phylodata 0.39.0

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🧬 PhyloData CLI

📥 Installation

Using pip

pip install phylodata

📖 Usage

# Process an experiment before uploading it to PhyloData
# (starts an interactive process in a web browser)
phylodata process

# Validate if a given JSON file contains valid PhyloData metadata
phylodata validate path/to/metadata.json

# Print the JSON schema for valid PhyloData metadata files
# (Use this to debug the JSON file, e.g. using https://www.jsonschemavalidator.net/)
phylodata schema

For Developers

🔧 Tech Stack

• Python: Requires Python 3.10+
• Streamlit: Web interface for data processing
• UV: Modern Python package manager and installer (no venv required)
• Just: Command runner used for development workflows

📋 Prerequisites

• Python 3.10+
• UV for dependency management
• Just for running commands

🛠️ Development Commands

Run these commands with just:

just test    # Run pytest tests with UV
just check   # Run ruff linter with auto-fix
just format  # Format code with ruff

In order to run a script using the dependencies, just preface it with uv python:

uv python my_script.py