Metadata-Version: 2.1
Name: cycquery
Version: 0.1.0
Summary: A tool to query EHR databases
Home-page: https://github.com/VectorInstitute/cyclops-query
License: Apache-2.0
Author: Vector AI Engineering
Author-email: cyclops@vectorinstitute.ai
Requires-Python: >=3.9,<3.11
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Dist: SQLAlchemy (>=1.4.32,<2.0.0)
Requires-Dist: dask[dataframe] (>=2023.10.0,<2024.0.0)
Requires-Dist: pandas (>=1.4.1,<2.0.0)
Requires-Dist: psycopg2 (>=2.9.6,<3.0.0)
Requires-Dist: pyarrow (>=11.0.0,<12.0.0)
Project-URL: Documentation, https://vectorinstitute.github.io/cyclops-query/
Project-URL: Repository, https://github.com/VectorInstitute/cyclops-query
Description-Content-Type: text/markdown

cyclops-query
--------------------------------------------------------------------------------

[![PyPI](https://img.shields.io/pypi/v/cycquery)](https://pypi.org/project/cycquery)
[![code checks](https://github.com/VectorInstitute/cyclops-query/actions/workflows/code_checks.yml/badge.svg)](https://github.com/VectorInstitute/cyclops-query/actions/workflows/code_checks.yml)
[![integration tests](https://github.com/VectorInstitute/cyclops-query/actions/workflows/integration_tests.yml/badge.svg)](https://github.com/VectorInstitute/cyclops-query/actions/workflows/integration_tests.yml)
[![docs](https://github.com/VectorInstitute/cyclops-query/actions/workflows/docs_deploy.yml/badge.svg)](https://github.com/VectorInstitute/cyclops-query/actions/workflows/docs_deploy.yml)
[![codecov](https://codecov.io/gh/VectorInstitute/cyclops-query/branch/main/graph/badge.svg)](https://codecov.io/gh/VectorInstitute/cyclops-query)
[![license](https://img.shields.io/github/license/VectorInstitute/cyclops-query.svg)](https://github.com/VectorInstitute/cyclops-query/blob/main/LICENSE)

``cyclops-query`` is a tool for querying EHR databases.

## 🐣 Getting Started

### Installing cyclops-query using pip

```bash
python3 -m pip install cycquery
```

## 🧑🏿‍💻 Developing

### Using poetry

The development environment can be set up using
[poetry](https://python-poetry.org/docs/#installation). Hence, make sure it is
installed and then run:

```bash
python3 -m poetry install
source $(poetry env info --path)/bin/activate
```

API documentation is built using [Sphinx](https://www.sphinx-doc.org/en/master/) and
can be locally built by:

```bash
cd docs
make html SPHINXOPTS="-D nbsphinx_allow_errors=True"
```

### Contributing

Contributing to ``cyclops-query`` is welcomed.
See [Contributing](https://vectorinstitute.github.io/cyclops-query/api/contributing.html) for
guidelines.


## 📚 [Documentation](https://vectorinstitute.github.io/cyclops-query/)


## 🎓 Citation

Reference to cite when you use ``cyclops-query`` in a project or a research paper:

```
@article {Krishnan2022.12.02.22283021,
	author = {Krishnan, Amrit and Subasri, Vallijah and McKeen, Kaden and Kore, Ali and Ogidi, Franklin and Alinoori, Mahshid and Lalani, Nadim and Dhalla, Azra and Verma, Amol and Razak, Fahad and Pandya, Deval and Dolatabadi, Elham},
	title = {CyclOps: Cyclical development towards operationalizing ML models for health},
	elocation-id = {2022.12.02.22283021},
	year = {2022},
	doi = {10.1101/2022.12.02.22283021},
	publisher = {Cold Spring Harbor Laboratory Press},
	URL = {https://www.medrxiv.org/content/early/2022/12/08/2022.12.02.22283021},
	journal = {medRxiv}
}
```

