EvoScientist 0.0.1.dev3__py3-none-any.whl → 0.1.0rc1__py3-none-any.whl

EvoScientist/middleware.py

@@ -1,80 +1,27 @@
 """Middleware configuration for the EvoScientist agent."""
 
-from __future__ import annotations
-
-from pathlib import Path
-from typing import TYPE_CHECKING
-
 from deepagents.backends import FilesystemBackend
 from deepagents.middleware.skills import SkillsMiddleware
 
-from .backends import MergedReadOnlyBackend
-from .memory import EvoMemoryMiddleware
-from .paths import MEMORY_DIR as _DEFAULT_MEMORY_DIR
-
-if TYPE_CHECKING:
-    from langchain.chat_models import BaseChatModel
-
-_DEFAULT_SKILLS_DIR = str(Path(__file__).parent / "skills")
-
 
 def create_skills_middleware(
-    skills_dir: str = _DEFAULT_SKILLS_DIR,
-    workspace_dir: str = ".",
-    user_skills_dir: str | None = None,
+    skills_dir: str = "./skills/",
+    workspace_dir: str = "./workspace/",
 ) -> SkillsMiddleware:
     """Create a SkillsMiddleware that loads skills.
 
-    Merges user-installed skills (./skills/) with system skills
-    (package built-in). User skills take priority on name conflicts.
+    All skills (system and user-installed) live in ./skills/.
+    The --user flag in install_skill.py also installs to ./skills/.
 
     Args:
-        skills_dir: Path to the system skills directory (package built-in)
-        workspace_dir: Path to the project root (user skills live under {workspace_dir}/skills/)
-        user_skills_dir: Optional explicit path for user-installed skills. If set,
-            this path is used directly instead of {workspace_dir}/skills.
+        skills_dir: Path to the skills directory
+        workspace_dir: Unused, kept for API compatibility
 
     Returns:
         Configured SkillsMiddleware instance
     """
-    if user_skills_dir is None:
-        user_skills_dir = str(Path(workspace_dir) / "skills")
-    merged = MergedReadOnlyBackend(
-        primary_dir=user_skills_dir,
-        secondary_dir=skills_dir,
-    )
+    skills_backend = FilesystemBackend(root_dir=skills_dir, virtual_mode=True)
     return SkillsMiddleware(
-        backend=merged,
+        backend=skills_backend,
         sources=["/"],
     )
-
-
-def create_memory_middleware(
-    memory_dir: str = str(_DEFAULT_MEMORY_DIR),
-    extraction_model: BaseChatModel | None = None,
-    trigger: tuple[str, int] = ("messages", 20),
-) -> EvoMemoryMiddleware:
-    """Create an EvoMemoryMiddleware for long-term memory.
-
-    Uses a FilesystemBackend rooted at ``memory_dir`` so that memory
-    persists across threads and sessions.
-
-    Args:
-        memory_dir: Path to the shared memory directory (not per-session).
-        extraction_model: Chat model for auto-extraction (optional; if None,
-            only prompt-guided manual memory updates via edit_file will work).
-        trigger: When to auto-extract. Default: every 20 human messages.
-
-    Returns:
-        Configured EvoMemoryMiddleware instance.
-    """
-    memory_backend = FilesystemBackend(
-        root_dir=memory_dir,
-        virtual_mode=True,
-    )
-    return EvoMemoryMiddleware(
-        backend=memory_backend,
-        memory_path="/MEMORY.md",
-        extraction_model=extraction_model,
-        trigger=trigger,
-    )

EvoScientist/stream/__init__.py

@@ -6,9 +6,6 @@ Provides:
 - ToolCallTracker: Incremental JSON parsing for tool parameters
 - ToolResultFormatter: Content-aware result formatting with Rich
 - Utility functions and constants
-- SubAgentState / StreamState: Stream state tracking
-- stream_agent_events: Async event generator
-- Display functions: Rich rendering for streaming and final output
 """
 
 from .emitter import StreamEventEmitter, StreamEvent
@@ -28,15 +25,6 @@ from .utils import (
     truncate_with_line_hint,
     get_status_symbol,
 )
-from .state import SubAgentState, StreamState, _parse_todo_items, _build_todo_stats
-from .events import stream_agent_events
-from .display import (
-    console,
-    formatter,
-    format_tool_result_compact,
-    create_streaming_display,
-    display_final_results,
-)
 
