/search

name: search
description: Unified academic paper search, citation chains, paper download (arXiv LaTeX/PDF, Sci-Hub), figure extraction from papers, LaTeX source reading, BibTeX fetching, web search, and browser automation for Cloudflare-protected sites (PRL, Science, Nature, Google Scholar).
compatibility: Requires Node.js 22+. Optional: browser-use CLI for browser automation. PyMuPDF and Pillow for figure extraction.
allowed-tools: Bash(search:*) Bash(browse:*) Bash(browser-use:*) Bash(extract-figures:*)

Search Skill

All information gathering in one place. Two CLI tools:

• `scripts/search` — paper search, citations, download, LaTeX source, BibTeX, web search, URL fetch
• `scripts/browse` — browser automation wrapper (uses browser-use with headed + Chrome profile defaults)

Setup

bash scripts/setup.sh

scripts/search

Paper Search

scripts/search papers "Rydberg atom quantum gate"
scripts/search papers "topological insulators" --source openalex --count 20
scripts/search papers "diffusion models" --source arxiv --count 15
scripts/search papers "air pollution health effects" --source crossref --count 20
scripts/search papers "quantum error correction" --from-year 2024 --sort date --count 20
# Author-filtered search: use last name as an indexed field, not free text.
# At least one of <query> or --author is required; both together = AND.
scripts/search papers "" --author "Lukin" --from-year 2025 --sort date --count 20
scripts/search papers "neutral atom arrays" --author "Bluvstein" --count 15

• **OpenAlex**: all fields, citation counts, DOIs. `--source openalex`
• **arXiv**: recent preprints, physics/CS/math. `--source arxiv`
• **CrossRef**: broadest coverage (120M+ records), all disciplines, non-English journals. `--source crossref`
• Default: all three.
• `--author <LastName>`: Filter by author last name. Maps to arXiv `au:`, OpenAlex `raw_author_name.search`, and CrossRef `query.author` — all indexed fields. Strongly preferred over putting the name in the free-text query, which treats the name as an unweighted keyword and routinely misses the target. Pair with `--from-year` for recent work by a specific researcher.
• `--from-year YYYY`: Only return papers published in YYYY or later.
• `--sort relevance|date`: Sort by relevance (default) or publication date (newest first).

Citation Chains

scripts/search citations W2057883617
scripts/search citations "10.1038/s41586-021-03819-2" --direction citations --limit 30
scripts/search citations 2301.07041 --direction references

Accepts: OpenAlex ID (W...), DOI, or arXiv ID. `--direction`: citations (forward), references (backward), both (default).

Paper Download

scripts/search download --arxiv 2301.07041 --output data/papers
scripts/search download --doi "10.1038/s41586-021-03819-2" --output data/papers
scripts/search download --url "https://example.com/paper.pdf" --output data/papers

• arXiv: tries LaTeX source first (tar.gz), falls back to PDF.
• DOI: auto-discovers working Sci-Hub mirror, downloads PDF.
• URL: direct download.
• Default `--output`: `data/papers/`

**Automatic reader dispatch (arXiv only).** After a successful `search download --arxiv <id>`, a background `reader` is dispatched automatically. It reads the paper's main text + figure manifest and writes two things in a single pass: methodology coverage (A/B/C/D: what's computed, what's demo'd, what goes in figures, what rigor bar) into `notes/methodology.md`, AND a per-paper literature entry (keyed by `cite_key`) into `notes/literature.md`. You never need to launch the reader manually. If it silently misses a paper (hook race, manual drop, DOI download), the research snapshot will surface an `<unprocessed_papers>` reminder asking you to `spawn_agent(agent="reader", ...)` for the gap.

LaTeX Source

scripts/search source 2301.07041
scripts/search source 2301.07041 --papers-dir data/papers --max-chars 50000

Downloads if not present, then returns concatenated .tex/.bib content. Much better than PDF for extracting equations, methods, citations.

BibTeX

scripts/search bib "10.1038/s41586-021-03819-2"
scripts/search bib "10.1038/s41586-021-03819-2" --save report/references.bib

Fetches BibTeX via doi.org content negotiation, falls back to CrossRef. `--save` appends to a .bib file (deduplicates by DOI).

Web Search (Brave)

scripts/search web "quantum error correction review 2024" --count 10

Requires `BRAVE_API_KEY` env var.

GitHub

# Repo search — find repositories by keyword
scripts/search github "quantum simulation" --count 10
scripts/search github "transformer inference" --from-year 2024 --sort date

# Code search — find code across public repos (via Sourcegraph)
scripts/search github "func NewRydbergHamiltonian" --code --count 5
scripts/search github "class QuantumCircuit" --code

# Read README — quick overview without cloning
scripts/search github qiskit/qiskit --readme

# Clone repo — shallow clone to local dir for deep analysis
scripts/search github qiskit/qiskit --clone --output /tmp

• **Repo search** (default): GitHub REST API. Sorted by stars (default) or `--sort date`. `--from-year YYYY` filters by creation date. Auth via `GITHUB_TOKEN` env var or `gh auth token` (optional, increases rate limit from 10 to 30 req/min).
• **Code search** (`--code`): Sourcegraph streaming API. Supports regex. Searches across most popular public repos. No auth needed.
• **README** (`--readme`): Fetches raw README markdown via GitHub API. Pass `owner/repo` as the query.
• **Clone** (`--clone`): `git clone --depth 1` (latest snapshot only, no history). Default output: `/tmp`. Pass `owner/repo` as the query.

URL Fetch

scripts/search fetch "https://example.com/page"

Strips HTML to plain text. For Cloudflare-protected sites, use `scripts/browse` instead.

scripts/browse

Browser automation via browser-use. Always launches in head