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https://github.com/biopragmatics/curies

🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python

https://github.com/biopragmatics/curies

Science Score: 36.0%

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
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
    Links to: zenodo.org
  • ○
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.8%) to scientific vocabulary

Keywords

curies obofoundry semantic-web uris

Keywords from Contributors

linkml owl knowledge-graph ontologies monarchinitiative linked-data rdf large-language-models information-extraction bioregistry
Last synced: 6 months ago · JSON representation

Repository

🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python

Basic Info
Statistics
  • Stars: 24
  • Watchers: 4
  • Forks: 6
  • Open Issues: 12
  • Releases: 69
Topics
curies obofoundry semantic-web uris
Created over 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing Funding License Code of conduct

README.md

CURIEs

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

Idiomatic conversion between URIs and compact URIs (CURIEs).

```python import curies

converter = curies.loadprefixmap({ "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:

```shell

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:

  1. A pre-defined prefix map to get from the web (bioregistry, go, obo, monarch, prefixcommons)
  2. 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.

🧑‍🤝‍🧑 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)

🚀 Installation

The most recent release can be installed from PyPI with:

console 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.

👐 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.

👋 Attribution

🙏 Acknowledgements

This package heavily builds on the trie data structure implemented in pytrie.

⚖️ License

The code in this package is licensed under the MIT License.

🍪 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/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: ```console $ 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: ```console python3 -m pip install cruft cruft update ``` More info on Cruft's update command is available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project). ### 🥼 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: ```console tox -e py ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/biopragmatics/curies/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```console 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`](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). #### Configuring ReadTheDocs 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! ### 📦 Making a Release #### Configuring Zenodo [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI to each release of your package. 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/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. 1. Register for an account on the [Python Package Index (PyPI)](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 #### Configuring your machine's connection to PyPI You have to do the following steps 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`. #### Uploading to PyPI After installing the package in development mode and installing `tox` with `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/curies/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/biopragmatics/curies/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.

Owner

  • Name: Biopragmatics Stack
  • Login: biopragmatics
  • Kind: organization

Software supporting biomedical semantics and pragmatics

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Last Year
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Nico Matentzoglu n****u@g****m 1
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 113,224 last-month
  • Total docker downloads: 1,262
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pypi.org: curies

Idiomatic conversion between URIs and compact URIs (CURIEs)

  • Versions: 70
  • Dependent Packages: 18
  • Dependent Repositories: 29
  • Downloads: 113,224 Last month
  • Docker Downloads: 1,262
Rankings
Dependent packages count: 0.8%
Downloads: 2.1%
Dependent repos count: 2.7%
Docker downloads count: 3.8%
Average: 6.8%
Forks count: 15.4%
Stargazers count: 16.1%
Maintainers (1)
cthoyt
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Last synced: 6 months ago

Dependencies

.github/workflows/tests.yml actions
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