diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
new file mode 100644
index 000000000..7017e7e46
--- /dev/null
+++ b/.github/workflows/Documentation.yml
@@ -0,0 +1,47 @@
+name: Documentation
+
+on:
+ push:
+ branches:
+ - 'master'
+ tags: '*'
+ workflow_dispatch:
+ schedule:
+ # Run on the 23rd hour every day
+ - cron: '0 23 * * *'
+
+jobs:
+ docs:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Julia
+ uses: julia-actions/setup-julia@v1
+ with:
+ version: '1'
+ - name: Set up Ruby 2.6
+ uses: actions/setup-ruby@v1
+ with:
+ ruby-version: '2.6.x'
+ - name: Install dependencies
+ run: |
+ julia --project=docs -e '
+ using Pkg
+ Pkg.activate(".")
+ Pkg.develop("Turing")
+ Pkg.instantiate()
+ Pkg.update()'
+ - name: Build and deploy (master)
+ run: |
+ julia --project=docs --color=yes make.jl
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+ TURING_VERSION: dev
+ - name: Build and deploy (stable)
+ run: |
+ git -C ~/.julia/dev/Turing checkout $(git -C ~/.julia/dev/Turing tag --sort version:refname | tail -n 1)
+ julia --project=docs --color=yes make.jl $(git -C ~/.julia/dev/Turing tag --sort version:refname | tail -n 1)
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 73c5104a6..648aebff7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,5 @@ _site/
.sass-cache/
.jekyll-cache/
.jekyll-metadata
-.gems/
\ No newline at end of file
+.gems/
+Manifest.toml
\ No newline at end of file
diff --git a/Manifest.toml b/Manifest.toml
deleted file mode 100644
index 3876b682e..000000000
--- a/Manifest.toml
+++ /dev/null
@@ -1,648 +0,0 @@
-# This file is machine-generated - editing it directly is not advised
-
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-
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-
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-version = "1.0.1"
-
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-git-tree-sha1 = "e3ef41a8746e0f1c0b8eba98257f3d0d00e5922b"
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-
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-
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-version = "0.4.0"
-
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-
-[[Bijectors]]
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-[[DataFrames]]
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diff --git a/Project.toml b/Project.toml
index 11eefb5d9..ed4edec1e 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,11 @@
+name = "docs"
+
[deps]
AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
+AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
+DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
Libtask = "6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f"
Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
diff --git a/_data/toc.yml b/_data/toc.yml
deleted file mode 100644
index c4051ff86..000000000
--- a/_data/toc.yml
+++ /dev/null
@@ -1,99 +0,0 @@
-- title: "USING TURING"
- url: "docs/using-turing/get-started"
- children:
- - title: "Getting Started"
- url: "docs/using-turing/get-started"
-
- - title: "Quick Start"
- url: "docs/using-turing/quick-start"
-
- - title: "Guide"
- url: "docs/using-turing/guide"
-
- - title: "Advanced Usage"
- url: "docs/using-turing/advanced"
-
- - title: "Automatic Differentiation"
- url: "docs/using-turing/autodiff"
-
- - title: "Performance Tips"
- url: "docs/using-turing/performancetips"
-
- - title: "Using DynamicHMC"
- url: "docs/using-turing/dynamichmc"
-
- - title: "Sampler Visualization"
- url: "docs/using-turing/sampler-viz"
-
-- title: "FOR DEVELOPERS"
- url: "docs/for-developers/"
- children:
- - title: "Turing Compiler Design"
- url: "docs/for-developers/compiler"
-
- - title: "Interface Guide"
- url: "docs/for-developers/interface"
-
- - title: "How Turing implements AbstractMCMC"
- url: "docs/for-developers/how_turing_implements_abstractmcmc"
-
- - title: "Variational Inference"
- url: "docs/for-developers/variational_inference"
-
-- title: "TUTORIALS"
- url: "tutorials"
- children:
- - title: "Home"
- url: "tutorials"
-
- - title: "Introduction to Turing"
- url: "tutorials/0-introduction"
-
- - title: "Gaussian Mixture Models"
- url: "tutorials/1-gaussianmixturemodel"
-
- - title: "Bayesian Logistic Regression"
- url: "tutorials/2-logisticregression"
-
- - title: "Bayesian Neural Networks"
- url: "tutorials/3-bayesnn"
-
- - title: "Hidden Markov Models"
- url: "tutorials/4-bayeshmm"
