Container Releases

Warning

Container-Only Releases

This documentation covers container releases only. Many NL-BIOMERO containers depend on underlying libraries that have their own separate release cycles and repositories.

Before releasing containers, ensure all dependent libraries are released first:

• BIOMERO Library - Release new version, then update BIOMERO_VERSION in .env

• OMERO Plugins (OMERO.biomero, OMERO.forms, etc.) - Release plugin, then update Dockerfile references

• OMERO ADI - Independent releases with own container builds

• Other Dependencies - Update base image versions, library versions, etc.

Example workflow:

1. Release BIOMERO library v2.1.0

2. Update NL-BIOMERO .env with BIOMERO_VERSION=v2.1.0

3. Update relevant Dockerfiles (server, web) with new library versions or requirements

4. Release NL-BIOMERO containers to build and distribute the updated images

This section covers the release process for NL-BIOMERO containers, including versioning, building, and distribution.

Release Overview

NL-BIOMERO uses an automated GitHub Actions workflow to build and publish Docker containers to Docker Hub upon each release. The containers are published to the cellularimagingcf organization.

Release Workflow

Container Build Automation

Main Repository (NL-BIOMERO)

• Trigger: GitHub release creation via the GitHub web interface

• Action: Automated Docker build and push to Docker Hub

• Containers Built: Most NL-BIOMERO containers (omeroserver, omeroweb, biomeroworker, etc.)

• Registry: Docker Hub - cellularimagingcf

OMERO ADI Submodule

• Repository: Separate repository (included as submodule)

• Versioning: Independent release cycle

• Action: Has its own GitHub Actions workflow

• Coordination: Update submodule reference in NL-BIOMERO when needed

Typical Release Process

1. Update Dependencies

   Update underlying library versions in relevant files:

   # Example: Update BIOMERO version
   # Edit .env file:
   BIOMERO_VERSION=v2.1.0
   
   # Example: Update other dependencies in Dockerfiles
   # server/Dockerfile, web/Dockerfile, etc.
   

2. Test Changes

   Build and test locally before releasing:

   # Build specific container
   docker-compose -f docker-compose-dev.yml build omeroserver
   
   # Test the full stack
   docker-compose -f docker-compose-dev.yml up -d
   

3. Create GitHub Release

   • Go to GitHub Releases page

   • Click “Create a new release”

   • Follow versioning guidelines (see below)

   • Write release notes describing changes

   • Mark as pre-release if applicable

4. Monitor Build Process

   • GitHub Actions will automatically trigger

   • Monitor the build process in the Actions tab

   • Verify containers are published to Docker Hub

5. Update Documentation

   • Update relevant documentation

   • Announce significant releases (see Communication section)

Versioning Guidelines

Semantic Versioning

NL-BIOMERO follows Semantic Versioning (MAJOR.MINOR.PATCH):

MAJOR (e.g., 1.0.0 → 2.0.0)

• Breaking changes that are not backward compatible

• Significant architectural changes

• API changes that require user intervention

MINOR (e.g., 1.0.0 → 1.1.0)

• New optional features

• New functionality that doesn’t break existing workflows

• New container services or plugins

PATCH (e.g., 1.0.0 → 1.0.1)

• Bug fixes

• Security updates

• Required feature updates that maintain compatibility

Pre-release Versions

For development and testing versions:

Alpha Releases

• Format: 1.0.0-alpha.1, 1.0.0-alpha.2

• Early development, may have significant issues

• Internal testing only

• Mark as “Pre-release” in GitHub to prevent becoming “latest”

Beta Releases

• Format: 1.0.0-beta.1, 1.0.0-beta.2

• Feature-complete but may have bugs

• Ready for broader testing

• Mark as “Pre-release” in GitHub to prevent becoming “latest”

Release Candidates

• No, beta is a release candidate

Release Examples

# Stable releases
v1.0.0    - Initial stable release
v1.1.0    - Added new BIOMERO workflows
v1.1.1    - Fixed import bug
v2.0.0    - Major UI overhaul (breaking changes)

# Pre-releases
v2.0.0-alpha.1  - Early development of v2.0
v2.0.0-beta.1   - Feature-complete v2.0 for testing

Dependency Management

Library Updates

BIOMERO Library

1. BIOMERO releases new version (separate repository)

2. Update BIOMERO_VERSION in .env file

3. Test integration with new BIOMERO version

4. Release new NL-BIOMERO version to build updated containers

OMERO Plugins

1. Plugin releases new version (e.g., OMERO.biomero, OMERO.forms)

2. Update version in relevant Dockerfile

3. Test plugin integration

4. Release new NL-BIOMERO version

Base Images

1. Monitor for security updates to base images (OMERO, PostgreSQL, etc.)

2. Update base image versions in Dockerfiles

3. Test compatibility

4. Release updated containers

Example Dependency Update

# 1. BIOMERO releases v2.1.0
# 2. Update NL-BIOMERO .env file:
BIOMERO_VERSION=v2.1.0

# 3. Test locally
docker-compose -f docker-compose-dev.yml build
docker-compose -f docker-compose-dev.yml up -d

# 4. Create release v1.2.0 on GitHub
# 5. GitHub Actions builds and publishes containers

OMERO ADI Submodule

Special Handling

The OMERO ADI component is managed as a Git submodule with independent versioning:

