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https://github.com/cthoyt/ols-client
🎡 Unified access to OLS instances like from the EBI and TIB
https://github.com/cthoyt/ols-client
ontologies ontology-lookup-services
Last synced: 16 days ago
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🎡 Unified access to OLS instances like from the EBI and TIB
- Host: GitHub
- URL: https://github.com/cthoyt/ols-client
- Owner: cthoyt
- License: mit
- Created: 2017-07-12T12:21:12.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2023-10-10T16:26:52.000Z (about 1 year ago)
- Last Synced: 2024-10-14T02:23:38.023Z (about 1 month ago)
- Topics: ontologies, ontology-lookup-services
- Language: Python
- Homepage: https://ols-client.readthedocs.io
- Size: 117 KB
- Stars: 11
- Watchers: 4
- Forks: 2
- Open Issues: 1
-
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
OLS Client
A client to the EBI Ontology Lookup Service (OLS) and other instances.
## 💪 Getting Started
One of several OLS clients can be instantiated and accessed with the same API:
```python
from ols_client import EBIClient
ebi_client = EBIClient()
ontologies = ebi_client.get_ontologies()
```
Further documentation can be found at
[ols-client.readthedocs.io](https://ols-client.readthedocs.io).
## 🚀 Installation
The most recent release can be installed from
[PyPI](https://pypi.org/project/ols_client/) with:
```bash
$ pip install ols_client
```
The most recent code and data can be installed directly from GitHub with:
```bash
$ pip install git+https://github.com/cthoyt/ols-client.git
```
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.md](https://github.com/cthoyt/ols-client/blob/master/.github/CONTRIBUTING.md) for more information on getting involved.
## 👋 Attribution
### ⚖️ License
The code in this package is licensed under the MIT License.
### Related
Since the creation of this repository, the EBI has also generated their
own client that can be found at https://github.com/Ensembl/ols-client and
on PyPI as `ebi-ols-client`.
### 🍪 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/cthoyt/ols-client.git
$ cd ols-client
$ 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/cthoyt/ols-client/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```shell
$ git clone git+https://github.com/cthoyt/ols-client.git
$ cd ols-client
$ 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/ols_client/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.