Merge pull request #68 from zenna/zt-prerelease

Zt prerelease

.travis.yml

@@ -12,14 +12,6 @@ notifications:
   email: false
 env:
   - DOCUMENTER_DEBUG="true" CONDA_JL_VERSION="2" PYTHON=""
-script:
-  - julia -e 'using Pkg; Pkg.activate(pwd())'
-  - julia -e 'using Pkg; Pkg.update()'
-  - julia -e 'using Pkg; Pkg.resolve()'
-  - julia -e 'using Pkg; Pkg.build("Omega")'
-  - julia -e 'using Pkg; Pkg.add("Test")'
-  - julia -e 'using Pkg; Pkg.add("Pkg")'
-  - julia --depwarn=no -e 'using Pkg; Pkg.test("Omega", coverage=true)'
 after_success:
   - julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())'
   - julia -e 'using Pkg; Pkg.add("Documenter"); include(joinpath("docs", "make.jl"))'

Manifest.toml

@@ -12,9 +12,9 @@ version = "0.3.1"
 
 [[Arpack]]
 deps = ["BinaryProvider", "Libdl", "LinearAlgebra", "Random", "SparseArrays", "Test"]
-git-tree-sha1 = "ffc099065b47835213386df346e4a8b807c320cd"
+git-tree-sha1 = "5b046410fb617d9cf2f8bc0edd5da05a2e5a2ad4"
 uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97"
-version = "0.2.2"
+version = "0.2.3"
 
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -27,27 +27,33 @@ version = "0.8.10"
 
 [[BinaryProvider]]
 deps = ["Libdl", "Pkg", "SHA", "Test"]
-git-tree-sha1 = "ffbf89cc49b073cffdb91381b7ee60557a03ec96"
+git-tree-sha1 = "38be61810f280c3c478f5c38aaf387f8f9199275"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
-version = "0.4.1"
+version = "0.5.1"
 
 [[Cassette]]
 deps = ["InteractiveUtils", "LinearAlgebra", "Test"]
-git-tree-sha1 = "97abd9e245237814b02d24e8e57c3bcbc2f59ac0"
+git-tree-sha1 = "26fee677e5047978ad52d25f3f00fc86cecd1297"
 uuid = "7057c7e9-c182-5462-911a-8362d720325c"
-version = "0.1.1"
+version = "0.1.2"
+
+[[CodecZlib]]
+deps = ["BinaryProvider", "Libdl", "Pkg", "Test", "TranscodingStreams"]
+git-tree-sha1 = "83cb3d65c37ea1364c2d5bf7bcea41843ba645dc"
+uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
+version = "0.5.0"
 
 [[ColorTypes]]
 deps = ["FixedPointNumbers", "Random", "Test"]
-git-tree-sha1 = "0e3209ba7418aed732e5c3818076b4400ee36c08"
+git-tree-sha1 = "f73b0e10f2a5756de7019818a41654686da06b09"
 uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
-version = "0.7.4"
+version = "0.7.5"
 
 [[Colors]]
 deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Pkg", "Printf", "Reexport", "Test"]
-git-tree-sha1 = "26f24e97782dd19d52cf97073c316897ac4d0e30"
+git-tree-sha1 = "8c89e0a9a583954eae3efcf6a531e51c02b38cee"
 uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.9.3"
+version = "0.9.4"
 
 [[CommonSubexpressions]]
 deps = ["Test"]
@@ -57,15 +63,15 @@ 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 = "277d3807440d9793421354b6680911fc95d91a84"
+git-tree-sha1 = "ff2595695fc4f14427358ce2593f867085c45dcb"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "1.0.1"
+version = "1.2.0"
 
 [[DataStructures]]
-deps = ["InteractiveUtils", "REPL", "Random", "Serialization", "Test"]
-git-tree-sha1 = "6e72a9098f5774601c8c8d6a4511a68270594910"
+deps = ["InteractiveUtils", "OrderedCollections", "REPL", "Random", "Serialization", "Test"]
+git-tree-sha1 = "8fc6e166e24fda04b2b648d4260cdad241788c54"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.11.0"
+version = "0.14.0"
 
