CLI Reference

The scitex-scholar command provides five subcommands. Every subcommand has --help for option listings.

scitex-scholar --help

Subcommands

single

Process a single paper from DOI or title through the full pipeline (resolve → enrich → download → organize).

scitex-scholar single --doi "10.1093/brain/awx173" --project my_project
scitex-scholar single --title "Seizure prediction with iEEG" --project my_project

parallel

Process multiple papers concurrently from a list.

scitex-scholar parallel --dois "10.1...,10.2..." --project my_project --num-workers 4

bibtex

Run the full pipeline across every entry in a BibTeX file. Resumable.

scitex-scholar bibtex --bibtex refs.bib --project my_project \
                      --num-workers 4 --browser-mode stealth

mcp

Start the deprecated standalone MCP server. Prefer the unified scitex serve server instead, which exposes scholar tools alongside the rest of the SciTeX ecosystem.

scitex-scholar mcp      # deprecated — use 'scitex serve'
scitex serve            # unified server, recommended

highlight

Overlay semantic highlights on a PDF. See Semantic PDF Highlighting.

export ANTHROPIC_API_KEY=sk-ant-...

scitex-scholar highlight paper.pdf                  # sentence-level, Haiku, default output
scitex-scholar highlight paper.pdf -o out.pdf
scitex-scholar highlight paper.pdf --model claude-sonnet-4-6
scitex-scholar highlight paper.pdf --stub           # offline keyword heuristic
scitex-scholar highlight paper.pdf --dry-run
scitex-scholar highlight paper.pdf --max-blocks 20  # smoke test

# Offline label-apply workflow
scitex-scholar highlight paper.pdf --labels-dump blocks.json
scitex-scholar highlight paper.pdf --labels-apply labels.json

Also available as a standalone module:

python -m scitex_scholar.pdf_highlight paper.pdf