A client to the EBI Ontology Lookup Service
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:
from ols_client import EBIClient ebi_client = EBIClient() ontologies = ebi_client.get_ontologies()
Further documentation can be found at ols-client.readthedocs.io.
The most recent release can be installed from PyPI with:
$ pip install ols_client
The most recent code and data can be installed directly from GitHub with:
$ pip install git+https://github.com/cthoyt/ols-client.git
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
The code in this package is licensed under the MIT License.
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
🛠️ For Developers
See developer instructions
The final section of the README is for if you want to get involved by making a code contribution.
To install in development mode, use the following:
$ git clone git+https://github.com/cthoyt/ols-client.git $ cd ols-client $ pip install -e .
After cloning the repository and installing
pip install tox, the unit tests in the
tests/ folder can be
run reproducibly with:
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/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
extra specified in the
texext can be added there. Additionally, they need to be added to the
extensions list in
📦 Making a Release
After installing the package in development mode and installing
pip install tox, the commands for making a new release are contained within the
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
docs/source/conf.pyto not have the
- Packages the code in both a tar archive and a wheel using
- Uploads to PyPI using
twine. Be sure to have a
.pypircfile 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
tox -e bumpversion minorafter.
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