Dev Container Features

A collection of reusable DevContainer Features for various development tools and workflows.

Features

This repository contains the following DevContainer Features:

• apptainer - Install Apptainer for HPC containerization
• cmdstan - Install CmdStan (Stan probabilistic programming system)
• renv-cache - Configure R with renv cache
• fit-sne - Install FIt-SNE for dimensionality reduction
• mermaid - Install Mermaid CLI for diagram generation
• repos - Manage multiple Git repositories

Usage

Each feature can be added to your devcontainer.json file. See the sections below for specific usage examples and options.

---

apptainer

Installs Apptainer, a container system widely used in High Performance Computing (HPC) environments.

Example

{
    "image": "mcr.microsoft.com/devcontainers/base:ubuntu",
    "features": {
        "ghcr.io/MiguelRodo/DevContainerFeatures/apptainer:1": {
            "timezone": "UTC"
        }
    }
}

Options

Option	Type	Default	Description
timezone	string	"UTC"	Timezone to configure in the container (e.g., "UTC", "Europe/London"). Required for proper Apptainer mounting behavior.

Notes

• Adds the ppa:apptainer/ppa repository
• Configures tzdata because Apptainer containers often inherit the host's /etc/localtime

---

cmdstan

Installs CmdStan, the command-line interface to Stan – a state-of-the-art platform for Bayesian probabilistic programming and statistical inference.

The feature downloads the official CmdStan release tarball, pre-compiles the Stan C++ toolchain during the image build, and configures the CMDSTAN environment variable system-wide so that the installation survives container rebuilds.

Example

{
    "image": "mcr.microsoft.com/devcontainers/base:ubuntu",
    "features": {
        "ghcr.io/MiguelRodo/DevContainerFeatures/cmdstan:1": {
            "version": "latest"
        }
    }
}

Options

Option	Type	Default	Description
version	string	"latest"	CmdStan version to install (e.g. "2.36.0"). Use "latest" to always pull the newest release.
installDir	string	"/opt/cmdstan"	Base directory under which the versioned CmdStan folder is created.
installRPackage	boolean	true	When true and R is present, install the cmdstanr R package and configure it to use the system CmdStan installation.

Notes

• Installs CmdStan to a system-wide path (not a user home directory) so the installation survives rebuilds
• Pre-compiles the Stan C++ toolchain during the image build (make build)
• Sets CMDSTAN and updates PATH via /etc/profile.d/cmdstan.sh and /etc/environment
• Compilation may take 3–10 minutes depending on available CPU cores

---

renv-cache

Configures R for development in VS Code, including library paths, GitHub tokens, and package restoration with renv cache.

Example

{
    "image": "mcr.microsoft.com/devcontainers/base:ubuntu",
    "features": {
        "ghcr.io/MiguelRodo/DevContainerFeatures/renv-cache:2": {
            "setRLibPaths": true,
            "restore": true
        }
    }
}

Options

Option	Type	Default	Description
setRLibPaths	boolean	true	Set default paths for R libraries (including for renv) to avoid reinstalling upon rebuild
ensureGitHubPatSet	boolean	true	If GITHUB_PAT is not set, attempt to set it from GH_TOKEN or GITHUB_TOKEN
restore	boolean	true	Whether to run package restoration using renvvv::renvvv_restore()
update	boolean	false	Whether to run package update using renvvv::renvvv_update(). If both restore and update are true, renvvv::renvvv_restore_and_update() is used
renvDir	string	"/usr/local/share/renv-cache/renv"	Path to directory containing subdirectories with renv.lock files
pkgExclude	string	""	Comma-separated list of packages to exclude from renv snapshot restore
usePak	boolean	false	Whether to use pak for package installation
debug	boolean	false	Print debug information during package restore
debugRenv	boolean	false	Print debug information during renv restore

Notes

• Runs automatically via postCreateCommand
• Sets up GitHub tokens for API access
• Configures R library paths and renv settings

---

fit-sne

Installs FIt-SNE (Fast Interpolation-based t-SNE) by compiling it from source along with the required FFTW 3.3.10 library.

Example

{
    "image": "mcr.microsoft.com/devcontainers/base:ubuntu",
    "features": {
        "ghcr.io/MiguelRodo/DevContainerFeatures/fit-sne:1": {
            "version": "1.2.1"
        }
    }
}

Options

Option	Type	Default	Description
version	string	"latest"	FIt-SNE version tag or commit SHA to install. Use "latest" for the default branch.

Notes

• Compiles from source, so installation may take a few minutes
• Installs required dependencies: build-essential, wget, git

---

mermaid

Installs Mermaid CLI to generate diagrams from .mmd files. Sets up a non-root user and Puppeteer configuration for headless rendering.

Example

{
    "image": "mcr.microsoft.com/devcontainers/base:ubuntu",
    "features": {
        "ghcr.io/MiguelRodo/DevContainerFeatures/mermaid:1": {
            "userName": "mermaiduser",
            "nodeVersion": "lts"
        }
    }
}

Options

Option	Type	Default	Description
userName	string	"mermaiduser"	Username under which Mermaid CLI will run
puppeteerConfigDir	string	"/usr/local/share/mermaid-config"	Directory to store Puppeteer configuration files
nodeVersion	string	"lts"	Node.js version to install if not present (e.g., "lts", "20", "18")

Notes

• Requires Node.js (will install if missing)
• Installs system dependencies required for Puppeteer

---

repos

Installs the repos CLI tool to manage multiple Git repositories. Automatically clones repositories defined in repos.list when the container starts.

Example

{
    "image": "mcr.microsoft.com/devcontainers/base:ubuntu",
    "features": {
        "ghcr.io/MiguelRodo/DevContainerFeatures/repos:2": {
            "runOnStart": true
        }
    }
}

Options

Option	Type	Default	Description
runOnStart	boolean	true	Automatically run 'repos' when the container starts

Usage

When runOnStart is true, the repos tool automatically executes on container start. Create a repos.list file in your project to define which repositories to clone.

To run manually:

repos

Notes

• Installs from the apt-miguelrodo APT repository
• Creates a post-start script at /usr/local/bin/repos-post-start
• For detailed usage, refer to the repos tool documentation

---

Development

Testing

Run tests for all features:

devcontainer features test --global-scenarios-only .

Publishing

Features are automatically published to GitHub Container Registry (GHCR) via GitHub Actions on release. They are available at:

ghcr.io/MiguelRodo/DevContainerFeatures/<feature-name>

License

See LICENSE file for details.