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Open Source Science

https://github.com/cthoyt/ols-client

🎡 Unified access to OLS instances like from the EBI and TIB

https://github.com/cthoyt/ols-client

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.8%) to scientific vocabulary

Keywords

ontologies ontology-lookup-services
Last synced: 9 months ago · JSON representation

Repository

🎡 Unified access to OLS instances like from the EBI and TIB

Basic Info
Statistics
  • Stars: 13
  • Watchers: 4
  • Forks: 2
  • Open Issues: 1
  • Releases: 12
Topics
ontologies ontology-lookup-services
Created almost 9 years ago · Last pushed 10 months ago
Metadata Files
Readme Contributing License Code of conduct

README.md

OLS Client

Tests PyPI PyPI - Python Version PyPI - License Documentation Status Codecov status Cookiecutter template from @cthoyt Ruff Contributor Covenant DOI

A client to the EBI Ontology Lookup Service.

💪 Getting Started

One of several OLS clients can be instantiated and accessed with the same API:

```python from ols_client import EBIClient

ebiclient = EBIClient() ontologies = ebiclient.get_ontologies() ```

Further documentation can be found at ols-client.readthedocs.io.

🚀 Installation

The most recent release can be installed from PyPI with uv:

console $ uv pip install ols_client

or with pip:

console $ python3 -m pip install ols_client

The most recent code and data can be installed directly from GitHub with uv:

console $ uv pip install git+https://github.com/cthoyt/ols-client.git

or with pip:

console $ python3 -m 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 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'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: ```console $ git clone git+https://github.com/cthoyt/ols-client.git $ cd ols-client $ uv pip install -e . ``` Alternatively, install using pip: ```console $ python3 -m pip install -e . ``` ### 🥼 Testing After cloning the repository and installing `tox` with `uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the unit tests in the `tests/` folder can be run reproducibly with: ```console $ tox -e py ``` 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: ```console $ 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 [`pyproject.toml`](pyproject.toml). `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).

🧑‍💻 For Maintainers

See maintainer instructions ### Initial Configuration #### Configuring ReadTheDocs [ReadTheDocs](https://readthedocs.org) is an external documentation hosting service that integrates with GitHub's CI/CD. Do the following for each repository: 1. Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/ 2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository 3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters) 4. Click next, and you're good to go! #### Configuring Archival on Zenodo [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI to each release of your package. Do the following for each repository: 1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click "grant" next to any organizations you want to enable the integration for, then click the big green "approve" button. This step only needs to be done once. 2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make a new repository, you'll have to come back to this After these steps, you're ready to go! After you make "release" on GitHub (steps for this are below), you can navigate to https://zenodo.org/account/settings/github/repository/cthoyt/ols-client to see the DOI for the release and link to the Zenodo record for it. #### Registering with the Python Package Index (PyPI) The [Python Package Index (PyPI)](https://pypi.org) hosts packages so they can be easily installed with `pip`, `uv`, and equivalent tools. 1. Register for an account [here](https://pypi.org/account/register) 2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email might not have been sent by default, so you might have to click the "options" dropdown next to your address to get to the "re-send verification email" button 3. 2-Factor authentication is required for PyPI since the end of 2023 (see this [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)). This means you have to first issue account recovery codes, then set up 2-factor authentication 4. Issue an API token from https://pypi.org/manage/account/token This only needs to be done once per developer. #### Configuring your machine's connection to PyPI This needs to be done once per machine. ```console $ uv tool install keyring $ keyring set https://upload.pypi.org/legacy/ __token__ $ keyring set https://test.pypi.org/legacy/ __token__ ``` Note that this deprecates previous workflows using `.pypirc`. ### 📦 Making a Release #### Uploading to PyPI After installing the package in development mode and installing `tox` with `uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run the following from the console: ```console $ tox -e finish ``` This script does the following: 1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to switch the version number in the `pyproject.toml`, `CITATION.cff`, `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 [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package) 3. Uploads to PyPI using [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package). 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. #### Releasing on GitHub 1. Navigate to https://github.com/cthoyt/ols-client/releases/new to draft a new release 2. Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made 3. Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit 4. Click the big green "Publish Release" button This will trigger Zenodo to assign a DOI to your release as well. ### Updating Package Boilerplate This project uses `cruft` to keep boilerplate (i.e., configuration, contribution guidelines, documentation configuration) up-to-date with the upstream cookiecutter package. Install cruft with either `uv tool install cruft` or `python3 -m pip install cruft` then run: ```console $ cruft update ``` More info on Cruft's update command is available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).

Owner

  • Name: Charles Tapley Hoyt
  • Login: cthoyt
  • Kind: user
  • Location: Bonn, Germany
  • Company: RWTH Aachen University

GitHub Events

Total
  • Release event: 1
  • Watch event: 3
  • Delete event: 2
  • Issue comment event: 2
  • Push event: 10
  • Pull request event: 2
  • Create event: 1
Last Year
  • Release event: 1
  • Watch event: 3
  • Delete event: 2
  • Issue comment event: 2
  • Push event: 10
  • Pull request event: 2
  • Create event: 1

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 78
  • Total Committers: 2
  • Avg Commits per committer: 39.0
  • Development Distribution Score (DDS): 0.013
Top Committers
Name Email Commits
Charles Tapley Hoyt c****t@g****m 77
Charles Tapley Hoyt c****t@u****m 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 5
  • Total pull requests: 3
  • Average time to close issues: about 1 year
  • Average time to close pull requests: about 10 hours
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.6
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cthoyt (2)
  • famosab (1)
  • PoGibas (1)
  • mastevb (1)
Pull Request Authors
  • cthoyt (4)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 23,808 last-month
  • Total docker downloads: 147
  • Total dependent packages: 2
  • Total dependent repositories: 7
  • Total versions: 14
  • Total maintainers: 1
pypi.org: ols-client

A client to the EBI Ontology Lookup Service

  • Versions: 14
  • Dependent Packages: 2
  • Dependent Repositories: 7
  • Downloads: 23,808 Last month
  • Docker Downloads: 147
Rankings
Docker downloads count: 3.0%
Dependent packages count: 3.1%
Downloads: 3.8%
Dependent repos count: 5.6%
Average: 9.7%
Stargazers count: 20.3%
Forks count: 22.6%
Maintainers (1)
cthoyt
Funding
  • https://github.com/sponsors/cthoyt
Last synced: 9 months ago

Dependencies

.github/workflows/tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v1 composite
pyproject.toml pypi