https://github.com/cthoyt/semantic-pydantic
Annotate data models in Pydantic and APIs in FastAPI with the Bioregistry to make them more FAIR
https://github.com/cthoyt/semantic-pydantic
Last synced: 21 days ago
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Annotate data models in Pydantic and APIs in FastAPI with the Bioregistry to make them more FAIR
- Host: GitHub
- URL: https://github.com/cthoyt/semantic-pydantic
- Owner: cthoyt
- License: mit
- Created: 2024-01-09T15:06:01.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-10T02:26:46.000Z (3 months ago)
- Last Synced: 2025-04-12T10:14:58.399Z (about 1 month ago)
- Language: Python
- Homepage: https://semantic-pydantic.readthedocs.io
- Size: 433 KB
- Stars: 5
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- Funding: .github/FUNDING.yml
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
Semantic Pydantic
Annotate your data models in Pydantic and APIs in FastAPI with the Bioregistry to make them more FAIR
## 💪 Getting Started
You can use one of the several extensions to Pydantic and FastAPI's `Field` classes.
```python
from pydantic import BaseModel, Field
from semantic_pydantic import SemanticField
class Scholar(BaseModel):
"""A model representing a researcher, who might have several IDs on different services."""
orcid: str = SemanticField(..., prefix="orcid")
name: str = Field(..., example="Charles Tapley Hoyt")
wos: str | None = SemanticField(default=None, prefix="wos.researcher")
dblp: str | None = SemanticField(default=None, prefix="dblp.author")
github: str | None = SemanticField(default=None, prefix="github")
scopus: str | None = SemanticField(default=None, prefix="scopus")
semion: str | None = SemanticField(default=None, prefix="semion")
publons: str | None = SemanticField(default=None, prefix="publons.researcher")
authorea: str | None = SemanticField(default=None, prefix="authorea.author")
```
Similarly, this can be used in FastAPI.
```python
from fastapi import FastAPI
from semantic_pydantic import SemanticPath
app = FastAPI(title="Semantic Pydantic Demo")
Scholar = ... # defined before
@app.get("/api/orcid/{orcid}", response_model=Scholar)
def get_scholar_from_orcid(orcid: str = SemanticPath(prefix="orcid")):
"""Get xrefs for a researcher in Wikidata, given ORCID identifier."""
... # full implementation in https://github.com/cthoyt/semantic-pydantic
return Scholar(...)
```
Here's what the Swagger UI looks like, including all the annotations on both the data model and endpoint arguments.
The demo can be run by cloning the repository, installing its requirements, and
running the self-contained `demo.py`.
## 🚀 Installation
The most recent release can be installed from
[PyPI](https://pypi.org/project/semantic_pydantic/) with:
```console
$ python3 -m pip install semantic_pydantic
```
The most recent code and data can be installed directly from GitHub with:
```shell
$ python3 -m pip install git+https://github.com/cthoyt/semantic-pydantic.git
```
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.md](https://github.com/cthoyt/semantic-pydantic/blob/master/.github/CONTRIBUTING.md)
for more information on getting involved.
## 👋 Attribution
### ⚖️ License
The code in this package is licensed under the MIT License.
### 💰 Funding
This work was initially funded by the Chan Zuckerberg Initiative (CZI) under award 2023-329850.
### 🍪 Cookiecutter
This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/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/semantic-pydantic.git
cd semantic-pydantic
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/cthoyt/semantic-pydantic/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```console
git clone git+https://github.com/cthoyt/semantic-pydantic.git
cd semantic-pydantic
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/cthoyt/semantic-pydantic
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/semantic_pydantic/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/semantic-pydantic/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.