Merge pull request #174 from CCPBioSim/158-review-community-docs

Update Community Documentation Post `v1.0.0`

Author: harryswift01

.github/CONTRIBUTING.md

@@ -1,42 +1,65 @@
-# How to contribute
+# Contributing to CodeEntropy
 
-We welcome contributions from external contributors, and this document
-describes how to merge code changes into this CodeEntropy. 
+Thank you for your interest in contributing to **CodeEntropy**!
+
+We’re excited to collaborate with developers, researchers, and community members to make CodeEntropy better for everyone.
+
+This guide explains how to set up your environment, make changes, and submit them for review. Whether you’re fixing a bug, improving documentation, or adding new features, every contribution makes a difference.
+
+---
 
 ## Getting Started
 
-* Make sure you have a [GitHub account](https://github.com/signup/free).
-* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub.
-* On your local machine,
-  [clone](https://help.github.com/articles/cloning-a-repository/) your fork of
-  the repository.
-
-## Making Changes
-
-* Add some really awesome code to your local fork.  It's usually a [good
-  idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/)
-  to make changes on a
-  [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
-  with the branch name relating to the feature you are going to add.
-* When you are ready for others to examine and comment on your new feature,
-  navigate to your fork of CodeEntropy on GitHub and open a [pull
-  request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
-  after you launch a PR from one of your fork's branches, all
-  subsequent commits to that branch will be added to the open pull request
-  automatically.  Each commit added to the PR will be validated for
-  mergability, compilation and test suite compliance; the results of these tests
-  will be visible on the PR page.
-* If you're providing a new feature, you must add test cases and documentation.
-* When the code is ready to go, make sure you run the test suite using pytest.
-* When you're ready to be considered for merging, check the "Ready to go"
-  box on the PR page to let the CodeEntropy devs know that the changes are complete.
-  The code will not be merged until this box is checked, the continuous
-  integration returns checkmarks,
-  and multiple core developers give "Approved" reviews.
-
-# Additional Resources
-
-* [General GitHub documentation](https://help.github.com/)
-* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/)
-* [A guide to contributing to software packages](http://www.contribution-guide.org)
-* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR)
+Before contributing, please review the [Developer Guide](https://codeentropy.readthedocs.io/en/latest/developer_guide.html).  
+It covers CodeEntropy’s architecture, setup instructions, and contribution workflow.
+
+If you’re new to the project, we also recommend:
+- Reading the [README](../README.md) for an overview and installation details.
+- Checking open [issues](https://github.com/CCPBioSim/CodeEntropy/issues) labeled **good first issue** to find beginner-friendly tasks.
+
+---
+
+## Submitting a Pull Request (PR)
+
+When you’re ready to submit your work:
+
+1. **Push your branch** to GitHub.  
+2. **Open a [pull request](https://help.github.com/articles/using-pull-requests/)** against the `main` branch.  
+3. **Fill out the PR template**, including:
+   - A concise summary of what your PR does  
+   - A list of all changes introduced  
+   - Details on how these changes affect the repository (features, tests, documentation, etc.)  
+4. **Verify before submission**:
+   - All tests pass  
+   - Pre-commit checks succeed  
+   - Documentation is updated where applicable  
+5. **Review process**:
+   - Your PR will be reviewed by the core development team.  
+   - At least **one approval** is required before merging.  
+
+We aim to provide constructive feedback quickly and appreciate your patience during the review process.
+
+---
+
+## Reporting Issues
+
+Found a bug or have a feature request?
+
+1. **Open a new issue** on GitHub.  
+2. Provide a **clear and descriptive title**.  
+3. Include:
+   - Steps to reproduce the issue (if applicable)  
+   - Expected vs. actual behavior  
+   - Relevant logs, screenshots, or input files  
+
+Well-documented issues help us address problems faster and keep CodeEntropy stable and robust.
+
+---
+
+## Additional Resources
+
+- [GitHub Docs](https://help.github.com/)
+
+---
+
+Thank you for helping improve **CodeEntropy**, your contributions make open source stronger!

