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.
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:
--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.
Other packages that convert between CURIEs and URIs:
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.
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
This package heavily builds on the trie
data structure implemented in pytrie.
The code in this package is licensed under the MIT License.
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
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/biopragmatics/curies.git
cd curies
python3 -m pip install -e .
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.
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.
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.
Zenodo is a long-term archival system that assigns a DOI to each release of your package.
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.
You only have to do the following steps once.
You have to do the following steps once per machine.
$ 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.
After installing the package in development mode and installing
tox with python3 -m pip install tox tox-uv,
run the following from the console:
tox -e finish
This script does the following:
pyproject.toml, CITATION.cff, src/curies/version.py,
and docs/source/conf.py to not have the -dev suffixuv builduv publish.tox -e bumpversion -- minor after.This will trigger Zenodo to assign a DOI to your release as well.
FAQs
Idiomatic conversion between URIs and compact URIs (CURIEs)
We found that curies demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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