Runtime CLI reference

The bijux-proteomics-runtime command manages canonical execution and run records. Use --json for machine-readable command output and --pretty for indented JSON. Unless a governed workflow specifies another location, write local run products beneath the repository artifacts/ directory.

Run or validate a sequence

Provide either an inline sequence or a FASTA file:

bijux-proteomics-runtime run \
  --sequence MKTIIALSYIFCLVFADYKDDDDK \
  --dry-run \
  --artifacts-dir artifacts/runtime \
  --json

--dry-run validates and plans without invoking tools. Omit it to execute. --rounds controls the number of rounds; --execution-mode accepts auto, gpu, or cpu.

Real structure providers are opt-in through --provider: esmfold, local_esmfold, rosettafold, local_rosettafold, or openprotein. Availability depends on installed extras and environment capabilities. If no provider is requested, runtime retains its governed default selection behavior.

Continue and inspect

bijux-proteomics-runtime resume CANDIDATE_ID \
  --artifacts-dir artifacts/runtime \
  --json

bijux-proteomics-runtime inspect-candidate CANDIDATE_ID --pretty

resume re-enters a candidate from governed state and accepts the same rounds, provider, artifact directory, and execution-mode controls used by run. Inspection is read-only and returns the recorded candidate state.

Compare and reproduce

bijux-proteomics-runtime compare RUN_A RUN_B --pretty
bijux-proteomics-runtime reproduce RUN_ID --json

Comparison reports differences between completed run records. Reproduction uses the stored run contract and rejects conditions that cannot support an honest replay. Neither command asserts scientific equivalence beyond the recorded comparison fields.

Import an external result

bijux-proteomics-runtime import-result \
  --sequence MKTIIALSYIFCLVFADYKDDDDK \
  --source artifacts/external/result.json \
  --engine-name example-engine \
  --engine-version 1.4.0 \
  --artifacts-dir artifacts/runtime \
  --json

The engine name, version, source path, and sequence are required. The resulting record preserves external provenance and remains distinguishable from a native runtime execution.

Export a report

bijux-proteomics-runtime export-report RUN_ID \
  --output artifacts/runtime/report.json \
  --pretty

The exported report is a view over the recorded run. Keep the underlying run bundle when audit, replay, or artifact verification is required.

Inspect runtime identity

bijux-proteomics-runtime identity

Identity output supports environment and version diagnosis. Record it with reproduction evidence when provider or dependency differences may matter.

HTTP API

Start the local application with:

bijux-proteomics-runtime api serve --host 127.0.0.1 --port 8000

Use --no-docs to disable interactive OpenAPI documentation and --reload only for local development. The api command group also exposes structured CLI views of health, status, history, artifacts, evidence-bundle, review-packet, and artifact or evidence lookups.

Exit and failure behavior

Invalid inputs, missing capabilities, provider failures, corrupt artifacts, and incompatible replay conditions remain explicit non-success results. Structured output should be retained with the artifact bundle; do not infer success from the presence of a partially written directory.

Historical users may invoke the same command group as agentic-proteins. Migrate automation to bijux-proteomics-runtime; the compatibility command is not the canonical name for new integrations.