PyPI - tooluniverse - Versions diffs - 0.1.0__tar.gz → 0.1.2__tar.gz - Mend

tooluniverse 0.1.0tar.gz → 0.1.2tar.gz

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tooluniverse-0.1.2/LICENSE ADDED Viewed

@@ -0,0 +1,21 @@
+MIT License
+Copyright (c) 2025 Artificial Intelligence for Medicine and Science @ Harvard
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

tooluniverse-0.1.2/PKG-INFO ADDED Viewed

@@ -0,0 +1,132 @@
+Metadata-Version: 2.2
+Name: tooluniverse
+Version: 0.1.2
+Summary: A collection of biomedical tools designed for use by Agentic AI.
+Home-page: https://github.com/mims-harvard/TxAgent
+Author: Shanghua Gao
+Author-email: shanghuagao@gmail.com
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: numpy
+Requires-Dist: graphql-core
+# ToolUniverse
+[![ProjectPage](https://img.shields.io/badge/Page-TxAgent-red)](https://zitniklab.hms.harvard.edu/TxAgent)
+[![PaperLink](https://img.shields.io/badge/PDF-TxAgent-red)]()
+[![TxAgent-PIP](https://img.shields.io/badge/Pip-TxAgent-blue)](https://pypi.org/project/txagent/)
+[![ToolUniverse-PIP](https://img.shields.io/badge/Pip-ToolUniverse-blue)](https://pypi.org/project/tooluniverse/)
+[![TxAgent](https://img.shields.io/badge/Code-TxAgent-purple)](https://github.com/mims-harvard/TxAgent)
+[![ToolUniverse](https://img.shields.io/badge/Code-ToolUniverse-purple)](https://github.com/mims-harvard/ToolUniverse)
+[![HuggingFace](https://img.shields.io/badge/HuggingFace-TxAgentT1-yellow)](https://huggingface.co/collections/mims-harvard/txagent-67c8e54a9d03a429bb0c622c)
+  <body>
+    <section class="hero">
+      <div class="hero-body">
+        <div class="container is-max-desktop">
+          <div class="columns is-centered">
+            <div class="column has-text-centered">
+              <h1 class="title is-1 publication-title">
+              </h1>
+              <div class="is-size-5 publication-authors">
+                <!-- Paper authors -->
+                <span class="author-block">
+                  <a href="https://shgao.site" target="_blank">Shanghua Gao</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a
+                    href="https://www.linkedin.com/in/richard-zhu-4236901a7/"
+                    target="_blank"
+                    >Richard Zhu</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://zlkong.github.io/homepage/" target="_blank"
+                    >Zhenglun Kong</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://www.ayushnoori.com/" target="_blank"
+                    >Ayush Noori</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a
+                    href="https://scholar.google.com/citations?hl=zh-CN&user=Awdn73MAAAAJ"
+                    target="_blank"
+                    >Xiaorui Su</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a
+                    href="https://www.linkedin.com/in/curtisginder/"
+                    target="_blank"
+                    >Curtis Ginder</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://sites.google.com/view/theo-t" target="_blank"
+                    >Theodoros Tsiligkaridis</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://zitniklab.hms.harvard.edu/" target="_blank"
+                    >Marinka Zitnik</a
+                  >
+              </div>
+ToolUniverse is a collection of biomedical tools designed for use by Agentic AI. It is a critical component of TxAgent, providing the agent with the ability to access and leverage a vast array of biomedical knowledge to solve complex therapeutic reasoning tasks. ToolUniverse includes 211 biomedical tools that address various aspects of drugs and diseases. These tools are linked to trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets and Monarch Initiative.
+![TxAgent](img/TxAgent_ToolUniverse.jpg)
+# Install
+### Install from source
+```
+python -m pip install . --no-cache-dir
+```
+### Install from Pypi
+Pip page (https://pypi.org/project/tooluniverse)
+```
+pip install tooluniverse
+```
+# Usage
+**Get all tools**
+```
+from tooluniverse import ToolUniverse
+tooluni = ToolUniverse()
+tooluni.load_tools()
+tool_name_list, tool_desc_list = tooluni.refresh_tool_name_desc()
+print(tool_name_list)
+print(tool_desc_list)
+```
+**Function call to a tool**
+```
+from tooluniverse import ToolUniverse
+tooluni = ToolUniverse()
+tooluni.load_tools()
+query = {"name": "get_indications_by_drug_name", "arguments": {"drug_name": "KISUNLA"}}
+tooluni.run(query)
+```
+## Citation
+```
+```
+## Contact
+If you have any questions or suggestions, please email [Shanghua Gao](mailto:shanghuagao@gmail.com) and [Marinka Zitnik](mailto:marinka@hms.harvard.edu).