 [[Dates]]
 deps = ["Printf"]
@@ -92,44 +98,38 @@ deps = ["LinearAlgebra", "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 = "c43dc10a52598ad76d61f8907b3b30f159ca146f"
+deps = ["Distributed", "LinearAlgebra", "PDMats", "Pkg", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"]
+git-tree-sha1 = "c24e9b6500c037673f0241a2783472b8c3d080c7"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.16.2"
+version = "0.16.4"
 
 [[FixedPointNumbers]]
 deps = ["Pkg", "Test"]
-git-tree-sha1 = "31cbf24d537a217475b37274df05de09882b53f1"
+git-tree-sha1 = "b8045033701c3b10bf2324d7203404be7aef88ba"
 uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
-version = "0.5.2"
+version = "0.5.3"
 
 [[Flux]]
-deps = ["AbstractTrees", "Adapt", "Colors", "DiffRules", "ForwardDiff", "GZip", "Juno", "LinearAlgebra", "MacroTools", "NNlib", "NaNMath", "Printf", "Random", "Reexport", "Requires", "SpecialFunctions", "Statistics", "StatsBase", "Test", "ZipFile"]
-git-tree-sha1 = "7cb08b05904dcb869a2a3bd35d97ad6eb77ce20f"
+deps = ["AbstractTrees", "Adapt", "CodecZlib", "Colors", "DiffRules", "ForwardDiff", "Juno", "LinearAlgebra", "MacroTools", "NNlib", "NaNMath", "Pkg", "Printf", "Random", "Reexport", "Requires", "SpecialFunctions", "Statistics", "StatsBase", "Test", "ZipFile"]
+git-tree-sha1 = "b9fc47f3eeb8062c9dac3a74bca9fd83f7e0fbf5"
 uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c"
-version = "0.6.3"
+version = "0.6.7"
 
 [[ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "InteractiveUtils", "LinearAlgebra", "NaNMath", "Pkg", "Random", "SparseArrays", "SpecialFunctions", "StaticArrays", "Test"]
-git-tree-sha1 = "0dd11038da4efce9ce457b1cf47a52eaf6251bd3"
+git-tree-sha1 = "8425a7d4e060bc2ded32d090bce910a187d6cce7"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "0.8.5"
-
-[[GZip]]
-deps = ["Libdl", "Pkg", "Test"]
-git-tree-sha1 = "ee443ef166b29282301468d8af403e1ed8f5412e"
-uuid = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
-version = "0.5.0"
+version = "0.9.0"
 
 [[InteractiveUtils]]
 deps = ["LinearAlgebra", "Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[Juno]]
 deps = ["Base64", "Logging", "Media", "Profile", "Test"]
-git-tree-sha1 = "f2d553719755f00f602cb226689c0bcfee023a1d"
+git-tree-sha1 = "3c29a199713e7ec62cfdc11f44d7760219d5f658"
 uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d"
-version = "0.5.2"
+version = "0.5.3"
 
 [[LibGit2]]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -162,30 +162,36 @@ version = "0.4.1"
 
 [[Missings]]
 deps = ["Dates", "InteractiveUtils", "SparseArrays", "Test"]
-git-tree-sha1 = "196528fa1df03df435025f52f9c1ff8356f94738"
+git-tree-sha1 = "adc26d2ee85a49c413464110d922cf21efc9d233"
 uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
-version = "0.3.0"
+version = "0.3.1"
 
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
 [[NNlib]]
 deps = ["Libdl", "LinearAlgebra", "MacroTools", "Requires", "Test"]
-git-tree-sha1 = "1375b53e79080b37705a4040c97f1ded4e332cac"
+git-tree-sha1 = "d7f65ad9734adea3c5a4c473bc65b365f8afbb2b"
 uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
-version = "0.4.1"
+version = "0.4.2"
 
