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Contributing to Medical-Image-Registration-Short-Course

👍🎉 First off, thanks for taking the time to contribute! 🎉👍

The Carpentries (Software Carpentry, Data Carpentry, and Library Carpentry) are open source projects, and we welcome contributions of all kinds: new lessons, fixes to existing material, bug reports, and reviews of proposed changes are all welcome.

Contributor Agreement

By contributing, you agree that we may redistribute your work under our license. In exchange, we will address your issues and/or assess your change proposal as promptly as we can, and help you become a member of our community. Everyone involved in The Carpentries agrees to abide by our code of conduct.

How to Contribute

The easiest way to get started is to file an issue to tell us about a spelling mistake, some awkward wording, or a factual error. This is a good way to introduce yourself and to meet some of our community members.

  1. If you have a GitHub account, or are willing to create one, but do not know how to use Git, you can open an issue (bug report, feature request, or something is not working) https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/issues/new/choose This allows us to assign the item to someone and to respond to it in a threaded discussion.

  2. If you are comfortable with Git, and would like to add or change material, you can submit a pull request (PR). Instructions for doing this are included below.

Note: if you want to build the website locally, please refer to [setting up][_setting_up].

Where to Contribute

  1. If you wish to change this lesson, add issues and pull requests here.
  2. If you wish to change the template used for workshop websites, please refer to [The Workbench documentation][template-doc].

What to Contribute

There are many ways to contribute, from writing new exercises and improving existing ones to updating or filling in the documentation and submitting bug reports about things that do not work, are not clear, or are missing. If you are looking for ideas, please see the list of issues for this repository, or the issues for Data Carpentry, Library Carpentry, and Software Carpentry projects.

Comments on issues and reviews of pull requests are just as welcome: we are smarter together than we are on our own. Reviews from novices and newcomers are particularly valuable: it's easy for people who have been using these lessons for a while to forget how impenetrable some of this material can be, so fresh eyes are always welcome.

What Not to Contribute

Our lessons already contain more material than we can cover in a typical workshop, so we are usually not looking for more concepts or tools to add to them. As a rule, if you want to introduce a new idea, you must (a) estimate how long it will take to teach and (b) explain what you would take out to make room for it. The first encourages contributors to be honest about requirements; the second, to think hard about priorities.

We are also not looking for exercises or other material that only run on one platform. Our workshops typically contain a mixture of Windows, macOS, and Linux users; in order to be usable, our lessons must run equally well on all three.

:octocat: Using GitHub

Setting up your repository locally.

  1. Generate your SSH keys as suggested here
  2. Clone the repository by typing (or copying) the following lines in a terminal
git clone git@github.com:HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course.git

Committing and pushing changes

  1. Create new branch using issue number
git checkout -b ISSUENUMBER-branch-name
  1. Commit changes and push to your branch
git add .
git commit -m 'short message (#ISSUENUMBER)'
git push origin ISSUENUMBER-branch-name
  1. Submit a Pull Request against the main branch.

Pull Request (PR) and merge to main branch

  1. Select branch that contain your commits.
  2. Click Compare and pull request and create PR for the associated branch.
  3. Type a title and description of your PR and create PR
  4. Please keep your PR in sync with the base branch.
git checkout main
git pull origin main
git checkout FEATURE_BRANCH
git rebase main
git push --force origin FEATURE_BRANCH

4.1 In case you are in a different MY_FEATURE_BRANCH branch, follow:

git checkout FEATURE_BRANCH
git pull origin FEATURE_BRANCH
git checkout MY_FEATURE_BRANCH 
git rebase FEATURE_BRANCH
git push --force origin MY_FEATURE_BRANCH
  1. Run pre-commit to tidy up code and documentation (see next section).
  2. Request a PR review. See collaborating-with-pull-requests for further details.
  3. Once your PRs has been approved, procced to merge it to main. See Merging a pull request
  4. Remove your merged branch from your repo and in the list of https://github.com/UCL/real-time-ai-for-surgery/branches
#Local git clear
git branch --merged | grep -v '\*\|master\|main\|develop' | xargs -n 1 git branch -d
#Remote git clear
git branch -r --merged | grep -v '\*\|master\|main\|develop' | sed 's/origin\///' | xargs -n 1 git push --delete origin

NB: The published copy of the lesson is usually in the main branch.

Each lesson has a team of maintainers who review issues and pull requests or encourage others to do so. The maintainers are community volunteers, and have final say over what gets merged into the lesson.

Other Resources

The Carpentries

The Carpentries is a global organisation with volunteers and learners all over the world. We share values of inclusivity and a passion for sharing knowledge, teaching and learning. There are several ways to connect with The Carpentries community listed at https://carpentries.org/connect/ including via social media, slack, newsletters, and email lists. You can also reach us by email.