 __all__ = [
     # Emitter
@@ -62,17 +50,4 @@ __all__ = [
     "count_lines",
     "truncate_with_line_hint",
     "get_status_symbol",
-    # State
-    "SubAgentState",
-    "StreamState",
-    "_parse_todo_items",
-    "_build_todo_stats",
-    # Events
-    "stream_agent_events",
-    # Display
-    "console",
-    "formatter",
-    "format_tool_result_compact",
-    "create_streaming_display",
-    "display_final_results",
 ]

EvoScientist/stream/utils.py

@@ -114,40 +114,34 @@ def format_tool_compact(name: str, args: dict | None) -> str:
     if name_lower == "execute":
         cmd = args.get("command", "")
         if len(cmd) > 50:
-            cmd = cmd[:47] + "\u2026"
+            cmd = cmd[:47] + "..."
         return f"execute({cmd})"
 
-    # File operations (with special case for memory files)
+    # File operations
     if name_lower == "read_file":
-        path = args.get("path", "")
-        if path.endswith("/MEMORY.md") or path == "/MEMORY.md":
-            return "Reading memory"
-        return f"read_file({_shorten_path(path)})"
+        path = _shorten_path(args.get("path", ""))
+        return f"read_file({path})"
 
     if name_lower == "write_file":
-        path = args.get("path", "")
-        if path.endswith("/MEMORY.md") or path == "/MEMORY.md":
-            return "Updating memory"
-        return f"write_file({_shorten_path(path)})"
+        path = _shorten_path(args.get("path", ""))
+        return f"write_file({path})"
 
     if name_lower == "edit_file":
-        path = args.get("path", "")
-        if path.endswith("/MEMORY.md") or path == "/MEMORY.md":
-            return "Updating memory"
-        return f"edit_file({_shorten_path(path)})"
+        path = _shorten_path(args.get("path", ""))
+        return f"edit_file({path})"
 
     # Search operations
     if name_lower == "glob":
         pattern = args.get("pattern", "")
         if len(pattern) > 40:
-            pattern = pattern[:37] + "\u2026"
+            pattern = pattern[:37] + "..."
         return f"glob({pattern})"
 
     if name_lower == "grep":
         pattern = args.get("pattern", "")
         path = args.get("path", ".")
         if len(pattern) > 30:
-            pattern = pattern[:27] + "\u2026"
+            pattern = pattern[:27] + "..."
         return f"grep({pattern}, {path})"
 
     # Directory listing
@@ -169,17 +163,16 @@ def format_tool_compact(name: str, args: dict | None) -> str:
     if name_lower == "task":
         sa_type = args.get("subagent_type", "").strip()
         task_desc = args.get("description", args.get("task", "")).strip()
-        task_desc = task_desc.split("\n")[0].strip() if task_desc else ""
         if sa_type:
             if task_desc:
                 if len(task_desc) > 50:
-                    task_desc = task_desc[:47] + "\u2026"
+                    task_desc = task_desc[:47] + "..."
                 return f"Cooking with {sa_type} — {task_desc}"
             return f"Cooking with {sa_type}"
         # Fallback if no subagent_type
         if task_desc:
             if len(task_desc) > 50:
-                task_desc = task_desc[:47] + "\u2026"
+                task_desc = task_desc[:47] + "..."
             return f"Cooking with sub-agent — {task_desc}"
         return "Cooking with sub-agent"
 
@@ -192,14 +185,14 @@ def format_tool_compact(name: str, args: dict | None) -> str:
     if name_lower in ("tavily_search", "internet_search"):
         query = args.get("query", "")
         if len(query) > 40:
-            query = query[:37] + "\u2026"
+            query = query[:37] + "..."
         return f"{name}({query})"
 
     # Think/reflection
     if name_lower == "think_tool":
         reflection = args.get("reflection", "")
         if len(reflection) > 40:
-            reflection = reflection[:37] + "\u2026"
+            reflection = reflection[:37] + "..."
         return f"think_tool({reflection})"
 
