tooluniverse 1.0.4__py3-none-any.whl → 1.0.5__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of tooluniverse might be problematic. Click here for more details.

Files changed (24) hide show
  1. tooluniverse/__init__.py +17 -5
  2. tooluniverse/agentic_tool.py +8 -2
  3. tooluniverse/data/agentic_tools.json +2 -2
  4. tooluniverse/data/odphp_tools.json +354 -0
  5. tooluniverse/default_config.py +1 -0
  6. tooluniverse/llm_clients.py +201 -0
  7. tooluniverse/mcp_tool_registry.py +3 -3
  8. tooluniverse/odphp_tool.py +226 -0
  9. tooluniverse/remote/boltz/boltz_mcp_server.py +2 -2
  10. tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +2 -2
  11. tooluniverse/smcp.py +204 -112
  12. tooluniverse/smcp_server.py +4 -7
  13. tooluniverse/test/test_claude_sdk.py +86 -0
  14. tooluniverse/test/test_odphp_tool.py +166 -0
  15. tooluniverse/test/test_openrouter_client.py +288 -0
  16. tooluniverse/test/test_stdio_hooks.py +1 -1
  17. tooluniverse/test/test_tool_finder.py +1 -1
  18. {tooluniverse-1.0.4.dist-info → tooluniverse-1.0.5.dist-info}/METADATA +100 -74
  19. {tooluniverse-1.0.4.dist-info → tooluniverse-1.0.5.dist-info}/RECORD +23 -18
  20. tooluniverse-1.0.5.dist-info/licenses/LICENSE +201 -0
  21. tooluniverse-1.0.4.dist-info/licenses/LICENSE +0 -21
  22. {tooluniverse-1.0.4.dist-info → tooluniverse-1.0.5.dist-info}/WHEEL +0 -0
  23. {tooluniverse-1.0.4.dist-info → tooluniverse-1.0.5.dist-info}/entry_points.txt +0 -0
  24. {tooluniverse-1.0.4.dist-info → tooluniverse-1.0.5.dist-info}/top_level.txt +0 -0
{tooluniverse-1.0.4.dist-info → tooluniverse-1.0.5.dist-info}/METADATA RENAMED
@@ -1,9 +1,9 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: tooluniverse
3
- Version: 1.0.4
3
+ Version: 1.0.5
4
4
  Summary: A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows.
5
5
  Author-email: Shanghua Gao <shanghuagao@gmail.com>
6
- Project-URL: Homepage, https://github.com/mims-harvard/TxAgent
6
+ Project-URL: Homepage, https://github.com/mims-harvard/ToolUniverse
7
7
  Requires-Python: >=3.10
8
8
  Description-Content-Type: text/markdown
9
9
  License-File: LICENSE
@@ -38,19 +38,28 @@ Requires-Dist: aiohttp
38
38
  Provides-Extra: dev
39
39
  Requires-Dist: pytest>=6.0; extra == "dev"
40
40
  Requires-Dist: pytest-cov>=2.0; extra == "dev"
41
+ Requires-Dist: pytest-timeout>=2.3.1; extra == "dev"
42
+ Requires-Dist: pytest-mock>=3.14.0; extra == "dev"
43
+ Requires-Dist: requests-mock>=1.12.1; extra == "dev"
41
44
  Requires-Dist: black>=22.0; extra == "dev"
42
45
  Requires-Dist: flake8>=4.0; extra == "dev"
43
46
  Requires-Dist: pre-commit>=2.0; extra == "dev"
44
47
  Provides-Extra: docs
45
48
  Requires-Dist: sphinx>=4.0; extra == "docs"
49
+ Requires-Dist: furo>=2024.8.6; extra == "docs"
46
50
  Requires-Dist: sphinx-rtd-theme>=1.0; extra == "docs"
47
51
  Requires-Dist: myst-parser>=0.18; extra == "docs"
52
+ Requires-Dist: linkify-it-py>=2.0.0; extra == "docs"
48
53
  Requires-Dist: sphinx-autobuild>=2021.3.14; extra == "docs"
49
54
  Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
50
55
  Requires-Dist: sphinx-tabs>=3.2.0; extra == "docs"
51
56
  Requires-Dist: sphinx-design>=0.3.0; extra == "docs"
52
57
  Requires-Dist: sphinx-notfound-page>=0.8; extra == "docs"
53
58
  Requires-Dist: sphinx-autodoc-typehints>=1.12.0; extra == "docs"
59
+ Provides-Extra: embedding
60
+ Requires-Dist: sentence-transformers>=5.1.0; extra == "embedding"
61
+ Requires-Dist: faiss-cpu>=1.12.0; extra == "embedding"
62
+ Requires-Dist: huggingface_hub>=0.34.0; extra == "embedding"
54
63
  Provides-Extra: graph
55
64
  Requires-Dist: flask>=2.0.0; extra == "graph"
56
65
  Requires-Dist: matplotlib>=3.5.0; extra == "graph"
@@ -66,11 +75,12 @@ Dynamic: license-file
66
75
 
67
76
  # <img src="docs/_static/logo.png" alt="ToolUniverse Logo" height="28" style="vertical-align: middle; margin-right: 8px;" /> ToolUniverse: Democratizing AI scientists
68
77
 
78
+ [![Paper](https://img.shields.io/badge/Paper-Arxiv-blue)](https://arxiv.org/abs/2509.23426)
69
79
  [![ToolUniverse-PIP](https://img.shields.io/badge/PyPI-ToolUniverse-blue)](https://pypi.org/project/tooluniverse/)
70
80
  [![ToolUniverse](https://img.shields.io/badge/Code-ToolUniverse-purple)](https://github.com/mims-harvard/ToolUniverse)
71
81
  [![Model context protocol (MCP)](https://img.shields.io/badge/Model_Context_Protocol_(MCP)_Supported-green)](README_USAGE.md#running-the-mcp-server)
72
- [![Documentation](https://img.shields.io/badge/Documentation-Available-green)](https://zitniklab.hms.harvard.edu/bioagent/)
73
- [![🌐Web Service](https://img.shields.io/badge/Web_Service-aiscientist.tools-blue)](https://aiscientist.tools)
82
+ [![Documentation](https://img.shields.io/badge/Documentation-Available-green)](https://zitniklab.hms.harvard.edu/ToolUniverse/)
83
+ [![🌐Web](https://img.shields.io/badge/Website-aiscientist.tools-blue)](https://aiscientist.tools)
74
84
  [![Slack](https://img.shields.io/badge/Slack-Join_Community-orange)](https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ)
75
85
 