tooluniverse-0.1.2/README.md ADDED Viewed

@@ -0,0 +1,118 @@
+# ToolUniverse
+[![ProjectPage](https://img.shields.io/badge/Page-TxAgent-red)](https://zitniklab.hms.harvard.edu/TxAgent)
+[![PaperLink](https://img.shields.io/badge/PDF-TxAgent-red)]()
+[![TxAgent-PIP](https://img.shields.io/badge/Pip-TxAgent-blue)](https://pypi.org/project/txagent/)
+[![ToolUniverse-PIP](https://img.shields.io/badge/Pip-ToolUniverse-blue)](https://pypi.org/project/tooluniverse/)
+[![TxAgent](https://img.shields.io/badge/Code-TxAgent-purple)](https://github.com/mims-harvard/TxAgent)
+[![ToolUniverse](https://img.shields.io/badge/Code-ToolUniverse-purple)](https://github.com/mims-harvard/ToolUniverse)
+[![HuggingFace](https://img.shields.io/badge/HuggingFace-TxAgentT1-yellow)](https://huggingface.co/collections/mims-harvard/txagent-67c8e54a9d03a429bb0c622c)
+  <body>
+    <section class="hero">
+      <div class="hero-body">
+        <div class="container is-max-desktop">
+          <div class="columns is-centered">
+            <div class="column has-text-centered">
+              <h1 class="title is-1 publication-title">
+              </h1>
+              <div class="is-size-5 publication-authors">
+                <!-- Paper authors -->
+                <span class="author-block">
+                  <a href="https://shgao.site" target="_blank">Shanghua Gao</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a
+                    href="https://www.linkedin.com/in/richard-zhu-4236901a7/"
+                    target="_blank"
+                    >Richard Zhu</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://zlkong.github.io/homepage/" target="_blank"
+                    >Zhenglun Kong</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://www.ayushnoori.com/" target="_blank"
+                    >Ayush Noori</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a
+                    href="https://scholar.google.com/citations?hl=zh-CN&user=Awdn73MAAAAJ"
+                    target="_blank"
+                    >Xiaorui Su</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a
+                    href="https://www.linkedin.com/in/curtisginder/"
+                    target="_blank"
+                    >Curtis Ginder</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://sites.google.com/view/theo-t" target="_blank"
+                    >Theodoros Tsiligkaridis</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://zitniklab.hms.harvard.edu/" target="_blank"
+                    >Marinka Zitnik</a
+                  >
+              </div>
+ToolUniverse is a collection of biomedical tools designed for use by Agentic AI. It is a critical component of TxAgent, providing the agent with the ability to access and leverage a vast array of biomedical knowledge to solve complex therapeutic reasoning tasks. ToolUniverse includes 211 biomedical tools that address various aspects of drugs and diseases. These tools are linked to trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets and Monarch Initiative.
+![TxAgent](img/TxAgent_ToolUniverse.jpg)
+# Install
+### Install from source
+```
+python -m pip install . --no-cache-dir
+```
+### Install from Pypi
+Pip page (https://pypi.org/project/tooluniverse)
+```
+pip install tooluniverse
+```
+# Usage
+**Get all tools**
+```
+from tooluniverse import ToolUniverse
+tooluni = ToolUniverse()
+tooluni.load_tools()
+tool_name_list, tool_desc_list = tooluni.refresh_tool_name_desc()
+print(tool_name_list)
+print(tool_desc_list)
+```
+**Function call to a tool**
+```
+from tooluniverse import ToolUniverse
+tooluni = ToolUniverse()
+tooluni.load_tools()
+query = {"name": "get_indications_by_drug_name", "arguments": {"drug_name": "KISUNLA"}}
+tooluni.run(query)
+```
+## Citation
+```
+```
+## Contact
+If you have any questions or suggestions, please email [Shanghua Gao](mailto:shanghuagao@gmail.com) and [Marinka Zitnik](mailto:marinka@hms.harvard.edu).

