https://github.com/biopragmatics/debio
🥮 Decentralized Biomedical Ontology
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.0%) to scientific vocabulary
Keywords
Repository
🥮 Decentralized Biomedical Ontology
Basic Info
- Host: GitHub
- Owner: biopragmatics
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://biopragmatics.github.io/debio/
- Size: 195 KB
Statistics
- Stars: 1
- Watchers: 4
- Forks: 1
- Open Issues: 1
- Releases: 2
Topics
Metadata Files
README.md
DeBiO
A community-curated, decentralized biomedical ontology.
👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved. This document also includes:
- Curation guidelines for new object properties
- Instructions for rebuilding the ontology
- Instructions for releasing the ontology to PyPI
🚀 Installation
The most recent release can be installed from PyPI with:
bash
$ pip install debio
The most recent code and data can be installed directly from GitHub with:
bash
$ pip install git+https://github.com/biopragmatics/debio.git
👋 Attribution
⚖️ License
The code in this package is licensed under the MIT License.
🍪 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/biopragmatics/debio.git $ cd debio $ 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/biopragmatics/debio/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell $ git clone git+https://github.com/biopragmatics/debio.git $ cd debio $ 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/debio/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.Owner
- Name: Biopragmatics Stack
- Login: biopragmatics
- Kind: organization
- Website: https://biopragmatics.github.io
- Twitter: biopragmatics
- Repositories: 9
- Profile: https://github.com/biopragmatics
Software supporting biomedical semantics and pragmatics
GitHub Events
Total
- Issues event: 2
- Watch event: 1
- Issue comment event: 1
Last Year
- Issues event: 2
- Watch event: 1
- Issue comment event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Charles Tapley Hoyt | c****t@g****m | 47 |
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 3
- Total pull requests: 2
- Average time to close issues: 8 days
- Average time to close pull requests: 3 days
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 1.67
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: 6 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lnanderson (2)
- cthoyt (1)
Pull Request Authors
- cthoyt (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 18 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
pypi.org: debio
A community-curated, decentralized biomedical ontology.
- Homepage: https://github.com/biopragmatics/debio
- Documentation: https://debio.readthedocs.io/
- License: MIT
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Latest release: 0.1.1
published almost 4 years ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- codecov/codecov-action v1 composite