ingest-metadata

Schema hosting relevant metadata for a data transformation conformant to the Biolink Model

Website

https://biolink.github.io/ingest-metadata

Repository Structure

• examples/ - example data
• project/ - project files (do not edit these)
• src/ - source files (edit these)
  • ingest_metadata
    • schema -- LinkML schema (edit this)
    • datamodel -- generated Python datamodel
• tests/ - Python tests

Developer Documentation

Prerequisites

This project uses uv for dependency management. Install uv first:

# On macOS and Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

# On Windows
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

# Alternative: using pip
pip install uv

Getting Started

1. Clone the repository:

git clone https://github.com/biolink/ingest-metadata.git
cd ingest-metadata

2. Install dependencies:

uv sync

3. Run tests:

make test

Development Commands

To run commands you may use good old make or the command runner just which is a better choice on Windows. Use the make command or duty commands to generate project artefacts:

• make help or just --list: list all pre-defined tasks
• make all or just all: make everything
• make deploy or just deploy: deploys site
• make install: install dependencies with uv
• uv sync: install dependencies directly with uv
• make test: run tests

Credits

This project was made with linkml-project-cookiecutter.