-
- - title: "Linear Regression"
- url: "tutorials/5-linearregression"
-
- - title: "Infinite Mixture Models"
- url: "tutorials/6-infinitemixturemodel"
-
- - title: "Bayesian Poisson Regression"
- url: "tutorials/7-poissonregression"
-
- - title: "Multinomial Logistic Regression"
- url: "tutorials/8-multinomiallogisticregression"
-
- - title: "Variational Inference"
- url: "tutorials/9-variationalinference"
-
- - title: "Bayesian Differential Equation"
- url: "tutorials/10-bayesiandiffeq"
-
-- title: "API"
- url: "docs/library"
- children:
- - title: "Turing"
- url: "docs/library"
- - title: "AdvancedHMC"
- url: "docs/library/advancedhmc/"
- - title: "Bijectors"
- url: "docs/library/bijectors/"
-
-- title: "CONTRIBUTING"
- url: "docs/contributing/guide"
- children:
- - title: "How to Contribute"
- url: "docs/contributing/guide"
-
- - title: "Style Guide"
- url: "docs/contributing/style-guide"
diff --git a/_docs/assets/Documenter.css b/_docs/assets/Documenter.css
deleted file mode 100644
index d9af5d6c9..000000000
--- a/_docs/assets/Documenter.css
+++ /dev/null
@@ -1,18 +0,0 @@
-div.wy-menu-vertical ul.current li.toctree-l3 a {
- font-weight: bold;
-}
-
-a.documenter-source {
- float: right;
-}
-
-.documenter-methodtable pre {
- margin-left: 0;
- margin-right: 0;
- margin-top: 0;
- padding: 0;
-}
-
-.documenter-methodtable pre.documenter-inline {
- display: inline;
-}
diff --git a/_docs/assets/mathjaxhelper.js b/_docs/assets/mathjaxhelper.js
deleted file mode 100644
index 3561b109f..000000000
--- a/_docs/assets/mathjaxhelper.js
+++ /dev/null
@@ -1,25 +0,0 @@
-MathJax.Hub.Config({
- "tex2jax": {
- inlineMath: [['$','$'], ['\\(','\\)']],
- processEscapes: true
- }
-});
-MathJax.Hub.Config({
- config: ["MMLorHTML.js"],
- jax: [
- "input/TeX",
- "output/HTML-CSS",
- "output/NativeMML"
- ],
- extensions: [
- "MathMenu.js",
- "MathZoom.js",
- "TeX/AMSmath.js",
- "TeX/AMSsymbols.js",
- "TeX/autobold.js",
- "TeX/autoload-all.js"
- ]
-});
-MathJax.Hub.Config({
- TeX: { equationNumbers: { autoNumber: "AMS" } }
-});
diff --git a/_docs/contributing/guide.md b/_docs/contributing/guide.md
deleted file mode 100644
index beaf3d1b6..000000000
--- a/_docs/contributing/guide.md
+++ /dev/null
@@ -1,58 +0,0 @@
----
-title: Contributing
----
-
-
-
-
-
-# Contributing
-
-
-Turing is an open source project. If you feel that you have some relevant skills and are interested in contributing, then please do get in touch. You can contribute by opening issues on GitHub or implementing things yourself and making a pull request. We would also appreciate example models written using Turing.
-
-
-Turing has a [style guide]({{site.baseurl}}/docs/contributing/style-guide). It is not strictly necessary to review it before making a pull request, but you may be asked to change portions of your code to conform with the style guide before it is merged.
-
-
-
-
-
-
-## How to Contribute
-
-
-
-
-
-
-### Getting Started
-
-
- * [Fork this repository](https://github.com/TuringLang/Turing.jl#fork-destination-box).
- * Clone your fork on your local machine: `git clone https://github.com/your_username/Turing.jl`.
- * Add a remote corresponding to this repository:
-
-
-`git remote add upstream https://github.com/TuringLang/Turing.jl`.
-
-
-
-
-
-
-### What Can I Do?
-
-
-Look at the [issues](https://github.com/TuringLang/Turing.jl/issues) page to find an outstanding issue. For instance, you could implement new features, fix bugs or write example models.
-
-
-
-
-
-
-### Git Workflow
-
-
-For more information on how the Git workflow typically functions, please see the [GitHub's introduction](https://guides.github.com/introduction/flow/) or [Julia's contribution guide](https://github.com/JuliaLang/julia/blob/master/CONTRIBUTING.md).
-
diff --git a/_docs/contributing/style-guide.md b/_docs/contributing/style-guide.md
deleted file mode 100644
index 3abdee766..000000000
--- a/_docs/contributing/style-guide.md
+++ /dev/null
@@ -1,735 +0,0 @@
----
-title: Style Guide
----
-
-
-
-
-
-# Style Guide
-
-
-This style guide is adapted from [Invenia](https://invenia.ca/labs/)'s style guide. We would like to thank them for allowing us to access and use it. Please don't let not having read it stop you from contributing to Turing! No one will be annoyed if you open a PR whose style doesn't follow these conventions; we will just help you correct it before it gets merged.