{tooluniverse-0.1.0 → tooluniverse-0.1.2}/setup.cfg RENAMED Viewed

@@ -1,6 +1,6 @@
 [metadata]
 name = tooluniverse
-version = 0.1.0
+version = 0.1.2
 description = A collection of biomedical tools designed for use by Agentic AI.
 author = Shanghua Gao
 author_email = shanghuagao@gmail.com
@@ -16,7 +16,7 @@ python_requires = >=3.6
 install_requires =
 	requests
 	numpy
-	graphql
+	graphql-core
 [options.packages.find]
 where = src

{tooluniverse-0.1.0 → tooluniverse-0.1.2}/src/tooluniverse/execute_function.py RENAMED Viewed

@@ -33,14 +33,19 @@ tool_type_mappings = {
 class ToolUniverse:
-    def __init__(self, tool_files=default_tool_files):
+    def __init__(self, tool_files=default_tool_files, keep_default_tools=True):
         # Initialize any necessary attributes here
         self.all_tools = []
         self.all_tool_dict = {}
         self.tool_category_dicts = {}
         if tool_files is None:
             tool_files = default_tool_files
+        elif keep_default_tools:
+            default_tool_files.update(tool_files)
+            tool_files = default_tool_files
         self.tool_files = tool_files
+        print("Tool files:")
+        print(tool_files)
         self.callable_functions = {}
     def load_tools(self, tool_type=None):
@@ -125,8 +130,10 @@ class ToolUniverse:
                 print(f"Tool name {each_name} not found in the loaded tools.")
         return picked_tool_list
-    def get_one_tool_by_one_name(self, tool_name):
+    def get_one_tool_by_one_name(self, tool_name, return_prompt=False):
             if tool_name in self.all_tool_dict:
+                if return_prompt:
+                    return self.prepare_one_tool_prompt(self.all_tool_dict[tool_name])
                 return self.all_tool_dict[tool_name]
             else:
                 print(f"Tool name {tool_name} not found in the loaded tools.")

