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BioDataFuse / pyBiodatafuse

Python package for biodatafuse project.
MIT License
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pyBioDataFuse

PyPI PyPI - Python Version PyPI - License Codecov status Cookiecutter template from @cthoyt Code style: black Contributor Covenant

💪 Getting Started

We introduce BioDataFuse, a query-based Python tool for seamless integration of biomedical databases. BioDataFuse establishes a modular framework for efficient data wrangling, enabling context-specific knowledge graph creation and supporting graph-based analyses. With a user-friendly interface, it enables users to dynamically create knowledge graphs from their input data. Supported by a robust Python package, pyBiodatafuse, this tool excels in data harmonization, aggregating diverse sources through modular queries. Moreover, BioDataFuse provides plugin capabilities for Cytoscape and Neo4j, allowing local graph hosting. Ongoing refinements enhance the graph utility through tasks like link prediction, making BioDataFuse a versatile solution for efficient and effective biological data integration.

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install pyBiodatafuse

The most recent code and data can be installed directly from GitHub with:

$ pip install git+https://github.com/BioDataFuse/pyBiodatafuse.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

📖 Citation

The work was started as part of the Elixir BioHackathon 2023 integrating and bringing together multiple Core Data Resources together.

Gadiya, Y., Ammar, A., Willighagen, E., Martinat, D., Sima, A. C., Balci, H., & Abbassi Daloii, T. (2023). BioHackEU23 report: Extending interoperability of experimental data using modular queries across biomedical resources. BioHackrXiv Preprints. https://doi.org/10.37044/osf.io/mhsqp

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions The final section of the README is for if you want to get involved by making a code contribution. ### Development Installation To install in development mode, use the following: ```bash $ git clone git+https://github.com/BioDataFuse/pyBiodatafuse.git $ cd pyBiodatafuse $ pip install -e . ``` ### 🥼 Testing After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be run reproducibly with: ```shell $ tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/BioDataFuse/pyBiodatafuse/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell $ git clone git+https://github.com/BioDataFuse/pyBiodatafuse.git $ cd pyBiodatafuse $ tox -e docs $ open docs/build/html/index.html ``` The documentation automatically installs the package as well as the `docs` extra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins like `texext` can be added there. Additionally, they need to be added to the `extensions` list in [`docs/source/conf.py`](docs/source/conf.py). ### 📦 Making a Release After installing the package in development mode and installing `tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment in `tox.ini`. Run the following from the shell: ```shell $ tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/pyBiodatafuse/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid the need for manual input at this step 4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped. 5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use `tox -e bumpversion -- minor` after.