     # Default: show first few params
@@ -207,12 +200,12 @@ def format_tool_compact(name: str, args: dict | None) -> str:
     for k, v in list(args.items())[:2]:
         v_str = str(v)
         if len(v_str) > 20:
-            v_str = v_str[:17] + "\u2026"
+            v_str = v_str[:17] + "..."
         params.append(f"{k}={v_str}")
 
     params_str = ", ".join(params)
     if len(params_str) > 50:
-        params_str = params_str[:47] + "\u2026"
+        params_str = params_str[:47] + "..."
 
     return f"{name}({params_str})"
 

EvoScientist/tools.py

@@ -106,70 +106,6 @@ async def tavily_search(
         return f"Search failed: {str(e)}"
 
 
-@tool(parse_docstring=True)
-def skill_manager(
-    action: Literal["install", "list", "uninstall"],
-    source: str = "",
-    name: str = "",
-) -> str:
-    """Manage user skills: install, list, or uninstall.
-
-    Use this tool when the user asks to:
-    - Install a skill (action="install", source required)
-    - List installed skills (action="list")
-    - Uninstall a skill (action="uninstall", name required)
-
-    Supported sources for install:
-    - Local path: "./my-skill" or "/path/to/skill"
-    - GitHub URL: "https://github.com/owner/repo/tree/main/skill-name"
-    - GitHub shorthand: "owner/repo@skill-name"
-
-    Args:
-        action: One of "install", "list", or "uninstall"
-        source: For install - local path or GitHub URL/shorthand
-        name: For uninstall - skill name to remove
-
-    Returns:
-        Result message
-    """
-    from .skills_manager import install_skill, list_skills, uninstall_skill
-
-    if action == "install":
-        if not source:
-            return "Error: 'source' is required for install action"
-        result = install_skill(source)
-        if result["success"]:
-            return (
-                f"Successfully installed skill: {result['name']}\n"
-                f"Description: {result.get('description', '(none)')}\n"
-                f"Path: {result['path']}\n\n"
-                f"Use load_skill to activate it."
-            )
-        else:
-            return f"Failed to install skill: {result['error']}"
-
-    elif action == "list":
-        skills = list_skills(include_system=False)
-        if not skills:
-            return "No user skills installed. Use action='install' to add skills."
-        lines = [f"Installed User Skills ({len(skills)}):"]
-        for skill in skills:
-            lines.append(f"  - {skill.name}: {skill.description}")
-        return "\n".join(lines)
-
-    elif action == "uninstall":
-        if not name:
-            return "Error: 'name' is required for uninstall action"
-        result = uninstall_skill(name)
-        if result["success"]:
-            return f"Successfully uninstalled skill: {name}"
-        else:
-            return f"Failed to uninstall skill: {result['error']}"
-
-    else:
-        return f"Unknown action: {action}. Use 'install', 'list', or 'uninstall'."
-
-
 @tool(parse_docstring=True)
 def think_tool(reflection: str) -> str:
     """Tool for strategic reflection on research progress and decision-making.

