# 🌿 ivybloom CLI
> **Command-line interface for ivy biosciences' computational biology and drug discovery platform**
[](https://badge.fury.io/py/ivybloom)
[](https://www.python.org/downloads/)
[](https://opensource.org/licenses/MIT)
[](https://docs.ivybiosciences.com/cli)
Accelerate your computational biology research with powerful command-line tools for protein structure prediction, drug discovery, ADMET analysis, and workflow automation.
## 🚀 Quick Start
### Installation
```bash
pip install ivybloom
```
### Authentication
```bash
# Browser-based login (recommended)
ivybloom auth login --browser
```
### Your First Job
```bash
# Predict protein structure
ivybloom run esmfold protein_sequence=MKLLVLGLVGFGVGFGVGFGVGFGVGFGVGFG
# Monitor progress
ivybloom jobs list
```
## ✨ Key Features
### 🧬 **Computational Biology Tools**
- **Protein Structure Prediction**: ESMFold, AlphaFold integration
- **Drug Discovery**: REINVENT, fragment-based design
- **ADMET Analysis**: Comprehensive property prediction
- **Molecular Analysis**: Solubility, toxicity, bioavailability
### 🔗 **Advanced Workflows**
- **Job Chaining**: Link multiple analyses seamlessly
- **Parallel Execution**: Run multiple optimizations simultaneously
- **Parameter Passing**: Results flow between pipeline stages
- **YAML Workflows**: Define complex multi-step processes
### 🎨 **Beautiful Interface**
- **Earth-Tone Design**: Professional, biology-inspired color scheme
- **Rich Formatting**: Progress bars, tables, status indicators
- **Multiple Formats**: JSON, YAML, CSV, table output
- **Real-Time Monitoring**: Live job progress tracking
### 🔐 **Enterprise Authentication**
- **Browser OAuth**: "Click here to login" experience
- **Device Flow**: Perfect for headless environments
- **API Keys**: Traditional authentication for automation
- **Secure Storage**: System keyring integration
## 📊 Platform Integration
The IvyBloom CLI seamlessly integrates with your existing workflow:
- **Shared Database**: Jobs appear in both CLI and web interface
- **Project Access**: Full project management capabilities
- **Account Management**: Usage tracking and limits
- **Cross-Platform**: macOS, Linux, Windows support
## 🔬 Research Use Cases
### Drug Discovery Pipeline
```bash
ivybloom workflows run protein_to_drug_pipeline.yaml \
--input protein_sequence=MKLLVL... \
--project-id drug-discovery-project
```
### Fragment-Based Design
```bash
ivybloom workflows run fragment_based_discovery.yaml \
--input target_protein=structure.pdb \
--parallel
```
### High-Throughput Screening
```bash
ivybloom workflows run virtual_screening.yaml \
--input compound_library=compounds.sdf \
--batch-size 10000
```
## 📚 Documentation
- **[Complete Documentation](docs/cli/README.md)** - Full feature guide
- **[Authentication Guide](docs/cli/guides/authentication.md)** - Setup and security
- **[Workflow Examples](docs/cli/examples/)** - Real-world pipelines
- **[API Reference](https://docs.ivybiosciences.com/api)** - Backend integration
## 🛠 Development
### Local Installation
```bash
git clone https://github.com/ivybiosciences/ivybloom-cli.git
cd ivybloom-cli
pip install -e .
```
### Testing
```bash
pip install -e ".[dev]"
pytest tests/
```
## 🤝 Contributing
We welcome contributions! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
## 📄 License
This project is licensed under the MIT License - see [LICENSE](LICENSE) for details.
