Update CodeEntropy Documentation to reflect changes made in v1.0.0

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,20 +1,20 @@
-### Summary
+## Summary
 <!-- Provide a brief description of the PR's purpose here. -->
 
-### Changes
+## Changes
 <!-- List all the changes introduced in this PR. -->
-Change 1 <!-- Rename Change 1 to reflect change title -->:
+### Change 1 <!-- Rename Change 1 to reflect change title -->:
 - <!-- Bullet point the changes in update 1. -->
 -  
 
-Change 2 <!-- Rename Change 2 to reflect change title -->:
+### Change 2 <!-- Rename Change 2 to reflect change title -->:
 - <!-- Bullet point the changes in update 2. -->
 -  
 
-Change 3 <!-- Rename Change 3 to reflect change title -->:
+### Change 3 <!-- Rename Change 3 to reflect change title -->:
 - <!-- Bullet point the changes in update 3. -->
 -  
 
-### Impact
+## Impact
 - <!-- Bullet point the expected impact this PR will have on the codebase. -->
 -  

.gitignore

@@ -117,3 +117,10 @@ Example/data/*.csv
 # trajectory file too big
 Example/data/1AKI_prod.trr
 Example/data/1AKI_prod.tpr
+
+# output directories, log file and outputs
+job*
+*.json
+*.err
+*.com
+*.txt

README.md

@@ -1,17 +1,19 @@
 [//]: # (Badges)
 [![CodeEntropy CI](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/project-ci.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/project-ci.yaml)
+[![Docs - Status](https://app.readthedocs.org/projects/codeentropy/badge/?version=latest)](https://codeentropy.readthedocs.io/en/latest/?badge=latest)
 ![PyPI - Version](https://img.shields.io/pypi/v/codeentropy?logo=pypi&logoColor=white)
 ![PyPI - Status](https://img.shields.io/pypi/status/codeentropy?logo=pypi&logoColor=white)
-![PyPI - Downloads](https://img.shields.io/pepy/dt/codeentropy?logo=pypi&logoColor=white&color=blue)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/CodeEntropy)
+![PyPI - Total Downloads](https://img.shields.io/pepy/dt/codeentropy?logo=pypi&logoColor=white&color=blue)
+![PyPI - Monthly Downloads](https://img.shields.io/pypi/dm/CodeEntropy?logo=pypi&logoColor=white&color=blue)
 [![Coverage Status](https://coveralls.io/repos/github/CCPBioSim/CodeEntropy/badge.svg?branch=main)](https://coveralls.io/github/CCPBioSim/CodeEntropy?branch=main)
-[![Docs - Status](https://app.readthedocs.org/projects/codeentropy/badge/?version=latest)](https://codeentropy.readthedocs.io/en/latest/?badge=latest)
 
 CodeEntropy
 ==============================
 CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.
 
 <p align="center">
-<img src="https://github.com/CCPBioSim/branding/blob/fbf562b1f5a9bf34440d0a537548591bad0bd206/logos/biosim-codeentropy_logo_grey.png" alt="CodeEntropy logo" width="300"/>
+<img src="docs/images/biosim-codeentropy_logo_grey.svg" alt="CodeEntropy logo" width="300"/>
 </p>
 
 See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information.

pyproject.toml

@@ -7,27 +7,32 @@ build-backend = "flit_core.buildapi"
 # See https://www.python.org/dev/peps/pep-0621/
 name = "CodeEntropy"
 dynamic = ["version"]
-description = "CodeEntropy tool with POSEIDON code integrated to form a complete and generally applicable set of tools for computing entropy of macromolecular systems from the forces sampled in a MD simulation."
+description = "CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics."
 authors = [
     {name = "Arghya 'Argo' Chakravorty", email = "arghyac@umich.edu"},
-    {name = "Jas Kalayan", email = "jas.kalayan@stfc.ac.uk"},
     {name = "Donald Chung-HK", email = "donald.chung@stfc.ac.uk"},
     {name = "Sarah Fegan", email = "sarah.fegan@stfc.ac.uk"},
-    {name = "Ioana Papa", email = "iapapa1@SHEFFIELD.AC.UK"},
-    {name = "Harry Swift", email = "harry.swift@stfc.ac.uk"}
+    {name = "James Gebbie-Rayet", email = "james.gebbie@stfc.ac.uk"},
+    {name = "Sarah Harris", email="sarah.harris@sheffield.ac.uk"},
+    {name = "Richard Henchman", email="rhen7213@uni.sydney.edu.au"},
+    {name = "Jonathan Higham", email="j.higham4@lancaster.ac.uk"},
+    {name = "Jas Kalayan", email = "jas.kalayan@stfc.ac.uk"},
+    {name = "Ioana Papa", email = "iapapa1@sheffield.ac.uk"},
 ]
 maintainers = [
-    {name = "Sarah Fegan", email = "sarah.fegan@stfc.ac.uk"},
     {name = "Harry Swift", email = "harry.swift@stfc.ac.uk"}
 ]
 readme = "README.md"
 license = { file = "LICENSE" }
 classifiers = [
     "Programming Language :: Python",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",
     "Natural Language :: English",
-    "Development Status :: 4 - Beta"
+    "Development Status :: 5 - Production/Stable"
 ]
 keywords = ["entropy", "macromolecular systems", "MD simulation"]
 requires-python = ">=3.11"
@@ -45,7 +50,9 @@ dependencies = [
 ]
 
 [project.urls]
-Source = "https://github.com/CCPBioSim/CodeEntropy"
+Homepage = "https://ccpbiosim.github.io/CodeEntropy/"
+Repository = "https://github.com/CCPBioSim/CodeEntropy"
+Documentation = "https://codeentropy.readthedocs.io"
 
 [project.optional-dependencies]
 testing = [