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pySBOL2\n![gh-action badge](https://github.com/SynBioDex/pySBOL2/workflows/Python%20package/badge.svg)\n![readthedocs badge](https://readthedocs.org/projects/pysbol2/badge/)\n\n**pySBOL2** is a pure Python implementation of the\nSBOL 2.3.0 standard [Synthetic Biology Open Language (SBOL)](https://sbolstandard.org/) - \nan open standard for the representation of *in silico* biological designs. It draws from [libSBOL](https://github.com/SynBioDex/libSBOL)\nand [pySBOL](https://github.com/SynBioDex/pySBOL).\n\nThis native Python library is intended to eventually supplant the original [pySBOL](https://github.com/SynBioDex/pySBOL) based on C++ wrappers.\n\nFor developers, please see [CONTRIBUTING.md](CONTRIBUTING.md).\n\n## INSTALLATION\n\nUse [pip](https://pip.pypa.io/) to install pySBOL2:\n\n```shell\npip install sbol2\n```\n\nIf you get a permission error, try using the `--user` flag:\n\n```shell\npip install --user sbol2\n```\n\n### Java dependency for offline validation/conversion\n\nBy default, pySBOL2 executes its validation and conversion with the online validator/converter. \nThese can also be done offline using the Java JAR file packaged with the library.\n\nJava requirements are: openjdk8 or later \n\nJava location defaults to `/usr/bin/java`, and can be adjusted by setting the `JAVA_LOCATION` config option:\n\n```\nConfig.setOption(ConfigOptions.JAVA_LOCATION, '/my/java/path')\n```\n\n## CODE EXAMPLE\n\nThis short example creates a Document, adds a ComponentDefinition\nto the Document, and then writes the resulting Document to an SBOL\nfile. Other examples are in the [examples](examples) directory.\n\n```\nimport sbol2\n\ndoc = sbol2.Document()\ncd = sbol2.ComponentDefinition('cd1')\ndoc.add(cd)\ndoc.write('my-sbol.xml')\n```\n\n## UNIT TESTS\n\nThe unit tests are not included when installing via pip. The unit\ntests are included in the source distribution. To access and\nrun the unit tests without [checking out from git](CONTRIBUTING.md),\ndownload the source distribution, unpack it, and run the unit tests.\n\n```shell script\npip download --no-binary sbol2 sbol2\ntar zxf sbol2-VERSION.tar.gz\ncd sbol2-VERSION\npython3 -m unittest discover test\n```\n\n## DOCUMENTATION\n\n[Full documentation for pySBOL2 is available here](https://pysbol.readthedocs.io).\n\n## ACKNOWLEDGEMENTS\n\nDevelopment of this library has been supported by the \n[DARPA Synergistic Discovery and Design (SD2)](https://www.darpa.mil/program/synergistic-discovery-and-design)\nprogram and [Raytheon BBN Technologies](http://bbn.com/).\n\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"./logo.jpg\" height=\"100\" /\u003e\n\u003c/p\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsynbiodex%2Fpysbol2","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsynbiodex%2Fpysbol2","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsynbiodex%2Fpysbol2/lists"}