 [[NaNMath]]
 deps = ["Compat"]
 git-tree-sha1 = "ce3b85e484a5d4c71dd5316215069311135fa9f2"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 version = "0.3.2"
 
+[[OrderedCollections]]
+deps = ["Pkg", "Random", "Serialization", "Test"]
+git-tree-sha1 = "85619a3f3e17bb4761fe1b1fd47f0e979f964d5b"
+uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+version = "1.0.2"
+
 [[PDMats]]
 deps = ["Arpack", "LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"]
-git-tree-sha1 = "484f7fbb6c382ab6bcfff4d134f9b51fa29ee562"
+git-tree-sha1 = "9e3e7a5c9b8cfdba8c01a1bcae38fe0144936fda"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.9.4"
+version = "0.9.5"
 
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
@@ -207,9 +213,9 @@ version = "0.6.0"
 
 [[QuadGK]]
 deps = ["DataStructures", "LinearAlgebra", "Test"]
-git-tree-sha1 = "7d61ca207f021be6574b365a1a077bea04935f19"
+git-tree-sha1 = "7e8dff9c205f36eceaf6e62a43ff851637ca45fc"
 uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
-version = "2.0.1"
+version = "2.0.2"
 
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets"]
@@ -262,17 +268,17 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[Spec]]
 deps = ["Cassette"]
-git-tree-sha1 = "3d74b2848fa5c7a4313d04b79314853f328af292"
+git-tree-sha1 = "275d533031b8c97b6ca38b83395a435524a3dc46"
 repo-rev = "master"
 repo-url = "https://github.com/zenna/Spec.jl"
 uuid = "526a04b8-654b-11e8-1588-db2a414f95b5"
-version = "0.1.0"
+version = "0.1.3"
 
 [[SpecialFunctions]]
-deps = ["BinDeps", "BinaryProvider", "Compat", "Libdl"]
-git-tree-sha1 = "d12f8917be3782f4b800ba16003b8d0d4858c2e5"
+deps = ["BinDeps", "BinaryProvider", "Libdl", "Test"]
+git-tree-sha1 = "c35c9c76008babf4d658060fc64aeb369a41e7bd"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "0.7.0"
+version = "0.7.1"
 
 [[StaticArrays]]
 deps = ["InteractiveUtils", "LinearAlgebra", "Random", "Statistics", "Test"]
@@ -304,6 +310,12 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
+[[TranscodingStreams]]
+deps = ["DelimitedFiles", "Pkg", "Random", "Test"]
+git-tree-sha1 = "a34a2d588e2d2825602bf14a24216d5c8b0921ec"
+uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
+version = "0.8.1"
+
 [[URIParser]]
 deps = ["Test", "Unicode"]
 git-tree-sha1 = "6ddf8244220dfda2f17539fa8c9de20d6c575b69"
@@ -323,14 +335,6 @@ git-tree-sha1 = "d26d1e85fb7e9d432a7bb0cd6e421e8a82928604"
 uuid = "b8865327-cd53-5732-bb35-84acbb429228"
 version = "0.3.1"
 
-[[ZenUtils]]
-deps = ["Spec"]
-git-tree-sha1 = "491d56ddfe16356a2b2a35f6238093884cf12925"
-repo-rev = "master"
-repo-url = "https://github.com/zenna/ZenUtils.jl"
-uuid = "8c7a6496-654a-11e8-0e4c-c7dc3dc823b6"
-version = "0.1.0"
-
 [[ZipFile]]
 deps = ["Printf", "Test"]
 git-tree-sha1 = "c191e56c849b1784cacbf7cd5e52cc672f1ae2db"

Project.toml

@@ -4,7 +4,6 @@ authors = ["Zenna Tavares <zennatavares@gmail.com>"]
 version = "0.1.0"
 
