Merge remote-tracking branch 'origin/main' into 251-docs-improve-readability-of-github-issues

Author: harryswift01

.github/workflows/project-ci.yaml

@@ -35,6 +35,7 @@ jobs:
         uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel: true       
 
   docs:
     runs-on: ubuntu-latest
@@ -68,4 +69,4 @@ jobs:
       - name: Run pre-commit
         run: |
           pre-commit install
-          pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+          pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

README.md

@@ -1,15 +1,13 @@
-[//]: # (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 - 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)
-
 CodeEntropy
 ==============================
+
+| Category       | Badges |
+|----------------|--------|
+| **Build**      | [![CodeEntropy CI](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/project-ci.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/project-ci.yaml) |
+| **Documentation** | [![Docs - Status](https://app.readthedocs.org/projects/codeentropy/badge/?version=latest)](https://codeentropy.readthedocs.io/en/latest/?badge=latest) |
+| **PyPI**       | ![PyPI - Status](https://img.shields.io/pypi/status/codeentropy?logo=pypi&logoColor=white) ![PyPI - Version](https://img.shields.io/pypi/v/codeentropy?logo=pypi&logoColor=white)  ![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)|
+| **Quality**    | [![Coverage Status](https://coveralls.io/repos/github/CCPBioSim/CodeEntropy/badge.svg?branch=main)](https://coveralls.io/github/CCPBioSim/CodeEntropy?branch=main) |
+
 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">
@@ -18,11 +16,6 @@ CodeEntropy is a Python package for computing the configurational entropy of mac
 
 See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information.
 
-## Copyright
-
-Copyright (c) 2025 CCPBioSim
-
-
 ## Acknowledgements
 
 Project based on