omnibioai-utils

Developer utilities, automation scripts, and ecosystem management tools for the OmniBioAI platform. Covers stack lifecycle management, build automation, CI/CD control, coverage reporting, GitHub project setup, and ecosystem health monitoring.

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Scripts

Stack Management

Script	Description
omnibioai-up.sh	Starts the full OmniBioAI stack in a tmux session
omnibioai-down.sh	Tears down the tmux session and stops all services
start_all.sh	Starts all OmniBioAI services sequentially
start_stack_tmux.sh	Launches the full stack in named tmux windows with port management
start-all-uis.sh	Starts all React frontend UIs and backend APIs
stop-all-uis.sh	Stops all running React UI dev servers
smoke_test_stack.sh	Runs HTTP health checks against all core service endpoints

Build Automation

Script	Description
build-all-new.sh	Builds and pushes all service images to GHCR (ghcr.io/man4ish)
build_all_tools.sh	Builds all bioinformatics tool images and pushes to ECR and GHCR
build_cython.sh	Compiles all high-priority Cython files across repos before Docker builds

Ecosystem Management

Script	Description
ecosystem_status.sh	Reports git branch and clean/dirty status across all 32 repos
clock_count.sh	Counts lines of code across the full ecosystem using cloc
run_coverage.sh	Aggregates pytest coverage reports across all repos into out/coverage/
disable_cicd.sh	Moves .github/workflows to workflows_disabled across all repos
update_descriptions.sh	Updates GitHub repo descriptions for all OmniBioAI repos via API
update_topics.sh	Sets GitHub topics for all OmniBioAI repos via gh api

Project Setup

Script / File	Description
setup_beta_project.py	Creates GitHub Project "OmniBioAI Beta Launch" with Board + Roadmap views, custom fields (Priority, Category, Repo, Due Date), and issues across all repos linked to the project
build-results.txt	Latest build results log

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Usage

Check ecosystem status

bash ecosystem_status.sh
# or from machine root:
bash utils/ecosystem_status.sh

Start the full stack

bash omnibioai-up.sh

Smoke test all services

bash smoke_test_stack.sh

Build and push all images to GHCR

bash build-all-new.sh

Run coverage across all repos

bash run_coverage.sh
# Output: ~/Desktop/machine/out/coverage/

Update all GitHub repo descriptions and topics

export GITHUB_TOKEN=<your_pat>
bash update_descriptions.sh
bash update_topics.sh

Set up GitHub Beta Launch project

export GITHUB_TOKEN=<your_pat>
python setup_beta_project.py --dry-run   # preview
python setup_beta_project.py             # execute

Disable CI/CD across all repos

bash disable_cicd.sh

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Requirements

# Shell utilities
sudo apt-get install tmux cloc

# Python (for setup_beta_project.py)
pip install PyGithub requests

# GitHub CLI (for update_topics.sh, update_descriptions.sh)
gh auth login

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Related Repositories

• omnibioai-ecosystem — Docker Compose stack wired by these scripts
• omnibioai-control-center — live health dashboard complementing smoke_test_stack.sh
• omnibioai-test-data — test suite run via these build and stack scripts