Set up documentation (#23)

* Set up documentation

* Update docs/make.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Author: devmotion

.github/workflows/CI.yml

@@ -6,6 +6,12 @@ on:
       - main
   pull_request:
 
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}

.github/workflows/CompatHelper.yml

@@ -24,8 +24,8 @@ jobs:
       - name: "Run CompatHelper"
         run: |
           import CompatHelper
-          CompatHelper.main()
+          CompatHelper.main(; subdirs=["", "docs"])
         shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/Docs.yml

@@ -0,0 +1,31 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          JULIA_DEBUG: Documenter # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955)
+        run: julia --project=docs/ docs/make.jl

.github/workflows/DocsCleanupPreview.yml

@@ -0,0 +1,26 @@
+name: DocsPreviewCleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.github/workflows/Format.yml

@@ -3,6 +3,12 @@ name: Format
 on:
   pull_request:
 
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   format:
     runs-on: ubuntu-latest
@@ -11,14 +17,15 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: 1
-      - name: Install JuliaFormatter and format code
+      - name: Format code
         run: |
-          using Pkg: Pkg
+          using Pkg
           Pkg.add(; name="JuliaFormatter", uuid="98e50ef6-434e-11e9-1051-2b60c6c9e899")
           using JuliaFormatter
           format("."; verbose=true)
         shell: julia --color=yes {0}
       - uses: reviewdog/action-suggester@v1
+        if: github.event_name == 'pull_request'
         with:
           tool_name: JuliaFormatter
           fail_on_error: true

.github/workflows/TagBot.yml

@@ -12,3 +12,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

README.md

@@ -2,7 +2,8 @@
 
 Julia implementation of elliptical slice sampling.
 
-[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://turinglang.github.io/EllipticalSliceSampling.jl/stable)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://turinglang.github.io/EllipticalSliceSampling.jl/dev)
 [![Build Status](https://github.com/TuringLang/EllipticalSliceSampling.jl/workflows/CI/badge.svg?branch=main)](https://github.com/TuringLang/EllipticalSliceSampling.jl/actions?query=workflow%3ACI%20branch%3Amain)
 [![Codecov](https://codecov.io/gh/TuringLang/EllipticalSliceSampling.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/TuringLang/EllipticalSliceSampling.jl)
 [![Coveralls](https://coveralls.io/repos/github/TuringLang/EllipticalSliceSampling.jl/badge.svg?branch=main)](https://coveralls.io/github/TuringLang/EllipticalSliceSampling.jl?branch=main)
@@ -16,99 +17,15 @@ This package implements elliptical slice sampling in the Julia language, as desc
 Elliptical slice sampling is a "Markov chain Monte Carlo algorithm for performing
 inference in models with multivariate Gaussian priors" (Murray, Adams & MacKay (2010)).
 
-Without loss of generality, the originally described algorithm assumes that the Gaussian
-prior has zero mean. For convenience we allow the user to specify arbitrary Gaussian
-priors with non-zero means and handle the change of variables internally.
+Please check the [documentation](https://turinglang.github.io/EllipticalSliceSampling.jl/stable)
+for more details.
 
-## Usage
+## Poster at JuliaCon 2021
 
-Probably most users would like to generate a MC Markov chain of samples from
-the posterior distribution by calling
-```julia
-sample([rng, ]ESSModel(prior, loglikelihood), ESS(), N[; kwargs...])
-```
-which returns a vector of `N` samples for approximating the posterior of
-a model with a Gaussian prior that allows sampling from the `prior` and
-evaluation of the log likelihood `loglikelihood`.
+[![EllipticalSliceSampling.jl: MCMC with Gaussian priors](http://img.youtube.com/vi/S5gUED7Uq2Q/0.jpg)](https://www.youtube.com/watch?v=S5gUED7Uq2Q)
 
-You can sample multiple chains in parallel with multiple threads or processes
-by running
-```julia
-sample([rng, ]ESSModel(prior, loglikelihood), ESS(), MCMCThreads(), N, nchains[; kwargs...])
-```
-or
-```julia
-sample([rng, ]ESSModel(prior, loglikelihood), ESS(), MCMCDistributed(), N, nchains[; kwargs...])
-```
+The slides are available as [Pluto notebook](https://talks.widmann.dev/2021/07/ellipticalslicesampling/).
 
