# libsbgnpy

> Python library for the Systems Biology Graphical Notation (SBGN)

The links below point to the markdown source of the documentation. [llms-full.txt](https://matthiaskoenig.github.io/libsbgnpy/llms-full.txt) contains all of it in a single file.

## Documentation

- [Home](https://matthiaskoenig.github.io/libsbgnpy/index.md): `libsbgnpy` is a python library to work with the Systems Biology Graphical Notation (SBGN).
- [Installation](https://matthiaskoenig.github.io/libsbgnpy/installation.md): `libsbgnpy` requires python >= 3.11 and is available from pypi.
- [Contributing](https://matthiaskoenig.github.io/libsbgnpy/development.md): Contributions are welcome.

## User guide

- [SBGN maps](https://matthiaskoenig.github.io/libsbgnpy/maps.md): The classes of `libsbgnpy.sbgn` are the python bindings of the SBGN-ML schema, generated with xsdata.
- [Reading and writing](https://matthiaskoenig.github.io/libsbgnpy/io.md): SBGN-ML documents are read and written with the functions of `libsbgnpy.io`, which use xsdata to map the XML onto the classes of `libsbgnpy.sbgn`.
- [Notes and extensions](https://matthiaskoenig.github.io/libsbgnpy/extensions.md): Every SBGN element inherits from `Sbgnbase` and therefore carries two containers for content the schema does not describe itself.
- [Render information](https://matthiaskoenig.github.io/libsbgnpy/render.md): SBGN says what a map means, not what it looks like.
- [Validation](https://matthiaskoenig.github.io/libsbgnpy/validation.md): Reading a document parses it, it does not check that it follows the SBGN-ML schema.
- [Images](https://matthiaskoenig.github.io/libsbgnpy/images.md): `libsbgnpy` does not draw maps itself.

## API reference

- [Overview](https://matthiaskoenig.github.io/libsbgnpy/api/index.md): The API reference is generated from the docstrings of the package.
- [sbgn](https://matthiaskoenig.github.io/libsbgnpy/api/sbgn.md): Python bindings of the SBGN-ML schema.
- [render](https://matthiaskoenig.github.io/libsbgnpy/api/render.md): Python bindings of the render extension used by SBGN-ML.
- [io](https://matthiaskoenig.github.io/libsbgnpy/api/io.md): Reading and writing of SBGN documents.
- [validator](https://matthiaskoenig.github.io/libsbgnpy/api/validator.md): Validation of SBGN documents against the SBGN XSD schema.
- [image](https://matthiaskoenig.github.io/libsbgnpy/api/image.md): Rendering of SBGN documents as images.
- [console](https://matthiaskoenig.github.io/libsbgnpy/api/console.md): Shared rich console.
- [log](https://matthiaskoenig.github.io/libsbgnpy/api/log.md): Logging of the package.

## Optional

- [Repository](https://github.com/matthiaskoenig/libsbgnpy): source code, issues and releases.
- [Sitemap](https://matthiaskoenig.github.io/libsbgnpy/sitemap.xml): all pages of the rendered site.
- [objects.inv](https://matthiaskoenig.github.io/libsbgnpy/objects.inv): the API objects of the reference as a sphinx inventory.