autonomous-lab 0.5.1__tar.gz

autonomous_lab-0.5.1/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Development tool caches
+.mypy_cache/
+.pytest_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+
+# Virtual environments
+.venv*/
+venv*/
+
+
+
+# Logs
+*.log
+
+# macOS
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Windows
+Thumbs.db
+ehthumbs.db
+Desktop.ini
+
+# Linux
+*~
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# Others
+.cursor/rules/
+uv.lock
+.mcp_feedback_settings.json
+test_reports/
+
+# Temporary test files
+test_*.py
+
+# User configuration files
+ui_settings.json
+.config/
+
+# Backup files
+*.bak
+*.backup
+*.orig
+
+# Environment files
+.env
+.env.local
+.env.*.local
+
+# Rust/Tauri build artifacts
+src-tauri/target/
+src-tauri/Cargo.lock
+src-tauri/WixTools/
+src-tauri/gen/
+
+
+
+
+# Tauri bundle outputs
+src-tauri/target/bundle/
+src-tauri/target/release/bundle/
+
+# Node.js (if using Tauri with frontend framework)
+node_modules/
+package-lock.json
+yarn.lock
+
+# Temporary build files
+*.tmp
+*.temp

autonomous_lab-0.5.1/.python-version

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+3.11

autonomous_lab-0.5.1/LICENSE

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+
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+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
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+   6. Trademarks. This License does not grant permission to use the trade
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+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
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+      License. However, in accepting such obligations, You may act only
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+
+   END OF TERMS AND CONDITIONS
+
+   Copyright 2025-2026 Albert Ying
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

autonomous_lab-0.5.1/NOTICE

@@ -0,0 +1,10 @@
+Autonomous Lab
+Copyright 2025-2026 Albert Ying
+
+This project contains code originally derived from work by:
+
+  - Fábio Ferreira (2024), MIT License
+  - Minidoracat (2024), MIT License (modifications and enhancements)
+
+The original MIT-licensed code has been substantially modified,
+extended, and re-architected for the Autonomous Lab project.