Separate Repository

• Repository: OMERO-Automated-Data-Import

• Independent versioning and release cycle

• Own GitHub Actions for container building

Submodule Updates

1. OMERO ADI releases new version independently

2. Update submodule reference in NL-BIOMERO:

cd biomero-importer
git fetch origin
git checkout v1.x.x  # Latest ADI release
cd ..
git add biomero-importer
git commit -m "Update OMERO ADI to v1.x.x"

3. Release new NL-BIOMERO version if ADI changes affect the platform

Coordination

• Most releases don’t require ADI updates

• Update ADI submodule only when necessary

• Test integration when updating submodule reference

Docker Hub Management

Container Registry

Organization: cellularimagingcf

Published Containers:

• cellularimagingcf/omeroserver

• cellularimagingcf/omeroworker

• cellularimagingcf/omeroweb

• cellularimagingcf/biomero

• cellularimagingcf/biomero-importer (from separate repo)

Tagging Strategy:

• latest - Latest stable release, but preferably use specific version tags

• vX.Y.Z - Specific version tags (e.g., v1.2.3)

• vX.Y - Minor version tags, updated with latest patch (e.g., v1.2)

• Pre-releases do not update latest tag

Repository Management

Automated Publishing

• GitHub Actions handles all container publishing

• No manual Docker Hub interactions needed

• Credentials managed via GitHub Secrets

Tag Management

• Stable releases automatically tagged as latest

• Pre-releases (alpha, beta, rc) maintain separate tags

• Version-specific tags are always created

Communication & Announcements

Release Communication

Significant Releases (major versions, important features):

1. NVVM Slack - Internal team communication

   📢 NL-BIOMERO v2.0.0 Released!
   
   Major updates:
   • New React-based UI via OMERO.biomero plugin
   • Enhanced BIOMERO workflow integration
   • Breaking changes: see migration guide
   
   Release notes: https://github.com/Cellular-Imaging-Amsterdam-UMC/NL-BIOMERO/releases/tag/v2.0.0
   

2. Image.sc Forum - Community announcements

   Post in appropriate categories: - Announcements Tag with e.g. - BIOMERO - OMERO - BIAFLOWS

Patch Releases (bug fixes):

• GitHub release notes sufficient

• Internal notification if critical fixes

Release Notes Template

## What's Changed

### 🚀 New Features
- Added new BIOMERO workflow XYZ
- Enhanced web interface with React components

### 🐛 Bug Fixes
- Fixed import issue with large datasets
- Resolved Metabase dashboard loading

### 📚 Documentation
- Updated deployment guide
- Added developer container documentation

### ⚠️ Breaking Changes
- Configuration format changed (see migration guide)
- Deprecated old API endpoints

### 🔧 Dependencies
- Updated BIOMERO to v2.1.0
- Updated OMERO base images to 5.6.17

**Full Changelog**: https://github.com/.../compare/v1.0.0...v2.0.0

Troubleshooting Releases

Common Issues

Build Failures

• Check GitHub Actions logs

• Verify Dockerfile syntax

• Test local builds before releasing

Dependency Conflicts

• Update dependency versions incrementally

• Test each dependency update separately

• Use development environment for testing

Docker Hub Issues

• Verify GitHub Secrets are configured

• Check Docker Hub organization permissions

• Monitor Docker Hub service status

Emergency Releases

For critical security fixes or major bugs:

1. Create hotfix branch from latest stable tag

2. Apply minimal fix (avoid feature additions)

3. Test thoroughly but expedite process

4. Release as patch version (increment PATCH number)

5. Communicate urgency in release notes and announcements

Best Practices

Release Checklist

Before creating a release:

□ All dependencies updated and tested
□ Local build and testing completed
□ Documentation updated for new features
□ Migration guide written (if breaking changes)
□ Release notes prepared
□ Version number follows semantic versioning
□ Pre-release marked appropriately (if applicable)

Release Quality

• Test thoroughly before releasing

• Use development environment for pre-release testing

• Coordinate with team for major releases

• Monitor post-release for issues

• Be prepared to create hotfix releases if needed

Related Documentation

• Developer Getting Started - Development setup

• Architecture Overview - System architecture

• GitHub Actions Documentation

• Docker Hub Documentation

• Semantic Versioning