-If you want to have more control about the sampling procedure (e.g., if you
-only want to save a subset of samples or want to use another stopping
-criterion), the function
-```julia
-AbstractMCMC.steps(
-    [rng,]
-    ESSModel(prior, loglikelihood),
-    ESS();
-    kwargs...
-)
-```
-gives you access to an iterator from which you can generate an unlimited
-number of samples.
-
-For more details regarding `sample` and `steps` please check the documentation of
-[AbstractMCMC.jl](https://github.com/TuringLang/AbstractMCMC.jl).
-
-### Prior
-
-You may specify Gaussian priors with arbitrary means. EllipticalSliceSampling.jl
-provides first-class support for the scalar and multivariate normal distributions
-in [Distributions.jl](https://github.com/JuliaStats/Distributions.jl). For
-instance, if the prior distribution is a standard normal distribution, you can
-choose
-```julia
-prior = Normal()
-```
-
-However, custom Gaussian priors are supported as well. For instance, if you want to
-use a custom distribution type `GaussianPrior`, the following methods should be
-implemented:
-```julia
-# state that the distribution is actually Gaussian
-EllipticalSliceSampling.isgaussian(::Type{<:GaussianPrior}) = true
-
-# define the mean of the distribution
-# alternatively implement `proposal(prior, ...)` and
-# `proposal!(out, prior, ...)` (only if the samples are mutable)
-Statistics.mean(dist::GaussianPrior) = ...
-
-# define how to sample from the distribution
-# only one of the following methods is needed:
-# - if the samples are immutable (e.g., numbers or static arrays) only
-#   `rand(rng, dist)` should be implemented
-# - otherwise only `rand!(rng, dist, sample)` is required
-Base.rand(rng::AbstractRNG, dist::GaussianPrior) = ...
-Random.rand!(rng::AbstractRNG, dist::GaussianPrior, sample) = ...
-```
-
-### Log likelihood
-
-In addition to the prior, you have to specify a Julia implementation of
-the log likelihood function. Here the predefined log densities and log
-likelihood functions in
-[Distributions.jl](https://github.com/JuliaStats/Distributions.jl) might
-be useful.
-
-### Progress monitor
-
-If you use a package such as [Juno](https://junolab.org/) or
-[TerminalLoggers.jl](https://github.com/c42f/TerminalLoggers.jl) that supports
-progress logs created by the
-[ProgressLogging.jl](https://github.com/JunoLab/ProgressLogging.jl) API, then you can
-monitor the progress of the sampling algorithm. If you do not specify a progress
-logging frontend explicitly,
-[AbstractMCMC.jl](https://github.com/TuringLang/AbstractMCMC.jl) picks a frontend
-for you automatically.
-
-## Bibliography
+## References
 
 Murray, I., Adams, R. & MacKay, D.. (2010). Elliptical slice sampling. Proceedings of Machine Learning Research, 9:541-548.

docs/.gitignore

@@ -0,0 +1,2 @@
+/Manifest.toml
+/build/

docs/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "0.27"

docs/make.jl

@@ -0,0 +1,17 @@
+using Documenter
+using EllipticalSliceSampling
+
+makedocs(;
+    sitename="EllipticalSliceSampling",
+    format=Documenter.HTML(),
+    modules=[EllipticalSliceSampling],
+    pages=["Home" => "index.md"],
+    strict=true,
+    checkdocs=:exports,
+)
+
+deploydocs(;
+    repo="github.com/TuringLang/EllipticalSliceSampling.jl.git",
+    devbranch="main",
+    push_preview=true,
+)

