https://github.com/synbiodex/pysbol2

A pure Python implementation of the SBOL standard.
https://github.com/synbiodex/pysbol2

Last synced: 4 days ago
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A pure Python implementation of the SBOL standard.

• Host: GitHub
• URL: https://github.com/synbiodex/pysbol2
• Owner: SynBioDex
• License: apache-2.0
• Created: 2019-05-03T21:46:05.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2024-04-11T18:18:24.000Z (9 months ago)
• Last Synced: 2024-04-14T10:00:50.074Z (9 months ago)
• Language: Python
• Size: 9.72 MB
• Stars: 20
• Watchers: 5
• Forks: 6
• Open Issues: 30
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.txt

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README

        
# pySBOL2

[![Build Status](https://travis-ci.org/SynBioDex/pySBOL2.svg?branch=master)](https://travis-ci.org/SynBioDex/pySBOL2)

[![Documentation Status](https://readthedocs.org/projects/pysbol/badge/?version=latest)](https://pysbol.readthedocs.io/en/latest/?badge=latest)

**pySBOL2** is a pure Python implementation of the

SBOL 2.3.0 standard [Synthetic Biology Open Language (SBOL)](https://sbolstandard.org/) - 

an open standard for the representation of *in silico* biological designs. It draws from [libSBOL](https://github.com/SynBioDex/libSBOL)

and [pySBOL](https://github.com/SynBioDex/pySBOL).

This native Python library is intended to eventually supplant the original [pySBOL](https://github.com/SynBioDex/pySBOL) based on C++ wrappers.

For developers, please see [CONTRIBUTING.md](CONTRIBUTING.md).

## INSTALLATION

Use [pip](https://pip.pypa.io/) to install pySBOL2:

```shell

pip install sbol2

```

If you get a permission error, try using the `--user` flag:

```shell

pip install --user sbol2

```

### Java dependency for offline validation/conversion

By default, pySBOL2 executes its validation and conversion with the online validator/converter. 

These can also be done offline using the Java JAR file packaged with the library.

Java requirements are: openjdk8 or later 

Java location defaults to `/usr/bin/java`, and can be adjusted by setting the `JAVA_LOCATION` config option:

```

Config.setOption(ConfigOptions.JAVA_LOCATION, '/my/java/path')

```

## CODE EXAMPLE

This short example creates a Document, adds a ComponentDefinition

to the Document, and then writes the resulting Document to an SBOL

file. Other examples are in the [examples](examples) directory.

```

import sbol2

doc = sbol2.Document()

cd = sbol2.ComponentDefinition('cd1')

doc.add(cd)

doc.write('my-sbol.xml')

```

## UNIT TESTS

The unit tests are not included when installing via pip. The unit

tests are included in the source distribution. To access and

run the unit tests without [checking out from git](CONTRIBUTING.md),

download the source distribution, unpack it, and run the unit tests.

```shell script

pip download --no-binary sbol2 sbol2

tar zxf sbol2-VERSION.tar.gz

cd sbol2-VERSION

python3 -m unittest discover test

```

## DOCUMENTATION

[Full documentation for pySBOL2 is available here](https://pysbol.readthedocs.io).

## ACKNOWLEDGEMENTS

Development of this library has been supported by the 

[DARPA Synergistic Discovery and Design (SD2)](https://www.darpa.mil/program/synergistic-discovery-and-design)

program and [Raytheon BBN Technologies](http://bbn.com/).