autonomous_lab-0.5.1/PKG-INFO

@@ -0,0 +1,153 @@
+Metadata-Version: 2.4
+Name: autonomous-lab
+Version: 0.5.1
+Summary: MCP server that turns any Senior-Junior workflow into an autonomous loop with a human decision maker. Seamless integration with Cursor, Claude Code, Codex, and any MCP client.
+Project-URL: Homepage, https://autolab.kejunying.com
+Project-URL: Repository, https://github.com/albert-ying/autonomous-lab
+Project-URL: Issues, https://github.com/albert-ying/autonomous-lab/issues
+Author: Albert Ying
+License: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Keywords: agent,ai,autonomous,claude-code,cursor,mcp,skill-container,workflow
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Libraries
+Requires-Python: >=3.11
+Provides-Extra: biotools
+Requires-Dist: biomni; extra == 'biotools'
+Provides-Extra: dependencies
+Requires-Dist: aiohttp>=3.8.0; extra == 'dependencies'
+Requires-Dist: fastapi>=0.115.0; extra == 'dependencies'
+Requires-Dist: fastmcp>=2.0.0; extra == 'dependencies'
+Requires-Dist: jinja2>=3.1.0; extra == 'dependencies'
+Requires-Dist: mcp>=1.9.3; extra == 'dependencies'
+Requires-Dist: psutil>=7.0.0; extra == 'dependencies'
+Requires-Dist: pyyaml>=6.0; extra == 'dependencies'
+Requires-Dist: uvicorn>=0.30.0; extra == 'dependencies'
+Requires-Dist: websockets>=13.0.0; extra == 'dependencies'
+Description-Content-Type: text/markdown
+
+# Autonomous Lab
+
+MCP server that turns any senior-junior workflow into an autonomous loop. AI handles the execution. You make the decisions.
+
+The server runs inside your existing agentic coding tool (Cursor, Claude Code, Codex CLI, Windsurf, or any MCP client). Your SKILL.md files become character configurations. The loop runs for hours without stopping. You step in as editor when the work is ready for judgment.
+
+## Install
+
+```bash
+# From PyPI
+uv pip install autonomous-lab
+
+# With biomedical toolkit (optional)
+uv pip install autonomous-lab[biotools]
+```
+
+## Quick start
+
+Add to your MCP client config (e.g. Cursor `~/.cursor/mcp.json`):
+
+```json
+{
+  "mcpServers": {
+    "autonomous-lab": {
+      "command": "uvx",
+      "args": ["autonomous-lab"],
+      "timeout": 600,
+      "env": {
+        "MCP_WEB_PORT": "8766"
+      }
+    }
+  }
+}
+```
+
+Or if you installed via `uv pip install`:
+
+```json
+{
+  "mcpServers": {
+    "autonomous-lab": {
+      "command": "autonomous-lab",
+      "timeout": 600,
+      "env": {
+        "MCP_WEB_PORT": "8766"
+      }
+    }
+  }
+}
+```
+
+Then tell your agent: "Initialize an autonomous lab project on [your topic]."
+
+## What it does
+
+Two AI personas (senior + junior) iterate on your project in a loop. They design, execute, write, and revise. You sit above them as the decision maker: editor, code reviewer, creative director, or whatever the domain calls for.
+
+The loop:
+
+```
+autolab_next → (AI acts as role) → autolab_record → lab_meeting → autolab_next → ...
+```
+
+When work is ready, you review it. Accept, request revisions, or reject. The loop continues until you're satisfied.
+
+## Key capabilities
+
+- **Skill containers**: configure characters with any combination of SKILL.md files you already have. A PI with `scanpy + scientific-writing + statistical-analysis` skills behaves differently from a Tech Lead with `react + typescript + code-review` skills.
+- **24-hour sessions**: the loop runs indefinitely. No timeout, no context loss. Sessions persist across disconnects with `autolab_resume`.
+- **Fully configurable**: YAML character profiles control personality, expertise, goals, and available tools. Swap them in seconds.
+- **Domain-agnostic**: research, software, consulting, legal, medical, creative, or anything with a senior-junior structure.
+- **Expert consultation**: invite domain specialists mid-session for one-off advice without breaking the loop.
+- **Verified citations**: built-in CrossRef integration for real, validated references (no hallucinated papers).
+- **Game-style monitoring UI**: browser dashboard shows live progress, iteration history, and editorial controls.
+
+## MCP tools
+
+| Tool | What it does |
+|------|-------------|
+| `autolab_init` | Initialize a new project |
+| `autolab_resume` | Resume an interrupted session |
+| `autolab_next` | Get the next role prompt (PI or Trainee) |
+| `autolab_record` | Record a completed turn |
+| `autolab_status` | Check project state |
+| `autolab_cite` | Search, validate, and format citations |
+| `autolab_consult` | Invite a domain expert |
+| `autolab_editorial` | Wait for editor decision |
+| `autolab_editor_act` | Execute editorial decision (AI fallback) |
+| `autolab_create_character` | Build a character profile |
+| `lab_meeting` | Pause for user feedback between turns |
+
+## Character example
+
+```yaml
+name: Dr. Maria Chen
+role: pi
+title: Computational Biology PI
+expertise: single-cell genomics, machine learning
+goal: discover cell-type-specific regulatory programs
+skills:
+  - scanpy
+  - scvi-tools
+  - scientific-writing
+  - statistical-analysis
+personality:
+  - "Visionary: spots novel research directions"
+  - "Rigorous: demands statistical reproducibility"
+```
+
+## Requirements
+
+- Python >= 3.11
+- An MCP-compatible client (Cursor, Claude Code, Codex CLI, Windsurf, etc.)
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE) and [NOTICE](NOTICE).

