literature-search

Literature Search (shared toolchain)

This skill is not a loop — it is the literature-retrieval dependency several loops use for paper discovery and novelty checks. It bundles tools/lit_search.py (a stdlib-only entrypoint) and the tools/lit/ package: Semantic Scholar (S2) for semantic search + snippets + the citation graph and arXiv for full-text reads (the keyless core), plus optional OpenAlex, Perplexity Sonar (ask), and bgpt.pro (bgpt) when their keys are set. Every subcommand prints JSON; on a terminal failure it prints {"error","fallback"} and exits non-zero so the caller degrades to its built-in WebSearch/WebFetch. No installs, Python ≥3.9.

How a loop uses it

A consuming loop resolves these once at setup and reuses them:

• <lit_skill_dir> — where this skill is installed. After cp -r loops/* ~/.claude/skills/ it sits as a sibling of the calling loop, e.g. ~/.claude/skills/literature-search/ (adjust per host). If it cannot be resolved, the caller falls back to WebSearch/WebFetch — depending on it never hard-breaks a loop, it only enriches it.
• <lit> — the literature CLI as a single command token: <lit_skill_dir>/tools/lit_search.py. The entrypoint is executable and carries a #!/usr/bin/env python3 shebang, so it runs directly with no python3 prefix. To reuse a cache across calls, append --cache-dir <sandbox_root>/literature/.cache after the subcommand (a per-subcommand flag, not global).
• <lit_py> — only needed for the fallback form on a host that doesn't honour the execute bit: <lit_py> <lit_skill_dir>/tools/lit_search.py, with <lit_py> = python3 (any ≥3.9 interpreter).

Invoke <lit> as one command — keep it a single shell token. In particular zsh does not word-split unquoted variables, so storing the two-word python3 .../lit_search.py in a variable and calling $VAR tries to exec one long (nonexistent) filename. Use the executable single-token form above, call the script path directly, or split explicitly (${=VAR} in zsh).

Subcommands

Subcommand	Use
<lit> search "<q>" [--year 2020-] [--min-citations N] [--limit N] [--source s2|openalex|both] [--sort relevance|citations|recent]	semantic discovery — related papers (titles, TLDR, abstract, citations, arxiv_id). Defaults to --source s2 (relevance); add openalex/both to widen discovery
<lit> snippet "<q>" [--limit N]	full-text passage search — pinpoint a verbatim fact/number without reading a paper
<lit> cite <paperId> --direction references|citations|recommend	walk the citation graph (backward / forward / "more like this")
<lit> fulltext <arxivId> [--mode auto|latex|pdf]	deep-read one paper's methods/results (HTML > LaTeX > PDF)
<lit> ask "<question>" [--model sonar|sonar-pro|sonar-reasoning]	Perplexity Sonar synthesis — a cited high-level answer (needs OPENROUTER_API_KEY; else use WebSearch)
<lit> bgpt "<q>" [--num N] [--days-back N]	bgpt.pro structured experimental-result/limitations extraction (free for 50 results, then BGPT_API_KEY)
<lit> keys [--init]	report which API keys are present (booleans only); --init writes/extends keys.env

The S2 + arXiv core (search/snippet/cite/fulltext) needs no keys. The optional extras (search --source openalex|both, ask, bgpt) widen discovery and synthesis when their keys are set.

API keys (the shared convention — optional, never block)

This skill is the canonical home for the project's key convention (it is the installed code that implements it). Keys live in one gitignored keys.env at the project root (the nearest .git ancestor of the working dir, else the CWD), shared by every skill in the project.

• Plain KEY=VALUE lines; # comments; blank lines ignored; 0600 perms.
• A real OS environment variable always wins over the file (CI/power users can just export).
• All keys are optional — a missing key degrades that one feature gracefully, down to WebSearch.
• Secrets never enter the conversation — the user edits keys.env themselves; skills read only presence as booleans, never values.

Onboarding flow: <lit> keys (report what's present) → <lit> keys --init (create/append slots, append-only, never overwrites; prints the path) → user opens keys.env and pastes the keys they want (in-session: ! $EDITOR ./keys.env) → <lit> keys again, then proceed. Never block on keys.

• S2_API_KEY (free) — the one most worth setting; a dedicated 1 req/s for search/snippet/cite.
• OPENALEX_EMAIL (free, any email) — OpenAlex "polite pool" for faster --source openalex|both.
• OPENROUTER_API_KEY (paid) — enables ask (Perplexity Sonar); without it ask is disabled.
• BGPT_API_KEY (free for 50 results, then paid) — enables bgpt beyond the free tier.

Constraints

• Stdlib only — never add a dependency or assume one is installed; it must run under bare python3.
• Self-contained — everything lives under this folder; no ../ escapes, no docs/ links.
• Fail closed to a fallback — on any source error, emit {"error","fallback"} and exit non-zero rather than raising, so callers degrade cleanly.