mett 0.0.1a1__tar.gz

mett-0.0.1a1/PKG-INFO

@@ -0,0 +1,248 @@
+Metadata-Version: 2.4
+Name: mett
+Version: 0.0.1a1
+Summary: Python client and CLI for the METT Data Portal API
+Author-email: microbiome-informatics <vikasg@ebi.ac.uk>
+License: MIT
+Keywords: microbiome,mgnify,genomics,api,cli
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: pydantic>=2.5
+Requires-Dist: typer>=0.12
+Requires-Dist: click>=8.1
+Requires-Dist: rich>=13.7
+Requires-Dist: requests>=2.31.0
+Requires-Dist: urllib3<3,>=1.26
+Requires-Dist: python-dateutil>=2.8.2
+Requires-Dist: typing_extensions>=4.7.0
+Requires-Dist: tomli>=2.0; python_version < "3.11"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.4; extra == "dev"
+Requires-Dist: pytest-mock>=3.11; extra == "dev"
+Requires-Dist: ruff>=0.5; extra == "dev"
+Requires-Dist: pre-commit>=3.5; extra == "dev"
+Requires-Dist: build>=1; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+
+# METT Data Portal Client
+
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![PyPI version](https://badge.fury.io/py/mett.svg)](https://badge.fury.io/py/mett)
+
+Python client library and command-line interface (CLI) for the METT Data Portal API. Access genomic data, experimental results, and protein interactions for gut microbiome research.
+
+## Features
+
+- 🚀 **High-level Python API** - Clean, intuitive interface for programmatic access
+- 💻 **Command-line Interface** - Powerful CLI with tab completion and rich output
+- 📊 **Multiple Output Formats** - JSON, TSV, and formatted tables
+- 🔒 **Flexible Authentication** - Environment variables or config file support
+- 📚 **Comprehensive Documentation** - Auto-generated API reference with examples
+- 🔄 **Auto-generated SDK** - Stays in sync with the API schema
+
+## Quick Start
+
+### Installation
+
+```bash
+pip install mett
+```
+
+### CLI Usage
+
+```bash
+# List all species
+mett species list
+
+# Search genomes
+mett genomes search --query "Bacteroides" --per-page 5
+
+# Get gene information
+mett genes get BU_ATCC8492_00001
+```
+
+### Python API
+
+```python
+from mett_dataportal import DataPortalClient
+
+# Initialize client
+client = DataPortalClient()
+
+# List species
+species = client.list_species()
+print(f"Found {len(species)} species")
+
+# Search genomes
+result = client.search_genomes(query="Bacteroides", per_page=5)
+print(f"Found {len(result.items)} genomes")
+```
+
+## Documentation
+
+### Quick Links
+
+- 📖 **[API Reference](docs/reference/api-reference.qmd)** - Complete API documentation with tabbed examples (Quarto format)
+- 📘 **[Usage Guide](docs/guides/USAGE.md)** - Detailed usage examples for CLI and Python API
+- ⚙️ **[Configuration Guide](docs/guides/CONFIGURATION.md)** - Authentication and configuration options
+- 🔧 **[Development Guide](docs/developers/DEVELOPMENT.md)** - Setup, testing, and contributing
+- 📦 **[Architecture Guide](docs/developers/ARCHITECTURE.md)** - Package architecture and design decisions
+
+### Viewing API Documentation
+
+The API reference is in Quarto format (`.qmd`). To view it:
+
+```bash
+# Generate from OpenAPI spec (if needed)
+python3 scripts/generate-api-docs.py
+
+# Render to HTML
+quarto render docs/reference/api-reference.qmd
+
+# Open in browser
+open docs/reference/api-reference.html
+```
+
+Or use preview mode (auto-reloads on changes):
+
+```bash
+quarto preview docs/reference/api-reference.qmd
+```
+
+The rendered HTML includes interactive tabs showing examples in three formats:
+- **Friendly CLI** - High-level `mett` commands
+- **Generic CLI** - `mett api request` commands
+- **cURL** - Raw HTTP requests
+
+For more information, see the [Documentation README](docs/README.md).