76
86
 
@@ -84,27 +94,34 @@ ToolUniverse is an ecosystem for creating AI scientist systems from any open or
84
94
  [![Visit Website](https://img.shields.io/badge/Visit_Website-AIScientist.Tools-4285F4?style=for-the-badge&logo=google-chrome&logoColor=white)](https://aiscientist.tools)
85
95
 
86
96
  [![Join Slack Community](https://img.shields.io/badge/Join_Slack_Community-Get_Help_&_Connect-FF6B6B?style=for-the-badge&logo=slack&logoColor=white)](https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ)
87
- [![Join WeChat Group](https://img.shields.io/badge/Join_WeChat_Group-Community_&_Discussion-07C160?style=for-the-badge&logo=wechat&logoColor=white)](https://zitniklab.hms.harvard.edu/bioagent/wechat_community.html)
97
+ [![Join WeChat Group](https://img.shields.io/badge/Join_WeChat_Group-Community_&_Discussion-07C160?style=for-the-badge&logo=wechat&logoColor=white)](https://aiscientist.tools/wechat)
88
98
 
89
99
  [![Follow on LinkedIn](https://img.shields.io/badge/Follow_on_LinkedIn-Professional_Updates-0077B5?style=for-the-badge&logo=linkedin&logoColor=white)](https://www.linkedin.com/in/tooluniverse-at-harvard-b9aa88385/)
90
100
  [![Follow on X](https://img.shields.io/badge/Follow_on_X-Latest_Updates-000000?style=for-the-badge&logo=x&logoColor=white)](https://x.com/ScientistTools)
91
101
 
92
102
  </div>
103
+ <p align="center">
104
+ <img src="https://github.com/user-attachments/assets/13ddb54c-4fcc-4507-8695-1c58e7bc1e68" width="600" />
105
+ </p>
93
106
 
94
- → **Complete Tool List**: [Available Tools](https://zitniklab.hms.harvard.edu/bioagent/tools/tools_config_index.html)
107
+ → **Complete Tool List**: [Available Tools](https://zitniklab.hms.harvard.edu/ToolUniverse/tools/tools_config_index.html)
95
108
 
96
109
  → **Check our website for direct tool usage**: [AIScientist.Tools](https://aiscientist.tools/)
97
110
 
98
111
 
99
112
  ## 🤖 Building AI Scientists with ToolUniverse in 5 minutes
100
- - **[Overview](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/index.html)**: Create AI scientists from any LLM
101
- - **[Claude Desktop Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/claude_desktop.html)**: Native MCP integration with Claude Desktop App
102
- - **[Claude Code Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/claude_code.html)**: AI scientist development in Claude Code environment
103
- - **[Gemini CLI Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/gemini_cli.html)**: Command-line scientific research with Google Gemini
104
- - **[Qwen Code Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/qwen_code.html)**: AI scientist workflows in Qwen Code environment
105
- - **[GPT Codex CLI Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/codex_cli.html)**: Terminal-based research with OpenAI Codex
106
- - **[ChatGPT API Integration](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/chatgpt_api.html)**: Programmatic research with ChatGPT function calling
107
113
 
114
+ [![YouTube Video](https://img.youtube.com/vi/fManSJlSs60/maxresdefault.jpg)](https://www.youtube.com/watch?v=fManSJlSs60)
115
+ *Click the image above to watch the ToolUniverse demonstration*
116
+ [(Also in Bilibili)](https://www.bilibili.com/video/BV1GynhzjEos/?share_source=copy_web&vd_source=b398f13447281e748f5c41057a2c6858)
117
+
118
+ - **[Overview](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/index.html)**: Create AI scientists from any LLM
119
+ - **[Claude Desktop Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/claude_desktop.html)**: Native MCP integration with Claude Desktop App
120
+ - **[Claude Code Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/claude_code.html)**: AI scientist development in Claude Code environment
121
+ - **[Gemini CLI Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/gemini_cli.html)**: Command-line scientific research with Google Gemini
122
+ - **[Qwen Code Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/qwen_code.html)**: AI scientist workflows in Qwen Code environment
123
+ - **[GPT Codex CLI Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/codex_cli.html)**: Terminal-based research with OpenAI Codex
124
+ - **[ChatGPT API Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/chatgpt_api.html)**: Programmatic research with ChatGPT function calling
108
125
 
109
126
  ## 🔬 What is ToolUniverse?
110
127
 
@@ -114,18 +131,19 @@ ToolUniverse addresses this challenge by providing a standardized ecosystem that
114
131
 
115
132
  **Key Features:**
116
133
 
117
- - [**AI-Tool Interaction Protocol**](https://zitniklab.hms.harvard.edu/bioagent/guide/interaction_protocol.html): Standardized interface governing how AI scientists issue tool requests and receive results
118
- - [**Universal AI Model Support**](https://zitniklab.hms.harvard.edu/bioagent/guide/building_ai_scientists/index.html): Works with any LLM, AI agent, or large reasoning model (GPT5, Claude, Gemini, Qwen, Deepseek, open models)
119
- - [**Easy to Load & Find & Call Tool**](https://zitniklab.hms.harvard.edu/bioagent/guide/index.html) (*[WebService](https://aiscientist.tools/), [PythonAPI](https://zitniklab.hms.harvard.edu/bioagent/api/modules.html), [MCP](https://zitniklab.hms.harvard.edu/bioagent/guide/mcp_support.html)*): Maps natural-language descriptions to tool specifications and executes tools with structured results
120
- - [**Tool Composition & Scientific Workflows**](https://zitniklab.hms.harvard.edu/bioagent/guide/tool_composition.html): Chains tools for sequential or parallel execution in self-directed scientific workflows
121
- - [**Continuous Expansion**](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/index.html): New tools can be easily registered locally or remotely without additional configuration
122
- - [**Multi-Agent Tool Creation & Optimization**](https://zitniklab.hms.harvard.edu/bioagent/guide/scientific_workflows.html): Multi-agent powered tool construction and iterative tool optimization
123
-
134
+ - [**AI-Tool Interaction Protocol**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/interaction_protocol.html): Standardized interface governing how AI scientists issue tool requests and receive results
135
+ - [**Universal AI Model Support**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/building_ai_scientists/index.html): Works with any LLM, AI agent, or large reasoning model (GPT5, Claude, Gemini, Qwen, Deepseek, open models)
136
+ - [**OpenRouter Integration**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/openrouter_support.html): Access 100+ models from OpenAI, Anthropic, Google, Qwen, and more through a single API
137
+ - [**Easy to Load & Find & Call Tool**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/index.html) (*[WebService](https://aiscientist.tools/), [PythonAPI](https://zitniklab.hms.harvard.edu/ToolUniverse/api/modules.html), [MCP](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/mcp_support.html)*): Maps natural-language descriptions to tool specifications and executes tools with structured results
138
+ - [**Tool Composition & Scientific Workflows**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tool_composition.html): Chains tools for sequential or parallel execution in self-directed scientific workflows
139
+ - [**Continuous Expansion**](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/index.html): New tools can be easily registered locally or remotely without additional configuration
140
+ - [**Multi-Agent Tool Creation & Optimization**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/scientific_workflows.html): Multi-agent powered tool construction and iterative tool optimization
124
141
 