autonomous_lab-0.5.1/README.md

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+# Autonomous Lab
+
+MCP server that turns any senior-junior workflow into an autonomous loop. AI handles the execution. You make the decisions.
+
+The server runs inside your existing agentic coding tool (Cursor, Claude Code, Codex CLI, Windsurf, or any MCP client). Your SKILL.md files become character configurations. The loop runs for hours without stopping. You step in as editor when the work is ready for judgment.
+
+## Install
+
+```bash
+# From PyPI
+uv pip install autonomous-lab
+
+# With biomedical toolkit (optional)
+uv pip install autonomous-lab[biotools]
+```
+
+## Quick start
+
+Add to your MCP client config (e.g. Cursor `~/.cursor/mcp.json`):
+
+```json
+{
+  "mcpServers": {
+    "autonomous-lab": {
+      "command": "uvx",
+      "args": ["autonomous-lab"],
+      "timeout": 600,
+      "env": {
+        "MCP_WEB_PORT": "8766"
+      }
+    }
+  }
+}
+```
+
+Or if you installed via `uv pip install`:
+
+```json
+{
+  "mcpServers": {
+    "autonomous-lab": {
+      "command": "autonomous-lab",
+      "timeout": 600,
+      "env": {
+        "MCP_WEB_PORT": "8766"
+      }
+    }
+  }
+}
+```
+
+Then tell your agent: "Initialize an autonomous lab project on [your topic]."
+
+## What it does
+
+Two AI personas (senior + junior) iterate on your project in a loop. They design, execute, write, and revise. You sit above them as the decision maker: editor, code reviewer, creative director, or whatever the domain calls for.
+
+The loop:
+
+```
+autolab_next → (AI acts as role) → autolab_record → lab_meeting → autolab_next → ...
+```
+
+When work is ready, you review it. Accept, request revisions, or reject. The loop continues until you're satisfied.
+
+## Key capabilities
+
+- **Skill containers**: configure characters with any combination of SKILL.md files you already have. A PI with `scanpy + scientific-writing + statistical-analysis` skills behaves differently from a Tech Lead with `react + typescript + code-review` skills.
+- **24-hour sessions**: the loop runs indefinitely. No timeout, no context loss. Sessions persist across disconnects with `autolab_resume`.
+- **Fully configurable**: YAML character profiles control personality, expertise, goals, and available tools. Swap them in seconds.
+- **Domain-agnostic**: research, software, consulting, legal, medical, creative, or anything with a senior-junior structure.
+- **Expert consultation**: invite domain specialists mid-session for one-off advice without breaking the loop.
+- **Verified citations**: built-in CrossRef integration for real, validated references (no hallucinated papers).
+- **Game-style monitoring UI**: browser dashboard shows live progress, iteration history, and editorial controls.
+
+## MCP tools
+
+| Tool | What it does |
+|------|-------------|
+| `autolab_init` | Initialize a new project |
+| `autolab_resume` | Resume an interrupted session |
+| `autolab_next` | Get the next role prompt (PI or Trainee) |
+| `autolab_record` | Record a completed turn |
+| `autolab_status` | Check project state |
+| `autolab_cite` | Search, validate, and format citations |
+| `autolab_consult` | Invite a domain expert |
+| `autolab_editorial` | Wait for editor decision |
+| `autolab_editor_act` | Execute editorial decision (AI fallback) |
+| `autolab_create_character` | Build a character profile |
+| `lab_meeting` | Pause for user feedback between turns |
+
+## Character example
+
+```yaml
+name: Dr. Maria Chen
+role: pi
+title: Computational Biology PI
+expertise: single-cell genomics, machine learning
+goal: discover cell-type-specific regulatory programs
+skills:
+  - scanpy
+  - scvi-tools
+  - scientific-writing
+  - statistical-analysis
+personality:
+  - "Visionary: spots novel research directions"
+  - "Rigorous: demands statistical reproducibility"
+```
+
+## Requirements
+
+- Python >= 3.11
+- An MCP-compatible client (Cursor, Claude Code, Codex CLI, Windsurf, etc.)
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE) and [NOTICE](NOTICE).