ols-py

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Documentation: https://ahida-development.github.io/ols-py

Source Code: https://github.com/ahida-development/ols-py

PyPI: https://pypi.org/project/ols-py/

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Python client for the Ontology Lookup Service

Current status:

• Now that OLS4 is released and OLS3 is no longer updated, this client will only support OLS4 going forward
• Some API endpoints may not be implemented, or schemas not fully described - please open an issue if you want anything added.

Features:

• Type annotated so you know which parameters can be used for each endpoint
• Responses validated and parsed with pydantic for easy access to response data

Example usage

from ols_py.client import Ols4Client
client = Ols4Client()
resp = client.search("MC1R", params={"ontology": "go"})
term = resp.response.docs[0]
print(term)
# SearchResultItem(
#   id=None, annotations=None, annotations_trimmed=None,
#   description=['A rhodopsin-like G-protein ... gamma-melanocyte-stimulating hormone.'],
#   iri='http://purl.obolibrary.org/obo/PR_000001146', label='melanocortin receptor',
#   obo_id='PR:000001146', ontology_name='go', ontology_prefix='GO', subset=None,
#   short_form='PR_000001146', synonyms=None, type='class'
#)
print(term.iri)
# http://purl.obolibrary.org/obo/PR_000001146

Installation

pip install ols-py

Development

• Clone this repository
• Requirements:
  • Poetry
  • Python 3.10+
• Create a virtual environment and install the dependencies

poetry install

• Activate the virtual environment

poetry shell

Testing

pytest

Documentation

The documentation is automatically generated from the content of the docs directory and from the docstrings of the public signatures of the source code. The documentation is updated and published as a Github project page automatically as part each release.

Releasing

Trigger the Draft release workflow (press Run workflow). This will update the changelog & version and create a GitHub release which is in Draft state.

Find the draft release from the GitHub releases and publish it. When a release is published, it'll trigger release workflow which creates PyPI release and deploys updated documentation.

Pre-commit

Pre-commit hooks run all the auto-formatters (e.g. black, isort), linters (e.g. mypy, flake8), and other quality checks to make sure the changeset is in good shape before a commit/push happens.

You can install the hooks with (runs for each commit):

pre-commit install

Or if you want them to run only for each push:

pre-commit install -t pre-push

Or if you want e.g. want to run all checks manually for all files:

pre-commit run --all-files

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This project was generated using the wolt-python-package-cookiecutter template.