142
+ <p align="center">
143
+ <img src="https://github.com/user-attachments/assets/eb15bd7c-4e73-464b-8d65-733877c96a51" width="888" />
144
+ </p>
125
145
 
126
146
 
127
- <!-- ![TxAgent](img/TxAgent_ToolUniverse.jpg) -->
128
-
129
147
  ## 🚀 Quick Start
130
148
 
131
149
  ```python
@@ -143,17 +161,17 @@ tu.load_tools() # Load 600+ scientific tools
143
161
  # 3. Use Find Tool operation to discover relevant tools
144
162
  tools = tu.run({
145
163
  "name": "Tool_Finder_Keyword",
146
- "arguments": {"query": "disease target associations"}
164
+ "arguments": {"description": "disease target associations", "limit": 10}
147
165
  })
148
166
 
149
167
  # 4. Use Call Tool operation to execute selected tool
150
168
  result = tu.run({
151
169
  "name": "OpenTargets_get_associated_targets_by_disease_efoId",
152
- "arguments": {"efoId": "EFO_0000249"}
170
+ "arguments": {"efoId": "EFO_0000537"} # hypertension
153
171
  })
154
172
  ```
155
173
 
156
- → **Complete Quick Start Tutorial**: [Quick Start Tutorial](https://zitniklab.hms.harvard.edu/bioagent/quickstart.html) [Getting Started Tutorial](https://zitniklab.hms.harvard.edu/bioagent/getting_started.html)
174
+ → **Complete Quick Start Tutorial**: [Quick Start Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/quickstart.html) [Getting Started Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/getting_started.html)
157
175
 
158
176
 
159
177
  ## 📦 Installation
@@ -164,7 +182,7 @@ result = tu.run({
164
182
  uv pip install tooluniverse
165
183
  ```
166
184
 
167
- → **Complete Installation Tutorial**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/bioagent/installation.html)
185
+ → **Complete Installation Tutorial**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/installation.html)
168
186
 
169
187
  ## 🔧 Usage & Integration
170
188
 
@@ -182,17 +200,18 @@ tu.load_tools()
182
200
  # Find relevant tools
183
201
  tools = tu.run({
184
202
  "name": "Tool_Finder_Keyword", # Tool_Finder (Embedding model, GPU required), Tool_Finder_LLM (LLM-based model)
185
- "arguments": {"query": "protein structure prediction"}
203
+ "arguments": {"description": "protein structure prediction", "limit": 10}
186
204
  })
187
205
 
188
206
  # Execute tools
189
207
  result = tu.run({
190
- "name": "UniProt_get_protein_info",
191
- "arguments": {"gene_symbol": "BRCA1"}
208
+ "name": "UniProt_get_function_by_accession",
209
+ "arguments": {"accession": "P05067"}
192
210
  })
211
+
193
212
  ```
194
213
 
195
- → **Complete Tutorials**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/bioagent/installation.html)
214
+ → **Complete Tutorials**: [Installation Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/installation.html)
196
215
 
