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Merge pull request #20 from HealthBioscienceIDEAS/15-reproducible-repo
15 - reproducible repo
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: "\U0001F41B Bug Report"
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about: If you are pretty sure you are getting a bug, please create a report to help us improve this work
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title: ''
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labels: bug
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assignees: ''
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---
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### 🐛Bug
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<!-- A clear and concise description of what the bug is. Please use a short, concise title for the bug and elaborate here -->
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### To reproduce
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<!-- What did you do? -->
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<!-- Please provide a minimal working example, if possible: https://stackoverflow.com/help/minimal-reproducible-example -->
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```python
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# Your code here
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```
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### Expected behavior
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<!-- What did you expect? -->
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<!-- A clear and concise description of what you expected to happen. -->
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### Actual behavior
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<!-- What did you get? -->
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<!-- A clear and concise description of what actually happens. -->
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<!-- If you have a code sample, error messages, stack traces, please provide it here as well -->
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```python-traceback
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# Paste the whole error stack trace here
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```
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### System info
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Output of your application
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```
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# Paste here the output of that command in a terminal
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```

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: "\U0001F680 Feature Request"
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about: Submit a proposal/request for a new feature
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title: ''
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labels: 'enhancement'
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assignees: ''
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---
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### 🚀 Feature
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<!-- A clear and concise description of the feature proposal -->
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### Motivation
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<!-- Please outline the motivation for the proposal. Is your feature request related to a problem? e.g., I'm always frustrated when [...]. If this is related to another GitHub issue, please link here too -->
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### Pitch
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<!-- A clear and concise description of what you want to happen. -->
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### Alternatives
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<!-- A clear and concise description of any alternative solutions or features you've considered, if any. -->
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### Additional context
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<!-- Add any other context or screenshots about the feature request here. -->

‎.github/ISSUE_TEMPLATE/not_working.md‎

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---
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name: "\U00002757 Something is not working"
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about: If something is not working as expected but you're not sure if it's a bug, please follow the instructions in this template.
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title: ''
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labels: ''
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assignees: ''
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---
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### Problem
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<!-- A clear and concise description of what the bug is. Please use a short, concise title for the bug and elaborate here -->
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### To reproduce
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<!-- What did you do? -->
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<!-- Please provide a minimal working example, if possible: -->
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<!-- https://stackoverflow.com/help/minimal-reproducible-example -->
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<!-- Here's another useful resource: "How To Ask Questions The Smart Way" -->
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<!-- http://www.catb.org/~esr/faqs/smart-questions.html -->
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```python
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# Your code here
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```
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### Expected behavior
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<!-- What did you expect? -->
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<!-- A clear and concise description of what you expected to happen. -->
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### Actual behavior
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<!-- What did you get? -->
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<!-- A clear and concise description of what actually happens. -->
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<!-- If you have a code sample, error messages, stack traces, please provide it here as well -->
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```python-traceback
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# Paste the *full* error stack trace here
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```
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### System info
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Output of application
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```
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# Paste here the output of that command in a terminal
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```

‎.github/pull_request_template.md‎

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<!-- Replace {issue_number} with the issue that will be closed after merging this PR -->
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## Description
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Fixes #{issue_number}: A few sentences describing the changes proposed in this pull request.
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## Type of change
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Please delete options accordingly to the description.
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<!-- Write an `x` in all the boxes that apply -->
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- [ ] Bug fix (non-breaking change which fixes an issue)
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- [ ] New feature (non-breaking change which adds functionality)
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- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
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- [ ] This change requires a documentation update
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### Suggested Checklist
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<!-- You do not need to complete all the items by the time you submit the pull request, but most likely the changes will only be merged if all the tasks are done. -->
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<!-- Write an `x` in all the boxes that apply -->
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- [ ] I have performed a self-review of my own code
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- [ ] I have made corresponding changes to the documentation
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- [ ] My changes generate no new warnings
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- [ ] I have commented my code, particularly in hard-to-understand areas
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- [ ] I have read the [`CONTRIBUTING`](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/blob/main/CONTRIBUTING.md) docs
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- [ ] My code passes, following the style guidelines `pre-commit run -a`
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- [ ] My code is properly tested with `pytest -sv tests`
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- [ ] This pull request is ready to be reviewed
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- [ ] Make sure your branch is up-to-date with main branch. See below a general example if `rebase` is need.
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```
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git checkout main
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git pull origin main
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git checkout FEATURE_BRANCH
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git rebase main
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#git status
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#edit conflicting files with your editor
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#git rebase --continue
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#git add .
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git push --force origin FEATURE_BRANCH
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```

‎CODE_OF_CONDUCT.md‎

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---
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title: "Contributor Code of Conduct"
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---
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# Contributor Covenant Code of Conduct
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As contributors and maintainers of this project,
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we pledge to follow the [The Carpentries Code of Conduct][coc].
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## Our Pledge
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Instances of abusive, harassing, or otherwise unacceptable behavior
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may be reported by following our [reporting guidelines][coc-reporting].
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to make participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies within all project spaces, and it also applies when
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an individual is representing the project or its community in public spaces.
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Examples of representing a project or community include using an official
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project e-mail address, posting via an official social media account, or acting
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as an appointed representative at an online or offline event. Representation of
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a project may be further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team opening a [new issue](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/issues).
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All complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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[homepage]: https://www.contributor-covenant.org
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For answers to common questions about this code of conduct, see
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https://www.contributor-covenant.org/faq
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[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
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[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html

