AlphaXiv

Hypatia bundles an alphaXiv client (@companion-ai/alpha-hub) for searching arXiv papers, reading AI-generated paper reports or full text, asking questions about a paper, and reading a paper’s linked code. alphaXiv covers arXiv papers; DOI-only papers are read through web fetch or Europe PMC instead.

Authentication

Sign in during hypatia setup or at any time:

hypatia alpha login

On a machine without a browser (SSH, Docker, WSL without a display), hypatia alpha login prints the sign-in URL. Open it in a browser on any machine and finish signing in. The browser then lands on a http://127.0.0.1:9876/callback?code=... page that fails to load; copy that full URL, paste it into the waiting terminal, and press Enter.

Check your authentication status:

hypatia alpha status

Agent tools

alpha_search, alpha_get_paper, alpha_ask_paper, and alpha_read_code are available only when you are signed in; without an account, Hypatia searches papers through Semantic Scholar, OpenAlex, and the other literature databases instead. Start a new Hypatia session after hypatia alpha login to get them.

Tool	Purpose
alpha_search	Search papers. Modes: semantic (default), keyword, agentic, both, all
alpha_get_paper	Fetch a paper’s AI-generated report, or raw full text with fullText, plus any local annotation. section or sections return only abstract, introduction, methodology, experiments, results, discussion, limitations, or conclusion when detectable
alpha_ask_paper	Ask a targeted question about a paper’s PDF
alpha_read_code	Read files from a paper’s GitHub repository; / gives an overview
alpha_annotate_paper	Write or clear a local note on a paper
alpha_list_annotations	List local paper notes

The lead agent calls these tools directly. The bundled evidence-scout does not load them; it runs hypatia alpha ... through its shell instead, after checking hypatia alpha status.

In chat, alpha_search shows a compact source, result-count, and recorded-duration summary. If alphaXiv falls back to OpenAlex, the summary names OpenAlex and shows the fallback reason. The both and all modes show separate group counts, which can overlap. alpha_get_paper shows a compact read summary and duration. Press Ctrl+O to expand the full result. hypatia_science_database_search uses the same compact display for the other literature sources, including source notes and errors.

CLI

The same client is available from the terminal:

hypatia alpha search "scaling laws"
hypatia alpha get 2401.12345
hypatia alpha ask 2401.12345 "What optimizer did they use?"
hypatia alpha code https://github.com/org/repo src/model.py

Storage

The alphaXiv client keeps its login state and local paper annotations under ~/.ahub, separate from Hypatia’s ~/.hypatia directory. Remove ~/.ahub to clear them during uninstall.

Without AlphaXiv

Hypatia works without an alphaXiv login. Paper discovery then goes through hypatia_science_database_search (Semantic Scholar, OpenAlex, arXiv ID lookup, PubMed, Europe PMC, bioRxiv/medRxiv, Crossref, CORE, DOAB) and web search, and full text comes from fetch_content on arXiv or open-access pages.