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 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 diff --git a/README.md b/README.md index 55360e0..d031bb6 100644 --- a/README.md +++ b/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.

-CodeEntropy logo +CodeEntropy logo

See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information. diff --git a/pyproject.toml b/pyproject.toml index c0f0504..7900c86 100644 --- a/pyproject.toml +++ b/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 = [