +[[Arpack]] +deps = ["BinaryProvider", "Libdl", "LinearAlgebra", "Random", "SparseArrays", "Test"] +git-tree-sha1 = "1ce1ce9984683f0b6a587d5bdbc688ecb480096f" +uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" +version = "0.3.0" + +[[AxisAlgorithms]] +deps = ["Compat", "WoodburyMatrices"] +git-tree-sha1 = "99dabbe853e4f641ab21a676131f2cf9fb29937e" +uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" +version = "0.3.0" + +[[AxisArrays]] +deps = ["Compat", "Dates", "IntervalSets", "IterTools", "Random", "RangeArrays", "Test"] +git-tree-sha1 = "2e2536e9e6f27c4f8d09d8442b61a7ae0b910c28" +uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" +version = "0.3.0" + +[[Base64]] +uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" + +[[Bijectors]] +deps = ["Distributions", "LinearAlgebra", "MappedArrays", "Random", "Reexport", "Requires", "StatsFuns", "Test"] +git-tree-sha1 = "09cecb9cdf0237e95731606927551f2199ac4840" +uuid = "76274a88-744f-5084-9051-94815aaf08c4" +version = "0.2.9" + +[[BinDeps]] +deps = ["Compat", "Libdl", "SHA", "URIParser"] +git-tree-sha1 = "12093ca6cdd0ee547c39b1870e0c9c3f154d9ca9" +uuid = "9e28174c-4ba2-5203-b857-d8d62c4213ee" +version = "0.8.10" + +[[BinaryProvider]] +deps = ["Libdl", "Pkg", "SHA", "Test"] +git-tree-sha1 = "055eb2690182ebc31087859c3dd8598371d3ef9e" +uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" +version = "0.5.3" + +[[CSTParser]] +deps = ["LibGit2", "Test", "Tokenize"] +git-tree-sha1 = "437c93bc191cd55957b3f8dee7794b6131997c56" +uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f" +version = "0.5.2" + +[[Calculus]] +deps = ["Compat"] +git-tree-sha1 = "f60954495a7afcee4136f78d1d60350abd37a409" +uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" +version = "0.4.1" + +[[CategoricalArrays]] +deps = ["Compat", "Future", "Missings", "Printf", "Reexport", "Requires"] +git-tree-sha1 = "94d16e77dfacc59f6d6c1361866906dbb65b6f6b" +uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" +version = "0.5.2" + +[[CodecZlib]] +deps = ["BinaryProvider", "Libdl", "Test", "TranscodingStreams"] +git-tree-sha1 = "36bbf5374c661054d41410dc53ff752972583b9b" +uuid = "944b1d66-785c-5afd-91f1-9de20f533193" +version = "0.5.2" + +[[ColorTypes]] +deps = ["FixedPointNumbers", "Random", "Test"] +git-tree-sha1 = "f73b0e10f2a5756de7019818a41654686da06b09" +uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" +version = "0.7.5" + +[[Colors]] +deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Printf", "Reexport", "Test"] +git-tree-sha1 = "9f0a0210450acb91c730b730a994f8eef1d3d543" +uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" +version = "0.9.5" + +[[CommonSubexpressions]] +deps = ["Test"] +git-tree-sha1 = "efdaf19ab11c7889334ca247ff4c9f7c322817b0" +uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" +version = "0.2.0" + +[[Compat]] +deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] +git-tree-sha1 = "84aa74986c5b9b898b0d1acaf3258741ee64754f" +uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" +version = "2.1.0" + +[[Conda]] +deps = ["Compat", "JSON", "VersionParsing"] +git-tree-sha1 = "b625d802587c2150c279a40a646fba63f9bd8187" +uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" +version = "1.2.0" + +[[Contour]] +deps = ["LinearAlgebra", "StaticArrays", "Test"] +git-tree-sha1 = "b974e164358fea753ef853ce7bad97afec15bb80" +uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" +version = "0.5.1" + +[[DataFrames]] +deps = ["CategoricalArrays", "CodecZlib", "Compat", "DataStreams", "Dates", "InteractiveUtils", "IteratorInterfaceExtensions", "LinearAlgebra", "Missings", "Printf", "Random", "Reexport", "SortingAlgorithms", "Statistics", "StatsBase", "TableTraits", "Tables", "Test", "TranscodingStreams", "Unicode", "WeakRefStrings"] +git-tree-sha1 = "9cfed75401d25d281076eb5d82de148ac2933f9e" +uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +version = "0.17.1" + +[[DataStreams]] +deps = ["Dates", "Missings", "Test", "WeakRefStrings"] +git-tree-sha1 = "69c72a1beb4fc79490c361635664e13c8e4a9548" +uuid = "9a8bc11e-79be-5b39-94d7-1ccc349a1a85" +version = "0.4.1" + +[[DataStructures]] +deps = ["InteractiveUtils", "OrderedCollections", "Random", "Serialization", "Test"] +git-tree-sha1 = "ca971f03e146cf144a9e2f2ce59674f5bf0e8038" +uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" +version = "0.15.0" + +[[Dates]] +deps = ["Printf"] +uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" + +[[DelimitedFiles]] +deps = ["Mmap"] +uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" + +[[DiffEqDiffTools]] +deps = ["LinearAlgebra", "Test"] +git-tree-sha1 = "30f82c63cb9d293513b360572e283c19577fcf82" +uuid = "01453d9d-ee7c-5054-8395-0335cb756afa" +version = "0.8.1" + +[[DiffResults]] +deps = ["Compat", "StaticArrays"] +git-tree-sha1 = "34a4a1e8be7bc99bc9c611b895b5baf37a80584c" +uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" +version = "0.0.4" + +[[DiffRules]] +deps = ["Random", "Test"] +git-tree-sha1 = "dc0869fb2f5b23466b32ea799bd82c76480167f7" +uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" +version = "0.0.10" + +[[Distributed]] +deps = ["Random", "Serialization", "Sockets"] +uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" + +[[Distributions]] +deps = ["Distributed", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "022e6610c320b6e19b454502d759c672580abe00" +uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" +version = "0.18.0" + +[[FFTW]] +deps = ["AbstractFFTs", "BinaryProvider", "Compat", "Conda", "Libdl", "LinearAlgebra", "Reexport", "Test"] +git-tree-sha1 = "29cda58afbf62f35b1a094882ad6c745a47b2eaa" +uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" +version = "0.2.4" + +[[FixedPointNumbers]] +deps = ["Test"] +git-tree-sha1 = "b8045033701c3b10bf2324d7203404be7aef88ba" +uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" +version = "0.5.3" + +[[Flux]] +deps = ["AbstractTrees", "Adapt", "CodecZlib", "Colors", "DelimitedFiles", "Juno", "LinearAlgebra", "MacroTools", "NNlib", "Pkg", "Random", "Reexport", "Requires", "SHA", "Statistics", "StatsBase", "Test", "Tracker", "ZipFile"] +git-tree-sha1 = "75e5a6850ad9d6129773171d9ba66be899a515ec" +uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" +version = "0.8.2" + +[[ForwardDiff]] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "InteractiveUtils", "LinearAlgebra", "NaNMath", "Random", "SparseArrays", "SpecialFunctions", "StaticArrays", "Test"] +git-tree-sha1 = "4c4d727f1b7e0092134fabfab6396b8945c1ea5b" +uuid = "f6369f11-7733-5829-9624-2563aa707210" +version = "0.10.3" + +[[Future]] +deps = ["Random"] +uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" + +[[GR]] +deps = ["Base64", "DelimitedFiles", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test"] +git-tree-sha1 = "537b61986d8a5fd21e577541f8f0735e481eb3ed" +uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" +version = "0.39.1" + +[[InteractiveUtils]] +deps = ["Markdown"] +uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" + +[[Interpolations]] +deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "Test", "WoodburyMatrices"] +git-tree-sha1 = "e8d1c381b1dc5343e5b6d37265acbe1de493d512" +uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" +version = "0.11.2" + +[[IntervalSets]] +deps = ["Compat"] +git-tree-sha1 = "9dc556002f23740de13946e8c2e41798e09a9249" +uuid = "8197267c-284f-5f27-9208-e0e47529a953" +version = "0.3.1" + +[[IterTools]] +deps = ["SparseArrays", "Test"] +git-tree-sha1 = "79246285c43602384e6f1943b3554042a3712056" +uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" +version = "1.1.1" + +[[IteratorInterfaceExtensions]] +deps = ["Test"] +git-tree-sha1 = "5484e5ede2a4137b9643f4d646e8e7b87b794415" +uuid = "82899510-4779-5014-852e-03e436cf321d" +version = "0.1.1" + +[[JSON]] +deps = ["Dates", "Distributed", "Mmap", "Sockets", "Test", "Unicode"] +git-tree-sha1 = "1f7a25b53ec67f5e9422f1f551ee216503f4a0fa" +uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" +version = "0.20.0" + +[[Juno]] +deps = ["Base64", "Logging", "Media", "Profile", "Test"] +git-tree-sha1 = "4e4a8d43aa7ecec66cadaf311fbd1e5c9d7b9175" +uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d" +version = "0.7.0" + +[[KernelDensity]] +deps = ["Distributions", "FFTW", "Interpolations", "Optim", "StatsBase", "Test"] +git-tree-sha1 = "c1048817fe5711f699abc8fabd47b1ac6ba4db04" +uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" +version = "0.5.1" + +[[LibGit2]] +uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" + +[[Libdl]] +uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" + +[[Libtask]] +deps = ["BinaryProvider", "Libdl", "Pkg", "Test"] +git-tree-sha1 = "74bec5e9fc6f0bc2b779edad5bbe668b4d753d63" +uuid = "6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f" +version = "0.2.7" + +[[LineSearches]] +deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf", "Test"] +git-tree-sha1 = "54eb90e8dbe745d617c78dee1d6ae95c7f6f5779" +uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" +version = "7.0.1" + +[[LinearAlgebra]] +deps = ["Libdl"] +uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + +[[Logging]] +uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" + +[[MCMCChains]] +deps = ["AxisArrays", "DataFrames", "Distributions", "KernelDensity", "LinearAlgebra", "Plots", "Random", "RecipesBase", "Serialization", "Showoff", "SpecialFunctions", "Statistics", "StatsBase"] +git-tree-sha1 = "0c2806774a855105b3825266fb3b71cb355e6ac7" +uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" +version = "0.3.7" + +[[MacroTools]] +deps = ["CSTParser", "Compat", "DataStructures", "Test"] +git-tree-sha1 = "daecd9e452f38297c686eba90dba2a6d5da52162" +uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" +version = "0.5.0" + +[[MappedArrays]] +deps = ["Test"] +git-tree-sha1 = "923441c5ac942b60bd3a842d5377d96646bcbf46" +uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" +version = "0.2.1" + +[[Markdown]] +deps = ["Base64"] +uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" + +[[Measures]] +deps = ["Test"] +git-tree-sha1 = "ddfd6d13e330beacdde2c80de27c1c671945e7d9" +uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" +version = "0.3.0" + +[[Media]] +deps = ["MacroTools", "Test"] +git-tree-sha1 = "75a54abd10709c01f1b86b84ec225d26e840ed58" +uuid = "e89f7d12-3494-54d1-8411-f7d8b9ae1f27" +version = "0.5.0" + +[[Missings]] +deps = ["Dates", 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"189a3867-3050-52da-a836-e630ba90ab69" +Requires = "ae029012-a4dd-5104-9daa-d747884805df" +SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" +StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c" diff --git a/REQUIRE b/REQUIRE index 45f73d0d8..b04b2ccc7 100644 --- a/REQUIRE +++ b/REQUIRE @@ -4,7 +4,7 @@ Requires 0.5.0 Reexport 0.2.0 Distributions 0.16.0 ForwardDiff 0.8.0 -MCMCChains 0.3.4 +MCMCChains 0.3.7 Libtask 0.2.5 Flux 0.6.7 MacroTools