A client to BioPortal and other OntoPortal instances.
Project description
OntoPortal Client
A client to BioPortal and other OntoPortal instances.
💪 Getting Started
One of several OntoPortal clients can be instantiated and accessed with the same API:
from ontoportal_client import BioPortalClient
bioportal_client = BioPortalClient()
ontologies = bioportal_client.get_ontologies()
Complete documentation can be found on ontoportal-client.readthedocs.io
🚀 Installation
$ pip install ontoportal_client
The most recent code and data can be installed directly from GitHub with:
$ pip install git+https://github.com/cthoyt/ontoportal-client.git
⚙️ Configuration
Configuration of the API tokens for for each of the clients is mediated by
pystow
. Using BioPortal as an example,
you can either:
- Pass the API key in the construtor of the client class
- Set the
BIOPORTAL_API_KEY
environment variable - Create a file
~/.config/bioportal.ini
and set theapi_key
value under the[bioportal]
section.
👐 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.
🍪 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/cthoyt/ontoportal-client.git
$ cd ontoportal-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:
$ 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/cthoyt/ontoportal-client.git
$ cd ontoportal-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
. 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/ontoportal_client/version.py
, anddocs/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.
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