Claude Code plugin: self-contained layout, skill-based routing, ML demo readiness

.claude-plugin/marketplace.json

@@ -0,0 +1,20 @@
+{
+  "name": "tooluniverse",
+  "owner": {
+    "name": "MIMS Harvard",
+    "url": "https://github.com/mims-harvard"
+  },
+  "metadata": {
+    "description": "ToolUniverse marketplace — 1000+ scientific research tools and 114 specialized skills for biology, chemistry, medicine, and data science.",
+    "version": "1.1.11"
+  },
+  "plugins": [
+    {
+      "name": "tooluniverse",
+      "source": "./plugin",
+      "description": "1000+ scientific tools (PubMed, UniProt, PubChem, TCGA, FAERS, ClinicalTrials.gov, etc.) + 114 research skills + MCP server + research slash commands.",
+      "category": "science",
+      "strict": false
+    }
+  ]
+}

.gitattributes

@@ -0,0 +1,27 @@
+# Files to exclude when users run `git archive` (e.g., GitHub release tarballs).
+# These are kept in the repo for development but shouldn't ship with the plugin.
+
+# Benchmark data (third-party content)
+temp_docs_and_tests/ export-ignore
+
+# Benchmark outputs and harness (not part of the plugin itself)
+skills/evals/ export-ignore
+
+# Development-only dirs
+tests/ export-ignore
+src/tooluniverse/tools_generated/ export-ignore
+docs/ export-ignore
+
+# Session / memory
+memory/ export-ignore
+*_SUMMARY.md export-ignore
+*_REPORT.md export-ignore
+SESSION_*.md export-ignore
+
+# Build output (regenerated)
+dist/ export-ignore
+
+# Version control metadata
+.github/ export-ignore
+.gitattributes export-ignore
+.gitignore export-ignore

.github/workflows/release-plugin.yml

@@ -0,0 +1,100 @@
+name: Release Claude Code Plugin
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Tag name to build (e.g., v1.1.12)'
+        required: true
+
+permissions:
+  contents: write
+
+jobs:
+  build-plugin-zip:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.inputs.tag || github.ref }}
+
+      - name: Determine tag name
+        id: tag
+        run: |
+          TAG="${{ github.event.inputs.tag || github.ref_name }}"
+          echo "name=$TAG" >> $GITHUB_OUTPUT
+          echo "Building plugin zip for $TAG"
+
+      - name: Build plugin artifact
+        run: |
+          set -euo pipefail
+          TAG="${{ steps.tag.outputs.name }}"
+          BUILD_DIR="build/tooluniverse-plugin-${TAG}"
+          mkdir -p "$BUILD_DIR"
+
+          # Copy plugin directory, resolving symlinks (skills/ uses symlinks)
+          cp -rL plugin/. "$BUILD_DIR/"
+
+          # Include a copy of the root marketplace manifest for optional
+          # "unzip and add as local marketplace" install path.
+          mkdir -p "$BUILD_DIR/../marketplace"
+          cp -r .claude-plugin "$BUILD_DIR/../marketplace/"
+
+          # Rewrite the marketplace source path to the extracted plugin dir
+          TAG_NAME="$TAG" python3 - <<'PY'
+          import json, os, pathlib
+          tag = os.environ["TAG_NAME"]
+          m = pathlib.Path("build/marketplace/.claude-plugin/marketplace.json")
+          data = json.loads(m.read_text())
+          for p in data.get("plugins", []):
+              if p.get("name") == "tooluniverse":
+                  p["source"] = f"./tooluniverse-plugin-{tag}"
+          m.write_text(json.dumps(data, indent=2) + "\n")
+          PY
+
+          # Stage a top-level zip root that contains both
+          ZIP_ROOT="build/zip-root"
+          mkdir -p "$ZIP_ROOT"
+          mv "$BUILD_DIR" "$ZIP_ROOT/"
+          mv build/marketplace/.claude-plugin "$ZIP_ROOT/"
+
+          cd "$ZIP_ROOT"
+          zip -r "../../tooluniverse-plugin-${TAG}.zip" .
+          cd -
+
+          ls -la tooluniverse-plugin-${TAG}.zip
+          unzip -l tooluniverse-plugin-${TAG}.zip | head -30
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: tooluniverse-plugin-${{ steps.tag.outputs.name }}
+          path: tooluniverse-plugin-*.zip
+          if-no-files-found: error
+
+      - name: Attach to GitHub Release
+        if: startsWith(github.ref, 'refs/tags/')
+        uses: softprops/action-gh-release@v2
+        with:
+          files: tooluniverse-plugin-*.zip
+          fail_on_unmatched_files: true
+          body: |
+            ### ToolUniverse Claude Code Plugin ${{ steps.tag.outputs.name }}
+
+            Install from GitHub (recommended):
+            ```bash
+            claude plugin marketplace add mims-harvard/ToolUniverse#${{ steps.tag.outputs.name }}
+            claude plugin install tooluniverse@tooluniverse
+            ```
+
+            Or offline: download `tooluniverse-plugin-${{ steps.tag.outputs.name }}.zip`, unzip, then
+            ```bash
+            claude plugin marketplace add ./unzipped-directory
+            claude plugin install tooluniverse@tooluniverse
+            ```
+
+            Full install guide: `skills/tooluniverse-claude-code-plugin/SKILL.md`