.github/workflows/release.yaml

@@ -48,8 +48,16 @@ jobs:
       - name: checkout
         uses: actions/checkout@v5.0.0
 
-      - name: Change version in repo
-        run: sed -i "s/__version__ =.*/__version__ = \"${{ github.event.inputs.version }}\"/g" CodeEntropy/__init__.py
+      - name: Change version in repo and CITATION.cff
+        run: |
+          # Update Python package version
+          sed -i "s/__version__ =.*/__version__ = \"${{ github.event.inputs.version }}\"/g" CodeEntropy/__init__.py
+
+          # Update CITATION.cff version and date-released
+          if [ -f CITATION.cff ]; then
+            sed -i -E "s/^(version:\s*).*/\1${{ github.event.inputs.version }}/" CITATION.cff
+            sed -i -E "s/^(date-released:\s*).*/\1'$(date -u +%F)'/" CITATION.cff
+          fi
 
       - name: send PR
         id: pr_id
@@ -61,6 +69,7 @@ jobs:
           body: |
             Update version
             - Update the __init__.py with new release
+            - Update CITATION.cff version & date-released
             - Auto-generated by [CI]
           committer: version-updater <vu.bot@users.noreply.github.com>
           author: version-updater <vu.bot@users.noreply.github.com>

CITATION.cff

@@ -56,6 +56,7 @@ authors:
     family-names: Swift
     email: harry.swift@stfc.ac.uk
     affiliation: 'STFC, Scientific Computing'
+    orcid: 'https://orcid.org/0009-0007-3323-753X'
 repository-code: 'https://github.com/CCPBioSim/CodeEntropy'
 url: 'https://ccpbiosim.github.io/CodeEntropy/'
 abstract: >-
@@ -75,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 0.3.6
-date-released: '2022-07-06'
+version: 1.0.3
+date-released: '2025-09-29'

CODE_OF_CONDUCT.md

@@ -2,76 +2,127 @@
 
 ## Our Pledge
 
-In the interest of fostering an open and welcoming environment, we as
-contributors and maintainers pledge to making participation in our project and
-our community a harassment-free experience for everyone, regardless of age,
-body size, disability, ethnicity, gender identity and expression, level of
-experience, nationality, personal appearance, race, religion, or sexual
-identity and orientation.
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
 
 ## Our Standards
 
-Examples of behavior that contributes to creating a positive environment include:
+Examples of behavior that contributes to a positive environment for our
+community include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
 
-Examples of unacceptable behavior by participants include:
+Examples of unacceptable behavior include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
 * Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
-
-## Our Responsibilities
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
-Project maintainers are responsible for clarifying the standards of acceptable
-behavior and are expected to take appropriate and fair corrective action in
-response to any instances of unacceptable behavior.
+## Enforcement Responsibilities
 
-Project maintainers have the right and responsibility to remove, edit, or
-reject comments, commits, code, wiki edits, issues, and other contributions
-that are not aligned to this Code of Conduct, or to ban temporarily or
-permanently any contributor for other behaviors that they deem inappropriate,
-threatening, offensive, or harmful.
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
 
-Moreover, project maintainers will strive to offer feedback and advice to
-ensure quality and consistency of contributions to the code.  Contributions
-from outside the group of project maintainers are strongly welcomed but the
-final decision as to whether commits are merged into the codebase rests with
-the team of project maintainers.
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
 
 ## Scope
 
-This Code of Conduct applies both within project spaces and in public spaces
-when an individual is representing the project or its community. Examples of
-representing a project or community include using an official project e-mail
-address, posting via an official social media account, or acting as an
-appointed representative at an online or offline event. Representation of a
-project may be further defined and clarified by project maintainers.
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
 
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting the project team at 'lpchungaa@gmail.com'. The project team will
-review and investigate all complaints, and will respond in a way that it deems
-appropriate to the circumstances. The project team is obligated to maintain
-confidentiality with regard to the reporter of an incident. Further details of
-specific enforcement policies may be posted separately.
+reported to the community leaders responsible for enforcement at
+ccpbiosim@stfc.ac.uk.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
 
-Project maintainers who do not follow or enforce the Code of Conduct in good
-faith may face temporary or permanent repercussions as determined by other
-members of the project's leadership.
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
 
 ## Attribution
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
-version 1.4, available at
-[http://contributor-covenant.org/version/1/4][version]
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CodeEntropy/__init__.py

@@ -1,9 +1,11 @@
 """
 CodeEntropy
 
-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.
+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.
 """
 
 __version__ = "1.0.3"