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docs: fix repository structure, add GCP + generic_sif_runner/workflow_runner, coverage #1

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man4ish merged 1 commit into from
Aug 8, 2026
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docs: fix repository structure, add GCP + generic_sif_runner/workflow_runner, coverage #1

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34 changes: 26 additions & 8 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ OmniBioAI’s Tool Execution Service (TES) to run individual tools across **mult
* Local Docker execution
* AWS Batch
* Azure Batch
* GCP Batch (`gs://` results upload)
* Kubernetes Jobs
* Slurm / HPC via TES adapters

Expand Down Expand Up @@ -78,14 +79,22 @@ omnibioai-tool-runtime/
├── pyproject.toml
├── omni_tool_runtime/
│ ├── __init__.py
│ ├── contract.py # ToolContract + read_contract_from_env() —
│ │ # the code implementing "Execution Contract" below
│ ├── run.py # Generic entrypoint: resolves TOOL_ID ->
│ │ # tools.{tool_id}.run and calls its main()
│ ├── result_uri.py # URI parsing & dispatch
│ ├── upload_result.py # Unified upload logic
│ └── uploaders/
│ ├── s3_uploader.py
│ └── azureblob_uploader.py
├── tools/
│ └── echo_test/
│ ├── __init__.py
│ ├── echo_test/ # Minimal reference implementation — see below
│ │ ├── __init__.py
│ │ └── run.py
│ ├── generic_sif_runner/ # The real, production tool — embedded in every
│ │ └── run.py # ECR/ACR/GCR image (see omnibioai-tes's README)
│ └── workflow_runner/
│ └── run.py
└── tests/
```
Expand All @@ -98,16 +107,21 @@ omnibioai-tool-runtime/
cd ~/Desktop/machine/omnibioai-tool-runtime
pytest tests/ -v --cov=.

# 100% coverage
# 99% coverage (verified 2026-08-07; 371 tests. Two lines in
# generic_sif_runner/run.py are the only gap)
# Covers: upload_result, S3 uploader, Azure uploader,
# echo_test tool, run lifecycle
# echo_test/generic_sif_runner/workflow_runner tools, run lifecycle
```

---

## Example Tool: `echo_test`

This is the **reference implementation** for all future tools.
This is a **minimal reference implementation** — small enough to read
end-to-end as a template for a new tool. The real, production tool
embedded in every ECR/ACR/GCR image is `tools/generic_sif_runner/` (see
[omnibioai-tes's README](../omnibioai-tes#generic_sif_runner)); a third,
`tools/workflow_runner/`, also ships here.

### Behavior

Expand Down Expand Up @@ -154,6 +168,7 @@ if __name__ == "__main__":
| ------- | ------------------------------------------------- |
| AWS | `s3://bucket/prefix/run_id/results.json` |
| Azure | `azureblob://account/container/path/results.json` |
| GCP | `gs://bucket/prefix/run_id/results.json` (via `google.cloud.storage`) |

The runtime:

Expand Down Expand Up @@ -304,10 +319,13 @@ tools:
- Unified runtime image embedded in all tool Docker images
- AWS Batch support (S3 result upload)
- Azure Batch support (Azure Blob result upload)
- Kubernetes Job support
- GCP Batch support (GCS result upload)
- Kubernetes Job support — the same image runs unmodified as a K8s Job's
container; no Kubernetes-specific code lives in this repo
- Deterministic execution contract
- Reference `echo_test` tool
- 100% test coverage
- Reference `echo_test` tool, plus the production `generic_sif_runner`
and `workflow_runner` tools
- 99% test coverage

### Intentionally not included (by design)
- No workflow orchestration
Expand Down
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