docs: minimal version

Author: cvigilv

docs/Project.toml

@@ -1,4 +1,6 @@
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 KEGGAPI = "e8256861-d17c-4800-bf17-838497555b93"
+LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"

docs/make.jl

@@ -17,10 +17,9 @@ makedocs(;
     pages = [
         "Home" => "index.md",
         "Manual" => Any[
-            "Guide" => "man/guide.md",
-            "man/functions.md",
-            "man/examples.md",
-            "man/workflow.md",
+            "Getting started" => "man/getting-started.md",
+            "Examples" => "man/examples.md",
+            "API reference" => "man/api.md",
         ],
     ],
 )

docs/src/index.md

@@ -1,13 +1,15 @@
 ```@meta
 CurrentModule = KEGGAPI
 ```
-
-# KEGGAPI
-
-Documentation for [KEGGAPI](https://github.com/bwbioinfo/KEGGAPI.jl).
-
-An API interface to [KEGG](https://www.genome.jp/kegg/)
-
-
-```@index
-```
+# KEGGAPI.jl
+
+A Julia interface for the [KEGG API](https://www.kegg.jp/kegg/rest/keggapi.html).
+The interface allows the functional annotation of genes, identification of metabolic processes
+and pathways, the exploration of reaction/pathway prevalence at different taxonomic levels and
+the identification of orthologous proteins for further analysis.
+
+KEGGAPI.jl aims to support all KEGG API endpoints provided by the
+["KEGGREST"](https://bioconductor.org/packages/release/bioc/html/KEGGREST.html) package for R
+(Tenenbaum and maintainers, 2025) and the
+["Bio.KEGG.REST"](https://biopython.org/docs/1.75/api/Bio.KEGG.REST.html) submodule from
+Biopython for Python.

docs/src/man/functions.md docs/src/man/api.mddocs/src/man/functions.md renamed to docs/src/man/api.md

@@ -1,5 +1,5 @@
-# KEGGAPI.jl Functions
+# API reference
 
 ```@autodocs
 Modules = [KEGGAPI]
-```
+```

docs/src/man/examples.md

@@ -1,4 +1,4 @@
-# Some Examples
+# Examples
 
 ## KEGGAPI.conv
 

docs/src/man/getting-started.md

@@ -0,0 +1,38 @@
+# Getting started with KEGGAPI.jl
+
+## Installation
+
+KEGGAPI.jl can be installed using the Julia package manager.
+From the Julia REPL, type `]` to enter the Pkg REPL mode and run
+
+```
+pkg> add https://github.com/cvigilv/KEGGAPI.jl
+```
+
+## Usage
+
+To use KEGGAPI.jl, simply import the package:
+
+```@setup examples
+using KEGGAPI
+```
+
+And use the interfaces to query the KEGG API. For example, to list all organisms in KEGG:
+```@example examples
+result = KEGGAPI.list("organism");
+```
+This returns a `KeggOrganismList` object with the API call, column names and data. The data can
+accessed by indexing into the respective fields of the object:
+```@example examples
+result.url
+```
+
+```@example examples
+result.colnames
+```
+
+```@example examples
+result.data
+```
+
+For more example usage, refer to the [examples](examples.md) page and the [API reference](api.md).