RFC: Add dev container configuration

[hoechenberger]

👩‍💻 The experience I'm implementing here

Screen.Recording.2023-12-18.at.15.29.08.mov

📚 Background

In the past year, I moved almost all my development work into dev containers.

A development container (or dev container for short) allows you to use a container as a full-featured development environment. It can be used to run an application, to separate tools, libraries, or runtimes needed for working with a codebase, and to aid in continuous integration and testing. Dev containers can be run locally or remotely, in a private or public cloud, in a variety of supporting tools and editors.

Until recently, one of the few development workflows I had not yet transitioned to use dev containers was MNE-Python. Reason was that the interactive figures don't work well in a notebook or web browser, and I didn't want to run an X server on my host just to display the figures.

💡 Solution

I created a dev container configuration that deploys a remote resktop feature. It allows for a remote connection via a VNC client, or via the web browser. Browser-based access even works inside VS Code with the built-in Simple Browser.

The dev container runs on Debian 11, installs MNE-python via conda-forge, followed by a pip-based editable install of the version in the checked-out repository.

🎯 Scope & target audience

• Provide a seamless, virtually setup-free development environment to any interested party on all supported platforms (macOS, Windows, Linux)
• Allow for development via GH Codespaces.

🔮 Future plans

• Use dev container as a basis to deliver containers of stable MNE releases to end-users.
• Add a feature that installs FreeSurfer.
• Add a feature that downloads the sample and testing datasets.

🏃‍♀️ Using the dev container

You need

• Docker Desktop
• VS Code with the Dev Containers extension
• a copy of this repository branch

Open the repository in VS Code and click on Reopen in Container in the bottom right.

The Debian docker image and dev container features including MNE will be downloaded and installed. Lastly, an editable install of MNE will be carried out.

The VNC server will be exposed on localhost:5901 (you can connect to it with any VNC client, e.g. Screen Sharing.app on macOS), and the web server can be reached on http://localhost:6080. The password is vscode.

You can now start developing and using MNE-Python. Interactive figures will appear on the screen exposed via the VNC server.

All development dependencies are installed (incl. pre-commit hooks, pytest etc.), and the editor is set to auto-format code via Ruff on saving.

The host SSH agent's socket is transparently forwarded into the container, meaning you should be able to use SSH immediately without requiring any further configuration.

The host's git configuration is copied to the container as well, so your name and email address are set correctly, too.

✋ Limitations

I currently enforce running an AMD64 Debian image on all platforms, including Apple Silicon. The native ARM64 wouldn't work as MNE-Python cannot be installed from conda-forge on this platform, as the migration of aarch64dependencies is still ongoing. To avoid this, all deps could be potentially installed from PyPI via pip, but I haven't tried this yet.

❓Thoughts?

What do you all think?

cc @cbrnr @britta-wstnr @agramfort @sappelhoff

[hoechenberger]

this could probably be trimmed down a little? not sure.

[hoechenberger]

The password for VNC access is vscode.

[drammock]

I like this idea / initiative! I've left mostly questions and a few comments, so I can understand better how the config works.

[drammock]

why are these needed? Will the user ever access a terminal in the container (and if so, won't it be a BASH terminal by default?)

[hoechenberger]

Yes, of course :) It's a complete development environment, and if you open a terminal, it will open a "remote" shell inside the Docker container.

The default shell is zsh with oh-my-zsh.

I'm trying to provide a nice and comfy shell experience through these plugins.

[drammock]

I'm trying to provide a nice and comfy shell experience through these plugins.

Another word for "comfy" is "familiar". I don't necessarily object to including zsh alongside bash but I'm dubious about making zsh the default here.

[lucasfcnunes]

MacOS users have zsh as the default shell and zsh is very close to bash.

[drammock]

yes, I know that since 2019 macOS uses zsh as the default shell. And I've heard that they're similar. What I'm questioning is why tailor the experience in a linux container to feel familiar to macOS users. Sticking with BASH seems like the natural default choice, and deviation from that feels like it needs to be justified.

