add build status

README.md

@@ -1,5 +1,9 @@
 # PoseCheck: Benchmarking Generated Poses
 
+[![python](https://img.shields.io/badge/-Python_3.8_%7C_3.9_%7C_3.10-blue?logo=python&logoColor=white)](https://github.com/pre-commit/pre-commit)
+
+[![build](https://github.com/cch1999/posecheck/actions/workflows/tests.yaml/badge.svg?branch=main)](https://github.com/cch1999/posecheck/actions/workflows/tests.yaml)
+
 <p align="center">
   <a href="">
     <img src="data/posecheck_logo.png" width="800"/>
@@ -78,7 +82,9 @@ print(f"Interactions of example molecule: {interactions}")
 
 ## Data from the paper
 
-WIP!
+
+The data for the paper can be found at the following Zenodo link:
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10208912.svg)](https://doi.org/10.5281/zenodo.10208912)
 
 
 ## Cite

changelog.md

@@ -0,0 +1,19 @@
+# Changelog
+
+## [1.1] - 18-01-2024
+
+### Changed
+- [IMPORTANT - PLEASE READ IF YOU INTEND TO PUBLISH] Changed the way strain energy is calculated. Previously, the strain energy was calculated as the difference between the energy of the raw output and a fully relaxed structure. This meant that the energy term of the raw output exploded due to slight imperfections in local bond lengths and angles and did not reflect global strain well. Now we perform a small bit of local relaxation (max displacement in the atom positions of 0.1 Å) and use the energy of this structure as the reference energy. This means that the strain energy is now a more accurate reflection of the global strain of the molecule.
+
+### Added
+- Data and notebooks needed to reproduce plots from the paper.
+- Validator that warms the user if `reduce` cannot be found.
+- CI tests
+- Full environment specs
+
+### Fixed
+- Improved doc string coverage
+
+## [1.0] - 24-09-2023
+
+Initial release of the software with basic features for chemical analysis.

dev.ipynb

@@ -0,0 +1,44 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "",
+     "evalue": "",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31mRunning cells with '/Users/charlie/micromamba/envs/posecheck/bin/python' requires the ipykernel package.\n",
+      "\u001b[1;31mRun the following command to install 'ipykernel' into the Python environment. \n",
+      "\u001b[1;31mCommand: 'conda install -p /Users/charlie/micromamba/envs/posecheck ipykernel --update-deps --force-reinstall'"
+     ]
+    }
+   ],
+   "source": [
+    "import torch"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.11.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}