.gitignore

@@ -174,3 +174,23 @@ DEVTU_*.md
 # Claude Code configuration
 .claude/
 .tooluniverse/
+
+# Benchmark outputs (large, machine-generated, no history value)
+skills/evals/bixbench/results_*.json
+skills/evals/lab-bench/results_*.json
+skills/evals/bixbench/retest_*.json
+skills/evals/*.log
+skills/evals/*/BENCHMARK_REPORT.md
+skills/evals/*/BIXBENCH_FULL_REPORT.md
+
+# Per-user auto-memory / private session notes (never push)
+memory/
+MEMORY.md
+CLAUDE.md
+
+# API keys & secrets
+.env
+.env.local
+credentials.json
+*_api_key*
+*_token*

plugin/.claude-plugin/marketplace.json

@@ -0,0 +1,18 @@
+{
+  "name": "tooluniverse-local",
+  "owner": {
+    "name": "MIMS Harvard"
+  },
+  "metadata": {
+    "description": "Local marketplace for the ToolUniverse plugin",
+    "version": "1.1.11"
+  },
+  "plugins": [
+    {
+      "name": "tooluniverse",
+      "description": "1000+ scientific research tools for biology, chemistry, medicine, and data science.",
+      "source": "./",
+      "strict": false
+    }
+  ]
+}

plugin/.claude-plugin/plugin.json

@@ -0,0 +1,11 @@
+{
+  "name": "tooluniverse",
+  "description": "1000+ scientific research tools for biology, chemistry, medicine, and data science. Access PubMed, UniProt, PubChem, TCGA, NHANES, GWAS Catalog, and hundreds more databases through a unified MCP interface. Includes 114 specialized research skills for genomics, drug discovery, clinical analysis, and more.",
+  "version": "1.1.11",
+  "author": {
+    "name": "MIMS Harvard"
+  },
+  "homepage": "https://aiscientist.tools",
+  "repository": "https://github.com/mims-harvard/ToolUniverse",
+  "license": "Apache-2.0"
+}

plugin/.mcp.json

@@ -0,0 +1,13 @@
+{
+  "mcpServers": {
+    "tooluniverse": {
+      "command": "uvx",
+      "args": ["--refresh", "tooluniverse"],
+      "env": {
+        "PYTHONIOENCODING": "utf-8",
+        "PYTORCH_MPS_HIGH_WATERMARK_RATIO": "0.0",
+        "PYTORCH_ENABLE_MPS_FALLBACK": "1"
+      }
+    }
+  }
+}

plugin/README.md

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+# ToolUniverse Plugin for Claude Code
+
+1000+ scientific research tools for biology, chemistry, medicine, and data science.
+
+## Install
+
+```bash
+# 1. Register the marketplace from GitHub
+claude plugin marketplace add mims-harvard/ToolUniverse
+
+# 2. Install the plugin
+claude plugin install tooluniverse@tooluniverse
+```
+
+Restart Claude Code. Done.
+
+**Full install guide** (troubleshooting, API keys, offline zip install, version pinning): see the [`tooluniverse-claude-code-plugin`](../skills/tooluniverse-claude-code-plugin/SKILL.md) skill.
+
+### Local development install
+
+```bash
+# From the repo root:
+claude plugin marketplace add ./
+claude plugin install tooluniverse@tooluniverse
+```
+
+## What's Included
+
+- **MCP Server**: Auto-configured via `.mcp.json`. Provides `find_tools`, `list_tools`, `get_tool_info`, `execute_tool` — accessing 1000+ scientific APIs.
+- **114 Research Skills**: Specialized workflows for genomics, drug discovery, clinical analysis, statistical modeling, data wrangling, and more.
+- **Slash Commands**: `/tooluniverse:find-tools`, `/tooluniverse:run-tool`
+- **Research Agent**: `/tooluniverse:researcher` — autonomous agent for complex multi-database research.
+
+## Usage
+
+```
+# Discover tools (MCP — good for exploration)
+/tooluniverse:find-tools protein structure prediction
+
+# Run a single tool via CLI (one-off Bash query)
+tu run UniProt_search '{"query": "BRCA1", "organism": "human"}'
+
+# Research a question (auto-plans tool calls, uses SDK for batches)
+/tooluniverse:research What are the top mutated genes in breast cancer?
+
+# Launch research agent for complex multi-database questions
+/tooluniverse:researcher What genes are associated with Alzheimer's disease?
+
+# Or just ask — the router skill auto-dispatches
+"What do we know about drug resistance mutations in EGFR?"
+```
+
+## Design Philosophy: CLI Default, SDK for Large Batches, MCP for Discovery
+
+- **CLI** (`tu run`): Default for most tool calls — simple, direct, output flows into conversation naturally
+- **Python SDK** (`from tooluniverse import ToolUniverse`): Use for large batches (5+ calls in a loop) — loads the registry once and avoids per-call startup overhead
+- **MCP tools** (`find_tools`, `get_tool_info`): Best for discovering which tools exist and checking parameters
+
+The plugin configures MCP for discovery and teaches the agent to use the CLI for most work, switching to the SDK only when looping over many items.
+
+## API Keys (Optional)
+
+Most tools work without API keys. For enhanced access:
+
+| Key | Source | Free? |
+|-----|--------|-------|
+| `NCBI_API_KEY` | https://www.ncbi.nlm.nih.gov/account/settings/ | Yes |
+| `SEMANTIC_SCHOLAR_API_KEY` | https://www.semanticscholar.org/product/api | Yes |
+| `ONCOKB_API_TOKEN` | https://www.oncokb.org/apiAccess | Academic |
+
+Set via environment variables or in the MCP server config.
+
+## Update
+
+The MCP server auto-updates via `uvx --refresh`. To update skills, re-install the plugin.
+
+## Links
+
+- [ToolUniverse Documentation](https://aiscientist.tools)
+- [GitHub Repository](https://github.com/mims-harvard/ToolUniverse)
+- [Tool Catalog](https://aiscientist.tools/tools)