197
216
  ### MCP Support
198
217
 
@@ -200,7 +219,7 @@ result = tu.run({
200
219
  # run one command to launch the tooluniverse mcp server
201
220
  tooluniverse-smcp
202
221
  ```
203
- → **Complete Tutorial**: [MCP Support](https://zitniklab.hms.harvard.edu/bioagent/guide/mcp_support.html)
222
+ → **Complete Tutorial**: [MCP Support](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/mcp_support.html)
204
223
 
205
224
 
206
225
  ## 🚀 AI Scientists Projects Powered by ToolUniverse
@@ -213,9 +232,11 @@ tooluniverse-smcp
213
232
 
214
233
 
215
234
  ---
216
- **Hypercholesterolemia Drug Discovery** [[Tutorial]](https://zitniklab.hms.harvard.edu/bioagent/tutorials/tooluniverse_case_study.html) [[Code]](https://colab.research.google.com/drive/1UwJ6RwyUoqI5risKQ365EeFdDQWOeOCv?usp=sharing)
235
+ **Hypercholesterolemia Drug Discovery** [[Tutorial]](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/tooluniverse_case_study.html) [[Code]](https://colab.research.google.com/drive/1UwJ6RwyUoqI5risKQ365EeFdDQWOeOCv?usp=sharing)
236
+ <p align="center">
237
+ <img src="https://github.com/user-attachments/assets/cc53e9b0-94d3-407d-a015-71762ddb9836" width="600" />
238
+ </p>
217
239
 
218
- ---
219
240
 
220
241
 
221
242
  ## 🤝 Contribution and Community
@@ -228,7 +249,7 @@ Please join our [Slack Channel](https://join.slack.com/t/tooluniversehq/shared_i
228
249
  - **Report Issues**: [GitHub Issues](https://github.com/mims-harvard/ToolUniverse/issues)
229
250
  - **Join Discussions**: [Slack Channel](https://github.com/mims-harvard/ToolUniverse/discussions)
230
251
  - **Contact**: Reach out to [Shanghua Gao](shanghuagao@gmail.com)/[Marinka Zitnik](marinka@hms.harvard.edu)
231
- - **Contribute**: See our [Contributing Tutorial](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/comprehensive_tool_guide.html)
252
+ - **Contribute**: See our [Contributing Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/comprehensive_tool_guide.html)
232
253
 
233
254
 
234
255
 
@@ -236,10 +257,10 @@ Please join our [Slack Channel](https://join.slack.com/t/tooluniversehq/shared_i
236
257
 
237
258
  - **[Shanghua Gao](https://shgao.site)**
238
259
  - **[Richard Zhu](https://www.linkedin.com/in/richard-zhu-4236901a7/)**
239
- - **[Pengwei Sui](mailto:pengwei_sui@hms.harvard.edu)**
260
+ - **[Pengwei Sui](https://psui3905.github.io/)**
240
261
  - **[Zhenglun Kong](https://zlkong.github.io/homepage/)**
241
262
  - **[Sufian Aldogom](mailto:saldogom@mit.edu)**
242
- - **[Yepeng Huang](mailto:yepeng_huang@hms.harvard.edu)**
263
+ - **[Yepeng Huang](https://yepeng.notion.site/Yepeng-Huang-16ad8dd1740080c28d4bd3e3d7c1080c)**
243
264
  - **[Ayush Noori](https://www.ayushnoori.com/)**
244
265
  - **[Reza Shamji](mailto:reza_shamji@hms.harvard.edu)**
245
266
  - **[Krishna Parvataneni](mailto:krishna_parvataneni@hms.harvard.edu)**
@@ -253,53 +274,63 @@ Please join our [Slack Channel](https://join.slack.com/t/tooluniversehq/shared_i
253
274
  Our comprehensive documentation covers everything from quick start to advanced workflows:
254
275
 
255
276
  ### 🚀 Getting Started
256
- - **[Quick Start Tutorial](https://zitniklab.hms.harvard.edu/bioagent/quickstart.html)**: 5-minute setup and first query
257
- - **[Installation](https://zitniklab.hms.harvard.edu/bioagent/installation.html)**: Complete installation options
258
- - **[Getting Started](https://zitniklab.hms.harvard.edu/bioagent/getting_started.html)**: Step-by-step tutorial
259
- - **[AI-Tool Protocol](https://zitniklab.hms.harvard.edu/bioagent/guide/interaction_protocol.html)**: Understanding the interaction protocol
277
+ - **[Quick Start Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/quickstart.html)**: 5-minute setup and first query
278
+ - **[Installation](https://zitniklab.hms.harvard.edu/ToolUniverse/installation.html)**: Complete installation options
279
+ - **[Getting Started](https://zitniklab.hms.harvard.edu/ToolUniverse/getting_started.html)**: Step-by-step tutorial
280
+ - **[AI-Tool Protocol](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/interaction_protocol.html)**: Understanding the interaction protocol
260
281
 
261
282
  ### 📖 User Guides
262
- - **[Loading Tools](https://zitniklab.hms.harvard.edu/bioagent/guide/loading_tools.html)**: Complete Tutorial to loading tools
263
- - **[Tool Discovery](https://zitniklab.hms.harvard.edu/bioagent/tutorials/finding_tools.html)**: Find tools by keyword, LLM, and embedding search
264
- - **[Tool Caller](https://zitniklab.hms.harvard.edu/bioagent/guide/tool_caller.html)**: Primary execution engine
265
- - **[Tool Composition](https://zitniklab.hms.harvard.edu/bioagent/guide/tool_composition.html)**: Chain tools into workflows
266
- - **[Scientific Workflows](https://zitniklab.hms.harvard.edu/bioagent/guide/scientific_workflows.html)**: Real-world research scenarios
267
- - **[MCP Support](https://zitniklab.hms.harvard.edu/bioagent/guide/mcp_support.html)**: Model Context Protocol integration
268
- - **[Logging](https://zitniklab.hms.harvard.edu/bioagent/guide/logging.html)**: Comprehensive logging configuration
283
+ - **[Loading Tools](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/loading_tools.html)**: Complete Tutorial to loading tools
