Improve technical instruction and add -version flag

README.md

@@ -12,6 +12,16 @@ Whalen, A, Ros-Freixedes, R, Wilson, DL, Gorjanc, G, Hickey, JM. (2018). Hybrid
 
 See https://alphapeel.readthedocs.io/en/latest
 
+Quick links:
+
+- [Installation](https://alphapeel.readthedocs.io/en/latest/get_started.html#install-software)
+
+- [Simple example](https://alphapeel.readthedocs.io/en/latest/get_started.html#an-example)
+
+- [How to use](https://alphapeel.readthedocs.io/en/latest/usage.html)
+
+- [Algorithm](https://alphapeel.readthedocs.io/en/latest/algorithm.html)
+
 ## Conditions of use
 
 AlphaPeel is fully and freely available for all use under the MIT License.

docs/source/algorithm.rst

@@ -1,3 +1,5 @@
+.. _algorithm:
+
 ==================
 Algorithm Overview
 ==================

docs/source/changelog.rst

@@ -1,14 +1,23 @@
 =========
 Changelog
 =========
-[1.3.1] - 2026-03-05
-====================
+
+.. 
+  If you are add a new entry to the changelog, please follow the format of the existing entries and 
+  add your changes to the top of the file under the [Unreleased] section. 
+  Please also include the pull request number and the GitHub username(s) of the contributor(s) who made the change.
+
+[Unreleased] - 2026-03-??
+=========================
 
 New features
 ------------
 * Allow a founding individual to have two different metafounders, e.g., one for the paternal lineage and one for the maternal lineage
   (:pr:`222`, :user:`RosCraddock`, :user:`gregorgorjanc`, :user:`XingerTang`).
 
+* Add a version option to the command line interface
+  (:pr:`237`, :user:`XingerTang`).
+
 Maintenance
 -----------
 
@@ -25,16 +34,15 @@ Maintenance
 
     - Reformatted the ``alt_allele_prob_file`` input to match the outputted ``alt_allele_prob_file``.
 
-
-[Unreleased] - 2026-02-12
-=========================
-
-Maintenance
------------
-
 * Updated the documentation to clarify inputs, outputs, and parameters
   (:pr:`219`, :user:`gregorgorjanc`).
 
+* Add collaboration guidelines to the documentation
+  (:pr:`224`, :user:`XingerTang`, :user:`RosCraddock`, :user:`AprilYuZhang`, :user:`gregorgorjanc`).
+
+* Updated the documentation to add more techincal instructions for developers and contributors
+  (:pr:`237`, :user:`XingerTang`).
+
 [1.3.0] - 2026-02-05
 ====================