evoscientist-0.1.0rc1.dist-info/METADATA

@@ -0,0 +1,199 @@
+Metadata-Version: 2.4
+Name: EvoScientist
+Version: 0.1.0rc1
+Summary: EvoScientist: Towards Self-Evolving AI Scientists for End-to-End Scientific Discovery
+Author: Xi Zhang
+Maintainer: Xi Zhang
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/EvoScientist/EvoScientist
+Project-URL: Bug Tracker, https://github.com/EvoScientist/EvoScientist/issues
+Project-URL: Documentation, https://github.com/EvoScientist/EvoScientist#readme
+Keywords: ai-scientific,scientific-discovery,self-evolving,ai-scientists,end-to-end
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: deepagents>=0.3.6
+Requires-Dist: langchain>=1.2
+Requires-Dist: langchain-anthropic>=1.3
+Requires-Dist: anthropic>=0.76
+Requires-Dist: tavily-python>=0.7
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rich>=14.0
+Requires-Dist: prompt-toolkit>=3.0
+Requires-Dist: python-dotenv>=1.0
+Requires-Dist: langgraph-cli[inmem]>=0.4
+Requires-Dist: httpx>=0.27
+Requires-Dist: markdownify>=0.14
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=5.0; extra == "dev"
+Dynamic: license-file
+
+<!-- Add logo here -->
+<h1 align="center">
+  <!-- <img src="./assets/CCD_icon_logo.png" alt="CCD Logo" height="27" style="position: relative; top: -2px;"/> -->
+  <strong>EvoScientist</strong>
+</h1>
+
+
+<div align="center">
+
+<a href="https://git.io/typing-svg"><img src="https://readme-typing-svg.demolab.com?font=Fira+Code&pause=1000&width=435&lines=Towards+Self-Evolving+AI+Scientists+for+End-to-End+Scientific+Discovery" alt="Typing SVG" /></a>
+
+[![Project Page](https://img.shields.io/badge/Project-Page-4285F4?style=for-the-badge&logo=googlelens&logoColor=4285F4)]()
+[![arXiv](https://img.shields.io/badge/arXiv-xxxx.xxxx-b31b1b?style=for-the-badge&logo=arxiv&logoColor=b31b1b)]()
+[![Gradio Demo](https://img.shields.io/badge/Gradio-Online_Demo-FFCC00?style=for-the-badge&logo=gradio&logoColor=yellow&labelColor=grey)]()
+[![Evaluation Split](https://img.shields.io/badge/HF-Test_Dataset-AECBFA?style=for-the-badge&logo=huggingface&logoColor=FFCC00&labelColor=grey)]()
+[![License](https://img.shields.io/badge/License-MIT-green?style=for-the-badge)]()
+
+</div>
+
+## 🔥 News
+> TODO
+- **[27 Sep 2025]** ⛳ Our preprint is now live on [arXiv] — check it out for details.
+
+
+## Overview
+> TODO
+
+
+## 📖 Contents
+- [⛏️ Installation](#️-installation)
+- [⚡ Quick Start](#-quick-start)
+  - [CLI Inference](#cli-inference)
+  - [Script Inference](#script-inference)
+  - [Web Interface](#web-interface)
+- [📊 Evaluation](#-evaluation)
+- [📝 Citation](#-citation)
+- [📚 Acknowledgments](#-acknowledgments)
+- [📦 Codebase Contributors](#-codebase-contributors)
+- [📜 License](#-license)
+
+## ⛏️ Installation
+
+> [!TIP]  
+> Use [`uv`](https://pypi.org/project/uv) for installation — it's faster and more reliable than `pip`.
+### For Development
+
+```Shell
+# Create and activate a conda environment
+conda create -n EvoSci python=3.11 -y
+conda activate EvoSci
+
+# Install in development (editable) mode
+pip install EvoScientist
+# or
+pip install -e .
+```
+
+### Option 1:
+Install the latest version directly from GitHub for quick setup:
+> TODO
+### Option 2: 
+If you plan to modify the code or contribute to the project, you can clone the repository and install it in editable mode:
+
+> TODO
+
+<details>
+<summary> 🔄 Upgrade to the latest code base </summary>
+
+```Shell
+git pull
+uv pip install -e .
+```
+
+</details>
+
+## ⚡ Quick Start
+
+### CLI Inference  
+You can perform inference directly from the command line using our CLI tool:
+
+![demo](./assets/EvoScientist_cli.png)
+
+```Shell
+python -m EvoScientist
+```
+**Optional arguments:**  
+
+> TODO
+
+### Script Inference
+```python
+from EvoScientist import agent
+from langchain_core.messages import HumanMessage
+from EvoScientist.utils import format_messages
+thread = {"configurable": {"thread_id": "1"}}
+question = "Hi?"
+last_len = 0
+
+for state in agent.stream(
+    {"messages": [HumanMessage(content=question)]},
+    config=thread,
+    stream_mode="values",
+):
+    msgs = state["messages"]
+    if len(msgs) > last_len:
+        format_messages(msgs[last_len:]) 
+        last_len = len(msgs)
+```
+
+
+### Web Interface  
+
+> TODO
+
+
+## 📊 Evaluation  
+
+> TODO
+
+## 📝 Citation
+
+If you find our paper and code useful in your research and applications, please cite using this BibTeX:
+
+> TODO
+
+## 📚 Acknowledgments
+
+This project builds upon the following outstanding open-source works:
+
+- [**Deep Agents**](https://github.com/langchain-ai/deepagents) — A framework for building AI agents that can interact with various tools and environments.
+- [**Deep Agents UI**](https://github.com/langchain-ai/deep-agents-ui) — A user interface for visualising and managing Deep Agents.
+
+We thank the authors for their valuable contributions to the open-source community.
+
+
+## 📦 Codebase Contributors
+
+<table>
+  <tbody>
+    <tr>
+      <td align="center">
+        <a href="https://youganglyu.github.io/">
+          <img src="https://youganglyu.github.io/images/profile.png"
+               width="100" height="100"
+               style="object-fit: cover; border-radius: 20%;" alt="Yougang Lyu"/>
+          <br />
+          <sub><b>Yougang Lyu</b></sub>
+        </a>
+      </td>
+      <td align="center">
+        <a href="https://x-izhang.github.io/">
+          <img src="https://x-izhang.github.io/author/xi-zhang/avatar_hu13660783057866068725.jpg"
+               width="100" height="100"
+               style="object-fit: cover; border-radius: 20%;" alt="Xi Zhang"/>
+          <br />
+          <sub><b>Xi Zhang</b></sub>
+        </a>
+      </td>
+    </tr>
+  </tbody>
+</table>
+
+For any enquiries or collaboration opportunities, please contact: [**youganglyu@gmail.com**](mailto:youganglyu@gmail.com)
+
+## 📜 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

