From bddc0d7ca828d2ba262ca9d3fc9af75617f5bca4 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Thu, 28 Aug 2025 08:14:13 +0100 Subject: [PATCH 1/5] change logo source within `README.md` to use locallly sourced file in docs rather than the hosted version --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 55360e0..893b929 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ 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.

-CodeEntropy logo +CodeEntropy logo

See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information. From 95f337b5b4db909fab197cabf528d47ad980a171 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Thu, 28 Aug 2025 08:39:38 +0100 Subject: [PATCH 2/5] include all folders and files generated by `CodeEntropy` wihtin the `.gitignore` file --- .gitignore | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.gitignore b/.gitignore index e27a228..f64f3de 100644 --- a/.gitignore +++ b/.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 From 25197843d76d9d99ebd68dc6d6848eb77d0fd36a Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Thu, 28 Aug 2025 08:44:34 +0100 Subject: [PATCH 3/5] upgrade the development status to `Production/Stable` as `CodeEntropy` is now at `v1.0.0` --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c0f0504..f1eb46f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ classifiers = [ "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" From 80304857b5e4ea55b475a5348c79e3b5c2a4b0aa Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 29 Aug 2025 08:46:52 +0100 Subject: [PATCH 4/5] update information within the `pyproject.toml` and `README.md` to reflect updates and changes made for `v1.0.0` --- README.md | 6 ++++-- pyproject.toml | 19 +++++++++++++------ 2 files changed, 17 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 893b929..d031bb6 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,12 @@ [//]: # (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 ============================== diff --git a/pyproject.toml b/pyproject.toml index f1eb46f..7900c86 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,23 +7,28 @@ 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", @@ -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 = [ From 12262d1edc7fc233190a76ae3c0848aa5507e78b Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 1 Sep 2025 09:24:21 +0100 Subject: [PATCH 5/5] cleaned and polished version of the `.github/PULL_REQUEST_TEMPLATE.md` --- .github/PULL_REQUEST_TEMPLATE.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 94cdb1a..41e7b7c 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,20 +1,20 @@ -### Summary +## Summary -### Changes +## Changes -Change 1 : +### Change 1 : - - -Change 2 : +### Change 2 : - - -Change 3 : +### Change 3 : - - -### Impact +## Impact - - \ No newline at end of file