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How to use GitHub Codespaces in your project

This page explains how to work with OpenSAFELY projects using GitHub Codespaces.

Warning

Codespaces are automatically deleted after a period of inactivity and any changes not pushed to the GitHub repo will be lost. For the opensafely organization, this period is 30 days.

Managing GitHub Codespaces🔗

How to create a codespace🔗

To create a Codespace, create a code repository first.

Once you have a research code repository to work in:

  1. In a web browser, go to your newly created research code repository on GitHub.
  2. Click the "Code" button
  3. Select "Create codespace on main".
  4. You will see a "Setting up your codespace" screen before the codespace is ready for use. It may take a few minutes before the codespace loads and displays the Visual Studio Code editor.

Info

For "Create codespace on main", "main" refers to the Git branch to use in the codespace.

If you are working on another repository branch, it is possible to select "New from options", which allows you to choose the branch.

How to stop a codespace🔗

See GitHub's documentation for how to stop a codespace.

Stopping a codespace is a specific action that makes the codespace inactive and stops the codespace from using CPU usage quota. You can resume working in a stopped codespace at a later time.

Because stopped codespaces are persistent, they still count against storage usage quota.

Note

Closing a browser that is running a codespace does not immediately stop a codespace.

Codespaces that GitHub consider to be idle due to a lack of user interaction or terminal activity will eventually timeout. But it is preferable to stop codespaces explicitly to save on usage.

How to restart a stopped codespace🔗

See GitHub's documentation for how to restart a stopped codespace.

How to delete a codespace🔗

See GitHub's documentation for how to delete a codespace.

Deleting a codespace removes the codespace entirely, preventing any further CPU or storage quota usage by the codespace.

Info

If you have changes in the codespace that have not been published to the repository, GitHub will warn you to confirm that you are sure you want to delete the codespace.

Developing OpenSAFELY projects in GitHub Codespaces🔗

How to save your work🔗

How to save the files in the codespace🔗

Note

Saving files in the codespace only ensures that changes persist in that codespace's storage. When the codespace is deleted, these changes will be lost unless they are pushed to the remote repository that GitHub hosts.

The remote repository is the one accessible at a GitHub URL, like, for example, https://github.com/opensafely/example-research-repository

If you work in the Visual Studio Code editor, changes that you make to the files in your codespace are saved automatically in the codespace.

If you work in RStudio, changes that you make to the files in your codespaces must be manually saved.

How to store your changes in your project's repository🔗

To do so, use your codespace's Visual Studio Code editor.

  1. Optionally, you may first wish to create a new branch for your changes if you have not already. See GitHub's documentation on how to create or switch to a branch.
  2. Commit your changes to the codespace's "local" copy of the Git repository. See GitHub's documentation on how to commit your changes.
  3. Push the changes from the codespace's "local" repository to the "remote" repository as hosted on GitHub. This makes your changes visible on GitHub's repository. See GitHub's documentation on how to push your changes.

Note

See GitHub's documentation on source control workflow in Codespaces.

How to run the OpenSAFELY CLI🔗

  • You can run the OpenSAFELY CLI in GitHub Codespaces. In the Visual Studio Code terminal, type opensafely and press Enter.
  • You should see the OpenSAFELY CLI help prompt.

Info

See the OpenSAFELY CLI documentation for more details.

How to use OpenSAFELY CLI to run the example project🔗

The research code repository that you created already has a minimal, working OpenSAFELY project in it.

  1. In the Visual Studio Code terminal, type opensafely run run_all and then press Enter to run the existing project.yaml.
  2. This may take a few moments to download the required Docker images, before the project is run.

You should see some information messages that should end something like:

=> generate_dataset
Completed successfully

Note

By default, the Visual Studio Code terminal that has opened should be in the correct directory (folder) that contains the project.yaml file.

If you have changed the terminal directory by using the cd change directory command, use cd to return to the directory containing project.yaml first.

$ cd /workspaces/"$RepositoryName"

How to access RStudio🔗

  1. In Visual Studio Code, select the "Ports" tab (next to "Terminal").
  2. Port 8787 should be listed — this is configured by the RStudio server.
  3. Right-click on port 8787 and select "Open in browser".
  4. A new browser tab/window appears with RStudio running.