## 🆘 Support
- **Documentation**: [docs.ivybiosciences.com/cli](https://docs.ivybiosciences.com/cli)
- **Issues**: [GitHub Issues](https://github.com/ivybiosciences/ivybloom-cli/issues)
- **Email**: [support@ivybiosciences.com](mailto:support@ivybiosciences.com)
---
**🌿 Computational Biology & Drug Discovery at Your Fingertips**
*Built with ❤️ by [Ivy Biosciences](https://ivybiosciences.com)*
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"description": "# \ud83c\udf3f ivybloom CLI\n\n> **Command-line interface for ivy biosciences' computational biology and drug discovery platform**\n\n[](https://badge.fury.io/py/ivybloom)\n[](https://www.python.org/downloads/)\n[](https://opensource.org/licenses/MIT)\n[](https://docs.ivybiosciences.com/cli)\n\nAccelerate your computational biology research with powerful command-line tools for protein structure prediction, drug discovery, ADMET analysis, and workflow automation.\n\n## \ud83d\ude80 Quick Start\n\n### Installation\n```bash\npip install ivybloom\n```\n\n### Authentication\n```bash\n# Browser-based login (recommended)\nivybloom auth login --browser\n```\n\n### Your First Job\n```bash\n# Predict protein structure\nivybloom run esmfold protein_sequence=MKLLVLGLVGFGVGFGVGFGVGFGVGFGVGFG\n\n# Monitor progress\nivybloom jobs list\n```\n\n## \u2728 Key Features\n\n### \ud83e\uddec **Computational Biology Tools**\n- **Protein Structure Prediction**: ESMFold, AlphaFold integration\n- **Drug Discovery**: REINVENT, fragment-based design\n- **ADMET Analysis**: Comprehensive property prediction\n- **Molecular Analysis**: Solubility, toxicity, bioavailability\n\n### \ud83d\udd17 **Advanced Workflows**\n- **Job Chaining**: Link multiple analyses seamlessly\n- **Parallel Execution**: Run multiple optimizations simultaneously \n- **Parameter Passing**: Results flow between pipeline stages\n- **YAML Workflows**: Define complex multi-step processes\n\n### \ud83c\udfa8 **Beautiful Interface**\n- **Earth-Tone Design**: Professional, biology-inspired color scheme\n- **Rich Formatting**: Progress bars, tables, status indicators\n- **Multiple Formats**: JSON, YAML, CSV, table output\n- **Real-Time Monitoring**: Live job progress tracking\n\n### \ud83d\udd10 **Enterprise Authentication**\n- **Browser OAuth**: \"Click here to login\" experience\n- **Device Flow**: Perfect for headless environments\n- **API Keys**: Traditional authentication for automation\n- **Secure Storage**: System keyring integration\n\n## \ud83d\udcca Platform Integration\n\nThe IvyBloom CLI seamlessly integrates with your existing workflow:\n- **Shared Database**: Jobs appear in both CLI and web interface\n- **Project Access**: Full project management capabilities\n- **Account Management**: Usage tracking and limits\n- **Cross-Platform**: macOS, Linux, Windows support\n\n## \ud83d\udd2c Research Use Cases\n\n### Drug Discovery Pipeline\n```bash\nivybloom workflows run protein_to_drug_pipeline.yaml \\\n --input protein_sequence=MKLLVL... \\\n --project-id drug-discovery-project\n```\n\n### Fragment-Based Design\n```bash\nivybloom workflows run fragment_based_discovery.yaml \\\n --input target_protein=structure.pdb \\\n --parallel\n```\n\n### High-Throughput Screening\n```bash\nivybloom workflows run virtual_screening.yaml \\\n --input compound_library=compounds.sdf \\\n --batch-size 10000\n```\n\n## \ud83d\udcda Documentation\n\n- **[Complete Documentation](docs/cli/README.md)** - Full feature guide\n- **[Authentication Guide](docs/cli/guides/authentication.md)** - Setup and security\n- **[Workflow Examples](docs/cli/examples/)** - Real-world pipelines\n- **[API Reference](https://docs.ivybiosciences.com/api)** - Backend integration\n\n## \ud83d\udee0 Development\n\n### Local Installation\n```bash\ngit clone https://github.com/ivybiosciences/ivybloom-cli.git\ncd ivybloom-cli\npip install -e .\n```\n\n### Testing\n```bash\npip install -e \".[dev]\"\npytest tests/\n```\n\n## \ud83e\udd1d Contributing\n\nWe welcome contributions! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.\n\n## \ud83d\udcc4 License\n\nThis project is licensed under the MIT License - see [LICENSE](LICENSE) for details.\n\n## \ud83c\udd98 Support\n\n- **Documentation**: [docs.ivybiosciences.com/cli](https://docs.ivybiosciences.com/cli)\n- **Issues**: [GitHub Issues](https://github.com/ivybiosciences/ivybloom-cli/issues)\n- **Email**: [support@ivybiosciences.com](mailto:support@ivybiosciences.com)\n\n---\n\n**\ud83c\udf3f Computational Biology & Drug Discovery at Your Fingertips**\n\n*Built with \u2764\ufe0f by [Ivy Biosciences](https://ivybiosciences.com)*\n",
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