-
-
-These conventions were originally written at Invenia, taking inspiration from a variety of sources including Python's [PEP8](http://legacy.python.org/dev/peps/pep-0008), Julia's [Notes for Contributors](https://github.com/JuliaLang/julia/blob/master/CONTRIBUTING.md), and Julia's [Style Guide](https://docs.julialang.org/en/latest/manual/style-guide/).
-
-
-What follows is a mixture of a verbatim copy of Invenia's original guide and some of our own modifications.
-
-
-
-
-
-
-## A Word on Consistency
-
-
-When adhering to this style it's important to realize that these are guidelines and not rules. This is [stated best in the PEP8](http://legacy.python.org/dev/peps/pep-0008/#a-foolish-consistency-is-the-hobgoblin-of-little-minds):
-
-
-> A style guide is about consistency. Consistency with this style guide is important. Consistency within a project is more important. Consistency within one module or function is most important.
-
-
-
-> But most importantly: know when to be inconsistent – sometimes the style guide just doesn't apply. When in doubt, use your best judgment. Look at other examples and decide what looks best. And don't hesitate to ask!
-
-
-
-
-
-
-
-## Synopsis
-
-
-Attempt to follow both the [Julia Contribution Guidelines](https://github.com/JuliaLang/julia/blob/master/CONTRIBUTING.md#general-formatting-guidelines-for-julia-code-contributions), the [Julia Style Guide](https://docs.julialang.org/en/latest/manual/style-guide/), and this guide. When convention guidelines conflict this guide takes precedence (known conflicts will be noted in this guide).
-
-
- * Use 4 spaces per indentation level, no tabs.
- * Try to adhere to a 92 character line length limit.
- * Use upper camel case convention for [modules](https://docs.julialang.org/en/latest/manual/modules/) and [types](https://docs.julialang.org/en/latest/manual/types/).
- * Use lower case with underscores for method names (note: Julia code likes to use lower case without underscores).
- * Comments are good, try to explain the intentions of the code.
- * Use whitespace to make the code more readable.
- * No whitespace at the end of a line (trailing whitespace).
- * Avoid padding brackets with spaces. ex. `Int64(value)` preferred over `Int64( value )`.
-
-
-
-
-
-
-## Editor Configuration
-
-
-
-
-
-
-### Sublime Text Settings
-
-
-If you are a user of Sublime Text we recommend that you have the following options in your Julia syntax specific settings. To modify these settings first open any Julia file (`*.jl`) in Sublime Text. Then navigate to: `Preferences > Settings - More > Syntax Specific - User`
-
-
-```json
-{
- "translate_tabs_to_spaces": true,
- "tab_size": 4,
- "trim_trailing_white_space_on_save": true,
- "ensure_newline_at_eof_on_save": true,
- "rulers": [92]
-}
-```
-
-
-
-
-
-
-### Vim Settings
-
-
-If you are a user of Vim we recommend that you add the following options to your `.vimrc` file.
-
-
-```
-set tabstop=4 " Sets tabstops to a width of four columns.
-set softtabstop=4 " Determines the behaviour of TAB and BACKSPACE keys with expandtab.
-set shiftwidth=4 " Determines the results of >>, <<, and ==.
-
-au FileType julia setlocal expandtab " Replaces tabs with spaces.
-au FileType julia setlocal colorcolumn=93 " Highlights column 93 to help maintain the 92 character line limit.
-```
-
-
-By default, Vim seems to guess that `.jl` files are written in Lisp. To ensure that Vim recognizes Julia files you can manually have it check for the `.jl` extension, but a better solution is to install [Julia-Vim](https://github.com/JuliaLang/julia-vim), which also includes proper syntax highlighting and a few cool other features.
-
-
-
-
-
-
-### Atom Settings
-
-
-Atom defaults preferred line length to 80 characters. We want that at 92 for julia. To change it:
-
-
-1. Go to `Atom -> Preferences -> Packages`.
-2. Search for the "language-julia" package and open the settings for it.
-3. Find preferred line length (under "Julia Grammar") and change it to 92.
-
-
-
-
-
-
-## Code Formatting
-
-
-
-
-
-
-### Function Naming
-
-
-Names of functions should describe an action or property irrespective of the type of the argument; the argument's type provides this information instead. For example, `buyfood(food)` should be `buy(food::Food)`.
-
-
-Names of functions should usually be limited to one or two lowercase words. Ideally write `buyfood` not `buy_food`, but if you are writing a function whose name is hard to read without underscores then please do use them.
