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Develop with OmniBioAI

OmniBioAI is roughly thirty separate repositories, most with their own language, framework, and test suite. This page is the routing point — it does not attempt to be a single manual for all of them. Where this site and a repository's own README disagree, the repository's own source wins; fix the summary here, not the other way around.

Verification vocabulary​

Every instruction across this documentation set uses precise terms, never implying more certainty than the evidence supports:

TermMeans
DOCUMENTEDA real walkthrough exists for this.
SOURCE_ONLYInferable by reading code/config; no prose walkthrough exists yet.
UNKNOWNGenuinely not established either way — not assumed working or broken.
CONFIGUREDPresent in source/registry. Not, by itself, tested, deployed, or operationally verified — see Testing & Quality for the full vocabulary this reuses.

A command that appears only in an older document, without matching current package/build configuration, is not treated as authoritative here.

What should I read first?​

  1. Repository Map — find which repository owns the kind of change you want to make.
  2. Local Development — toolchain requirements, environment setup, safe local-development boundaries, and how generated documentation gets regenerated.
  3. Containers — canonical bases, plugin image contracts, architecture validation, and release evidence.
  4. The detail page for your area: Architecture, Plugins & Integrations, Workflows & TES, API, or Troubleshooting.

What can I safely run locally?​

Nothing in this documentation set instructs you to connect to production infrastructure, reuse production credentials, or run a destructive operational procedure as a normal development step. See Local Development for what each component actually supports, and its "secret-safe local development" section for the short list of things no document here will ever tell you to do.

How do I run tests, and what does passing prove?​

Testing & Quality is authoritative for this across the whole ecosystem — test-source presence, execution, coverage, and CI enforcement are kept as separate facts there, and this page does not repeat or loosen that discipline. A repository containing many test files does not by itself mean a large number of tests currently pass; a coverage configuration does not by itself mean coverage is measured or enforced.

How do I regenerate generated artifacts?​

If your change affects a generated catalog family (plugins, integrations, reference data, TES tools/backends, workflows, the API reference, or the biomedical knowledge inventory), see Local Development for the source → generator → verify → validate → build contract. Never hand-edit a generated file — every generated page states this, and a verification step exists specifically to catch it.

Where are the architecture, security, and operations docs?​

  • Architecture — the platform's actual routing and service boundaries, evidence-bounded.
  • operator guidance — identity, authorization, audit, and data protection, with the same verification-state discipline as this page.
  • operator guidance and operator guidance — deployment-facing concerns; most of this does not apply to local development, and this documentation set does not imply otherwise.

A practical definition of done​

Not every repository has identical gates. Where applicable to your change:

  • You changed the repository that actually owns this behavior (see the Repository Map).
  • Relevant tests were updated alongside the source change.
  • Focused tests for the changed area were run locally.
  • If you touched a generated catalog in omnibioai-docs: the owning generator was re-run, its --verify mode passes, and nothing generated was hand-edited.
  • Security implications were considered for any change touching authentication, authorization, tenant scoping, audit, secrets, or sensitive data — see operator guidance.
  • Documentation was updated where the change affects other developers.
  • No secret, credential, or machine-specific absolute path was committed.

Component task guides​