Refactor documentation structure and update 'Get Started' guide for c…

…larity
camilogarciabotero · Oct 30, 2024 · 5c2edbb · 5c2edbb
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diff --git a/docs/make.jl b/docs/make.jl
@@ -4,33 +4,8 @@ using DocumenterVitepress
 
 DocMeta.setdocmeta!(GeneFinder, :DocTestSetup, :(using GeneFinder); recursive = true)
 
-# makedocs(;
-#     modules = [GeneFinder],
-#     authors = "Camilo García-Botero",
-#     repo = "https://github.com/camilogarciabotero/GeneFinder.jl/",
-#     sitename = "GeneFinder.jl",
-#     format = Documenter.HTML(;
-#         mathengine=MathJax3(),
-#         # prettyurls = get(ENV, "CI", "false") == "true",
-#         canonical = "https://camilogarciabotero.github.io/GeneFinder.jl",
-#         repolink = "https://github.com/camilogarciabotero/GeneFinder.jl",
-#         edit_link = "main",
-#     ),
-#     pages = [
-#         "Home" => "index.md",
-#         "Finding ORFs" => "naivefinder.md",
-#         "Scoring ORFs" => "features.md",
-#         "A Simple Coding Rule" => "simplecodingrule.md",
-#         "Wrtiting ORFs In Files" => "iodocs.md",
-#         "API" => "api.md",
-#         # "Roadmap" => "roadmap.md",
-#     ],
-#     warnonly = true,
-# )
-
 deploydocs(; repo = "https://github.com/camilogarciabotero/GeneFinder.jl", devbranch = "main")
 
-
 fmt = DocumenterVitepress.MarkdownVitepress(
     repo = "https://github.com/camilogarciabotero/GeneFinder.jl",
     devbranch = "main",
@@ -39,11 +14,15 @@ fmt = DocumenterVitepress.MarkdownVitepress(
 pgs = [
     "Home" => "index.md",
     "Get Started" => "getstarted.md",
-    "Finding ORFs" => "naivefinder.md",
-    "Scoring ORFs" => "features.md",
-    "A Simple Coding Rule" => "simplecodingrule.md",
-    "Wrtiting ORFs In Files" => "iodocs.md",
-    "API" => "api.md",
+    "Usage" => [
+        "Finding ORFs" => "naivefinder.md",
+        "Scoring ORFs" => "features.md",
+        "A Simple Coding Rule" => "simplecodingrule.md",
+        "Writing ORFs In Files" => "iodocs.md",
+    ],
+    "Reference" => [
+        "API" => "api.md",
+    ],
 ]
 
 makedocs(;

diff --git a/docs/src/getstarted.md b/docs/src/getstarted.md
@@ -2,7 +2,7 @@
 
 The main package function is `findorfs`. Under the hood, the `findorfs` function is an interface for different gene finding algorithms that can be plugged using the `finder` keyword argument. By default it uses the `NaiveFinder` algorithm, which is a simple algorithm that finds all (non-outbounded) ORFIs in a DNA sequence (see the [NaiveFinder](https://camilogarciabotero.github.io/GeneFinder.jl/dev/api/#GeneFinder.NaiveFinder-Union{Tuple{Union{BioSequences.LongDNA{N},%20BioSequences.LongSubSeq{BioSequences.DNAAlphabet{N}}}},%20Tuple{N}}%20where%20N) documentation for more details).
 
-> [!NOTE] 
+!!! note
   The `minlen` kwarg in the `NaiveFinder` mehtod has been set to 6nt, so it will catch random ORFIs not necesarily genes thus it might consider `dna"ATGTGA"` -> `aa"M*"` as a plausible ORFI.
 
 Here is an example of how to use the `findorfs` function with the `NaiveFinder` algorithm: