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https://github.com/gold-standard-phantoms/bids-pydantic
Pydantic model generator for BIDS metadata
https://github.com/gold-standard-phantoms/bids-pydantic
Last synced: 2 days ago
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Pydantic model generator for BIDS metadata
- Host: GitHub
- URL: https://github.com/gold-standard-phantoms/bids-pydantic
- Owner: gold-standard-phantoms
- License: mit
- Created: 2023-06-08T14:50:48.000Z (over 1 year ago)
- Default Branch: master
- Last Pushed: 2024-02-06T22:04:30.000Z (9 months ago)
- Last Synced: 2024-10-12T00:41:29.464Z (about 1 month ago)
- Language: Python
- Size: 81.1 KB
- Stars: 5
- Watchers: 2
- Forks: 3
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
- awesome-bids - BIDS-pydantic - pydantic-models](https://pypi.org/project/BIDS-pydantic-models/). (Tools / others)
README
# BIDS-pydantic
## Overview
BIDS-pydantic will pull a specified version (from v1.7.0 onwards, tested up to v1.7.0)
of the BIDS metadata schema which is used in the JSON BIDS sidecar, from the
[official BIDS GitHub page](https://github.com/bids-standard/bids-specification/),
and create corresponding [pydantic](https://pydantic-docs.helpmanual.io/) models, which
will provide BIDS data validation using python type annotations.
Alternatively, the BIDS-pydantic-models package will only install the models for direct
use in your Python software.
More information on the use of the models [can be found here.](./models/README.md)
## Table of Contents
- [Quickstart](#quickstart)
- [Installation](#installation)
- [Usage](#usage)
- [Development](#development)
- [Acknowledgements](#acknowledgements)
- [License](#license)
## How To Contribute
Got a great idea for something to implement in BIDS-pydantic, or maybe you have just
found a bug?
[Create an issue](https://github.com/gold-standard-phantoms/bids-pydantic/issues)
to get in touch with the development team and we’ll take it from there.
## Quickstart
If you just want to use the models in your project. Download the pydantic models file
for the BIDS schema version you wish to use from the [models](models) directory, and
add it to your code-base. These files are generated using the `bids-pydantic make -a`
command (see below).
Alternatively, you can just run:
```sh
$ pip install bids-pydantic-models
```
More information on the use of the models [can be found here.](./models/README.md)
If you want to use the command line tool to generate the models, keep reading this README.
## Installation
Install with:
```sh
$ pip install bids-pydantic
```
BIDS-pydantic can be installed as a module directly from the python package index.
For more information how to use a python package in this
way please see [https://docs.python.org/3/installing/index.html](https://docs.python.org/3/installing/index.html)
### Python Version
We recommend using the latest version of Python. BIDS-pydantic supports Python 3.9 and newer.
### Dependencies
These distributions will be installed automatically when installing BIDS-pydantic.
- [pydantic](https://pydantic-docs.helpmanual.io/)
- [datamodel-code-generator](https://github.com/koxudaxi/datamodel-code-generator)
## Usage
The primary commands can be viewed with the command `bids-pydantic`:
```
usage: bids-pydantic [-h] {list,make} ...
Run one of a set of commands. For example: `bids-pydantic list`, or `bids-pydantic make`. Run either
command with `-h` e.g. `bids-pydantic make -h` to get help for that command.
optional arguments:
-h, --help show this help message and exit
command:
{list,make} subcommand to run
```
The `list` command help can be viewed with the command `bids-pydantic list -h`:
```
usage: bids-pydantic list [-h]
Queries the GitHub API and lists the available supported BIDS schema versions. Only tested up to v1.7.0.
optional arguments:
-h, --help show this help message and exit
```
The `make` command help can be viewed with the command `bids-pydantic make -h`:
```
usage: bids-pydantic make [-h] [--output OUTPUT] [--output-all OUTPUT_ALL]
[--schema-version [SCHEMA_VERSION]]
Make a new python file(s) containing BIDS compliant pydantic models
optional arguments:
-h, --help show this help message and exit
--output OUTPUT, -o OUTPUT
The output python filename to create (will output to stdout console if not
specified).
--output-all OUTPUT_ALL, -a OUTPUT_ALL
Find all parsable schemas and output each to the provided directory. Will create
filenames such as bids_schema_model_v_1_7_0.py, etc. Will overwrite any files in
that directory with the same name.
--schema-version [SCHEMA_VERSION]
The BIDS schema version to use. e.g. 1.7.0 - supported versions can be
discovered using the list command. If a version is not specified v1.7.0 will be
used.
--input INPUT, -i INPUT
Specify an input BIDS metadata (yml) file to use instead of downloading a version
from GitHub. Cannot be used with --schema-version or --output-all
```
## Development
Development dependencies should be installed using `pip install -r requirements/dev.txt -U`, and `pre-commit install` then run to install code-quality Git hooks.
Development should be carried out using Python 3.8. Development must comply with a few code styling/quality rules and processes:
- Before pushing any code, make sure the `CHANGELOG.md` is updated as per the instructions in the `CHANGELOG.md` file. tox should also be run to ensure that tests and code-quality checks pass.
- The README.md file should be updated with any usage or development instructions.
- Ensure that a good level of test coverage is kept. The test reports will be committed to the CI system when testing is run, and these will be made available during code review. If you wish to view test coverage locally, run `coverage report`.
- To ensure these code quality rules are kept to, [pre-commit](https://pre-commit.com/) should be installed (see the `requirements/dev.txt`), and `pre-commit install` run when first cloning this repo. This will install some pre-commit hooks that will ensure any committed code meets the minimum code-quality and is formatted correctly _before_ being committed to Git. This will ensure that tests will pass on CI system after code is pushed. The tools should also be included in any IDEs/editors used, where possible. To run manually, run `precommit run --all-files`. The following software tools will be run:
- [mypy](https://github.com/python/mypy)
- [pylint](https://pylint.org/)
- [black](https://black.readthedocs.io/en/stable/)
- [isort](https://isort.readthedocs.io/en/latest/)
- [pyupgrade](https://github.com/asottile/pyupgrade)
## Acknowledgements
Conversion from schema to pydantic models is carried out using [datamodel-code-generator](https://github.com/koxudaxi/datamodel-code-generator).
Data validation is performed using [pydantic](https://pydantic-docs.helpmanual.io/).
## License
> You can check out the full license [here](LICENSE)
> This project is licensed under the terms of the **MIT** license.