docs/src/index.md

@@ -0,0 +1,114 @@
+# EllipticalSliceSampling
+
+*Julia implementation of elliptical slice sampling.*
+
+## Overview
+
+This package implements elliptical slice sampling in the Julia language, as described in
+[Murray, Adams & MacKay (2010)](http://proceedings.mlr.press/v9/murray10a/murray10a.pdf).
+
+Elliptical slice sampling is a "Markov chain Monte Carlo algorithm for performing
+inference in models with multivariate Gaussian priors" (Murray, Adams & MacKay (2010)).
+
+Without loss of generality, the originally described algorithm assumes that the Gaussian
+prior has zero mean. For convenience we allow the user to specify arbitrary Gaussian
+priors with non-zero means and handle the change of variables internally.
+
+## Poster at JuliaCon 2021
+
+[![EllipticalSliceSampling.jl: MCMC with Gaussian priors](http://img.youtube.com/vi/S5gUED7Uq2Q/0.jpg)](https://www.youtube.com/watch?v=S5gUED7Uq2Q)
+
+The slides are available as [Pluto notebook](https://talks.widmann.dev/2021/07/ellipticalslicesampling/).
+
+## Usage
+
+Probably most users would like to generate a MC Markov chain of samples from
+the posterior distribution by calling
+```julia
+sample([rng, ]ESSModel(prior, loglikelihood), ESS(), N[; kwargs...])
+```
+which returns a vector of `N` samples for approximating the posterior of
+a model with a Gaussian prior that allows sampling from the `prior` and
+evaluation of the log likelihood `loglikelihood`.
+
+You can sample multiple chains in parallel with multiple threads or processes
+by running
+```julia
+sample([rng, ]ESSModel(prior, loglikelihood), ESS(), MCMCThreads(), N, nchains[; kwargs...])
+```
+or
+```julia
+sample([rng, ]ESSModel(prior, loglikelihood), ESS(), MCMCDistributed(), N, nchains[; kwargs...])
+```
+
+If you want to have more control about the sampling procedure (e.g., if you
+only want to save a subset of samples or want to use another stopping
+criterion), the function
+```julia
+AbstractMCMC.steps(
+    [rng,]
+    ESSModel(prior, loglikelihood),
+    ESS();
+    kwargs...
+)
+```
+gives you access to an iterator from which you can generate an unlimited
+number of samples.
+
+For more details regarding `sample` and `steps` please check the documentation of
+[AbstractMCMC.jl](https://github.com/TuringLang/AbstractMCMC.jl).
+
+### Prior
+
+You may specify Gaussian priors with arbitrary means. EllipticalSliceSampling.jl
+provides first-class support for the scalar and multivariate normal distributions
+in [Distributions.jl](https://github.com/JuliaStats/Distributions.jl). For
+instance, if the prior distribution is a standard normal distribution, you can
+choose
+```julia
+prior = Normal()
+```
+
+However, custom Gaussian priors are supported as well. For instance, if you want to
+use a custom distribution type `GaussianPrior`, the following methods should be
+implemented:
+```julia
+# state that the distribution is actually Gaussian
+EllipticalSliceSampling.isgaussian(::Type{<:GaussianPrior}) = true
+
+# define the mean of the distribution
+# alternatively implement `proposal(prior, ...)` and
+# `proposal!(out, prior, ...)` (only if the samples are mutable)
+Statistics.mean(dist::GaussianPrior) = ...
+
+# define how to sample from the distribution
+# only one of the following methods is needed:
+# - if the samples are immutable (e.g., numbers or static arrays) only
+#   `rand(rng, dist)` should be implemented
+# - otherwise only `rand!(rng, dist, sample)` is required
+Base.rand(rng::AbstractRNG, dist::GaussianPrior) = ...
+Random.rand!(rng::AbstractRNG, dist::GaussianPrior, sample) = ...
+```
+
+### Log likelihood
+
+In addition to the prior, you have to specify a Julia implementation of
+the log likelihood function. Here the predefined log densities and log
+likelihood functions in
+[Distributions.jl](https://github.com/JuliaStats/Distributions.jl) might
+be useful.
+
+### Progress monitor
+
+If you use a package such as [Juno](https://junolab.org/) or
+[TerminalLoggers.jl](https://github.com/c42f/TerminalLoggers.jl) that supports
+progress logs created by the
+[ProgressLogging.jl](https://github.com/JunoLab/ProgressLogging.jl) API, then you can
+monitor the progress of the sampling algorithm. If you do not specify a progress
+logging frontend explicitly,
+[AbstractMCMC.jl](https://github.com/TuringLang/AbstractMCMC.jl) picks a frontend
+for you automatically.
+
+## References
+
+Murray, I., Adams, R. & MacKay, D.. (2010). Elliptical slice sampling. Proceedings of Machine Learning Research, 9:541-548.