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ef16689 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 | # Contributing to Biomni
Thank you for your interest in contributing to Biomni! We're building the infrastructure layer for biomedical AI agents, and we welcome contributions from the community. Contributors with significant contributions will be invited to co-author publications in top-tier journals and conferences.
## Getting Started
Before contributing, please ensure you:
- Have tested your changes locally
- Follow the existing code style and conventions
- Include appropriate documentation
## Types of Contributions
### 🛠️ Adding a New Tool
Tools are implemented as Python functions in `biomni/tool/XXX.py`, organized by subject area.
**Steps:**
1. **Implement and test** your function locally. If it requires additional software, create installation script and append it into `biomni_env/new_software_{VERSION}.sh`
2. **Choose the appropriate subject** category (e.g. database, biochemistry, etc.)
3. **Create a tool description** in `biomni/tool/tool_description/XXX.py` following the existing format
*Tip: Use this helper to auto-generate descriptions:*
```python
from biomni.utils import function_to_api_schema
from biomni.llm import get_llm
llm = get_llm('claude-sonnet-4-20250514')
desc = function_to_api_schema(function_code, llm)
```
4. **Create a test prompt** that uses your tool and verify the agent works correctly
5. **Submit a pull request** for review, don't forget to include your test prompt as well
### 📊 Adding New Data
If the data source has web API, follow this process:
**Steps:**
1. **Verify uniqueness** - ensure no overlap with existing data
2. **Add a new query_XX function** to `biomni/tool/database.py`, follow the format from the other functions.
3. **Create a tool description** in `biomni/tool/tool_description/database.py` following the existing format
If the data source has no API access, follow the process below:
**Steps:**
1. **Verify uniqueness** - ensure no overlap with existing data
2. **Prepare download link** with verified redistribution rights
3. **Add entry** to `data_lake_dict` in `biomni/env_desc.py`
4. **Submit a pull request** with the download link
Then, make a PR.
### 💻 Adding New Software
**Steps:**
1. **Test locally** to ensure no conflicts with existing environments
2. **Create installation script** and append it into `biomni_env/new_software_{VERSION}.sh`
3. **Add entry** to `library_content_dict` in `biomni/env_desc.py`
4. **Submit a pull request** including:
- Installation bash script
- Screenshot demonstrating no environment conflicts
### 🎯 Adding a New Benchmark
Create benchmarks in the `biomni/task/` folder.
**Required implementation:**
```python
class YourBenchmark:
def __init__(self):
# Initialize benchmark
pass
def __len__(self):
# Return dataset size
pass
def get_example(self, index):
# Return dataset item at index
pass
def evaluate(self):
# Evaluation logic (flexible input format)
pass
def output_class(self):
# Return expected agent output format
pass
```
**Steps:**
1. **Create benchmark file** in `biomni/task/[benchmark_name].py`
2. **Implement required methods** as shown above
3. **Provide data download link** for associated datasets
4. **Submit a pull request**
### 🐛 Bug Fixes & Enhancements
We welcome all bug fixes and enhancements to the existing codebase!
**Create an issue to discuss with the Biomni team first.**
**Guidelines:**
- Clearly describe the issue or enhancement
- Include tests when applicable
- Follow existing code patterns
- Update documentation if needed
## Submission Process
1. **Fork** the repository
2. **Create a feature branch** from `main`
3. **Make your changes** following the guidelines above
4. **Test thoroughly** in your local environment
5. **Submit a pull request** with a clear description
## Review Process
The Biomni team will review all pull requests promptly. We may request changes or provide feedback to ensure code quality and consistency.
## Questions?
If you have questions about contributing, please open an issue or reach out to the maintainers.
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*Together, let's build the future of biomedical AI agents!*
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