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install mett
+```
+
+### From Source
+
+#### Recommended (with `uv`)
+
+```bash
+git clone https://github.com/your-org/mett-dataportal-client.git
+cd mett-dataportal-client
+
+# Create a virtual environment and install all dependencies from pyproject.toml
+uv sync --all-extras --dev
+
+# Run the CLI via uv (no manual activation needed)
+uv run mett --help
+```
+
+### Running tests and linting
+
+With `uv` (recommended):
+
+```bash
+# Install all dev dependencies (if not already done)
+uv sync --all-extras --dev
+
+# Run tests
+uv run pytest -v
+
+# Run Ruff lint and formatting checks
+uv run ruff check mett_dataportal/ scripts/ tests/
+uv run ruff format --check mett_dataportal/ scripts/ tests/
+
+# (Optional) Run pre-commit hooks on all files
+uv run pre-commit run --all-files
+```
+
+#### Alternative (classic `pip` workflow)
+
+If you prefer not to use `uv`, you can still work with a standard virtual environment:
+
+```bash
+python -m venv .venv
+source .venv/bin/activate
+
+pip install --upgrade pip
+pip install -e ".[dev]"
+
+# CLI is now on PATH inside the venv
+mett --help
+```
+
+## Requirements
+
+- Python 3.10+
+- See `pyproject.toml` for full dependency list
+
+## Project Structure
+
+```
+mett-dataportal-client/
+├── mett_dataportal/          # Main package
+│   ├── cli/                  # CLI commands (organized by API type)
+│   │   ├── core/             # Core APIs (system, species, genomes, genes)
+│   │   ├── experimental/    # Experimental APIs (drugs, proteomics, etc.)
+│   │   └── interactions/    # Interaction APIs (PPI, TTP)
+│   ├── client.py             # High-level API client
+│   ├── config.py             # Configuration management
+│   └── utils.py              # Utility functions
+├── mett_dataportal_sdk/      # Auto-generated SDK
+├── docs/                      # Documentation
+│   ├── guides/                # User guides
+│   │   ├── USAGE.md          # Usage examples
+│   │   └── CONFIGURATION.md  # Configuration guide
+│   ├── developers/            # Developer documentation
+│   │   └── DEVELOPMENT.md    # Development guide
+│   ├── reference/             # API reference
+│   │   ├── api-reference.qmd # Main API reference (Quarto)
+│   │   └── cli-examples*.md  # Example files
+│   └── assets/                # Static assets (CSS, etc.)
+├── scripts/                   # Utility scripts
+└── tests/                     # Test suite
+```
+
+## Contributing
+
+We welcome contributions! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Make your changes
+4. Run tests and linting (see **Running tests and linting** above)
+5. Commit your changes (`git commit -m 'Add amazing feature'`)
+6. Push to the branch (`git push origin feature/feature/amazing-feature`)
+7. Open a Pull Request
+
+## License
+
+MIT License - see LICENSE file for details.
+
+## Support
+
+- **Issues**: [GitHub Issues](https://github.com/your-org/mett-dataportal-client/issues)
+- **Documentation**: See [docs/](docs/) directory
+- **Email**: vikasg@ebi.ac.uk
+
+## Acknowledgments
+
+Built for the METT Data Portal project. Special thanks to all contributors.
+
+---
+
+**Note**: For development environments without SSL certificates, you may need to set:
+```bash
+export METT_VERIFY_SSL=false
+```

mett-0.0.1a1/README.md

@@ -0,0 +1,214 @@
+# METT Data Portal Client
+
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![PyPI version](https://badge.fury.io/py/mett.svg)](https://badge.fury.io/py/mett)
+
+Python client library and command-line interface (CLI) for the METT Data Portal API. Access genomic data, experimental results, and protein interactions for gut microbiome research.