[hoechenberger]

Both shells are first-class citizens in the MS dev containers. By default, both are shipped, hence I'm shipping both too. The plugins listed here make the zsh experience better and superior to the Bash experience. I have not yet decided which shell shall be the default one. However, I'm surprised this seems to be so controversial. VS Code clearly displays which shell is being used, and when spawning a new terminal, one can select the shell from a dropdown menu. Besides, I don't see how the choice of shell matters as long as one doesn't do shell programming; and this is an MNE dev container, no generic Linux Shell Programming dev container. Like I said, I haven't decided yet which default I think would be best; but It's quite obvious to me though that the zsh prompt looks better and the shell provides more help during interactive use (history substring search being one of those invaluable features; git support being another).

[drammock]

I have not yet decided which shell shall be the default one.

This is news to me; you originally set zsh as default (which I noticed at the time), then removed that setting in 7d5c6a2 after my earlier comments. It seems a bit disingenuous to now say "why is this so controversial, they're both included and I haven't chosen a default".

That said, I'm happy if both are included and it's easy (and documented) for users to switch the shell they get in their container. Ideally this would be a one-time config (not something that needs doing every time the container is launched) if that's possible

[hoechenberger]

This is news to me; you originally set zsh as default (which I noticed at the time), then removed that setting in 7d5c6a2 after my earlier comments

Ah, I see!! No, this was actually a misunderstanding. The default login shell always was Bash, and the setting you're referring to controls which shell should be spawned by default when creating a new terminal without explicitly selecting a shell. This was in fact an accidental setting that I copied over from another dev container config I'm working with. But this setting never changed the (login) default shell to zsh, nor dropped bash or something :) I had however forgotten to properly set up mamba and conda for bash – something I realized and fixed after your comment / question.

That said, I'm happy if both are included and it's easy (and documented) for users to switch the shell they get in their container. Ideally this would be a one-time config (not something that needs doing every time the container is launched) if that's possible

Yep, I'm open for this! for now I'm really still trying to make things work and experimenting a bit! Let's save the heated debates for later! 😁🤗

Oh and, happy holidays to you all!!!

[drammock]

seems like fertile ground for bikeshedding. Is there a way for the container to pick up the user's local settings? If not, then can you indicate which of these settings are truly necessary for the container to work, which are not necessary but clearly a good idea (e.g., don't restore port forwards?), and which are your preferences (perhaps "format on type" fits here)?

[hoechenberger]

Thanks for you feedback, @drammock
I will respond to your remaining comments later tonight or tomorrow

[hoechenberger]

would be good to get this "into" 1.7, but i'm not sure if i'll be able to finish it in time

i know it's devs-only but it would be nice to have a reference to this in the 1.7 stable docs

[larsoner]

would be good to get this "into" 1.7, but i'm not sure if i'll be able to finish it in time

In this case let's not mark it for 1.7 -- let's only mark the things that are blockers for release (which should happen this week ideally). If it gets merged in time though that's great (nothing stopping it if you can get it done)!

[hoechenberger]

ok I'm fine with that!

[hoechenberger]

Using uv now for installation instead of pip, cuts down download & install time by a HUGE amount on my machine

[larsoner]

Can you open this branch in VS Code but not use the dev container? ... You will see that two tasks will be started (but quit gracefully, stating that they're not running in the container).

Yeah and that seems to be the default behavior, and I think I see those:

How much of an annoyance is that to you?

If it happened every time it would be too much. But there is a button suggesting I can tell it not to ask again, and having to cilck "Don't show again ..." once seems fine!

[hoechenberger]

Thanks for testing, @larsoner

The button you're referring to will unfortunately only disable the dialog asking whether you want to open the folder in a dev container; the terminal output from your first screenshot would not be hidden by that.
(These are tasks, defined in tasks.json, that run automatically)

Seems I'll need to think a little more about this…

btw how do you like the uv-based installation? Blazingly fast, no?

[larsoner]

btw how do you like the uv-based installation? Blazingly fast, no?

Haven't tried it, on a plane at the moment! ✈️

the terminal output from your first screenshot would not be hidden by that... Seems I'll need to think a little more about this…

Ahh. That part doesn't bother me too much based on my workflow but I could see it being problematic for others. Maybe at the end of the script there is some way to tell vscode to close the terminal rather than requiring an enter keypress or something.

[hoechenberger]

Have a safe trip!

[hoechenberger]

• Currently blocked by Cannot build HTML docs #12653
• Still needs a changelog entry