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https://github.com/biopragmatics/semra
🛣️ Semantic Mapping Reasoning Assembler (SeMRA): tooling for semantic mappings
https://github.com/biopragmatics/semra
biopragmatics mappings ontology-merging semantic-mappings
Last synced: 26 days ago
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🛣️ Semantic Mapping Reasoning Assembler (SeMRA): tooling for semantic mappings
- Host: GitHub
- URL: https://github.com/biopragmatics/semra
- Owner: biopragmatics
- License: mit
- Created: 2023-04-12T10:20:43.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-05-02T15:17:42.000Z (8 months ago)
- Last Synced: 2024-10-06T10:37:12.802Z (3 months ago)
- Topics: biopragmatics, mappings, ontology-merging, semantic-mappings
- Language: Jupyter Notebook
- Homepage: https://semra.readthedocs.io
- Size: 896 KB
- Stars: 5
- Watchers: 3
- Forks: 1
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
SeMRA
Semantic mapping reasoner and assembler
[](https://zenodo.org/badge/latestdoi/626870339)
This software provides:
1. An object model for semantic mappings (based on SSSOM)
2. Functionality for assembling and reasoning over
semantic mappings at scale
3. A provenance model for automatically generated mappings
4. A confidence model granular at the curator-level,
mapping set-level, and community feedback-level
We also provide an accompanying raw semantic mapping database on Zenodo at
https://zenodo.org/records/11082039.
## 🚀 Installation
The most recent release can be installed from
[PyPI](https://pypi.org/project/semra/) with:
```shell
pip install semra
```
The most recent code and data can be installed directly from GitHub with:
```shell
pip install git+https://github.com/biopragmatics/semra.git
```
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.md](https://github.com/biopragmatics/semra/blob/master/.github/CONTRIBUTING.md) for more information on getting involved.
## 👋 Attribution
### ⚖️ License
The code in this package is licensed under the MIT License.
### 🍪 Cookiecutter
This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/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/semra.git
cd semra
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/semra/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```shell
git clone git+https://github.com/biopragmatics/semra.git
cd semra
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).
The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using
[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html).
The [`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration you'll need.
You can also set up continuous integration on GitHub to check not only that
Sphinx can build the documentation in an isolated environment (i.e., with ``tox -e docs-test``)
but also that [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
### 📦 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/semra/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.