From aae2e04108e92ed9a6e45da81f6345c7d844f027 Mon Sep 17 00:00:00 2001
From: Emmanuel Lujan <lujan.emmanuel@gmail.com>
Date: Wed, 5 Jun 2024 11:54:22 -0400
Subject: [PATCH] First update to documentation.

---
 docs/make.jl                        | 23 ++++++++++++++---------
 docs/src/how-to-run-the-examples.md | 28 +++++++++++-----------------
 2 files changed, 25 insertions(+), 26 deletions(-)

diff --git a/docs/make.jl b/docs/make.jl
index ecd9db4d..cf17d070 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -12,21 +12,25 @@ DocMeta.setdocmeta!(
     recursive = true,
 )
 
+
 bib = CitationBibliography(joinpath(@__DIR__, "citation.bib"))
 
 # Generate examples
 
-#const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
-#const OUTPUT_DIR = joinpath(@__DIR__, "src/generated")
+const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
+const OUTPUT_DIR   = joinpath(@__DIR__, "src/generated")
+
+examples = [
+    "Subsampling, compute descriptors, and fit ACE" => "Na/fit-dpp-ace-na"
+]
 
-#examples = Pair{String,String}[]
+for (_, name) in examples
+    example_filepath = joinpath(EXAMPLES_DIR, string(name, ".jl"))
+    Literate.markdown(example_filepath, OUTPUT_DIR, documenter=true)
+end
 
-#for (_, name) in examples
-#    example_filepath = joinpath(EXAMPLES_DIR, string(name, ".jl"))
-#    Literate.markdown(example_filepath, OUTPUT_DIR, documenter = true)
-#end
+examples = [title=>joinpath("generated", string(name, ".md")) for (title, name) in examples]
 
-#examples = [title => joinpath("generated", string(name, ".md")) for (title, name) in examples]
 
 makedocs(
       root    =  joinpath(dirname(pathof(PotentialLearning)), "..", "docs"),
@@ -39,9 +43,10 @@ makedocs(
       highlightsig = true,
       sitename = "PotentialLearning.jl",
       expandfirst = [],
-      draft = false,
+      draft = false,    
       pages = ["Home" => "index.md",
                "How to run the examples" => "how-to-run-the-examples.md",
+               "Examples" => examples,
                "API" => "api.md"],
       format = Documenter.HTML(;
         prettyurls = get(ENV, "CI", "false") == "true",
diff --git a/docs/src/how-to-run-the-examples.md b/docs/src/how-to-run-the-examples.md
index a5fd45b7..a063835a 100644
--- a/docs/src/how-to-run-the-examples.md
+++ b/docs/src/how-to-run-the-examples.md
@@ -1,7 +1,6 @@
 # How to run the examples
 
 ## Add registries
-
 Open a Julia REPL (`$ julia`), type `]` to enter the Pkg REPL, and add the following registries:
 ```julia
     pkg> registry add https://github.com/JuliaRegistries/General
@@ -10,32 +9,27 @@ Open a Julia REPL (`$ julia`), type `]` to enter the Pkg REPL, and add the follo
     pkg> registry add https://github.com/ACEsuit/ACEregistry
 ```
 
-## Install the dependencies of the `examples` folder project
-
+## Clone repository and access an example folder
 Clone `PotentialLearning.jl` repository in your working directory.
 ```shell
     $ git clone git@github.com:cesmix-mit/PotentialLearning.jl.git
 ```
-Open a Julia REPL activating the `examples`  folder project.
-```shell
-    $ julia --project=PotentialLearning.jl/examples
-```
- Type `]` to enter the Pkg REPL and instantiate.
-```julia
-    pkg> instantiate
-```
-
-## Run an example
-
 Access to any folder within `PotentialLearning.jl/examples`. E.g.
 ```shell
-    $ cd PotentialLearning.jl/examples/ACE
+    $ cd PotentialLearning.jl/examples/Na
 ```
+
+## Run example
 Open a Julia REPL, activate the `examples` folder project, and define the number of threads.
 ```julia
-    $ julia --project=../ --threads=4
+    $ julia --project=./ --threads=4
+```
+Type `]` to enter the Pkg REPL and instantiate.
+```julia
+    pkg> instantiate
 ```
 Finally, include the example file.
 ```julia
-    julia> include("fit-ace.jl")
+    julia> include("fit-dpp-ace-na.jl")
 ```
+