linkml-arrays

This repository serves as an example repository showcasing the support for loading and dumping N-dimensional arrays, including labeled arrays in LinkML. The examples are a work in progress, which are used at the same time to develop the metadata model for arrays in LinkML.

Dumpers and loaders

The repository currently includes dumpers and loaders examples for yaml, hdf5, numpy and zarr.

Data

Temperature dataset

The schema defining the labeled array according to the linkml array metamodel can be found here tests/input/temperature_schema.yaml. The schema defines a DataArray similar to an xarray.DataArray. The schema includes an array of values TemperaturesInKMatrix, and labeled dimensions which correspond to the concept of coordinates in xarray.

Quick reference for common commands

uv run gen-pydantic tests/input/temperature_schema.yaml > tests/array_classes_lol.py

Acknowledgements

This cookiecutter project was developed from the monarch-project-template template and will be kept up-to-date using cruft.