evoscientist-0.1.0rc1.dist-info/RECORD

@@ -0,0 +1,21 @@
+EvoScientist/EvoScientist.py,sha256=9q0iSru5zrwXMvK1sUtExGF4YAkIq2HZiJINuMRBz7o,4601
+EvoScientist/__init__.py,sha256=yj4YJUPldtq4xx8geadIoZ1n-BmgsM2Z_S2W8ld9S1k,702
+EvoScientist/__main__.py,sha256=P5USQ_BiiY0TBhtajGMuX5AMXlQ5joz1kvljHeacqmA,91
+EvoScientist/backends.py,sha256=yKI5fofVd3sDxJp5BEaqPsXjIOrKrpge1KnFG-X7gzU,12321
+EvoScientist/cli.py,sha256=TsLj8Dgkr0gRgVSpnazx1qRvF4X-yw6qRSqqK7c94VE,49399
+EvoScientist/middleware.py,sha256=3ibUbv0jFyzRNcKBy7V2oZqIHQu-NSPWt1C3EHgj0lY,836
+EvoScientist/prompts.py,sha256=ni-qHoEoM703xtfD4J3IlvwAWPcW8gcNiCBVjRJoy3g,10692
+EvoScientist/subagent.yaml,sha256=yoFlMJWitLlYuOe4_44EPG6vjpNP_txHBlqr-kNX2GM,6130
+EvoScientist/tools.py,sha256=oYaJN8tl_NCw6PLFFNRZbjPB9-VriVcpVb6Zp-d_xVQ,4223
+EvoScientist/utils.py,sha256=GuWMRMkPHYgUOtoPZA0ErIt4FUBE4NMkz_OZluxYyRo,6801
+EvoScientist/stream/__init__.py,sha256=cO30Ujs7mVB1pZjI0AXgaggmPeV6jXgBjt6AKYH42kQ,1219
+EvoScientist/stream/emitter.py,sha256=zmdn8vIXNgkgoWRtanrMtPN2GlsHmZtdFmoqCry3o_o,2978
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+evoscientist-0.1.0rc1.dist-info/licenses/LICENSE,sha256=NsYFy5JSm90lmXcPNQuthVTCVaVcbT4XZ9h5HpAoGIo,1069
+evoscientist-0.1.0rc1.dist-info/METADATA,sha256=FHHeFCQVotPc5FG1Z-cmz1blHtf_gyFGxyxrG5rclCg,5936
+evoscientist-0.1.0rc1.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+evoscientist-0.1.0rc1.dist-info/entry_points.txt,sha256=AQTfRSD-9-fgD1ViOdbGcvhsNeaUNgvmNqLkNY7o7Zw,55
+evoscientist-0.1.0rc1.dist-info/top_level.txt,sha256=XBZouSd9lQfNn0Fus6jQb9nqdXzAbKyzh987Jt3A2-A,13
+evoscientist-0.1.0rc1.dist-info/RECORD,,

evoscientist-0.1.0rc1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+evoscientist = EvoScientist.cli:main