Contributing

This project follows the all contributors specification. Contributions in many different ways are welcome!

Contribution Types

Report Bugs

Report bugs at https://github.com/TranslationalML/pacsifier/issues.

If you are reporting a bug, please include:

  • Your operating system name and version.

  • Any details about your local setup that might be helpful in troubleshooting.

  • Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.

Write Documentation

PACSIFIER could always use more documentation, whether as part of the official pacsifier docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to create an issue at https://github.com/TranslationalML/pacsifier/issues.

If you are proposing a feature:

  • Explain in detail how it would work.

  • Keep the scope as narrow as possible, to make it easier to implement.

  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!

Ready to contribute? Here’s how to set up PACSIFIER for local development.

  1. Fork the repository of PACSIFIER on GitHub.

  2. Clone your fork locally:

    git clone git@github.com:your_name_here/pacsifier.git
cd pacsifier

  3. Create a branch for local development:

    git checkout -b name-of-your-bug-fix-or-feature

  4. Now you can make your changes locally.

Important

Please keep your commit the most specific to a change it describes. It is highly advice to track unstaged files with git status, add a file involved in the change to the stage one by one with git add <file>. The use of git add . is highly disencouraged. When all the files for a given change are staged, commit the files with a brieg message using git commit -m "<type>[optional scope]: <description>" that describes your change and where <type> can be fix for a bug fix, feat for a new feature, refactor for a code change that neither fixes a bug nor adds a feature, docs for documentation, ci for continuous integration testing, and test for adding missing tests or correcting existing tests. This follows the Angular conventional commits, please see https://www.conventionalcommits.org/en/v1.0.0-beta.4/ for more details.

  1. When you’re done making changes, push your branch to GitHub:

    git push origin name-of-your-bugfix-or-feature

  2. Submit a pull request through the GitHub website.

    Important

    Please make sure that the pull request is made against the main branch.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. If the pull request adds functionality, the docs should be updated (See documentation build instructions).

  2. Make sure that the tests pass (See instructions for testing )

CI/CD Pipeline: Under the Hood

PACSIFIER uses GitHub Actions for continuous integration (CI) and continuous deployment (CD).

The CI/CD is defined by two workflow files in .github/workflows/:

build-test-deploy.yml — Main pipeline

This workflow runs on pull requests and releases. It performs the following steps:

  1. Build: Build the Docker image of PACSIFIER and the Python package wheel.

  2. Test: Run the pytest test suite using the built Docker image.

  3. Validate: Validate the .zenodo.json metadata file.

  4. Deploy (on release only):

    • Publish the Python package to PyPI.

    • Push the Docker image to Quay.io.

graph LR subgraph "Stages" build["Build Docker + wheel"] test["Test (pytest)"] validate["Validate .zenodo.json"] deploy_pypi["Deploy to PyPI"] deploy_docker["Push to Quay.io"] end build --> test test --> validate validate -->|on release| deploy_pypi validate -->|on release| deploy_docker

docs.yml — Documentation pipeline

This workflow builds the Sphinx documentation and deploys it to GitHub Pages on pushes to the main branch.

Not listed as a contributor?

This is easy, PACSIFIER has the all contributors bot installed.

Just comment on Issue or Pull Request (PR), asking @all-contributors to add you as contributor:

@all-contributors please add <github_username> for <contributions>

<contribution>: See the Emoji Key Contribution Types Reference for a list of valid contribution types.

The all-contributors bot will create a PR to add you in the README and reply with the pull request details.

When the PR is merged you will have to make an extra Pull Request where you have to:

  1. add your entry in the zenodo.json (for that you will need an ORCID ID - https://orcid.org/). Doing so, you will appear as a contributor on Zenodo in the future version releases of PACSIFIER. Zenodo is used by PACSIFIER to publish and archive each of the version release with a unique Digital Object Identifier (DOI), which can then be used for citation.

  2. update the content of the table in docs/contributors.rst with the new content generated by the bot in the README. Doing so, you will appear in the Contributing Page.

This document has been inspired and adapted from these great contributing guidelines.