Merge pull request #127 from dwijenchawra/master

mykelk · web-flow · commit f30ac4625e2a · 2021-05-05T09:30:24.000-07:00
Migrated documentation from Jupyter to Documenter.jl
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -0,0 +1,27 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - master
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.6'
+      - name: Install LuaLatex
+        run: sudo apt-get install texlive-full && sudo apt-get install texlive-latex-extra && sudo mktexlsr && sudo updmap-sys
+      - 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
+        run: julia --project=docs/ docs/make.jl
+
diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,7 @@
 
 .DS_Store
 
+doc/build/
+doc/site/
+/docs/build/
+/.idea/
diff --git a/.travis.yml b/.travis.yml
@@ -1,14 +1,34 @@
+# Documentation: http://docs.travis-ci.com/user/languages/julia
 language: julia
-coveralls: true
-os:
-  - linux
-  - osx 
-  - windows
+notifications:
+  email: false
 julia:
   - 1.0
-  - 1
-matrix:
+  - 1.5
+  - nightly
+os:
+  - linux
+
+cache:
+  directories:
+    - ~/.julia/artifacts
+jobs:
+  fast_finish: true
   allow_failures:
-    - julia: 1.0
-notifications:
-  email: false
+    - julia: nightly
+  include:
+    - stage: "Documentation"
+      julia: 1.5
+      os: linux
+      script:
+        - julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd()));
+          Pkg.instantiate()'
+        - julia --project=docs/ docs/make.jl
+      after_success: skip
+after_success:
+  - |
+    julia -e '
+      using Pkg
+      Pkg.add("Coverage")
+      using Coverage
+      Coveralls.submit(process_folder())'
diff --git a/Project.toml b/Project.toml
@@ -22,6 +22,8 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
 
 [compat]
 DataFrames = "0.21,0.22"
@@ -40,6 +42,7 @@ Requires = "1.0.1"
 SpecialFunctions = "0.8,0.10,1.0,1.1,1.2"
 StatsBase = "0.25,0.26,0.27,0.28,0.29,0.30,0.31,0.32,0.33"
 julia = "1"
+Documenter = "0.26"
 
 [extras]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
diff --git a/README.md b/README.md
@@ -2,6 +2,6 @@
 
 This library supports representation, inference, and learning in Bayesian networks.
 
-Please read the [documentation](http://nbviewer.ipython.org/github/sisl/BayesNets.jl/blob/master/doc/BayesNets.ipynb).
+Please read the [documentation](https://sisl.github.io/BayesNets.jl/dev/index.html).
 
-[![Build Status](https://travis-ci.org/sisl/BayesNets.jl.svg?branch=master)](https://travis-ci.org/sisl/BayesNets.jl) [![Coverage Status](https://coveralls.io/repos/sisl/BayesNets.jl/badge.svg?branch=master&service=github)](https://coveralls.io/github/sisl/BayesNets.jl?branch=master)
+[![Build Status](https://github.com/sisl/BayesNets.jl/actions/workflows/main.yml/badge.svg)](https://travis-ci.org/sisl/BayesNets.jl) [![Coverage Status](https://coveralls.io/repos/sisl/BayesNets.jl/badge.svg?branch=master&service=github)](https://coveralls.io/github/sisl/BayesNets.jl?branch=master)
diff --git a/docs/.gitignore b/docs/.gitignore
diff --git a/docs/BayesNets.ipynb b/docs/BayesNets.ipynb
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -0,0 +1,8 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "0.26"
+
+[extras]
+TikzGraphs = "b4f28e30-c73f-5eaf-a395-8a9db949a742"
diff --git a/docs/make.jl b/docs/make.jl
@@ -0,0 +1,29 @@
+push!(LOAD_PATH, "../src")
+import Pkg
+Pkg.add("BayesNets")
+Pkg.add("TikzPictures")
+Pkg.add("TikzGraphs")
+Pkg.add("Documenter")
+Pkg.add("Discretizers")
+Pkg.add("RDatasets")
+using Documenter, BayesNets, TikzGraphs, TikzPictures, Discretizers, RDatasets
+
+makedocs(
+    modules = [BayesNets, TikzPictures, TikzGraphs, Discretizers, RDatasets],
+    format = Documenter.HTML(
+        mathengine = Documenter.MathJax2()
+    ),
+    sitename = "BayesNets.jl",
+    pages = [
+        "Table of Contents" => [
+            "index.md",
+            "install.md",
+            "usage.md",
+            "concepts.md"
+        ]
+    ]
+)
+
+deploydocs(
+    repo = "github.com/sisl/BayesNets.jl.git",
+)
diff --git a/docs/src/concepts.md b/docs/src/concepts.md
@@ -0,0 +1,10 @@
+# Concepts
+
+
+## Bayesian Networks
+
+A Bayesian Network (BN) represents a probability distribution over a set of variables, ``P(x_1, x_2, \ldots, x_n)``. 
+Bayesian networks leverage variable relations in order to efficiently decompose the joint distribution into smaller conditional probability distributions.
+
+A BN is defined by a directed acyclic graph and a set of conditional probability distributions. Each node in the graph corresponds to a variable ``x_i`` and is associated with a conditional probability distribution ``P(x_i \mid \text{parents}(x_i))``.
+
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -0,0 +1,9 @@
+# [BayesNets](https://github.com/sisl/BayesNets.jl)
+
+*A Julia package for Bayesian Networks*
+
+### Table of Contents
+
+```@contents
+Pages = ["install.md", "usage.md", "concepts.md]
+```
diff --git a/docs/src/install.md b/docs/src/install.md
@@ -0,0 +1,6 @@
+# Installation
+
+```julia
+Pkg.add("BayesNets");
+```
+Default visualization of the network structure is provided by the GraphPlot package. However, we recommend using tex-formatted graphs provided by the TikzGraphs package. Installation requirements for TikzGraphs (e.g., PGF/Tikz and pdf2svg) are provided [here](http://nbviewer.ipython.org/github/sisl/TikzGraphs.jl/blob/master/doc/TikzGraphs.ipynb). Simply run using `TikzGraphs` in your Julia session to automatically switch to tex-formatted graphs (thanks to the Requires.jl package).
diff --git a/docs/src/usage.md b/docs/src/usage.md
diff --git a/test/test_docs.jl b/test/test_docs.jl
