devcontainer

Development container focused on Python (with first-class R support) providing a reproducible, batteries‑included environment. It ships with the VS Code Dev Containers extension assets, curated tooling, and a consistent tagging strategy for deterministic rebuilds.

Table of Contents

1. Published Container
2. Quick Start
3. Using in SDF TRE
4. Documentation
5. What's Included
6. R Language Support
7. VS Code Server
8. Adding Extensions
9. Automated Builds & Tag Strategy
10. Contributing
11. License

📦 Published Container

Built and published automatically to GitHub Container Registry (GHCR):

• Registry: ghcr.io
• Image: ghcr.io/smartdatafoundry/devcontainer
• Tag Families:
  • latest – Most recent stable main build
  • main – Moving pointer to HEAD of main
  • main-<branch-sha> – Immutable build for a specific main commit
  • pr-<number> – Ephemeral preview for a pull request
  • vscode-<vscode-sha> – Locks VS Code Server version (container content may still move)
  • vscode-<vscode-sha>-<branch-sha> – Fully reproducible (VS Code Server + container commit)

Recommended:

• Daily development: latest
• CI / Reproducibility: vscode-<vscode-sha>-<branch-sha>
• VS Code Server pin only: vscode-<vscode-sha>

🚀 Quick Start

Using the Published Container

Add this to your .devcontainer/devcontainer.json:

{
  "name": "Python Development",
  "image": "ghcr.io/smartdatafoundry/devcontainer:latest"
}

Using in SDF Trusted Research Environment

See the SDF TRE Setup Guide for:

• Manual Dev Containers extension install & extraction
• Podman configuration
• Proxy / network specifics
• Troubleshooting in constrained environments

Using This Repository Directly

1. Clone this repository
2. Open in VS Code
3. Select "Reopen in Container" when prompted

📚 Documentation

Topic	Reference
SDF TRE usage	SDF_TRE_SETUP.md
Full container internals	DEVCONTAINER.md
Reusable publish workflow	docs/BUILD_PUBLISH_CONTAINER.md
Dev Container Specification	https://containers.dev

🛠️ What's Included

• Base: Ubuntu 24.04 (Noble) via Microsoft's devcontainers base image
• Python: System Python with development tools (via devcontainer feature)
• R: Full R language support with development tools (via Rocker Project devcontainer feature)
• Git: Latest version with configuration support
• Shell: Zsh with Oh My Zsh (via common-utils feature)
• Quarto: Document publishing platform (latest version)
• Marimo: Markdown presentation tool, alternative to Jupyter Notebooks
• VS Code Extensions (curated):
  • Continue (AI assistant)
  • Black (Python formatting)
  • Jupyter
  • Marimo
  • Markdown All in One
  • Rainbow CSV
  • (See .devcontainer/vscode-init/extensions-to-install.txt for authoritative list)
• VS Code Server: Pre-installed for immediate development

📊 R Language Support

This dev container includes comprehensive R language support through the Rocker Project's devcontainer features. The R feature provides:

Features Available

• R Installation: Latest R version via apt package manager
• Development Tools: devtools, renv for package management
• IDE Integration:
  • languageserver package for VS Code R extension support
  • httpgd package for interactive graphics
  • rmarkdown for document generation
• Jupyter Integration: R kernel for Jupyter notebooks
• Interactive Console: radian (enhanced R console with syntax highlighting)
• Debugging Support: vscDebugger package for VS Code R debugging

⚙️ VS Code Server

Pre-installed. Pin a version using the tag families described above or via build arg VSCODE_COMMIT. For environment-specific considerations (e.g. TRE) see SDF_TRE_SETUP.md.

Adding New Extensions

To add new VS Code extensions to the container, follow these steps:

1. Open the appropriate file in .devcontainer/vscode-init/:
   • extensions-to-install.txt for extensions to install directly
   • extensions-to-download.txt for extensions that need to be downloaded
2. Add the identifier of the desired extension in the format publisher.extensionName on a new line.
3. Save the changes to the extension file.
4. Commit and push the changes to your repository to trigger the build workflow with the updated extensions

🔄 Automated Builds & Tag Strategy

Workflow: .github/workflows/build-devcontainer.yml

Triggers:

• Pull Requests touching devcontainer/workflow files → build + pr-<number> tag
• Manual dispatch (with required vscode_commit input) → publish full tag set

Outputs per production run:

• latest, main, main-<branch-sha>
• vscode-<vscode-sha>, vscode-<vscode-sha>-<branch-sha>

Manual build steps:

1. Open Actions → Build and Publish Dev Container
2. Run workflow, supplying VS Code Server commit hash
3. Await completion & verify tags on GHCR package page

Tag usage quick reference:

Need	Tag
Stable rolling	latest
Immutable main snapshot	main-<sha>
Test PR	pr-<number>
Pin VS Code Server only	vscode-<vscode-sha>
Full reproducibility	vscode-<vscode-sha>-<sha>

Reusable generic Docker workflow documentation: see docs/BUILD_PUBLISH_CONTAINER.md.

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🤝 Contributing & License

Contribution workflow is standard GitHub Flow. See section above plus open issues for opportunities.

License: MIT

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