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:
- 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.
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)
The most recent release can be installed from PyPI with:
$ pip install curies
This package currently supports both Pydantic v1 and v2. See the Pydantic migration guide for updating your code.
Warning
Pydantic v1 support will be dropped on October 31st, 2024,
coincident with the obsolescence of Python 3.8.
This will be accompanied by the v0.8.0 release of the curies
package.
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.
See developer instructions
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/cthoyt/curies.git
$ cd curies
$ pip install -e .
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.
The documentation can be built locally using the following:
$ git clone git+https://github.com/cthoyt/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 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
.
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/curies/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.