Merge pull request tskit-dev#103 from hyanwong/msprime-sections

Put the msprime advances examples as sections

Author: jeromekelleher

_toc.yml

@@ -23,9 +23,11 @@ parts:
   # TODO this will be broken down more finely as we add more content
   chapters:
   - file: no_mutations
-  - file: demography
-  - file: bottlenecks
-  - file: introgression
+  - file: msprime
+    sections:
+    - file: demography
+    - file: bottlenecks
+    - file: introgression
   - file: completing-forward-sims
 - caption: Forward time simulations
   # TODO port/add forward simulation contents

bottlenecks.md

@@ -11,6 +11,8 @@ kernelspec:
   name: python3
 ---
 
+(sec_msprime_bottlenecks)=
+
 # Instantaneous Bottlenecks
 
 **Konrad Lohse and Jerome Kelleher**

demography.md

@@ -11,6 +11,8 @@ kernelspec:
   name: python3
 ---
 
+(sec_msprime_demography)=
+
 # Demography
 
 **Georgia Tsambos**

introgression.md

@@ -11,6 +11,8 @@ kernelspec:
   name: python3
 ---
 
+(sec_msprime_introgression)=
+
 # Introgression 
 
 **Jerome Kelleher and Konrad Lohse**

msprime.md

@@ -1,5 +1,23 @@
+---
+jupytext:
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.12
+    jupytext_version: 1.9.1
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
 
-# Advanced msprime topics 
+(sec_msprime)=
 
-These are advanced topics in msprime or examples of how to 
-do some particular things in msprime.
+# Advanced {program}`msprime` topics 
+
+These are advanced topics in [msprime](https://tskit.dev/msprime) or examples of how to 
+do some particular things with it. This chapter is broken down into the following
+sections:
+
+```{tableofcontents}
+```