lx-dtypes 0.1.1

lx-data-types

lx-data-models

CodeCov (Main)

CodeCov (Dev)

lx-dtypes provides strongly typed, Pydantic-powered data models for Lux Group medical research projects. The package ships opinionated validators, utilities for ingestion/export, and a common vocabulary so downstream services can reason about patient examinations, knowledge-base entries, and related clinical data.

Features

• Comprehensive Pydantic models covering patient records, exam findings, and knowledge-base entities.
• Data loaders/encoders that normalize multiple file formats into the same abstractions.
• Utilities for working with Lux Research tooling (paths, logging, export helpers, etc.).
• Ready-to-run pytest suite with coverage and optional type-checking.

Installation

Install the latest release from PyPI (coming soon):

pip install lx-dtypes

For contributors and power users, install with the development extras:

pip install "lx-dtypes[dev]"

Quick Start

from lx_dtypes import __version__
from lx_dtypes.models.patient import Patient

patient = Patient.model_validate({
		"id": "1234",
		"first_name": "Ada",
		"last_name": "Lovelace",
})

print(patient.full_name)
print(__version__)

Development

git clone https://github.com/wg-lux/lx-data-models
cd lx-data-models
python -m venv .venv && source .venv/bin/activate
pip install -e ".[dev]"

Migrations

The following command shortcuts are available for managing migratons, see line below for what they do:

mkmigrations

"uv run python manage.py makemigrations ${DJANGO_APP_NAME}";

migrate

"uv run python manage.py migrate";

runserver

"uv run python manage.py runserver";

resetdb

"rm -f db.sqlite3";

resetmigrations

rm -rf ${DJANGO_APP_DIR}/migrations/;
uv run python manage.py makemigrations ${DJANGO_APP_NAME};

Initialized Models

Some pydantic models with ForwardRefs require initialization before use. Import initialized models from lx_dtypes.utils.initialized_models

If you encounter this error when using a model, you may add it there.

Example for the PatientLedger model which references Examiner. This would cause a circular import, therefore we just use the Examiner model during TYPE_CHECKING in the PatientLedger model file and rebuild the model here.

from lx_dtypes.models.examiner import (
    Examiner,  # for model rebuild # type: ignore # noqa: F401
)

PatientLedger.model_rebuild()

Test & Lint

pytest
ruff check lx_dtypes tests
mypy lx_dtypes

Documentation

Install the documentation extras (included in .[dev]) and build the HTML site with Sphinx:

pip install -e ".[docs]"
make -C docs html
# open docs/_build/html/index.html in your browser

Use make -C docs linkcheck to verify outbound references before publishing to Read the Docs or GitHub Pages.

Release Process

1. Update CHANGELOG.md and bump the version in pyproject.toml.
2. Run formatting, linting, type-checking, and the full test suite.
3. Build artifacts with python -m build and verify with twine check dist/*.
4. Trigger the "Publish" GitHub workflow (either via tag/release or manual dispatch). Trusted Publisher entries for test.pypi.org and pypi.org should already reference the publish.yml workflow and the testpypi/pypi environments; approve those environments as needed and the workflow will push to TestPyPI first, then PyPI.

Contributing

See CONTRIBUTING.md for the full workflow, coding standards, and release guidelines. Bug reports and pull requests are welcome!

License

Distributed under the MIT License. See LICENSE for details.