victus-processing is the local command surface for paper-processing work.
Run commands through uv from the repository root:
uv run victus-processing --help
Use built-in help as the runtime source of truth for exact flags:
uv run victus-processing <group> --help
uv run victus-processing <group> <command> --help
metadata-extraction: discovers candidates, fetches metadata by DOI, andbibliography-export: generates DOI-only BibTeX from canonical metadata forpdf-intake: links manually obtained PDFs to metadata and stores canonicalpaper_pdf_links.jsonl from existingpdf-processing: converts PDF artifacts to Markdown and structured paper JSON.evidence-extraction: classifies processed papers, maps experiments, buildstesting-pipeline: runs the PDF-processing and evidence chain in per-paperdata/testing.data-layout: creates local runtime directories.Create the expected local data/ layout:
uv run victus-processing data-layout create
Run the main local paper-processing flow:
uv run victus-processing metadata-extraction explore --mode broad-nutrition
uv run victus-processing bibliography-export generate-bib
uv run victus-processing pdf-intake link --metadata-id meta:s2:example --pdf data/artifacts/intake/pdfs/example.pdf
uv run victus-processing pdf-processing run
uv run victus-processing evidence-extraction run
Backfill links for existing PDF artifacts:
uv run victus-processing pdf-intake backfill-links --overwrite
Use --limit while testing or debugging:
uv run victus-processing pdf-processing markdown --limit 1
uv run victus-processing pdf-processing json-from-markdown --markdown data/artifacts/markdown/{paper_id}.md
uv run victus-processing pdf-processing json-from-markdown --input-dir data/artifacts/markdown --shuffle --limit 5
uv run victus-processing pdf-processing run --limit 1
uv run victus-processing evidence-extraction run --limit 1
uv run victus-processing processing-state refresh
uv run victus-processing testing-pipeline run --limit 1
Refresh the paper processing dashboard from data/artifacts inputs and
PostgreSQL output tables:
uv run victus-processing processing-state refresh --csv data/reports/exports/paper_processing_state.csv
Infisical-backed CLI inspection:
uv run victus-infisical-env run --env dev --path / -- victus-processing --help
Useful forms:
uv run victus-infisical-env export --env dev --path / --output .env
uv run victus-infisical-env run --env dev --path / -- victus-processing pdf-processing run --limit 1
Export final scientific PostgreSQL tables to CSV and Parquet:
uv run victus-postgres-export --output-dir data/reports/exports/postgres
Smoke-test CLI routing after changing command behavior:
uv run pytest tests/test_cli_smoke.py -q
Related: Operations.