https://github.com/henriqueslab/docker-rxiv-maker
Docker image building infrastructure for rxiv-maker with weekly and on-demand builds
https://github.com/henriqueslab/docker-rxiv-maker
Last synced: 9 months ago
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Docker image building infrastructure for rxiv-maker with weekly and on-demand builds
- Host: GitHub
- URL: https://github.com/henriqueslab/docker-rxiv-maker
- Owner: HenriquesLab
- Created: 2025-08-24T08:22:49.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2025-09-08T16:46:08.000Z (9 months ago)
- Last Synced: 2025-09-08T18:09:13.492Z (9 months ago)
- Language: Shell
- Size: 188 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Docker Infrastructure for Rxiv-Maker
Docker image building infrastructure for rxiv-maker with **pre-installed rxiv-maker via UV** for direct terminal usage.
## 🆕 NEW POLICY: Pre-installed Terminal-Focused Architecture
**MAJOR CHANGE**: We have shifted from runtime dependency injection to **pre-installed rxiv-maker** during Docker build time.
### Key Changes:
- ✅ **rxiv-maker pre-installed via UV** during Docker build
- ✅ **Direct terminal usage** - no runtime installation needed
- ✅ **Faster startup** - immediate rxiv-maker availability
- ✅ **Consistent versions** - locked at build time
- ❌ **No more runtime dependency injection** (old approach deprecated)
## Build Schedule
- **Weekly Builds**: Every Monday at 2 AM UTC with latest rxiv-maker version
- **On-Demand Builds**: Manual workflow dispatch for testing and hotfixes
- **Release Builds**: Triggered by main rxiv-maker releases with version tags
## Repository Structure
```
docker-rxiv-maker/
├── .github/
│ ├── workflows/
│ │ ├── build-weekly.yml # Weekly scheduled builds
│ │ ├── build-on-demand.yml # Manual trigger builds
│ │ └── build-release.yml # Release-triggered builds
│ └── scripts/
│ └── builder.py # Docker build automation
├── images/
│ └── base/ # Base Docker images
│ ├── Dockerfile # NEW: UV pre-installation Dockerfile
│ ├── build.sh # Build script
│ └── Makefile # Management commands
├── scripts/ # NEW: Terminal-focused helper scripts
│ ├── workspace-setup.sh # Interactive workspace setup
│ └── usage.sh # Usage instructions
├── docs/ # Documentation
└── tests/ # Build verification tests
```
## Image Details
### Base Images (`images/base/`)
- **Repository**: `henriqueslab/rxiv-maker-base`
- **Tags**: `latest`, `v2.5.x` (new versioning for UV-based images)
- **Architecture**: AMD64, ARM64 (native performance)
- **Purpose**: Production-ready images with **pre-installed rxiv-maker via UV**
- **Features**:
- ✅ rxiv-maker ready for immediate use
- ✅ Complete LaTeX distribution (TeX Live)
- ✅ Python 3.11 with scientific libraries
- ✅ R with graphics packages
- ✅ Mermaid.ink API integration
- ✅ No browser dependencies
- ✅ Optimized image size
## 🚀 Quick Start (NEW TERMINAL-FOCUSED WORKFLOW)
### Interactive Terminal Usage (Recommended)
**NEW**: Start an interactive terminal session and use rxiv-maker directly:
```bash
# Start interactive container with your manuscript
docker run -it --rm -v $(pwd):/workspace henriqueslab/rxiv-maker-base:latest
# Inside container: Use rxiv-maker directly (pre-installed!)
rxiv pdf ./my-manuscript/
rxiv validate ./my-manuscript/
rxiv --help
# Optional: Set up workspace structure
workspace-setup.sh
```
### Direct Command Execution
**NEW**: Run rxiv-maker commands directly without interactive shell:
```bash
# Generate PDF (one command)
docker run --rm -v $(pwd):/workspace henriqueslab/rxiv-maker-base:latest rxiv pdf .
# Validate manuscript (one command)
docker run --rm -v $(pwd):/workspace henriqueslab/rxiv-maker-base:latest rxiv validate .
# View usage instructions
docker run --rm henriqueslab/rxiv-maker-base:latest usage.sh
```
### Helper Scripts (Available in Container)
```bash
# Inside container - helper scripts available globally:
usage.sh # Usage instructions
workspace-setup.sh # Interactive workspace setup
rxiv --version # Check pre-installed version
```
## 🔄 Migration from Old Architecture
If you were using the old "runtime dependency injection" approach:
### OLD (Deprecated):
```bash
# OLD: Runtime dependency injection approach
docker run -it --rm -v $(pwd):/workspace henriqueslab/rxiv-maker-base:latest dev-mode.sh
docker run --rm -v $(pwd):/workspace henriqueslab/rxiv-maker-base:latest install-project-deps.sh
```
### NEW (Current):
```bash
# NEW: Direct terminal usage (rxiv-maker pre-installed)
docker run -it --rm -v $(pwd):/workspace henriqueslab/rxiv-maker-base:latest
# Then inside container: rxiv pdf ./my-manuscript/
```
## Benefits of New Architecture
| Aspect | OLD (Runtime Injection) | NEW (Pre-installed) |
|--------|------------------------|-------------------|
| **Startup Time** | ~30-60s (dependency installation) | ~2-3s (immediate) |
| **Reliability** | Depends on PyPI availability | Pre-built, always works |
| **Version Consistency** | Runtime variations possible | Locked at build time |
| **Offline Usage** | Requires internet for first run | Works completely offline |
| **Usage Complexity** | Requires setup scripts | Direct rxiv commands |
## Docker Image Building
### Local Development
```bash
# Build new UV-based image locally
cd images/base
./build.sh # Build for local development
./build.sh --push # Build and push to registry
```
### Build Configuration
- Uses **UV for rxiv-maker installation** during build time
- Includes terminal-focused helper scripts
- Optimized for immediate terminal usage
- No runtime dependency installation needed
## Troubleshooting
### Common Issues
**Problem**: "rxiv command not found"
**Solution**: You may be using an old image. Pull latest: `docker pull henriqueslab/rxiv-maker-base:latest`
**Problem**: Scripts not found (workspace-setup.sh, usage.sh)
**Solution**: These are included in images v2.5.0+. Update your image.
**Problem**: Looking for old dev-mode.sh or install-project-deps.sh
**Solution**: These are deprecated. Use the new direct terminal approach.
## Backwards Compatibility
- **Images v2.4.x and earlier**: Used APT + runtime dependency injection
- **Images v2.5.x and later**: Use UV + pre-installation (current)
- **Migration**: Update your workflows to use direct rxiv commands instead of setup scripts
## Documentation
- [Usage Instructions](scripts/usage.sh) - Available in container
- [Workspace Setup](scripts/workspace-setup.sh) - Available in container
- [Build Process](docs/) - Technical documentation
---
**Architecture Version**: v2.5.0-uv-preinstalled
**Last Updated**: September 2025
**Breaking Change**: Yes - migrated from runtime injection to pre-installation