Merge pull request #154 from sisl/plot_updates

Compat updates + minor documentation changes

Author: dylan-asmar

.gitignore

@@ -13,3 +13,5 @@ doc/build/
 doc/site/
 /docs/build/
 /.idea/
+
+Manifest.toml

Project.toml

@@ -1,6 +1,6 @@
 name = "BayesNets"
 uuid = "ba4760a4-c768-5bed-964b-cf806dc591cb"
-version = "3.5.0"
+version = "3.5.1"
 
 [deps]
 CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8"
@@ -9,7 +9,6 @@ DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Discretizers = "6e83dbb3-75ca-525b-8ae2-3751f0dd50b4"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GraphPlot = "a2cc645c-3eea-5389-862e-a155d0052231"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
@@ -31,8 +30,7 @@ DataFrames = "0.22,1.0,1.1"
 DataStructures = "0.11,0.12,0.13,0.14,0.15,0.16,0.17,0.18"
 Discretizers = "3.0"
 Distributions = "0.17,0.18,0.19,0.20,0.21,0.22,0.23,0.24,0.25"
-Documenter = "0.26, 0.27"
-GraphPlot = "0.5"
+GraphPlot = "0.6"
 Graphs = "1.0"
 IterTools = "1.3"
 LightXML = "0.8,0.9"

docs/Project.toml

@@ -0,0 +1,10 @@
+[deps]
+BayesNets = "ba4760a4-c768-5bed-964b-cf806dc591cb"
+Discretizers = "6e83dbb3-75ca-525b-8ae2-3751f0dd50b4"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b"
+TikzGraphs = "b4f28e30-c73f-5eaf-a395-8a9db949a742"
+TikzPictures = "37f6aa50-8035-52d0-81c2-5a1d08754b2d"
+
+[compat]
+Documenter = "1"

docs/make.jl

@@ -1,30 +1,27 @@
-push!(LOAD_PATH, "../src")
-import Pkg
-Pkg.develop(path=".")
-Pkg.add("TikzPictures")
-Pkg.add("TikzGraphs")
-Pkg.add("Documenter")
-Pkg.add("Discretizers")
-Pkg.add("RDatasets")
 using Documenter, BayesNets, TikzGraphs, TikzPictures, Discretizers, RDatasets
 
+page_order = [
+    "index.md",
+    "install.md",
+    "usage.md",
+    "concepts.md",
+    "api.md"
+]
+
 makedocs(
-    modules = [BayesNets, TikzPictures, TikzGraphs, Discretizers, RDatasets],
+    modules = [BayesNets],
     format = Documenter.HTML(
-        mathengine = Documenter.MathJax2()
+        mathengine = Documenter.MathJax2(),
+        size_threshold_ignore=["api.md"]
     ),
     sitename = "BayesNets.jl",
     pages = [
-        "Table of Contents" => [
-            "index.md",
-            "install.md",
-            "usage.md",
-            "concepts.md"
-        ]
-    ]
+        "Table of Contents" => page_order
+    ],
+    warnonly = [:missing_docs]
 )
 
 deploydocs(
     repo = "github.com/sisl/BayesNets.jl.git",
+    push_preview=true
 )
-return true

docs/src/api.md

@@ -0,0 +1,5 @@
+# API Documentation
+
+```@autodocs
+Modules = [BayesNets, BayesNets.CPDs, BayesNets.CPDs.ProbabilisticGraphicalModels, BayesNets.Tables]
+```

docs/src/index.md

@@ -5,5 +5,5 @@
 ### Table of Contents
 
 ```@contents
-Pages = ["install.md", "usage.md", "concepts.md]
+Pages = Main.page_order
 ```

src/learning.jl

@@ -70,7 +70,6 @@ end
     ScoreComponentCache
 Used to store scores in a priority queue such that graph search algorithms know
 when a particular construction has already been made.
-    cache[ⱼ](parentsⱼ, score) for the ith variable with parents parents
 """
 const ScoreComponentCache = Vector{PriorityQueue{Vector{Int}, Float64}} # parent indeces -> score