CLI Reference

The scitex-scholar command provides a Click-based noun-verb subcommand interface. Every group has --help; pass --help-recursive at the top level for a full overview, --version/-V for the installed version, and --json (where supported) for machine-readable output.

scitex-scholar --help
scitex-scholar --help-recursive
scitex-scholar --version
scitex-scholar paper --help
scitex-scholar library --help

Top-level groups

paper

Operate on a paper / batch of papers.

# Single paper from DOI or title (was: ``single``)
scitex-scholar paper fetch --doi "10.1093/brain/awx173" --project my_project
scitex-scholar paper fetch --title "Seizure prediction with iEEG" --project my_project

# Multiple papers in parallel (was: ``parallel``)
scitex-scholar paper fetch-batch --dois 10.1/x --dois 10.2/y --project my_project --num-workers 4

Mutating verbs (fetch, fetch-batch, import, build, etc.) accept --dry-run and -y/--yes.

bibtex

Operate on a BibTeX file.

# Process every entry (was: top-level ``bibtex --bibtex …``)
scitex-scholar bibtex import --bibtex refs.bib --project my_project \
                             --num-workers 4 --browser-mode stealth

mcp

MCP server commands (Model Context Protocol).

scitex-scholar mcp start                  # start stdio server
scitex-scholar mcp start --dry-run        # print plan, exit
scitex-scholar mcp list-tools             # print scholar_* tool names
scitex-scholar mcp list-tools --json      # machine-readable
scitex-scholar mcp doctor                 # check fastmcp + handler imports
scitex-scholar mcp install --claude-code  # config snippet

Prefer the unified scitex serve server when integrating with the rest of the SciTeX ecosystem.

pdf

PDF post-processing. See Semantic PDF Highlighting.

export ANTHROPIC_API_KEY=sk-ant-...

scitex-scholar pdf highlight paper.pdf
scitex-scholar pdf highlight paper.pdf -o out.pdf
scitex-scholar pdf highlight paper.pdf --model claude-sonnet-4-6
scitex-scholar pdf highlight paper.pdf --stub
scitex-scholar pdf highlight paper.pdf --dry-run
scitex-scholar pdf highlight paper.pdf --max-blocks 20

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

Also available as a standalone module:

python -m scitex_scholar.pdf_highlight paper.pdf

library

Library-tree management.

# Symlink <project>/.scitex/scholar/library → ~/.scitex/scholar/library/
scitex-scholar library link-project-tree .

# Replace a library-symlink with a bib-filtered real directory
scitex-scholar library materialize <link_path> --bib refs.bib

# Replace a materialized directory with a symlink to ~/.scitex/scholar/library
scitex-scholar library dematerialize <path>

# Library SQLite index
scitex-scholar library db build --dry-run
scitex-scholar library db build
scitex-scholar library db migrate
scitex-scholar library db lookup --doi 10.1/x --json
scitex-scholar library db list --limit 20 --json
scitex-scholar library db audit --json

skills

Bundled SciTeX-Scholar skill leaves (under src/scitex_scholar/_skills/scitex-scholar/).

scitex-scholar skills list
scitex-scholar skills list --json
scitex-scholar skills get 04_cli-reference
scitex-scholar skills install            # symlink into ~/.claude/skills/
scitex-scholar skills install --copy --force --dry-run

Python API introspection

scitex-scholar list-python-apis           # one name per line
scitex-scholar list-python-apis -v        # with signatures
scitex-scholar list-python-apis --json    # machine-readable

Migration from pre-1.3.0

The pre-1.3.0 top-level commands (single, parallel, top-level bibtex --bibtex, highlight, link-project-tree, materialize, dematerialize, db) still work but emit a one-line DeprecationWarning on stderr and will be removed in 1.4.0. See the project CHANGELOG.md for the full migration table.