284
+ - **[Tool Discovery](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/finding_tools.html)**: Find tools by keyword, LLM, and embedding search
285
+ - **[Tool Caller](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tool_caller.html)**: Primary execution engine
286
+ - **[Tool Composition](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/tool_composition.html)**: Chain tools into workflows
287
+ - **[Scientific Workflows](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/scientific_workflows.html)**: Real-world research scenarios
288
+ - **[MCP Support](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/mcp_support.html)**: Model Context Protocol integration
289
+ - **[Logging](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/logging.html)**: Comprehensive logging configuration
269
290
 
270
291
  ### 🛠️ Advanced Features
271
- - **[Hooks System](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/index.html)**: Intelligent output processing
272
- - **[Hook Configuration](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/hook_configuration.html)**: Configure hooks for different outputs
273
- - **[File Save Hook](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/file_save_hook.html)**: Save tool outputs to files
274
- - **[Summarization Hook](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/summarization_hook.html)**: Summarize tool outputs
275
- - **[Server Stdio Hooks](https://zitniklab.hms.harvard.edu/bioagent/guide/hooks/server_stdio_hooks.html)**: Server communication hooks
276
- - **[Expert Feedback](https://zitniklab.hms.harvard.edu/bioagent/tutorials/expert_feedback.html)**: Human-in-the-loop consultation
277
- - **[Agentic Tools](https://zitniklab.hms.harvard.edu/bioagent/tutorials/agentic_tools_tutorial.html)**: AI-powered tool development
278
- - **[Case Study](https://zitniklab.hms.harvard.edu/bioagent/tutorials/tooluniverse_case_study.html)**: End-to-end drug discovery workflow
279
- - **[Tool Optimization](https://zitniklab.hms.harvard.edu/bioagent/tutorials/optimization/Tool_Description_Optimizer_Tutorial.html)**: Optimize tool descriptions for better performance
292
+ - **[Hooks System](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/index.html)**: Intelligent output processing
293
+ - **[Hook Configuration](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/hook_configuration.html)**: Configure hooks for different outputs
294
+ - **[File Save Hook](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/file_save_hook.html)**: Save tool outputs to files
295
+ - **[Summarization Hook](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/summarization_hook.html)**: Summarize tool outputs
296
+ - **[Server Stdio Hooks](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/hooks/server_stdio_hooks.html)**: Server communication hooks
297
+ - **[Expert Feedback](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/expert_feedback.html)**: Human-in-the-loop consultation
298
+ - **[Agentic Tools](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/agentic_tools_tutorial.html)**: AI-powered tool development
299
+ - **[Case Study](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/tooluniverse_case_study.html)**: End-to-end drug discovery workflow
300
+ - **[Tool Optimization](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/optimization/Tool_Description_Optimizer_Tutorial.html)**: Optimize tool descriptions for better performance
280
301
 
281
302
  ### 🔧 Expanding ToolUniverse
282
- - **[Architecture](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/architecture.html)**: System architecture overview
283
- - **[Local Tool Registration](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/local_tool_registration.html)**: Create custom tools
284
- - **[Remote Tool Registration](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/remote_tool_registration.html)**: Integrate external services
285
- - **[Contributing Tools](https://zitniklab.hms.harvard.edu/bioagent/expand_tooluniverse/comprehensive_tool_guide.html)**: Complete contribution guide
286
- - **[Adding Tools Tutorial](https://zitniklab.hms.harvard.edu/bioagent/tutorials/addtools/Adding_Tools_Tutorial.html)**: Step-by-step tool addition guide
287
- - **[MCP Tool Registration](https://zitniklab.hms.harvard.edu/bioagent/tutorials/addtools/mcp_tool_registration_en.html)**: Register tools via MCP
303
+ - **[Architecture](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/architecture.html)**: System architecture overview
304
+ - **[Local Tool Registration](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/local_tool_registration.html)**: Create custom tools
305
+ - **[Remote Tool Registration](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/remote_tool_registration.html)**: Integrate external services
306
+ - **[Contributing Tools](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/comprehensive_tool_guide.html)**: Complete contribution guide
307
+ - **[Adding Tools Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/addtools/Adding_Tools_Tutorial.html)**: Step-by-step tool addition guide
308
