Curies
๐ธ Idiomatic conversion between URIs and compact URIs (CURIEs) in Python
Install / Use
/learn @biopragmatics/CuriesREADME
Idiomatic conversion between URIs and compact URIs (CURIEs).
import curies
converter = curies.load_prefix_map({
"CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
# ... and so on
})
>>> converter.compress("http://purl.obolibrary.org/obo/CHEBI_1")
'CHEBI:1'
>>> converter.expand("CHEBI:1")
'http://purl.obolibrary.org/obo/CHEBI_1'
Full documentation is available at curies.readthedocs.io.
CLI Usage
This package comes with a built-in CLI for running a resolver web application or a IRI mapper web application:
# Run a resolver
python -m curies resolver --host 0.0.0.0 --port 8764 bioregistry
# Run a mapper
python -m curies mapper --host 0.0.0.0 --port 8764 bioregistry
The positional argument can be one of the following:
- A pre-defined prefix map to get from the web (bioregistry, go, obo, monarch, prefixcommons)
- A local file path or URL to a prefix map, extended prefix map, or one of
several formats. Requires specifying a
--format.
The framework can be swapped to use Flask (default) or FastAPI with
--framework. The server can be swapped to use Werkzeug (default) or Uvicorn
with --server. These functionalities are also available programmatically, see
the docs for more information.
๐งโ๐คโ๐ง Related
Other packages that convert between CURIEs and URIs:
- https://github.com/prefixcommons/prefixcommons-py (Python)
- https://github.com/prefixcommons/curie-util (Java)
- https://github.com/geneontology/curie-util-py (Python)
- https://github.com/geneontology/curie-util-es5 (Node.js)
- https://github.com/endoli/curie.rs (Rust)
- https://github.com/cthoyt/curies4j (Java)
- https://github.com/biopragmatics/curies.rs (Rust, Node.js, Python)
๐ Installation
The most recent release can be installed from PyPI with:
python3 -m pip install curies
As of v0.8, this package only supports Pydantic v2. v0.6.x and v0.7.x had cross-version support for Pydantic v1 and v2. v0.5.x and before only supported Pydantic v1. See the Pydantic migration guide for updating your code.
๐ Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
Users
See
who's using curies.
๐ Attribution
๐ Acknowledgements
This package heavily builds on the trie
data structure implemented in pytrie.
โ๏ธ License
The code in this package is licensed under the MIT License.
๐ช Cookiecutter
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
๐ ๏ธ For Developers
<details> <summary>See developer instructions</summary>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/biopragmatics/curies.git
$ cd curies
$ uv --preview pip install -e .
Alternatively, install using legacy pip with UV_PREVIEW mode enabled until the
uv build backend becomes a stable feature:
$ UV_PREVIEW=1 python3 -m pip install -e .
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. Update with the following:
python3 -m pip install cruft
cruft update
More info on Cruft's update command is available here.
๐ฅผ Testing
After cloning the repository and installing tox with
python3 -m pip install tox tox-uv, the unit tests in the tests/ folder can
be run reproducibly with:
tox -e py
Additionally, these tests are automatically re-run with each commit in a GitHub Action.
๐ Building the Documentation
The documentation can be built locally using the following:
git clone git+https://github.com/biopragmatics/curies.git
cd curies
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. sphinx plugins like
texext can be added there. Additionally, they need to be added to the
extensions list in docs/source/conf.py.
The documentation can be deployed to ReadTheDocs using
this guide. The
.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.
Configuring ReadTheDocs
- Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/
- Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository
- You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
- Click next, and you're good to go!
๐ฆ Making a Release
Configuring Zenodo
Zenodo is a long-term archival system that assigns a DOI to each release of your package.
- 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.
- 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/biopragmatics/curies to see the DOI for the release and link to the Zenodo record for it.
Registering with the Python Package Index (PyPI)
You only have to do the following steps once.
- Register for an account on the Python Package Index (PyPI)
- 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
- 2-Factor authentication is required for PyPI since the end of 2023 (see this blog post from PyPI). This means you have to first issue account recovery codes, then set up 2-factor authentication
- Issue an API token from https://pypi.org/manage/account/token
Related Skills
node-connect
346.4kDiagnose OpenClaw node connection and pairing failures for Android, iOS, and macOS companion apps
frontend-design
107.2kCreate distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, or applications. Generates creative, polished code that avoids generic AI aesthetics.
openai-whisper-api
346.4kTranscribe audio via OpenAI Audio Transcriptions API (Whisper).
qqbot-media
346.4kQQBot ๅฏๅชไฝๆถๅ่ฝๅใไฝฟ็จ <qqmedia> ๆ ็ญพ๏ผ็ณป็ปๆ นๆฎๆไปถๆฉๅฑๅ่ชๅจ่ฏๅซ็ฑปๅ๏ผๅพ็/่ฏญ้ณ/่ง้ข/ๆไปถ๏ผใ