tooluniverse-0.1.2/src/tooluniverse.egg-info/PKG-INFO ADDED Viewed

@@ -0,0 +1,132 @@
+Metadata-Version: 2.2
+Name: tooluniverse
+Version: 0.1.2
+Summary: A collection of biomedical tools designed for use by Agentic AI.
+Home-page: https://github.com/mims-harvard/TxAgent
+Author: Shanghua Gao
+Author-email: shanghuagao@gmail.com
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: numpy
+Requires-Dist: graphql-core
+# ToolUniverse
+[![ProjectPage](https://img.shields.io/badge/Page-TxAgent-red)](https://zitniklab.hms.harvard.edu/TxAgent)
+[![PaperLink](https://img.shields.io/badge/PDF-TxAgent-red)]()
+[![TxAgent-PIP](https://img.shields.io/badge/Pip-TxAgent-blue)](https://pypi.org/project/txagent/)
+[![ToolUniverse-PIP](https://img.shields.io/badge/Pip-ToolUniverse-blue)](https://pypi.org/project/tooluniverse/)
+[![TxAgent](https://img.shields.io/badge/Code-TxAgent-purple)](https://github.com/mims-harvard/TxAgent)
+[![ToolUniverse](https://img.shields.io/badge/Code-ToolUniverse-purple)](https://github.com/mims-harvard/ToolUniverse)
+[![HuggingFace](https://img.shields.io/badge/HuggingFace-TxAgentT1-yellow)](https://huggingface.co/collections/mims-harvard/txagent-67c8e54a9d03a429bb0c622c)
+  <body>
+    <section class="hero">
+      <div class="hero-body">
+        <div class="container is-max-desktop">
+          <div class="columns is-centered">
+            <div class="column has-text-centered">
+              <h1 class="title is-1 publication-title">
+              </h1>
+              <div class="is-size-5 publication-authors">
+                <!-- Paper authors -->
+                <span class="author-block">
+                  <a href="https://shgao.site" target="_blank">Shanghua Gao</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a
+                    href="https://www.linkedin.com/in/richard-zhu-4236901a7/"
+                    target="_blank"
+                    >Richard Zhu</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://zlkong.github.io/homepage/" target="_blank"
+                    >Zhenglun Kong</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://www.ayushnoori.com/" target="_blank"
+                    >Ayush Noori</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a
+                    href="https://scholar.google.com/citations?hl=zh-CN&user=Awdn73MAAAAJ"
+                    target="_blank"
+                    >Xiaorui Su</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a
+                    href="https://www.linkedin.com/in/curtisginder/"
+                    target="_blank"
+                    >Curtis Ginder</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://sites.google.com/view/theo-t" target="_blank"
+                    >Theodoros Tsiligkaridis</a
+                  >,</span
+                >
+                <span class="author-block">
+                  <a href="https://zitniklab.hms.harvard.edu/" target="_blank"
+                    >Marinka Zitnik</a
+                  >
+              </div>
+ToolUniverse is a collection of biomedical tools designed for use by Agentic AI. It is a critical component of TxAgent, providing the agent with the ability to access and leverage a vast array of biomedical knowledge to solve complex therapeutic reasoning tasks. ToolUniverse includes 211 biomedical tools that address various aspects of drugs and diseases. These tools are linked to trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets and Monarch Initiative.
+![TxAgent](img/TxAgent_ToolUniverse.jpg)
+# Install
+### Install from source
+```
+python -m pip install . --no-cache-dir
+```
+### Install from Pypi
+Pip page (https://pypi.org/project/tooluniverse)
+```
+pip install tooluniverse
+```
+# Usage
+**Get all tools**
+```
+from tooluniverse import ToolUniverse
+tooluni = ToolUniverse()
+tooluni.load_tools()
+tool_name_list, tool_desc_list = tooluni.refresh_tool_name_desc()
+print(tool_name_list)
+print(tool_desc_list)
+```
+**Function call to a tool**
+```
+from tooluniverse import ToolUniverse
+tooluni = ToolUniverse()
+tooluni.load_tools()
+query = {"name": "get_indications_by_drug_name", "arguments": {"drug_name": "KISUNLA"}}
+tooluni.run(query)
+```
+## Citation
+```
+```
+## Contact
+If you have any questions or suggestions, please email [Shanghua Gao](mailto:shanghuagao@gmail.com) and [Marinka Zitnik](mailto:marinka@hms.harvard.edu).

