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GitHub repositories

This section provides information on the git repositories for each OpenSAFELY research project.

The repository, or repo, contains all the analysis scripts, codelists, released outputs, and other research objects needed to understand and run the project. Changes to the repo are audited using git, a version control system for recording, sharing and collaborating on code. The repo's canonical location is on GitHub, a website that makes it easier to use git, and adds extra collaboration and security tools on top. You can download a copy of the repo ("clone"), create a development "branch", make changes ("commit") on that branch, then upload these changes ("push") back to the remote repo on GitHub — for more details see the GitHub and Git section.

GitHub is the means by which code in the repository is passed to the server to be run against the OpenSAFELY database — it is the only entry point between the secure server and the outside world. GitHub is also the means by which approved disclosure-safe outputs are released from the secure server to researchers.

Repository visibility🔗

In accordance with the Principles of OpenSAFELY, we expect all code from all users to be made public. As technical users will know, a public GitHub repository is visible by anyone on the internet, but only specified people will have the ability to change it.

How to make your code public🔗

You can request that a private repository is made public at any time by contacting tech support.

Publishing older repositories that contain results as well as code🔗

In earlier versions of OpenSAFELY, all results released from the secure server after disclosivity checking went directly to the GitHub repository containing the code for the project. Because of this, for older repositories the OpenSAFELY team and you must check that there are no outstanding results which still require approval from NHS England in your repository, before that repository is made public. If you are unsure whether this applies to your repository then you should contact tech support.

When you need to make your code public🔗

A repository must be made public if it forms part of a publication. We have guide to publishing repositories that you must read. During the development stage of a project, a repository may be kept private, so that only members of the OpenSAFELY GitHub organisation are able to view it. We welcome people sharing code in public while they are developing, where they wish to do so, but we recognise that for many this would be a little like drafting a paper entirely in public, so it is not a requirement. Even when there is no publication, we expect all repositories to become public, within twelve months after code execution. During our pilot phase of OpenSAFELY Users, if we encounter edge cases proposing that a particular repo should be excepted from this policy we will develop an open and structured Exceptions Process.

Warning

You should never commit files or content that should not be made public to the repository. All committed files, whether on the main branch or on development branches, will remain in the git history of the repository even after they have been deleted. These might include for example patient- or commercially-sensitive data from other sources, internal institutional documentation or forms, and incomplete manuscript drafts.

Creating a repository for a new project🔗

For ease of use, we have created a research template that you should use for your study. Go to the OpenSAFELY research template repo on GitHub. Click the green button that says  Use this template .

Fill in the details:

  • owner: select your personal GitHub for testing/experimenting, or select the opensafely organisation for a bona fide OpenSAFELY-approved study. The repo can be transferred into opensafely later if needed.
  • repository name: It needs to be short but informative — browse existing repo names for inspiration.
  • Description: This will appear at the top of the repo on GitHub. No more than a sentence is needed as the repo should be explained fully in the README.
  • public / private: See Repository access to make the the right choice for your study.
  • Include all branches: Leave unchecked.

And submit. You will now be at the GitHub landing page for the repo.

You should also download a copy of this repo to your machine so you can work on it locally. This is necessary because you can:

  • develop your code using familiar editing tools
  • test and run code without disturbing other contributors

To clone your new repository to your machine, follow these instructions which explains cloning both via GitHub Desktop or via the command line. When this is done, you should have a folder whose name is the same as the repo on your machine.

Note that if someone else wants to commit to your recently created OpenSAFELY repo, they may need to wait up to an hour for the necessary write permissions to be granted.

Repository structure🔗

README.md🔗

This file introduces your project, helps people understand the purpose of the repo, and how to navigate and use the code.

Any new repo will include a template README. It should be updated to briefly describe the intended study and to reflect the repo's current status as a work in progress. The README should also be updated frequently to reflect changes to the repo, and should certainly be up-to-date before publication of any research outputs.

The README is written in Markdown. If you're not familiar with Markdown syntax, read this guide on GitHub-flavoured Markdown. There's a handy cheatsheet for the most useful Markdown syntax.

You can update the README directly in GitHub. Click the edit button (a little pencil in the top-right), change the text, and commit the changes. This is a standard commit so there's no need to write more than "first README update", but typically commits should have a bit more detail than that.

project.yaml🔗

This file defines a "pipeline": how all the components of your analysis can run together, efficiently, either on the server or locally on your computer. See the pipeline documentation for more information.

.github/🔗

This is an important folder, used internally by GitHub, that you can happily ignore. Do not delete.

analysis/🔗

By convention, this folder contains:

  • Any study_definition.py script that defines the study definition
  • Analysis scripts in R, Python or Stata

codelists/🔗

This contains a .txt document listing the codelists that you want to retrieve from OpenCodelists, and the .csv files of the retrieved codelists themselves. You should not edit the CSV files directly; see the codelists documentation for more on how to update the codelists.

output/🔗

This folder contains:

  • the input.csv file containing the (dummy or real) dataset. You will only have access to the dummy version of this dataset when working locally.
  • By convention, any other files outputted by the analysis scripts that convert input.csv into study results, tables, figures, etc.

Be aware that input.csv is included in the .gitignore file (see below), which means it can't be (easily) committed and uploaded to GitHub.

You don't have to store things in these locations, but that's the convention we suggest.

released_outputs/🔗

Outputs that have been reviewed (and possibly edited) to ensure they are not disclosive are stored here.

docs/🔗

Used for documentation.

(other folders)/🔗

Feel free to add more folders to the repo and organise your project as you wish. However, we recommend including all active scripts and codelists in the analysis/ and codelists/ folders.

If you don't want any additional files or folders to be accidentally pushed to the remote repo, use .gitignore.

.gitignore🔗

This is a text document, used by git, which lists all the files and folders that you don't want to be uploaded to the remote repo on GitHub when you push changes from your local repo (untracked files). As a system for keeping private files private, it's vulnerable to human error so don't rely on it for this purpose.

Instructions for how to list ignored files properly in .gitignore.

If you need to create an empty folder to save files in, put a file in the folder that is tracked by git — by convention this is a .gitkeep file.

If you want to create an empty folder to save files in, but you never want its contents to be committed to the repo, you can add a .gitignore file to that folder with the following contents:

# Ignore all files in this folder
*

# Apart from this very file
!/.gitignore

This can be useful if you want to, for example, add a output/plots/ subfolder to put your analysis plots into without having to check and create that folder explicitly every time in the analysis script. This is necessary because the contents of the output/ folder is ignored by the default .gitignore in the root (the top-level) of the repository.