Add stub files

jeromekelleher · jeromekelleher · commit 97e044184166 · 2025-11-20T13:47:15.000Z
diff --git a/docs/_config.yml b/docs/_config.yml
@@ -4,7 +4,7 @@
 title: sc2ts manual
 author: sc2ts developers
 logo: sc2ts.png
-copyright: "2024"
+copyright: "2025"
 only_build_toc_files: true
 
 execute:
diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -1,6 +1,14 @@
 format: jb-book
 root: intro
 parts:
+  - caption: Getting started
+    chapters:
+      - file: installation
+  - caption: Usage
+    chapters:
+      - file: inference
+      - file: arg_analysis
+      - file: alignments_analysis
   - caption: Interfaces
     chapters:
       - file: cli
diff --git a/docs/alignments_analysis.md b/docs/alignments_analysis.md
@@ -0,0 +1 @@
+# Alignments analysis
diff --git a/docs/arg_analysis.md b/docs/arg_analysis.md
@@ -0,0 +1 @@
+# ARG analysis
diff --git a/docs/inference.md b/docs/inference.md
@@ -0,0 +1,2 @@
+# Inference
+
diff --git a/docs/installation.md b/docs/installation.md
@@ -0,0 +1,11 @@
+# Installation
+
+
+Install sc2ts from PyPI:
+
+```sh
+python -m pip install sc2ts
+```
+
+This installs the minimal version of sc2ts which provides the Python interfaces to
+analyse a
