Feature request: native support for Docker/Apptainer over remote SSH

[cullen-molitor]

Summary

I'd like to request an option in Positron for launching console sessions (R or Python) inside containerized environments like Docker or Apptainer (formerly Singularity) images. I know this is an option locally with Dev containers, so my request is focused on working over SSH on a remote host.

Motivation

I see from dev-containers documentation that this is not supported currently, where it says:

Containers are not supported in environments that are already remote (such as Remote SSH, WSL, and Posit Workbench).

I mostly want to voice my support for implementing this functionality. I work as a data scientist on academic HPC clusters, and containers can be super helpful in my research for a few reasons:

1. Reproducibility across projects. Different projects pin to different R versions and package versions. Rather than fighting against system R, I use Apptainer images so the entire stack (R version, system libraries like GDAL/PROJ, R packages) is frozen.
2. System dependencies on shared HPC. I can't apt install on a cluster, so containers are the cleanest path to libraries like GDAL, NetCDF, openMPI, or specific GEOS versions. I have found that dependencies can be a nightmare with the available modules and too many versions.
3. Old R versions for collaborators / replication. Replicating an analysis sometimes means running R 3.6 or earlier (especially with geospatial analysis). Containers are an easy to use solution that is easy to share with collaborators.

Current workaround

Right now I have two viable workarounds but both have major drawbacks.

1. Launch the apptainer with and interactive R session in the terminal and then set it up to send commands to the terminal with cmd + shift + enter (whereas cmd + enter sends to console). This is fine for doing a bit of development before submitting a job, but you do not get things like the plot pane or session pane so it has limited value over simply using VS Code.
2. Spoof the ark kernel to point to an Apptainer manually. It works, but it's fiddly to set up, breaks easily (every Positron update), and isn't a documented/supported path.

Request

A configuration option that would allow the use of containers over remote SSH. Specifically it would be nice to:

• Specify a container image (Docker image name, or path to a .sif / Apptainer image)
• Specify bind mounts, env vars, and the runtime (docker, podman, apptainer, singularity)
• Have Positron launch the R or Python kernel with that container, with the console, plots pane, environment pane, etc. all functioning normally

Alternatively, I would appreciate someone pointing me towards a better method or workaround than what I am doing currently!

Thanks! Love positron so far!

[jmcphers]

It is true that you currently can't mix remote SSH and dev containers, but you might be able to use one or the other in this case. You can, for example, start the container on the remote host, run sshd inside the container, and then use regular remote SSH to connect to it.

We are tracking nested remote functionality (connecting to a dev container from a remote session) in #11867 if you'd like to add some context/upvotes.

It sounds like your request though is not to run the entire Positron IDE inside a container (which is what the existing dev container feature does) but to run individual R and Python sessions in containers, with each session in its own container. Does that sound right?

Related issue: #8300

[cullen-molitor]

Hello, thanks for the quick reply!

Your first solution sounds interesting and something I will try out today.

To be honest, I don't know exactly what I want other than generally being able to use containers on a remote host while being able to use the plot pane and data viewer. If the easiest way to implement that is to modify the current dev container workflow then I am on board with that!

My workaround with spoofing ark was out of ignorance and only accomplished with some help from Claude. Maybe others would find value in being able to select containers for the R session without launching positron in it? I don't think I know enough to ask concisely, sorry.