scitoolkit

A package manager and runtime for scientific AI tools. Lets researchers publish toolkits to the SciToolkit registry and use them in coding agents (Claude Code, Codex) or in scripts via the Model Context Protocol.

Each toolkit installs into its own isolated Python environment, so dependency conflicts between toolkits are never a problem.

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Quickstart

pip install scitoolkit

# Install a toolkit from the registry
stk install arxiv-search

# See what you have
stk list

# Serve installed toolkits over MCP stdio
stk serve

stk is a shorter alias for scitoolkit; both ship with the package and behave identically.

To use the served toolkits in Claude Code, add this to its MCP config:

{
  "mcpServers": {
    "scitoolkit": {
      "command": "scitoolkit",
      "args": ["serve"]
    }
  }
}

Claude Code will spawn its own scitoolkit serve subprocess and discover all installed toolkits' tools. To watch tool calls fire in real time, run stk logs in another terminal.

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Authoring a toolkit

stk init my-toolkit              # scaffold from template
# stk init my-toolkit --with-setup   # if your toolkit needs a setup.py
cd my-toolkit
# write your tools in tools/ ; write skills in skills/
stk validate                     # check structure
stk login                        # one-time, browser-flow auth (per-user)
stk publish                      # ship it

stk login (no toolkit name) does a browser-flow that gives you a per-user token good for any toolkit you own or collaborate on. Legacy per-toolkit tokens are still accepted (stk login my-toolkit) but deprecated.

For the agent-assisted authoring flow (recommended for first toolkits), see https://scitoolkit.org/docs/scaffold-with-an-agent.

For the full author guide — toolkit layout, tool conventions, skills, groups, expected_toolkits, configuration — see https://scitoolkit.org/docs/authoring and https://scitoolkit.org/docs/configuration.

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What's in scitoolkit 0.3.0

Commands:

• init, validate, login, whoami, logout, publish — author and ship toolkits.
• search, install, uninstall, list — manage installed toolkits.
• serve — run installed toolkits as an MCP stdio server. Supports positional toolkit names, --group, --enable-tool, --disable-tool, --dry-run, --call-timeout.
• setup <toolkit> — run a toolkit's setup.py (--reset, --check).
• config <show|edit|path|set|unset|validate> — manage per-toolkit config files at ~/.scitoolkit/config/<toolkit>.yaml.
• logs — tail the serve log with Rich coloring.
• groups — manage named tool subsets that span toolkits.

Features:

• Configuration system. Toolkits declare a config: block in toolkit.yaml (seven types: string, secret, path, integer, float, boolean, choice); users fill it at install time or by editing ~/.scitoolkit/config/<toolkit>.yaml. Toolkits with more involved setup ship a setup.py with full prompts, downloads (resumable, SHA256-verified, auto-extracting tar/zip with zip-slip defense), and derived-state writes via ctx.set_config(...).
• Per-user auth. scitoolkit login does a browser-flow that stores a per-user token good for any toolkit you own or collaborate on. Legacy per-toolkit tokens still work but are deprecated.
• Multi-tier execution: same-Python toolkits run in venv, different-Python toolkits run under conda (auto-detected). Docker mode coming in 3B.
• Per-tool selection: enable or disable individual tools per serve session or persistently in ~/.scitoolkit/serve.yaml.
• Skills surfacing: a toolkit's skills/*.md files are auto-mirrored to ~/.claude/skills/ so Claude Code discovers them. Symlinked on POSIX for live edits, copied on Windows.
• Agent-friendly flags: every state-modifying command supports --yes, --no, --no-input. Non-TTY stdin auto-applies non-interactive behavior.
• Versioning safeguards: publish blocks "version already exists" and "version decrease" with helpful suggestions before upload.
• Crash resilience: per-toolkit subprocess auto-restart with exponential backoff. A crashed toolkit doesn't take the orchestrator down.
• Python 3.12+ required.

See CHANGELOG.md for the full release history.

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Architecture

The package has three pieces:

• CLI (this package) — installed locally, manages toolkit environments and serves tools.
• Backend (api.scitoolkit.org) — registry, auth, tarball storage.
• Website (scitoolkit.org) — discover and manage published toolkits.

Each installed toolkit runs in its own subprocess in its own Python environment. The scitoolkit serve orchestrator aggregates them and exposes the union as a single MCP server upstream. Failures in one toolkit don't affect others.

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Contributing

Issues and PRs are welcome at https://github.com/adroman/scitoolkit.

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License

MIT. See LICENSE.

Links

• Website: https://scitoolkit.org
• Backend API: https://api.scitoolkit.org
• GitHub: https://github.com/adroman/scitoolkit
• Issues: https://github.com/adroman/scitoolkit/issues