 [deps]
-Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -14,4 +13,11 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Spec = "526a04b8-654b-11e8-1588-db2a414f95b5"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
-ZenUtils = "8c7a6496-654a-11e8-0e4c-c7dc3dc823b6"
+
+[extras]
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test", "InteractiveUtils", "Pkg"]

REQUIRE

@@ -1,6 +1,9 @@
-julia 0.6
+julia 0.7
 Flux
 Distributions
 PDMats
 ProgressMeter
-Spec
+Spec
+
+# Will probably remove
+UnicodePlots

docs/make.jl

@@ -16,8 +16,10 @@ makedocs(
     "Causal Inference" => "causal.md",
     "Higher Order Inference" => "higher.md",
     "Built-in Distributions" => "distributions.md",
-    "Omega" => "omega.md",
     "Cheat Sheet" => "cheatsheet.md",
+    "Internals" => ["Overview" => "internalsoverview.md",
+                    "Ω" => "omega.md",
+                    "RandVar" => "randvar.md"],
     "Contribution Guide" => "contrib.md",
   ]
 )

docs/src/cheatsheet.md

@@ -11,6 +11,11 @@ The major functions that you will use in Omega are:
 - [rid(x, θ)]()  : distribution interventional distribution of `x` given `θ`  
 - [rcd(x, θ) or x ∥ θ]()  : random conditional distribution of `x` given `θ`
 
+## FAQ
+
+- How to sample from a joint distribution (more than one random variable at a time)?
+Pass a tuple of random variables, e.g: `rand((x, y, z))`.
+
 ## Built-in Distributions
 
 [bernoulli(w)](distributions.md#Omega.bernoulli) [boolbernoulli(w)](distributions.md#Omega.boolbernoulli)
@@ -19,7 +24,7 @@ categorical
 constant
 exponential
 gammarv
-inversegamma
+invgamma
 kumaraswamy
 logistic
 poisson
@@ -32,6 +37,6 @@ rademacher
 RejectionSample
 MI
 SSMH
+SSMHDrift
 HMC
-SGHMC
 HMCFAST

docs/src/conditionalindependence.md

@@ -2,10 +2,6 @@
 
 Previously we saw that we could use `ciid` to turn a function rng into a `RandVar`.
 
-## Independent Random Variables
-
-Use `iid(x)` to create a random variable that is identical in distribution to `x` but but independent.
-
 ## Conditionally Independent Random Variables
 
 Use `ciid(x)` to create a random variable that is identical in distribution to `x` but conditionally independent given its parents.
@@ -15,4 +11,8 @@ Use `ciid(x)` to create a random variable that is identical in distribution to `
 y1 = normal(μ, 1.0)
 y2 = ciid(y1)
 rand((y1, y2))
+```
+
+```@docs
+ciid
 ```

docs/src/index.md

@@ -5,12 +5,16 @@ It was developed by [Zenna Tavares](http://zenna.org) with help from Javier Burr
 
 ## Quick Start
 
-Omega is built in Julia 0.7 but not yet in the official Julia Package repository.  You can still easily install it from a Julia repl with:
+Omega is built in Julia 1.0 but not yet in the official Julia Package repository.  You can still easily install it from a Julia repl with:
 
 ```julia
-(v0.7) pkg> add https://github.com/zenna/Omega.jl.git
+(v1.0) pkg> add https://github.com/zenna/Omega.jl.git
 ```
 
+Note: You will likely manually add the following dependencies, but if you use Omega from its environment, these will be downloaded automatically:
+- https://github.com/zenna/Spec.jl
+- https://github.com/zenna/ZenUtils.jl
+
 Check Omega is working and gives reasonable results with: 
 
 ```julia
@@ -27,7 +31,11 @@ With that, see the [Tutorial](basictutorial.md) for a run through of the main fe
 We want your contributions!
 
 - Probabilistic models
-- Contribute an inference procedure
+Please add probabilistic models and model families to https://github.com/zenna/OmegaModels.jl
+
+- Inference procedures
+
+
 
 
 ## Citation