+ - **[MCP Tool Registration](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/addtools/mcp_tool_registration_en.html)**: Register tools via MCP
288
309
 
289
310
  ### 📚 API Reference
290
- - **[API Directory](https://zitniklab.hms.harvard.edu/bioagent/api/modules.html)**: Complete module listing
291
- - **[Core Modules](https://zitniklab.hms.harvard.edu/bioagent/api/tooluniverse.html)**: Main ToolUniverse class and utilities
292
- - **[Tool Classes](https://zitniklab.hms.harvard.edu/bioagent/api/tooluniverse.base_tool.html)**: Base tool classes and implementations
293
- - **[Compose Scripts](https://zitniklab.hms.harvard.edu/bioagent/api/tooluniverse.compose_scripts.html)**: Tool composition utilities
294
- - **[MCP Integration](https://zitniklab.hms.harvard.edu/bioagent/api/tooluniverse.mcp_integration.html)**: Model Context Protocol support
311
+ - **[API Directory](https://zitniklab.hms.harvard.edu/ToolUniverse/api/modules.html)**: Complete module listing
312
+ - **[Core Modules](https://zitniklab.hms.harvard.edu/ToolUniverse/api/tooluniverse.html)**: Main ToolUniverse class and utilities
313
+ - **[Tool Classes](https://zitniklab.hms.harvard.edu/ToolUniverse/api/tooluniverse.base_tool.html)**: Base tool classes and implementations
314
+ - **[Compose Scripts](https://zitniklab.hms.harvard.edu/ToolUniverse/api/tooluniverse.compose_scripts.html)**: Tool composition utilities
315
+ - **[MCP Integration](https://zitniklab.hms.harvard.edu/ToolUniverse/api/tooluniverse.mcp_integration.html)**: Model Context Protocol support
295
316
 
296
- → **Browse All Documentation**: [ToolUniverse Documentation](https://zitniklab.hms.harvard.edu/bioagent/)
317
+ → **Browse All Documentation**: [ToolUniverse Documentation](https://zitniklab.hms.harvard.edu/ToolUniverse/)
297
318
 
298
319
 
299
320
  ### Citation
300
321
 
301
322
  ```
302
- @misc{gao2025txagent,
323
+ @article{gao2025democratizingaiscientistsusing,
324
+ title={Democratizing AI scientists using ToolUniverse},
325
+ author={Shanghua Gao and Richard Zhu and Pengwei Sui and Zhenglun Kong and Sufian Aldogom and Yepeng Huang and Ayush Noori and Reza Shamji and Krishna Parvataneni and Theodoros Tsiligkaridis and Marinka Zitnik},
326
+ year={2025},
327
+ eprint={2509.23426},
328
+ archivePrefix={arXiv},
329
+ primaryClass={cs.AI},
330
+ url={https://arxiv.org/abs/2509.23426},
331
+ }
332
+
333
+ @article{gao2025txagent,
303
334
  title={TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools},
304
335
  author={Shanghua Gao and Richard Zhu and Zhenglun Kong and Ayush Noori and Xiaorui Su and Curtis Ginder and Theodoros Tsiligkaridis and Marinka Zitnik},
305
336
  year={2025},
@@ -310,11 +341,6 @@ Our comprehensive documentation covers everything from quick start to advanced w
310
341
  }
311
342
  ```
312
343
 
313
-
314
- ### Acknowledgments
315
-
316
- ToolUniverse is developed by the [Zitnik Lab](https://zitniklab.hms.harvard.edu/) at Harvard Medical School in collaboration with MIT Lincoln Laboratory. We thank the scientific community for their valuable feedback and contributions.
317
-
318
344
  ---
319
345
 
320
346
  *Democratizing AI agents for science with ToolUniverse.*
{tooluniverse-1.0.4.dist-info → tooluniverse-1.0.5.dist-info}/RECORD RENAMED
@@ -1,6 +1,6 @@
1
- tooluniverse/__init__.py,sha256=DXdZsB6gSGAubWpPjZDJZGo_PeH8l3BeJ-NeKsuY5Co,13944
1
+ tooluniverse/__init__.py,sha256=cTSgL2DN923MpPxGYeoPri3bW5u4GtNbDhU0YNXsgZM,14420
2
2
  tooluniverse/admetai_tool.py,sha256=nEfq7dwvFqjDryKv3nivGoBSRap6LT7_m76iMu72Q6E,3009
3
- tooluniverse/agentic_tool.py,sha256=y8M_6LzTGxrpndLms_M9-ycC10Ppp0S3EphExl5RrBo,20645
3
+ tooluniverse/agentic_tool.py,sha256=9hfcoXDzhIK8T7lxzvLp5633S5hL12kcuvMJWLzxbi4,21028
4
4
  tooluniverse/alphafold_tool.py,sha256=NkKQttC0MfuetCTTcWTFEG2MdhyKwy3jb5TR4odiqAw,4658
5
5
  tooluniverse/base_tool.py,sha256=uA-wGrs1drEJJbIp24YfWWWWfNGeMqEQo1tI6r3csEg,5664
6
6
  tooluniverse/boltz_tool.py,sha256=Kfcymeu6FRRpWLw7dWhEON4PUBTsHuBiTAPJlYH5ZGs,7930
@@ -10,7 +10,7 @@ tooluniverse/ctg_tool.py,sha256=3nR_F-YGpxVmTa6u5xi-mrTmLSH7OBehP4EJo-CQS0Y,4605
10
10
  tooluniverse/custom_tool.py,sha256=w2LMMRT82byxSNYPBKmuEJ2lbKktDJt_iW0Ew24M5VY,2701
11
11
  tooluniverse/dailymed_tool.py,sha256=sxIs0xYwX0CVlkhHaPwvGV-Oo1OW2tvsWZypAWujt9k,3800
12
12
  tooluniverse/dataset_tool.py,sha256=cmcCz_SFs7V78EZDNLesnQ2Qe9fVz1jOLghrpwe8hM8,11371
13
- tooluniverse/default_config.py,sha256=OFQwgrO1SOHpbAErDvXxkfEsd1kAlxUPI9MO6EwqFvU,7287
13
+ tooluniverse/default_config.py,sha256=hANCqLH8bqMQTNqnI9SbwTPi6dbtu8luh4Qz0X_HphY,7355
14
14
  tooluniverse/efo_tool.py,sha256=J4tjPFlNa9KhmQTEToBZN-m8jMuF1IKf2yQb1dyTeXI,1394
15
15
  tooluniverse/embedding_database.py,sha256=ua-yIyv3dPq2GHdyZmiwZyaUlkKYyV3nslB4H9asvDo,24682
16
16
  tooluniverse/embedding_sync.py,sha256=Cq3g64MjNXXpiImrzPMNsCTvGZeEI9009OlHOD3EloI,14669
@@ -23,12 +23,13 @@ tooluniverse/graphql_tool.py,sha256=y7ztNyb9hn4OdSGKhLsHev_snkNgbAwJZL8ZGHm0LEk,
23
23
  tooluniverse/gwas_tool.py,sha256=hq4VhB93DhczZo0xRGjGS9AtdKWL0O_XQy3eoV_fi8E,12351
24
24
  tooluniverse/hpa_tool.py,sha256=siRA0usQ0Rggloy3VL1b56QlytabndXS8Xzc9H3uWs8,64998
25
25
  tooluniverse/humanbase_tool.py,sha256=xojNboYvFrW_LAzOzKaexp6tvyGSbUazpMfOvX5ETXY,15006
