{"id":51510289,"url":"https://github.com/man4ish/omnibioai-utils","last_synced_at":"2026-07-08T05:01:58.291Z","repository":{"id":365328940,"uuid":"1271610976","full_name":"man4ish/omnibioai-utils","owner":"man4ish","description":"Developer utilities and automation scripts for the OmniBioAI ecosystem — stack lifecycle management, image builds, coverage reporting, CI/CD control, and GitHub project automation.","archived":false,"fork":false,"pushed_at":"2026-06-16T21:05:22.000Z","size":33,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-06-16T23:07:56.472Z","etag":null,"topics":["bash","omnibioai","python","utliities"],"latest_commit_sha":null,"homepage":"","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/man4ish.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-06-16T20:54:16.000Z","updated_at":"2026-06-16T21:05:26.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/man4ish/omnibioai-utils","commit_stats":null,"previous_names":["man4ish/omnibioai-utils"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/man4ish/omnibioai-utils","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/man4ish%2Fomnibioai-utils","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/man4ish%2Fomnibioai-utils/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/man4ish%2Fomnibioai-utils/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/man4ish%2Fomnibioai-utils/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/man4ish","download_url":"https://codeload.github.com/man4ish/omnibioai-utils/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/man4ish%2Fomnibioai-utils/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35252324,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-08T02:00:06.796Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bash","omnibioai","python","utliities"],"created_at":"2026-07-08T05:01:57.414Z","updated_at":"2026-07-08T05:01:58.265Z","avatar_url":"https://github.com/man4ish.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# omnibioai-utils\n\nDeveloper 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.\n\n---\n\n## Scripts\n\n### Stack Management\n\n| Script | Description |\n|--------|-------------|\n| `omnibioai-up.sh` | Starts the full OmniBioAI stack in a tmux session |\n| `omnibioai-down.sh` | Tears down the tmux session and stops all services |\n| `start_all.sh` | Starts all OmniBioAI services sequentially |\n| `start_stack_tmux.sh` | Launches the full stack in named tmux windows with port management |\n| `start-all-uis.sh` | Starts all React frontend UIs and backend APIs |\n| `stop-all-uis.sh` | Stops all running React UI dev servers |\n| `smoke_test_stack.sh` | Runs HTTP health checks against all core service endpoints |\n\n### Build Automation\n\n| Script | Description |\n|--------|-------------|\n| `build-all-new.sh` | Builds and pushes all service images to GHCR (`ghcr.io/man4ish`) |\n| `build_all_tools.sh` | Builds all bioinformatics tool images and pushes to ECR and GHCR |\n| `build_cython.sh` | Compiles all high-priority Cython files across repos before Docker builds |\n\n### Ecosystem Management\n\n| Script | Description |\n|--------|-------------|\n| `ecosystem_status.sh` | Reports git branch and clean/dirty status across all 32 repos |\n| `clock_count.sh` | Counts lines of code across the full ecosystem using `cloc` |\n| `run_coverage.sh` | Aggregates pytest coverage reports across all repos into `out/coverage/` |\n| `disable_cicd.sh` | Moves `.github/workflows` to `workflows_disabled` across all repos |\n| `update_descriptions.sh` | Updates GitHub repo descriptions for all OmniBioAI repos via API |\n| `update_topics.sh` | Sets GitHub topics for all OmniBioAI repos via `gh api` |\n\n### Project Setup\n\n| Script / File | Description |\n|---------------|-------------|\n| `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 |\n| `build-results.txt` | Latest build results log |\n\n---\n\n## Usage\n\n### Check ecosystem status\n```bash\nbash ecosystem_status.sh\n# or from machine root:\nbash utils/ecosystem_status.sh\n```\n\n### Start the full stack\n```bash\nbash omnibioai-up.sh\n```\n\n### Smoke test all services\n```bash\nbash smoke_test_stack.sh\n```\n\n### Build and push all images to GHCR\n```bash\nbash build-all-new.sh\n```\n\n### Run coverage across all repos\n```bash\nbash run_coverage.sh\n# Output: ~/Desktop/machine/out/coverage/\n```\n\n### Update all GitHub repo descriptions and topics\n```bash\nexport GITHUB_TOKEN=\u003cyour_pat\u003e\nbash update_descriptions.sh\nbash update_topics.sh\n```\n\n### Set up GitHub Beta Launch project\n```bash\nexport GITHUB_TOKEN=\u003cyour_pat\u003e\npython setup_beta_project.py --dry-run   # preview\npython setup_beta_project.py             # execute\n```\n\n### Disable CI/CD across all repos\n```bash\nbash disable_cicd.sh\n```\n\n---\n\n## Requirements\n\n```bash\n# Shell utilities\nsudo apt-get install tmux cloc\n\n# Python (for setup_beta_project.py)\npip install PyGithub requests\n\n# GitHub CLI (for update_topics.sh, update_descriptions.sh)\ngh auth login\n```\n\n---\n\n## Related Repositories\n\n- [`omnibioai-ecosystem`](../omnibioai-ecosystem) — Docker Compose stack wired by these scripts\n- [`omnibioai-control-center`](../omnibioai-control-center) — live health dashboard complementing `smoke_test_stack.sh`\n- [`omnibioai-test-data`](../omnibioai-test-data) — test suite run via these build and stack scripts\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fman4ish%2Fomnibioai-utils","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fman4ish%2Fomnibioai-utils","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fman4ish%2Fomnibioai-utils/lists"}