Isabelle-MCP

MCP server that lets AI agents (Claude Code, Codex, …) drive the Isabelle theorem prover through its LSP/PIDE commands — fully autonomously, with no human in the loop.

Python ≥ 3.12 | v0.1.0 (MVP)

Purpose

This MCP server exists so that Claude / Codex can issue Isabelle LSP commands without any human mediation. The entire Isabelle process is encapsulated behind the MCP tools — it exposes no UI to the user. The agent works by editing .thy/.ML files on disk and calling the tools to evaluate them and query proof states; nobody watches or steers the prover interactively.

This server is not designed for human–AI collaboration (there is no jEdit/VSCode front-end in the picture). It implements a single AI ↔ Isabelle, no-human-in-the-loop model.

⚠️ One agent per server instance. This server holds a single Isabelle session with global mutable state — one set of open documents, one caret/perspective, and one evaluation in flight at a time. It is single-threaded and not concurrency-safe: pointing multiple agents at one instance, or interleaving concurrent requests, corrupts the evaluation/caret/ document state with catastrophic, hard-to-debug results. The server runs over stdio, so each agent already gets its own dedicated server process (and its own isabelle vscode_server) — just don't share one or drive it concurrently.

[!IMPORTANT] Patch Isabelle first — this server does not work on a stock Isabelle. It drives isabelle vscode_server through PIDE LSP requests (PIDE/output_at_position, PIDE/cancel_execution, …) that only exist after applying the my-better-isabelle-prover patches:

>

``bash pip install my-better-isabelle-prover # via pip or uv tool; needs Python ≥ 3.12 my-better-isabelle patch # apply patches + rebuild the Scala components my-better-isabelle status # verify: every patch reports "applied" ``

>

isabelle-mcp install checks this (when isabelle is reachable) and refuses to register the server against an unpatched Isabelle. The server re-checks at run time too: every isabelle_launch verifies the patches (via its bundled copy of the patch manager) and refuses to start an unpatched Isabelle — bypass with isabelle-mcp --skip-patch-check for hand-patched setups the patch manager cannot recognize. Compatibility notes (PEP 668, non-global Isabelle, …) are in AGENTS.md.

Quick Start

pip install isabelle-mcp      # or: uv tool install isabelle-mcp

# register into Claude Code / Codex (auto-detects whichever is installed):
isabelle-mcp install

For Claude Desktop, register manually instead (~/.config/claude/claude_desktop_config.json):

{
  "mcpServers": {
    "isabelle": {
      "command": "isabelle-mcp"
    }
  }
}

Tools

All positions are 1-indexed. File paths must be absolute.

PIDE tools (goal, command_output) are best-effort wrappers around async PIDE notifications and may time out.

Development

pip install -e ".[dev]"             # editable install from a checkout
pytest                              # unit tests
pytest -m integration               # requires running Isabelle
python -m mypy src/                 # type checking

Architecture

server.py         FastMCP entry point — tool registration, lifespan
lsp_client.py     JSON-RPC 2.0 client for isabelle vscode_server
tools/            Tool implementations (one file per tool)
utils/            Position conversion, URI handling, HTML parsing
models.py         Pydantic output models

License

See LICENSE.