+
+## Features
+
+- 🚀 **High-level Python API** - Clean, intuitive interface for programmatic access
+- 💻 **Command-line Interface** - Powerful CLI with tab completion and rich output
+- 📊 **Multiple Output Formats** - JSON, TSV, and formatted tables
+- 🔒 **Flexible Authentication** - Environment variables or config file support
+- 📚 **Comprehensive Documentation** - Auto-generated API reference with examples
+- 🔄 **Auto-generated SDK** - Stays in sync with the API schema
+
+## Quick Start
+
+### Installation
+
+```bash
+pip install mett
+```
+
+### CLI Usage
+
+```bash
+# List all species
+mett species list
+
+# Search genomes
+mett genomes search --query "Bacteroides" --per-page 5
+
+# Get gene information
+mett genes get BU_ATCC8492_00001
+```
+
+### Python API
+
+```python
+from mett_dataportal import DataPortalClient
+
+# Initialize client
+client = DataPortalClient()
+
+# List species
+species = client.list_species()
+print(f"Found {len(species)} species")
+
+# Search genomes
+result = client.search_genomes(query="Bacteroides", per_page=5)
+print(f"Found {len(result.items)} genomes")
+```
+
+## Documentation
+
+### Quick Links
+
+- 📖 **[API Reference](docs/reference/api-reference.qmd)** - Complete API documentation with tabbed examples (Quarto format)
+- 📘 **[Usage Guide](docs/guides/USAGE.md)** - Detailed usage examples for CLI and Python API
+- ⚙️ **[Configuration Guide](docs/guides/CONFIGURATION.md)** - Authentication and configuration options
+- 🔧 **[Development Guide](docs/developers/DEVELOPMENT.md)** - Setup, testing, and contributing
+- 📦 **[Architecture Guide](docs/developers/ARCHITECTURE.md)** - Package architecture and design decisions
+
+### Viewing API Documentation
+
+The API reference is in Quarto format (`.qmd`). To view it:
+
+```bash
+# Generate from OpenAPI spec (if needed)
+python3 scripts/generate-api-docs.py
+
+# Render to HTML
+quarto render docs/reference/api-reference.qmd
+
+# Open in browser
+open docs/reference/api-reference.html
+```
+
+Or use preview mode (auto-reloads on changes):
+
+```bash
+quarto preview docs/reference/api-reference.qmd
+```
+
+The rendered HTML includes interactive tabs showing examples in three formats:
+- **Friendly CLI** - High-level `mett` commands
+- **Generic CLI** - `mett api request` commands
+- **cURL** - Raw HTTP requests
+
+For more information, see the [Documentation README](docs/README.md).
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install mett
+```
+
+### From Source
+
+#### Recommended (with `uv`)
+
+```bash
+git clone https://github.com/your-org/mett-dataportal-client.git
+cd mett-dataportal-client
+
+# Create a virtual environment and install all dependencies from pyproject.toml
+uv sync --all-extras --dev
+
+# Run the CLI via uv (no manual activation needed)
+uv run mett --help
+```
+
+### Running tests and linting
+
+With `uv` (recommended):
+
+```bash
+# Install all dev dependencies (if not already done)
+uv sync --all-extras --dev
+
+# Run tests
+uv run pytest -v
+
+# Run Ruff lint and formatting checks
+uv run ruff check mett_dataportal/ scripts/ tests/
+uv run ruff format --check mett_dataportal/ scripts/ tests/
+
+# (Optional) Run pre-commit hooks on all files
+uv run pre-commit run --all-files
+```
+
+#### Alternative (classic `pip` workflow)
+
+If you prefer not to use `uv`, you can still work with a standard virtual environment:
+
+```bash
+python -m venv .venv
+source .venv/bin/activate
+
+pip install --upgrade pip
+pip install -e ".[dev]"
+
+# CLI is now on PATH inside the venv
+mett --help
+```
+
+## Requirements
+
+- Python 3.10+
+- See `pyproject.toml` for full dependency list
+
+## Project Structure
+
+```
+mett-dataportal-client/
+├── mett_dataportal/          # Main package
+│   ├── cli/                  # CLI commands (organized by API type)
+│   │   ├── core/             # Core APIs (system, species, genomes, genes)
+│   │   ├── experimental/    # Experimental APIs (drugs, proteomics, etc.)
+│   │   └── interactions/    # Interaction APIs (PPI, TTP)
+│   ├── client.py             # High-level API client
+│   ├── config.py             # Configuration management
+│   └── utils.py              # Utility functions
+├── mett_dataportal_sdk/      # Auto-generated SDK
+├── docs/                      # Documentation
+│   ├── guides/                # User guides
+│   │   ├── USAGE.md          # Usage examples
+│   │   └── CONFIGURATION.md  # Configuration guide
+│   ├── developers/            # Developer documentation
+│   │   └── DEVELOPMENT.md    # Development guide
+│   ├── reference/             # API reference
+│   │   ├── api-reference.qmd # Main API reference (Quarto)
+│   │   └── cli-examples*.md  # Example files
+│   └── assets/                # Static assets (CSS, etc.)
