Package Stack — Hypatia Docs

Hypatia is built on stock Pi and uses curated Pi packages for its capabilities. Hypatia itself is a Pi package: its package.json pi manifest declares its extension, prompts, skills, theme, and subagent definitions. Hypatia launches Pi with PI_CODING_AGENT_DIR=~/.hypatia/agent and lists itself and its core packages in ~/.hypatia/agent/settings.json as local-path packages, so subagents load the same tools as the main session.

See Pi’s upstream docs for packages, extensions, and skills.

Core packages

These are npm dependencies of Hypatia, installed with it and loaded unmodified from its install directory.

Package	Purpose
`pi-subagents`	The `subagent` tool, `/subagents`, and `/run`; powers delegated and parallel research runs
`pi-web-access`	`web_search`, `source_check`, `fetch_content`, and `get_search_content` for web search and page, PDF, and GitHub retrieval
`pi-docparser`	`document_parse`, `document_search`, and `document_screenshot` for local PDFs, Office documents, spreadsheets, and images
`pi-btw`	`/btw` side conversations while the main research agent is busy
`@companion-ai/alpha-hub`	alphaXiv client library behind Hypatia’s `alpha_*` tools and `hypatia alpha`

They update when you upgrade Hypatia. You do not need to install them individually.

Bundled research extension

Hypatia’s own extension registers these tools and commands:

Group	Contents
AlphaXiv tools	`alpha_search`, `alpha_get_paper`, `alpha_ask_paper`, `alpha_read_code`, `alpha_annotate_paper`, `alpha_list_annotations`
Science database search	`hypatia_science_database_search` over Semantic Scholar, OpenAlex, arXiv IDs, PubMed, Europe PMC, bioRxiv/medRxiv, Crossref, CORE, and DOAB
Hugging Face Hub tools	`hf_dataset_info`, `hf_repo_files`, `hf_repo_read_file`
Commands	`/help`, `/init`, `/outputs`, `/model-routes`, `/tools`, `/service-tier`

Optional packages

Install on demand with hypatia packages install <preset>.

Package	Preset	Purpose
`@samfp/pi-memory`	`memory`	Preference and correction memory across sessions
`@luxusai/pi-hindsight`	`hindsight`	Hindsight-backed long-term memory. Requires a Hindsight server or Hindsight Cloud account

To search past Hypatia sessions without a package, search the session files directly:

rg -n "protein folding" ~/.hypatia/sessions

Installing and managing packages

List core packages and optional presets:

hypatia packages list

Install a specific optional preset:

hypatia packages install memory

Updating packages

Update the optional packages you installed, through Pi’s own pi update --extensions:

hypatia update

Update one package, by preset name or Pi package source:

hypatia update memory

Core packages are not touched by hypatia update because they ship with Hypatia; to update them, upgrade Hypatia itself (rerun the installer from the Installation guide, or npm install -g @tquang122/hypatia@latest).

Runtime versions

The package manifest targets Pi 1.1.0 and bundles pi-subagents 0.74.0, pi-web-access 0.35.0, pi-docparser 4.0.0, pi-btw 0.7.1, and Alpha Hub 0.1.6. Pi is declared through peer dependencies; the other packages are installed with Hypatia and loaded unmodified. Every release is checked by booting the installed CLI in Pi RPC mode on Linux, macOS, and Windows.