{tooluniverse-0.1.0 → tooluniverse-0.1.2}/src/tooluniverse.egg-info/SOURCES.txt RENAMED Viewed

@@ -1,3 +1,4 @@
+LICENSE
 README.md
 pyproject.toml
 setup.cfg

{tooluniverse-0.1.0 → tooluniverse-0.1.2}/src/tooluniverse.egg-info/requires.txt RENAMED Viewed

@@ -1,3 +1,3 @@
 requests
 numpy
-graphql
+graphql-core

tooluniverse-0.1.0/PKG-INFO DELETED Viewed

@@ -1,54 +0,0 @@
-Metadata-Version: 2.2
-Name: tooluniverse
-Version: 0.1.0
-Summary: A collection of biomedical tools designed for use by Agentic AI.
-Home-page: https://github.com/mims-harvard/TxAgent
-Author: Shanghua Gao
-Author-email: shanghuagao@gmail.com
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-Requires-Dist: requests
-Requires-Dist: numpy
-Requires-Dist: graphql
-# ToolUniverse
-ToolUniverse is a collection of biomedical tools designed for use by Agentic AI.
-# Install
-### Local install
-```
-python -m pip install . --no-cache-dir
-```
-### Install from PIP
-```
-pip install tooluniverse
-```
-### Usage
-Get all tools
-```
-from tooluniverse import ToolUniverse
-tooluni = ToolUniverse()
-tooluni.load_tools()
-tool_name_list, tool_desc_list = tooluni.refresh_tool_name_desc()
-print(tool_name_list)
-print(tool_desc_list)
-```
-Function call to a tool
-```
-from tooluniverse import ToolUniverse
-tooluni = ToolUniverse()
-tooluni.load_tools()
-tooluni.refresh_tool_name_desc()
-query = {"name": "get_indications_by_drug_name", "arguments": {"drug_name": "KISUNLA"}}
-tooluni.run(query)
-```

tooluniverse-0.1.0/README.md DELETED Viewed

@@ -1,41 +0,0 @@
-# ToolUniverse
-ToolUniverse is a collection of biomedical tools designed for use by Agentic AI.
-# Install
-### Local install
-```
-python -m pip install . --no-cache-dir
-```
-### Install from PIP
-```
-pip install tooluniverse
-```
-### Usage
-Get all tools
-```
-from tooluniverse import ToolUniverse
-tooluni = ToolUniverse()
-tooluni.load_tools()
-tool_name_list, tool_desc_list = tooluni.refresh_tool_name_desc()
-print(tool_name_list)
-print(tool_desc_list)
-```
-Function call to a tool
-```
-from tooluniverse import ToolUniverse
-tooluni = ToolUniverse()
-tooluni.load_tools()
-tooluni.refresh_tool_name_desc()
-query = {"name": "get_indications_by_drug_name", "arguments": {"drug_name": "KISUNLA"}}
-tooluni.run(query)
-```

tooluniverse-0.1.0/src/tooluniverse.egg-info/PKG-INFO DELETED Viewed

@@ -1,54 +0,0 @@
-Metadata-Version: 2.2
-Name: tooluniverse
-Version: 0.1.0
-Summary: A collection of biomedical tools designed for use by Agentic AI.
-Home-page: https://github.com/mims-harvard/TxAgent
-Author: Shanghua Gao
-Author-email: shanghuagao@gmail.com
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-Requires-Dist: requests
-Requires-Dist: numpy
-Requires-Dist: graphql
-# ToolUniverse
-ToolUniverse is a collection of biomedical tools designed for use by Agentic AI.
-# Install
-### Local install
-```
-python -m pip install . --no-cache-dir
-```
-### Install from PIP
-```
-pip install tooluniverse
-```
-### Usage
-Get all tools
-```
-from tooluniverse import ToolUniverse
-tooluni = ToolUniverse()
-tooluni.load_tools()
-tool_name_list, tool_desc_list = tooluni.refresh_tool_name_desc()
-print(tool_name_list)
-print(tool_desc_list)
-```
-Function call to a tool
-```
-from tooluniverse import ToolUniverse
-tooluni = ToolUniverse()
-tooluni.load_tools()
-tooluni.refresh_tool_name_desc()
-query = {"name": "get_indications_by_drug_name", "arguments": {"drug_name": "KISUNLA"}}
-tooluni.run(query)
-```