+├── scripts/                   # Utility scripts
+└── tests/                     # Test suite
+```
+
+## Contributing
+
+We welcome contributions! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Make your changes
+4. Run tests and linting (see **Running tests and linting** above)
+5. Commit your changes (`git commit -m 'Add amazing feature'`)
+6. Push to the branch (`git push origin feature/feature/amazing-feature`)
+7. Open a Pull Request
+
+## License
+
+MIT License - see LICENSE file for details.
+
+## Support
+
+- **Issues**: [GitHub Issues](https://github.com/your-org/mett-dataportal-client/issues)
+- **Documentation**: See [docs/](docs/) directory
+- **Email**: vikasg@ebi.ac.uk
+
+## Acknowledgments
+
+Built for the METT Data Portal project. Special thanks to all contributors.
+
+---
+
+**Note**: For development environments without SSL certificates, you may need to set:
+```bash
+export METT_VERIFY_SSL=false
+```

mett-0.0.1a1/mett.egg-info/PKG-INFO

@@ -0,0 +1,248 @@
+Metadata-Version: 2.4
+Name: mett
+Version: 0.0.1a1
+Summary: Python client and CLI for the METT Data Portal API
+Author-email: microbiome-informatics <vikasg@ebi.ac.uk>
+License: MIT
+Keywords: microbiome,mgnify,genomics,api,cli
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: pydantic>=2.5
+Requires-Dist: typer>=0.12
+Requires-Dist: click>=8.1
+Requires-Dist: rich>=13.7
+Requires-Dist: requests>=2.31.0
+Requires-Dist: urllib3<3,>=1.26
+Requires-Dist: python-dateutil>=2.8.2
+Requires-Dist: typing_extensions>=4.7.0
+Requires-Dist: tomli>=2.0; python_version < "3.11"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.4; extra == "dev"
+Requires-Dist: pytest-mock>=3.11; extra == "dev"
+Requires-Dist: ruff>=0.5; extra == "dev"
+Requires-Dist: pre-commit>=3.5; extra == "dev"
+Requires-Dist: build>=1; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+
+# METT Data Portal Client
+
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![PyPI version](https://badge.fury.io/py/mett.svg)](https://badge.fury.io/py/mett)
+
+Python client library and command-line interface (CLI) for the METT Data Portal API. Access genomic data, experimental results, and protein interactions for gut microbiome research.
+
+## Features
+
+- 🚀 **High-level Python API** - Clean, intuitive interface for programmatic access
+- 💻 **Command-line Interface** - Powerful CLI with tab completion and rich output
+- 📊 **Multiple Output Formats** - JSON, TSV, and formatted tables
+- 🔒 **Flexible Authentication** - Environment variables or config file support
+- 📚 **Comprehensive Documentation** - Auto-generated API reference with examples
+- 🔄 **Auto-generated SDK** - Stays in sync with the API schema
+
+## Quick Start
+
+### Installation
+
+```bash
+pip install mett
+```
+
+### CLI Usage
+
+```bash
+# List all species
+mett species list
+
+# Search genomes
+mett genomes search --query "Bacteroides" --per-page 5
+
+# Get gene information
+mett genes get BU_ATCC8492_00001
+```
+
+### Python API
+
+```python
+from mett_dataportal import DataPortalClient
+
+# Initialize client
+client = DataPortalClient()
+
+# List species
+species = client.list_species()
+print(f"Found {len(species)} species")
+
+# Search genomes
+result = client.search_genomes(query="Bacteroides", per_page=5)
+print(f"Found {len(result.items)} genomes")
+```
+
+## Documentation
+
+### Quick Links
+
+- 📖 **[API Reference](docs/reference/api-reference.qmd)** - Complete API documentation with tabbed examples (Quarto format)
+- 📘 **[Usage Guide](docs/guides/USAGE.md)** - Detailed usage examples for CLI and Python API
+- ⚙️ **[Configuration Guide](docs/guides/CONFIGURATION.md)** - Authentication and configuration options
+- 🔧 **[Development Guide](docs/developers/DEVELOPMENT.md)** - Setup, testing, and contributing
+- 📦 **[Architecture Guide](docs/developers/ARCHITECTURE.md)** - Package architecture and design decisions
+
+### Viewing API Documentation
+
+The API reference is in Quarto format (`.qmd`). To view it:
+
+```bash
+# Generate from OpenAPI spec (if needed)
+python3 scripts/generate-api-docs.py
+
+# Render to HTML
+quarto render docs/reference/api-reference.qmd
+
+# Open in browser
+open docs/reference/api-reference.html
+```
+
+Or use preview mode (auto-reloads on changes):
+
+```bash
+quarto preview docs/reference/api-reference.qmd
+```
+
+The rendered HTML includes interactive tabs showing examples in three formats:
+- **Friendly CLI** - High-level `mett` commands
+- **Generic CLI** - `mett api request` commands
+- **cURL** - Raw HTTP requests
+
+For more information, see the [Documentation README](docs/README.md).
