Using development containers with Visual Studio Code

Scilpy comes pre-equiped with a development container recipe for Visual Studio Code. You can use it to develop Scilpy on any platform (Windows, Linux, Mac) without having to install any dependencies on your host machine.

Prerequisites

The only requirement is to have Docker and Visual Studio Code installed, with the Dev Containers extension activated.

Launching the container

  1. Clone the Scilpy repository locally with Visual Studio Code and open it.

  2. Open the command palette (Ctrl+Shift+P) and select Remote-Containers: Reopen in Container.

  3. Wait for the container to build and start. You can monitor the progress in the bottom left corner of the window.

Using the container

Once the container is running, you can use Visual Studio Code as you would normally. The only difference is that the code is running inside the container, so you can use all the tools and dependencies that are installed in it, such as ANTs, FSL and mrtrix. The container is also equiped with offscreen rendering capabilities, so scripts generating figures should work.

Note

The only accessible path from outside the container is the Scilpy repository. If you want to access other files, you will have to mount them in the container. See this page for more information.

Note

The container is running as a non-root user, so you might have to change the permissions of some files and folders to be able to write to them.