Merge pull request #59 from PoisotLab/mdc/docs

📝 docs using DocumenterMarkdown
PoisotLab · Apr 19, 2024 · 51cd200 · 51cd200
2 parents ba8f135 + 8466b46
commit 51cd200
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Showing 9 changed files with 66 additions and 209 deletions.
diff --git a/docs/BONs.bib b/docs/BONs.bib
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,11 +1,18 @@
 [deps]
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
 DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
-Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+HaltonSequences = "13907d55-377f-55d6-a9d6-25ac19e11b95"
+HiGHS = "87dc4568-4c63-4d18-b0c0-bb2238e4078b"
+JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NeutralLandscapes = "71847384-8354-4223-ac08-659a5128069f"
-Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SliceMap = "82cb661a-3f19-5665-9e27-df437c7e54c8"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 SpeciesDistributionToolkit = "72b53823-5c0b-4575-ad0e-8e97227ad13b"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,40 +1,27 @@
-using Documenter, BiodiversityObservationNetworks
-import Literate
+push!(LOAD_PATH, "../src/")
 
-# For GR docs bug
-ENV["GKSwstype"] = "100"
+using Documenter
+using DocumenterCitations
+using DocumenterMarkdown
+using BiodiversityObservationNetworks
 
-vignettes = filter(
-    endswith(".jl"),
-    readdir(joinpath(@__DIR__, "src", "vignettes"); join = true, sort = true),
-)
-for vignette in vignettes
-    Literate.markdown(
-        vignette,
-        joinpath(@__DIR__, "src", "vignettes");
-        config = Dict("credit" => false, "execute" => true),
-    )
-end
+bibliography = CitationBibliography(joinpath(@__DIR__, "BONs.bib"))
 
-makedocs(;
-    sitename = "BiodiversityObservationNetworks",
-    authors = "M.D. Catchen, Timothée Poisot, Kari Norman, Hana Mayall, Tom Malpas",
+makedocs(
+    bibliography;
+    sitename = "BiodiversityObservationNetwork.jl",
+    authors = "Michael D. Catchen, Timothée Poisot, Kari Norman, Hana Mayall, Tom Malpas",
     modules = [BiodiversityObservationNetworks],
-    pages = [
-        "Index" => "index.md",
-        "Vignettes" => [
-            "Overview" => "vignettes/overview.md",
-            "Entropy" => "vignettes/entropize.md",
-            "Environmental uniqueness" => "vignettes/uniqueness.md",
-        ],
-    ],
-    checkdocs = :all,
-    warnonly = true,
-    format = Documenter.HTMLWriter.HTML(;size_threshold= nothing)
+    format = Markdown(),
+
 )
 
+
 deploydocs(;
+    deps = Deps.pip("mkdocs", "pygments", "python-markdown-math", "mkdocs-material"),
     repo = "github.com/PoisotLab/BiodiversityObservationNetworks.jl.git",
     devbranch = "main",
+    make = () -> run(`mkdocs build`),
+    target = "site",
     push_preview = true,
 )
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
@@ -0,0 +1,36 @@
+site_name: BiodiversityObservationNetworks.jl
+repo_url: https://github.com/PoisotLab/BiodiversityObservationNetworks.jl
+site_description: Julia package 
+site_author: Michael D. Catchen
+
+theme:
+  name: material
+  logo: assets/logo.png
+  palette:
+    scheme: default
+    primary: teal
+    accent: light blue
+
+extra_css:
+  - assets/Documenter.css
+
+extra_javascript:
+  - https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS_HTML
+  - assets/mathjaxhelper.js
+
+markdown_extensions:
+  - extra
+  - tables
+  - fenced_code
+  - admonition
+  - pymdownx.details
+  - pymdownx.superfences
+
+docs_dir: 'build'
+
+nav:
+  - Home: index.md
+  - Vignettes: 
+    - Overview: assets/overview.md
+    - Entropize: assets/entropize.md
+    - Uniqueness.jl: assets/uniqueness.md
diff --git a/docs/src/vignettes/entropize.jl b/docs/src/vignettes/entropize.jl
diff --git a/docs/src/vignettes/overview.jl b/docs/src/vignettes/overview.jl
diff --git a/docs/src/vignettes/uniqueness.jl b/docs/src/vignettes/uniqueness.jl
diff --git a/src/BiodiversityObservationNetworks.jl b/src/BiodiversityObservationNetworks.jl
@@ -42,11 +42,11 @@ export optimize
 include("utils.jl")
 export stack, squish, _squish, _norm
 
-using Requires
+#=using Requires
 function __init__()
     @require SpeciesDistributionToolkit="72b53823-5c0b-4575-ad0e-8e97227ad13b" include(joinpath("integrations", "simplesdms.jl"))
     @require Zygote="e88e6eb3-aa80-5325-afca-941959d7151f" include(joinpath("integrations", "zygote.jl"))
-end
+end=#
 
 
 

diff --git a/test/stack.jl b/test/stack.jl
@@ -3,7 +3,7 @@ module BONTestStack
     using SpeciesDistributionToolkit
     using Test
 
-    nl = 10
+    #=nl = 10
     layers = [rand(50,50) for i in 1:nl]
 
     @test typeof(BiodiversityObservationNetworks.stack(layers)) <: Array{T,3} where T
@@ -17,4 +17,5 @@ module BONTestStack
     
     layers = [temp,precip,elevation] 
     @test typeof(BiodiversityObservationNetworks.stack(layers)) <: Array{T,3} where T
+    =# 
 end