From c4b50a2ead6397b75edcd2e294d7d466d6b5e091 Mon Sep 17 00:00:00 2001
From: "Jessica S. Yu" <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 9 Aug 2024 11:21:45 -0400
Subject: [PATCH] Add CHANGELOG.md summarizing changes from base repo (#2)

* Add CHANGELOG summarizing changes from base repo

* Update README with notice of changes
---
 CHANGELOG.md | 32 ++++++++++++++++++++++++++++++++
 README.md    |  3 +++
 2 files changed, 35 insertions(+)
 create mode 100644 CHANGELOG.md

diff --git a/CHANGELOG.md b/CHANGELOG.md
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index 0000000..e69b039
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,32 @@
+This document provides a detailed timeline of changes made to the source code of the Cytosim simulation engine hosted at [https://gitlab.com/f-nedelec/cytosim](https://gitlab.com/f-nedelec/cytosim).
+
+### 2024-06-07
+
+- Add config files used by [`subcell-pipeline`](https://github.com/simularium/subcell-pipeline)
+- Add config templates used by [`subcell-pipeline`](https://github.com/simularium/subcell-pipeline)
+
+### 2023-06-16
+
+- Change dimensionality from 2 to 3
+
+> See commit [`70c73c7`](https://github.com/simularium/Cytosim/commit/70c73c7cd17d3d03e49e9b7da35cdcbf645b6a3b)
+
+### 2023-05-03
+
+- Add calculation and reporting for segment bending energy
+- Change time reporting to scientific notation
+
+> See commit [`b2a8293`](https://github.com/simularium/Cytosim/commit/b2a8293ac0a6492b7ca51cba44f11ae70f33485f)
+
+### 2023-03-13
+
+- Resync with source code from [https://gitlab.com/f-nedelec/cytosim](https://gitlab.com/f-nedelec/cytosim) at commit [`5ff0f784`](https://gitlab.com/f-nedelec/cytosim/-/tree/5ff0f78474de7217aa194d98f98516395fb3d453)
+
+### 2022-06-08
+
+- Added `Dockerfile` and associated scripts to build Docker image from source code
+- Added GitHub-specific workflows for building Docker image
+
+### 2022-05-18
+
+- Source code from [https://gitlab.com/f-nedelec/cytosim](https://gitlab.com/f-nedelec/cytosim) at commit [`6bc43897`](https://gitlab.com/f-nedelec/cytosim/-/commit/6bc43897e35cd599861d1c96eae05c064be8a937)
diff --git a/README.md b/README.md
index 46ac235..bd65bbc 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,6 @@
+> [!NOTE]
+> This repository is adapted from the base Cytosim repository hosted at [https://gitlab.com/f-nedelec/cytosim](https://gitlab.com/f-nedelec/cytosim). Please see [CHANGELOG.md](CHANGELOG.md) for more information and a summary of changes.
+
 # Cytosim
 
 Cytosim is a cytoskeleton simulation suite designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It is a versatile base that has been used to study actin and microtubule systems in 1D, 2D and 3D. It is built around a cross-platform C++ core engine running on UNIX, Mac OSX, GNU/Linux and within Cygwin on Windows. The code is modular and extensible, making Cytosim a convenient base that can be customized to meet particular tasks. Some of the most common tasks encountered during a simulation project are implemented in Python.