26
- tooluniverse/llm_clients.py,sha256=UPcK0H68ryEDdkuKgu17QNroIXmYa6eUu8XNfwHSmkM,14630
26
+ tooluniverse/llm_clients.py,sha256=iA0a_TS3KM4REd-BZP-dehv-OKsEXIX07foJebdrS5I,22093
27
27
  tooluniverse/logging_config.py,sha256=SWM8TCrv0RZJZbC8NNwy8h04V9BvqSVyzwJFcW43eFI,7212
28
28
  tooluniverse/mcp_client_tool.py,sha256=R2WWAbnjzCFEKfeddTvtZTSZqtnvKRayV2ha2xdV9EU,28741
29
29
  tooluniverse/mcp_integration.py,sha256=9VtFDFbcVIuKO_sd1gFrOd-R0r6uxlYRjdsOKiqV1zs,13912
30
- tooluniverse/mcp_tool_registry.py,sha256=IoeEaLN7RoA7UZ_rCw4S63LGGvmXci0YmKkdvPPzvPA,31812
30
+ tooluniverse/mcp_tool_registry.py,sha256=H9jCzhywtkgm7I4d-zj0eV9Xmt1ZUXubX0XiPGL5pUs,31795
31
31
  tooluniverse/medlineplus_tool.py,sha256=__D7W2Khl05WllMnoV4Owv3pyl5EXS1lzEJmAE7PbD0,13214
32
+ tooluniverse/odphp_tool.py,sha256=xOuXOoZC55cWfX-rYfPY6E5h6gCMd4yO1u_R1oBpoMk,8897
32
33
  tooluniverse/openalex_tool.py,sha256=cR6K4ycFTarXxkNM_Rm2ULNu3K4QJX0ukK-7YVZiLcg,8066
33
34
  tooluniverse/openfda_adv_tool.py,sha256=t5kffba0iNDVtFHYPtfLW8ql4dKLaWwdcFnE9cNmNWE,10168
34
35
  tooluniverse/openfda_tool.py,sha256=AetafmFr1IygGAL8p1-URsNahVdN52tN0FvToTlkcMw,27425
@@ -41,8 +42,8 @@ tooluniverse/reactome_tool.py,sha256=ngmJXCcQfsu5d8XcX258ZHW4DIBi45sSjYNwUBk8nxo
41
42
  tooluniverse/remote_tool.py,sha256=ywb5xaJBqOT38_r5FBVoF3QFQDcLvfOH5AQrT-g7Fcs,3368
42
43
  tooluniverse/restful_tool.py,sha256=H7alq_vO3G4iVgZIZrrWh9vq2ForJN52Fl7_QOq7yaM,4409
43
44
  tooluniverse/semantic_scholar_tool.py,sha256=3gMHF-ReyNsP74oV7LzphhkhjYOX44F4JpnvIafaWPY,1970
44
- tooluniverse/smcp.py,sha256=D53npbXtNLN4snGpFyzU-jqyMVYt4MrpoA3DVNlStHo,99797
45
- tooluniverse/smcp_server.py,sha256=MfpamnRfn0P1YImIkmdIri7U_z4v2HOI0-NsBB3OySI,34598
45
+ tooluniverse/smcp.py,sha256=i2nvJqZLx4XkGkioG25VVgQOFgQJW_QK4OpbS_jC-QY,104959
46
+ tooluniverse/smcp_server.py,sha256=S-l8Z-wHrxTBrNZ3CdDfkV9Y0Y_BmD8UcF7NUQUX5uw,34316
46
47
  tooluniverse/tool_finder_embedding.py,sha256=O0WMCT6z7a_pDDew04QtpyPk_qzfGCX_647rsrBs0ug,11239
47
48
  tooluniverse/tool_finder_keyword.py,sha256=_Nt4-C1RranoywTk8vi6MePWPoNqFwOhafMDiTYl_SU,23480
48
49
  tooluniverse/tool_finder_llm.py,sha256=W63BDow6ioWQJgkpuhS3f0f4lb48uT_Jzc_bTqhBKE8,27361
@@ -67,7 +68,7 @@ tooluniverse/compose_scripts/tool_metadata_generator.py,sha256=JAcLhXnmsZMzRjNRF
67
68
  tooluniverse/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
68
69
  tooluniverse/data/admetai_tools.json,sha256=08LCNSCZJxL6ZuPF1mVfbdlh9f2X5tnEwIYU7RcLLSM,6497
69
70
  tooluniverse/data/adverse_event_tools.json,sha256=EDU_X8r4YtMnVt7SJpyimdo3FlcSNFSdvckWLShDODA,12752
70
- tooluniverse/data/agentic_tools.json,sha256=ABlMWxS06u-xqGHEDDEizUpprQ4MfDg1NXSKSWTo8x4,103299
71
+ tooluniverse/data/agentic_tools.json,sha256=uRaWGpxL7DyS5ufiP6tHrAATL-uIqVzZhDK4VXLu81Y,103250
71
72
  tooluniverse/data/alphafold_tools.json,sha256=--JO9z9fQM95t5dphrBoKKr28HKWg7iQOUm1hQYhEOk,10628
72
73
  tooluniverse/data/boltz_tools.json,sha256=_pMSRBkO3uj4vjYnQ7H6qbZFa4rzc9Looj6zHRyIkMg,303
73
74
  tooluniverse/data/chembl_tools.json,sha256=aQfFyFlUNz_y9ZTO3dNje4QGhqt7rLv6j5YdMJR2-x8,747
@@ -94,6 +95,7 @@ tooluniverse/data/mcp_client_tools_example.json,sha256=gnubP44yiaRp1LRHhREsa9t93
94
95
  tooluniverse/data/mcpautoloadertool_defaults.json,sha256=I1Z6Xnno6BRX7u9Ec4LlXlz-384GWpaBafPVHsqTr_c,998
95
96
  tooluniverse/data/medlineplus_tools.json,sha256=Jxy4Mqw6l6VYKfQ1sS54iR5SdDJFqVSryPHAgUWV5MQ,7236
96
97
  tooluniverse/data/monarch_tools.json,sha256=-uyhy-FlYBCmP0_biespZcuBHwcvOPmxX4gNYnTmgMU,3568
98
+ tooluniverse/data/odphp_tools.json,sha256=OYmtX7Ux4-9lwz7vbUkKG1g9nQXqAPHgPufdSuHavdM,14602
97
99
  tooluniverse/data/openalex_tools.json,sha256=6y-1rqRAwR8dzxT3E5sroTdzfl4OVJMxdLSPcIBb-vQ,1736
98
100
  tooluniverse/data/opentarget_tools.json,sha256=IZGLUbQWC--u_DSNoGGMtI9V9YFxucHB1ESqglJWCY8,67795
99
101
  tooluniverse/data/output_summarization_tools.json,sha256=9BxZAkzexsDp8jGMKUHW3LIRThZjleRjYRvk0y-bxEs,3944
@@ -125,7 +127,7 @@ tooluniverse/data/packages/scientific_computing_tools.json,sha256=YhGZIvllzmesF2
125
127
  tooluniverse/data/packages/single_cell_tools.json,sha256=HxHygdgtQM6kObnPdCqUTSwNI8Cux1LoOeYXuxxjjtw,36069
126
128
  tooluniverse/data/packages/structural_biology_tools.json,sha256=tQw78Ot6i9PWGUX3yVsZOgeOqZOhqTeh9mQVahZaUec,31755
127
129
  tooluniverse/data/packages/visualization_tools.json,sha256=yS-M_H3px6Ea-De-Km8v_gVMPa2Vdt6LmAPU-Zsai3c,25177
128
- tooluniverse/remote/boltz/boltz_mcp_server.py,sha256=oAqO8j52M4ntn1Ihdjclj6nJwHxRTbyxIF6efi_G_jU,2088
130
+ tooluniverse/remote/boltz/boltz_mcp_server.py,sha256=jvCd_6YSK_jJ11JXgG6IXU-UFWHL92DLJiN_Rpsxd0k,2088
129
131
  tooluniverse/remote/depmap_24q2/depmap_24q2_mcp_tool.py,sha256=6G_8MZuohXrt-jMmt8jVEsHHIPgL1IP5vcJHp4Coeb4,18994
130
132
  tooluniverse/remote/expert_feedback/human_expert_mcp_tools.py,sha256=WeXuIjus7bsWmvRwhCwX6tPrzu_1Sjj-Ml_xqWIKomA,72921
131
133
  tooluniverse/remote/expert_feedback/simple_test.py,sha256=rv_UN4oHH6BNmYVuPKRfPdIEjtdFvG0MXYoNOIHqXvg,535
@@ -134,7 +136,7 @@ tooluniverse/remote/expert_feedback/web_only_interface.py,sha256=47DEQpj8HBSa-_T
134
136
  tooluniverse/remote/immune_compass/compass_tool.py,sha256=jpxfMNDH7UWF4FiFzLB-JyfQYNUB8ZA6somvqkEtDH0,14423
135
137
