yamaa for Python

Python package for yamaa, a domain-specific language for clinical trial data standardization.

Runs yamaa specifications that transform ODM XML data into SDTM and ADaM datasets, and generates define.xml, with the same Rust engine as the R package:

import yamaa

project = yamaa.project("project.yaml")
run = project.spec("DM").run()      # one dataset, built in memory
run.output, run.issues, run.report
run.save()                          # write the dataset and its run report
project.run("adam").save()          # every ADaM dataset

The R and Python API page describes every call, and the introduction explains the specification language.

Installation

From its 1.0.0 release candidates on, yamaa is published on PyPI. A candidate is a pre-release there, so name it, for example python -m pip install --pre yamaa==1.0.0rc1. Once 1.0.0 is out, install the newest release with:

python -m pip install yamaa

The wheels cover CPython 3.12 and later on Linux x86_64 and aarch64, macOS arm64 and Windows x64. The Linux wheels are manylinux_2_28 and need glibc 2.28 or later, for example RHEL 8, Ubuntu 20.04 or Debian 10; elsewhere, pip builds the source archive, as described below.

Every release is also published as GitHub release assets, and yamaa 0.4.0 only there: download the wheel for your platform from the GitHub release, then install it:

python -m pip install ./yamaa-0.4.0-<wheel-tags>.whl

The 0.4.0 Linux wheel is manylinux_2_34 and needs glibc 2.34 or later.

Or install the standalone source archive from the same release. Building it uses your default Rust toolchain, which must be Rust 1.90 or later for 0.4.0, and Rust 1.82 or later from 0.5.0 on, with Cargo, a C compiler and GNU make:

python -m pip install ./yamaa-0.4.0.tar.gz

The build downloads the locked Rust crates from crates.io, and pip's build isolation fetches maturin. To build offline, fill the Cargo cache first, install maturin 1.9.6 and pass --no-build-isolation.

To set up the development version from GitHub, install uv, the pinned Rust toolchain and a C compiler, then run:

git clone https://github.com/elong0527/yamaa.git
cd yamaa
make setup

The development package requires only Polars and packaging at runtime. Its optional style extra adds the Python YAML readers used by the style checker; from a source checkout, install it with python -m pip install './python[style]'. The test extra also includes these readers, plus PyArrow, lxml and Pydantic for independent artifact and conformance checks. make setup installs it.

The release guidance lists the supported Python versions and platforms.

Contributing

We welcome contributions to yamaa. Please read the contributing guide to get started.

License

This project is licensed under the terms of the MIT license. The package also bundles third-party components, whose license notices ship as its LICENSE-*.txt files.