Package Health Score

72 / 100

security
No known security issues
popularity
Limited
maintenance
Healthy
community
Sustainable

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Popularity

Limited

GitHub Stars: 4
Forks: 8
Contributors: 10

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package pyBiodatafuse, we found that it has been starred 4 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Dec 2, 2024
Direct Vulnerabilities: 0
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0
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0
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0
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Indirect Vulnerabilities: 0
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0
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0
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License Risk: 0
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All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

MIT

Security Policy

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Maintenance

Healthy

Commit Frequency

Open Issues: 29
Open PR: 3
Last Release: 21 days ago
Last Commit: 2 months ago

Further analysis of the maintenance status of pyBiodatafuse based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that pyBiodatafuse demonstrates a positive version release cadence with at least one new version released in the past 3 months.

In the past month we didn't find any pull request activity or change in issues status has been detected for the GitHub repository.

Community

Sustainable

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 10
Funding: No

This project has seen only 10 or less contributors.

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Package

Python Versions Compatibility: >=3.8

Age: 1 year
Latest Release: 21 days ago
Dependencies: 5 Direct
Versions: 6
Maintainers: 0
Wheels: OS Independent

Readme

pyBioDataFuse

<a href="https://pypi.org/project/pyBiodatafuse">
    <img src="https://img.shields.io/pypi/v/pyBiodatafuse" alt="PyPI">
</a>
<a href="https://pypi.org/project/pyBiodatafuse">
    <img src="https://img.shields.io/pypi/pyversions/pyBiodatafuse" alt="PyPI - Python Version">
</a>
<a href="https://github.com/BioDataFuse/pyBiodatafuse/blob/main/LICENSE">
    <img src="https://img.shields.io/pypi/l/pyBiodatafuse" alt="PyPI - License">
</a>

<a href="https://codecov.io/gh/BioDataFuse/pyBiodatafuse/branch/main">
    <img alt="Codecov status" src="https://codecov.io/gh/BioDataFuse/pyBiodatafuse/branch/main/graph/badge.svg">
</a>  
<a href="https://github.com/cthoyt/cookiecutter-python-package">
    <img src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" alt="Cookiecutter template from @cthoyt"> 
</a>
<a href="https://github.com/psf/black">
    <img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg">
</a>
<a href="https://github.com/BioDataFuse/pyBiodatafuse/blob/main/.github/CODE_OF_CONDUCT.md">
    <img alt="Contributor Covenant" src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg">
</a>

💪 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.

To know more about the package, read our documentation here.

Creating your own graph

To generate your own graph, check out our tutorial notebook in examples.

🚀 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:

$ 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:

$ tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

$ 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. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in 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:

$ tox -e finish

This script does the following:

Uses Bump2Version to switch the version number in the setup.cfg, src/pyBiodatafuse/version.py, and docs/source/conf.py to not have the -dev suffix
Packages the code in both a tar archive and a wheel using build
Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
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.

pyBiodatafuse dependencies

click matplotlib networkx requests sparqlwrapper

FAQs

What is pyBiodatafuse?

A python package for integrating data from multiple resources. Visit Snyk Advisor to see a full health score report for pyBiodatafuse, including popularity, security, maintenance & community analysis.

Is pyBiodatafuse popular?

The python package pyBiodatafuse receives a total of 47 weekly downloads. As such, pyBiodatafuse popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is pyBiodatafuse well maintained?

We found that pyBiodatafuse demonstrated a healthy version release cadence and project activity. It has a community of 10 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is pyBiodatafuse safe to use?

The python package pyBiodatafuse was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 21 December-2024, at 11:06 (UTC).

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