-
-
-
-
-
-
-### Method Definitions
-
-
-Only use short-form function definitions when they fit on a single line:
-
-
-```julia
-# Yes:
-foo(x::Int64) = abs(x) + 3
-# No:
-foobar(array_data::AbstractArray{T}, item::T) where {T<:Int64} = T[
- abs(x) * abs(item) + 3 for x in array_data
-]
-
-# No:
-foobar(
- array_data::AbstractArray{T},
- item::T,
-) where {T<:Int64} = T[abs(x) * abs(item) + 3 for x in array_data]
-# Yes:
-function foobar(array_data::AbstractArray{T}, item::T) where T<:Int64
- return T[abs(x) * abs(item) + 3 for x in array_data]
-end
-```
-
-
-When using long-form functions [always use the `return` keyword](https://groups.google.com/forum/#!topic/julia-users/4RVR8qQDrUg):
-
-
-```julia
-# Yes:
-function fnc(x)
- result = zero(x)
- result += fna(x)
- return result
-end
-# No:
-function fnc(x)
- result = zero(x)
- result += fna(x)
-end
-
-# Yes:
-function Foo(x, y)
- return new(x, y)
-end
-# No:
-function Foo(x, y)
- new(x, y)
-end
-```
-
-
-Functions definitions with parameter lines which exceed 92 characters should separate each parameter by a newline and indent by one-level:
-
-
-```julia
-# Yes:
-function foobar(
- df::DataFrame,
- id::Symbol,
- variable::Symbol,
- value::AbstractString,
- prefix::AbstractString="",
-)
- # code
-end
-
-# Ok:
-function foobar(df::DataFrame, id::Symbol, variable::Symbol, value::AbstractString, prefix::AbstractString="")
- # code
-end
-# No:
-function foobar(df::DataFrame, id::Symbol, variable::Symbol, value::AbstractString,
- prefix::AbstractString="")
-
- # code
-end
-# No:
-function foobar(
- df::DataFrame,
- id::Symbol,
- variable::Symbol,
- value::AbstractString,
- prefix::AbstractString="",
- )
- # code
-end
-```
-
-
-
-
-
-
-### Keyword Arguments
-
-
-When calling a function always separate your keyword arguments from your positional arguments with a semicolon. This avoids mistakes in ambiguous cases (such as splatting a `Dict`).
-
-
-```julia
-# Yes:
-xy = foo(x; y=3)
-# No:
-xy = foo(x, y=3)
-```
-
-
-
-
-
-
-### Whitespace
-
-
-Avoid extraneous whitespace in the following situations:
-
-
- * Immediately inside parentheses, square brackets or braces.
-
-
-```julia
-Yes: spam(ham[1], [eggs])
-No: spam( ham[ 1 ], [ eggs ] )
-```
-
-
- * Immediately before a comma or semicolon:
-
-
-```julia
-Yes: if x == 4 @show(x, y); x, y = y, x end
-No: if x == 4 @show(x , y) ; x , y = y , x end
-```
-
-
- * When using ranges unless additional operators are used:
-
-
-```julia
-Yes: ham[1:9], ham[1:3:9], ham[1:3:end]
-No: ham[1: 9], ham[1 : 3: 9]
-```
-
-
-```julia
-Yes: ham[lower:upper], ham[lower:step:upper]
-Yes: ham[lower + offset : upper + offset]
-Yes: ham[(lower + offset):(upper + offset)]
-No: ham[lower + offset:upper + offset]
-```
-
-
- * More than one space around an assignment (or other) operator to align it with another:
-
-
-```julia
-# Yes:
-x = 1
-y = 2
-long_variable = 3
-
-# No:
-x = 1
-y = 2
-long_variable = 3
-```
-
-
- * When using parametric types:
-
-
-```julia
-# Yes:
-f(a::AbstractArray{T, N}) where {T<:Real, N} = ...
-g(a::AbstractArray{<:Real, N}) where {N} = ...
-
-# No:
-f(a::AbstractArray{T, N}) where {T <: Real, N} = ...
-g(a::AbstractArray{<: Real, N}) where {N} = ...
-```
-
-
- * Always surround these binary operators with a single space on either side: assignment ($=$), [updating operators](https://docs.julialang.org/en/latest/manual/mathematical-operations/#Updating-operators-1) ($+=$, $-=$, etc.), [numeric comparisons operators](https://docs.julialang.org/en/latest/manual/mathematical-operations/#Numeric-Comparisons-1) ($==$, $<$, $>$, $!=$, etc.). Note that this guideline does not apply when performing assignment in method definitions.
-
-
-```julia
-Yes: i = i + 1
-No: i=i+1
-
-Yes: submitted += 1
-No: submitted +=1
-
-Yes: x^2 < y
-No: x^2