  tooluniverse/remote/pinnacle/pinnacle_tool.py,sha256=Oprd2RyMCZF-NsMjkZMpPOB2apCfws7C3IWIn_U3JxQ,14632
136
138
  tooluniverse/remote/transcriptformer/transcriptformer_tool.py,sha256=ZU_TT340LBwjTuowTaQV6QcANcsjYimA4CVSJHdU0c0,25229
137
- tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py,sha256=gsfs-a3RZ7kwauO3uWNJjEOEi2ctHva3iRUtEYqjS6U,2352
139
+ tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py,sha256=Ve5x3VCKkuiFdphEm36frk-2xbo19ojrCTW9yK3iHxA,2352
138
140
  tooluniverse/remote/uspto_downloader/uspto_downloader_tool.py,sha256=hkDmSVh2-KEc56YhmgtwrgIwkYMFXR2fN1jrIL9vVlk,4460
139
141
  tooluniverse/scripts/filter_tool_files.py,sha256=IZZIeSmBfHKntno790er1hQHSDcrxfdIHZwZ-Lvq7I4,6415
140
142
  tooluniverse/scripts/generate_tool_graph.py,sha256=X_TpGcJ29CFH49Djzsz4gs8VvjDe0CcF6KFWU_hJHDI,12727
@@ -147,6 +149,7 @@ tooluniverse/test/test_agentic_tool_azure_models.py,sha256=2T3R_rm2jZ-tVe8b_3RI2
147
149
  tooluniverse/test/test_alphafold_tool.py,sha256=Hj-ITZqWO-U8OVNveVtmLVACiOAzwUYh1COwjcIaxrQ,3459
148
150
  tooluniverse/test/test_api_key_validation_min.py,sha256=esWQywax1fSLvinZ_LXbLVVqUxstqmlkIV0ZfAj7sPg,1976
149
151
  tooluniverse/test/test_chem_tool.py,sha256=N_ARBvouWyJMgWL1yMXSg1w407fBB-CZxJysFVRE6uY,1589
152
+ tooluniverse/test/test_claude_sdk.py,sha256=iHfmbxEns-_0RTzlLHfZEuIl45AAaVXr1KGnudnJ_Y4,2617
150
153
  tooluniverse/test/test_compose_lieraturereview.py,sha256=qNkgXHXJm7Ekiw9e0mcgtqs1z5c-MeE3qy0RoexF9Tg,1956
151
154
  tooluniverse/test/test_compose_tool.py,sha256=reRhUWhSuWwuorWF0jbDQHhIEd14UTq_GDSe0Wwl0v4,16607
152
155
  tooluniverse/test/test_dailymed.py,sha256=Dttqr6XNhFQaT34mg2TimQYaePN6aOn8BsOMj26Vm6w,2594
@@ -169,7 +172,9 @@ tooluniverse/test/test_list_built_in_tools.py,sha256=fLnCHCwoF1kWd28joMPwrYXi0b1
169
172
  tooluniverse/test/test_mcp_server.py,sha256=n3C3UuU9D-E6m6PbooWUgWwshLzncXDEmn0U9ugapaY,6631
170
173
  tooluniverse/test/test_mcp_tool.py,sha256=q6a9MCjFggK6KRy8F9h14tV2BezNVj63v6tDFaST-ys,8290
171
174
  tooluniverse/test/test_medlineplus.py,sha256=hQ2QyeHmF8BkCXMn9vW0SNImAcqd5jkZz_FhaZbZS7A,7332
175
+ tooluniverse/test/test_odphp_tool.py,sha256=sM_SnrC2sqVcgWUb44oRlrHVk9c9AX6F5Kb4c5wADqw,7178
172
176
  tooluniverse/test/test_openalex_tool.py,sha256=xZ2Mp54ci2nCs3eaA2OJVrbsShAytg5D-Wt2aEHw00o,862
177
+ tooluniverse/test/test_openrouter_client.py,sha256=15qifIjnxSndFujxVWWk6I9RJM5DsoPhAELfh-0OPR4,10743
173
178
  tooluniverse/test/test_opentargets.py,sha256=WlFQiif8rph4GT-LABU9NOlSOc5vRCIG0gyp3nVRmy0,862
174
179
  tooluniverse/test/test_pubchem_tool.py,sha256=gtYLmIlsFiWANallZwsftjnFdDeVpCSWglemjj6HVrI,4381
175
180
  tooluniverse/test/test_pubtator_tool.py,sha256=cs-Gl7HlOY9jowCMJVzj1IY9VHBoy2J-Yj08Vy_mxsg,1212
@@ -177,17 +182,17 @@ tooluniverse/test/test_rcsb_pdb_tool.py,sha256=bLI5zSWSZiyTmG_yyLf3mkroI6MZVnnp9
177
182
  tooluniverse/test/test_reactome.py,sha256=X3lV4z5sjYnpO3ntH6wc9DluKHgB6GL0z5j7YavFrtA,1784
178
183
  tooluniverse/test/test_semantic_scholar_tool.py,sha256=7ZQOIqivfIMc7yPCzGwWGrxNphvYHK_fZAlrdUAEzKE,705
179
184
  tooluniverse/test/test_software_tools.py,sha256=fJeS_9k-cysYzsic75QrQAC_bNxWRVk_vazoldNz0KA,5781
180
- tooluniverse/test/test_stdio_hooks.py,sha256=UDuZCOM7Rcz2hYQdCFwJDXgoth5qLMlHLMxp55pYNVQ,9187
185
+ tooluniverse/test/test_stdio_hooks.py,sha256=m6gdh6Vs9VsqKwagV7T8RZ8ioyy2BDEqsWXr_wzrUIM,9187
181
186
  tooluniverse/test/test_tool_description_optimizer.py,sha256=CuuxSYfb8kHjz9fHmJ8bGhpAIAmqIvUb6mYrt1H5F64,1320
182
- tooluniverse/test/test_tool_finder.py,sha256=6piRAEMR-9dKr2zaurRZd4dqZLpDMbach4jrq1fgP-c,741
187
+ tooluniverse/test/test_tool_finder.py,sha256=Lp2X2irIC--TsYMosxWGgqxy1vFJcUuGv0b5a3LlR8s,747
183
188
  tooluniverse/test/test_tool_finder_llm.py,sha256=nZTYavGePiNt5Z2smmNLhkO3dz-_P_RcUTv8J1vDzVs,8997
184
189
  tooluniverse/test/test_tools_find.py,sha256=vP9EV04iXXmejoY2rDhEM0Yc9uHEO2qEmd8s-YfvY4M,5797
185
190
  tooluniverse/test/test_uniprot_tools.py,sha256=V0x7aQjjlE-wS5alFWviHNwC3saHiEE5pMMqAcbokaw,2582
186
191
  tooluniverse/test/test_uspto_tool.py,sha256=y2VQBMbiHCTAmvXhBosHrc1innstUl9UMWNoPaBv-RY,2311
187
192
  tooluniverse/test/test_xml_tool.py,sha256=tx-w_psZ801C2kM6aDbBzR8QV3Vgu1p2zP6zExhjpVs,3602
188
- tooluniverse-1.0.4.dist-info/licenses/LICENSE,sha256=Unq9Y3buGL9J0vFop03FYZiVweytt1xdgLIh2n9ck2c,1115
189
- tooluniverse-1.0.4.dist-info/METADATA,sha256=724WaE2RW8W6CIVl-IM0-ud7iVvjQr66cqWWMm4R0Wg,18404
190
- tooluniverse-1.0.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
191
- tooluniverse-1.0.4.dist-info/entry_points.txt,sha256=Z_znqzUc_XR9ZIXViavqNAwBkwM4XYfC9h7LoBbAAog,600
192
- tooluniverse-1.0.4.dist-info/top_level.txt,sha256=zZ8YeCJ5FAkEwdd_mxsFtSCQMBDgBdxrrmHo3RNBiWs,13
193
- tooluniverse-1.0.4.dist-info/RECORD,,
193
+ tooluniverse-1.0.5.dist-info/licenses/LICENSE,sha256=0P0qDClpVzrnQUe3QAu7V-alszSBa-6hVHXyn9Xe60k,11351
194
+ tooluniverse-1.0.5.dist-info/METADATA,sha256=aa0FEMJExvBLUEf11_siI_L1YdmGk_ctqGMgk6NNxiA,20322
195
+ tooluniverse-1.0.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
196
+ tooluniverse-1.0.5.dist-info/entry_points.txt,sha256=Z_znqzUc_XR9ZIXViavqNAwBkwM4XYfC9h7LoBbAAog,600
197
+ tooluniverse-1.0.5.dist-info/top_level.txt,sha256=zZ8YeCJ5FAkEwdd_mxsFtSCQMBDgBdxrrmHo3RNBiWs,13
198
+ tooluniverse-1.0.5.dist-info/RECORD,,