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install mett
+```
+
+### From Source
+
+#### Recommended (with `uv`)
+
+```bash
+git clone https://github.com/your-org/mett-dataportal-client.git
+cd mett-dataportal-client
+
+# Create a virtual environment and install all dependencies from pyproject.toml
+uv sync --all-extras --dev
+
+# Run the CLI via uv (no manual activation needed)
+uv run mett --help
+```
+
+### Running tests and linting
+
+With `uv` (recommended):
+
+```bash
+# Install all dev dependencies (if not already done)
+uv sync --all-extras --dev
+
+# Run tests
+uv run pytest -v
+
+# Run Ruff lint and formatting checks
+uv run ruff check mett_dataportal/ scripts/ tests/
+uv run ruff format --check mett_dataportal/ scripts/ tests/
+
+# (Optional) Run pre-commit hooks on all files
+uv run pre-commit run --all-files
+```
+
+#### Alternative (classic `pip` workflow)
+
+If you prefer not to use `uv`, you can still work with a standard virtual environment:
+
+```bash
+python -m venv .venv
+source .venv/bin/activate
+
+pip install --upgrade pip
+pip install -e ".[dev]"
+
+# CLI is now on PATH inside the venv
+mett --help
+```
+
+## Requirements
+
+- Python 3.10+
+- See `pyproject.toml` for full dependency list
+
+## Project Structure
+
+```
+mett-dataportal-client/
+├── mett_dataportal/          # Main package
+│   ├── cli/                  # CLI commands (organized by API type)
+│   │   ├── core/             # Core APIs (system, species, genomes, genes)
+│   │   ├── experimental/    # Experimental APIs (drugs, proteomics, etc.)
+│   │   └── interactions/    # Interaction APIs (PPI, TTP)
+│   ├── client.py             # High-level API client
+│   ├── config.py             # Configuration management
+│   └── utils.py              # Utility functions
+├── mett_dataportal_sdk/      # Auto-generated SDK
+├── docs/                      # Documentation
+│   ├── guides/                # User guides
+│   │   ├── USAGE.md          # Usage examples
+│   │   └── CONFIGURATION.md  # Configuration guide
+│   ├── developers/            # Developer documentation
+│   │   └── DEVELOPMENT.md    # Development guide
+│   ├── reference/             # API reference
+│   │   ├── api-reference.qmd # Main API reference (Quarto)
+│   │   └── cli-examples*.md  # Example files
+│   └── assets/                # Static assets (CSS, etc.)
+├── scripts/                   # Utility scripts
+└── tests/                     # Test suite
+```
+
+## Contributing
+
+We welcome contributions! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Make your changes
+4. Run tests and linting (see **Running tests and linting** above)
+5. Commit your changes (`git commit -m 'Add amazing feature'`)
+6. Push to the branch (`git push origin feature/feature/amazing-feature`)
+7. Open a Pull Request
+
+## License
+
+MIT License - see LICENSE file for details.
+
+## Support
+
+- **Issues**: [GitHub Issues](https://github.com/your-org/mett-dataportal-client/issues)
+- **Documentation**: See [docs/](docs/) directory
+- **Email**: vikasg@ebi.ac.uk
+
+## Acknowledgments
+
+Built for the METT Data Portal project. Special thanks to all contributors.
+
+---
+
+**Note**: For development environments without SSL certificates, you may need to set:
+```bash
+export METT_VERIFY_SSL=false
+```