From 68c3b966fe8f5fc2caef7f1282575e51e2334868 Mon Sep 17 00:00:00 2001
From: niklasmueboe <niklasmueboe@github.com>
Date: Wed, 12 Jun 2024 11:20:04 +0200
Subject: [PATCH] update docs

---
 docs/Project.toml |  7 +++++++
 docs/make.jl      | 23 ++++++++++++++++++++++-
 docs/src/api.md   | 20 ++++++++++++++++++++
 docs/src/index.md | 23 ++++++++++++++---------
 4 files changed, 63 insertions(+), 10 deletions(-)
 create mode 100644 docs/Project.toml
 create mode 100644 docs/src/api.md

diff --git a/docs/Project.toml b/docs/Project.toml
new file mode 100644
index 0000000..f6490ec
--- /dev/null
+++ b/docs/Project.toml
@@ -0,0 +1,7 @@
+[deps]
+Documenter           = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
+StereoSSAM           = "4c4340ea-7f9e-46b4-8512-61f1f6c41a11"
+
+[compat]
+Documenter = "1.3"
diff --git a/docs/make.jl b/docs/make.jl
index 9fef554..e114b62 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -1,4 +1,25 @@
 using Documenter
+using DocumenterInterLinks
 using StereoSSAM
 
-makedocs(; sitename="StereoSSAM.jl")
\ No newline at end of file
+links = InterLinks(
+    # "CategoricalArrays" => "https://categoricalarrays.juliadata.org/stable/",
+    # "DimensionalData" => "https://rafaqz.github.io/DimensionalData.jl/dev/",
+    "Muon" => "https://scverse.org/Muon.jl/dev/",
+    "SparseArrays" => (
+        "https://docs.julialang.org/en/v1/stdlib/SparseArrays/",
+        "https://docs.julialang.org/en/v1/objects.inv",
+    ),
+)
+
+makedocs(;
+    sitename="StereoSSAM.jl",
+    pages=[
+        "Home" => "index.md",
+        "Example analysis" => "examples/ExampleAnalysis.md",
+        "Reference API" => "api.md",
+    ],
+    authors="Niklas Müller-Bötticher",
+    plugins=[links],
+    format=Documenter.HTML(; size_threshold_ignore=["examples/ExampleAnalysis.md"]),
+)
\ No newline at end of file
diff --git a/docs/src/api.md b/docs/src/api.md
new file mode 100644
index 0000000..2218ae5
--- /dev/null
+++ b/docs/src/api.md
@@ -0,0 +1,20 @@
+# Reference API
+
+Documentation for `StereoSSAM.jl`'s public interface.
+
+## Index
+
+```@index
+Pages = ["api.md"]
+```
+
+## API
+
+```@autodocs
+Modules = [
+    StereoSSAM.IO,
+    StereoSSAM.Utils,
+    StereoSSAM.KDE,
+    StereoSSAM.LocalMax,
+]
+```
diff --git a/docs/src/index.md b/docs/src/index.md
index 8d39934..d310c85 100644
--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -1,15 +1,20 @@
-# StereoSSAM.jl Documentation
+# StereoSSAM.jl
 
-```@contents
-```
+TODO general introduction
 
-## Functions
+reference to python repo
 
-```@autodocs
-Modules = [StereoSSAM]
-```
+## Citation
+
+If you use `StereoSSAM.jl` for your research please consider citing
+TODO
 
 ## Index
 
-```@index
-```
\ No newline at end of file
+```@contents
+Pages = [
+    "examples/ExampleAnalysis.md",
+    "api.md",
+]
+Depth = 3
+```