AnIML specifications

This repository implements the original AnIML XSD specification as markdown data model to make use of code generation tools.

Usage

Code generation

To generate the code, run the following command:

md-models pipeline -i gen.toml

This will generate the following files:

• schemes/animl.json
• docs/model.md
• typescript/src/index.ts

Python

As an alternative to the code generation, you can use the mdmodels Python library to dynamically generate Python PyDantic models and use them in your code.

from mdmodels import DataModel

animl = DataModel.from_github(
    repo="FAIRChemistry/animl-specification",
    branch="main",
    path="specifications/animl.md",
)

# You can now use the animl model in your code
animldoc = animl.AnIML(
    # ...
)

Rust

Similar to the Python example, you can use the mdmodels macro functions to dynamically generate serde-compatible Rust structs.

use mdmodels_macro::parse_mdmodel;

parse_mdmodel!("specifications/animl.md");

// You can now use the animl struct in your code
let animl = AnIMLBuilder::default()
    .sample_set(SampleSetBuilder::default().build())
    .build();