‎CONTRIBUTING.md‎

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## Contributing
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# Contributing to `Medical-Image-Registration-Short-Course`
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👍🎉 First off, thanks for taking the time to contribute! 🎉👍
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[The Carpentries][cp-site] ([Software Carpentry][swc-site], [Data
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Carpentry][dc-site], and [Library Carpentry][lc-site]) are open source
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mistake, some awkward wording, or a factual error. This is a good way to
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introduce yourself and to meet some of our community members.
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1. If you do not have a [GitHub][github] account, you can [send us comments by
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email][contact]. However, we will be able to respond more quickly if you use
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one of the other methods described below.
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1. If you have a [GitHub][github] account, or are willing to [create
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one][github-join], but do not know how to use Git,
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you can open an issue (bug report, feature request, or something is not working)
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https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/issues/new/choose
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This allows us to assign the item to someone and to respond to it in a threaded discussion.
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2. If you have a [GitHub][github] account, or are willing to [create
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one][github-join], but do not know how to use Git, you can report problems
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or suggest improvements by [creating an issue][issues]. This allows us to
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assign the item to someone and to respond to it in a threaded discussion.
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3. If you are comfortable with Git, and would like to add or change material,
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2. If you are comfortable with Git, and would like to add or change material,
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you can submit a pull request (PR). Instructions for doing this are
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[included below](#using-github).
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Note: if you want to build the website locally, please refer to [The Workbench
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documentation][template-doc].
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Note: if you want to build the website locally, please refer to [setting up][_setting_up].
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### Where to Contribute
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### Using GitHub
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### :octocat: Using GitHub
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#### Committing and pushing changes
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1. Clone this repo
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#### Setting up your repository locally.
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1. Generate your SSH keys as suggested [here](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent)
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2. Clone the repository by typing (or copying) the following lines in a terminal
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```
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git clone git@github.com:HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course.git
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git clone git@github.com:UCL/real-time-ai-for-surgery.git
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```
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2. Create new branch using issue number
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#### Committing and pushing changes
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1. Create new branch using issue number
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2. Commit changes and push to your branch
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3. Submit a Pull Request against the `main` branch.
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### Other Resources
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#### The Carpentries
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[swc-lessons]: https://software-carpentry.org/lessons/
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[template-doc]: https://carpentries.github.io/workbench/

‎README.md‎

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## Medical-Image-Registration-Short-Course
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<div style="text-align: center;" align="center">
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<h1> :medical_symbol: Medical-Image-Registration-Short-Course </h1>
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<h2> <a href="https://healthbioscienceideas.github.io/Medical-Image-Registration-Short-Course/">:page_with_curl: Sandpaper</a> </h2>
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</div>
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This is the lesson repository for [Medical-Image-Registration-Short-Course](https://healthbioscienceideas.github.io/Medical-Image-Registration-Short-Course)
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## Setting up and preview sandpaper
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## :nut_and_bolt: Setting up and preview sandpaper
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See [details](_setting_up) to setup sandpaper and its dependencies. Otherwise you are ready to preview your work:
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```
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R
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sandpaper::build_lesson()
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## 🤝 Contributing
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Medical-Image-Registration-Short-Course follows the [Contributor Covenant Code of Conduct](CODE_OF_CONDUCT.md).
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Contributions, issues and feature requests are welcome, so feel free to open new [issues](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/issues/new/choose).
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We also suggest to checking [the contributing guide](CONTRIBUTING.md).
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## :octocat: Cloning repository
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* Generate your SSH keys as suggested [here](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent)
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* Clone the repository by typing (or copying) the following lines in a terminal
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```
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git clone git@github.com:HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course.git
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```
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## Maintainers
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* [Dave Cash](https://github.com/davecash75)
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* [Jamie Mcclelland](https://github.com/jamie-mcclelland)
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## Contributors
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This project exists thanks to all the people who contribute.
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* [Dave Cash](https://github.com/davecash75)
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* [Jamie Mcclelland](https://github.com/jamie-mcclelland)
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* [Milan Malfait](https://github.com/milanmlft)
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* [Zakaria Senousy](https://github.com/zsenousy)
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* [Stephen Thompson](https://github.com/thompson318)
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* [Miguel Xochicale](https://github.com/mxochicale)
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## Licensing and copyright
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Copyright 2024 University College London.
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`Medical-Image-Registration-Short-Course` is released under the CC BY 4.0 license.
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Please see the [license file](LICENSE.md) for details.
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## Acknowledgements
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Funded by [UKRI Innovation Scholars](https://www.ukri.org/opportunity/innovation-scholars-data-science-training-in-health-bioscience/) Health and Bioscience IDEAS project (MR/V03863X/1)

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