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Excel-to-SBOL\n\n**Excel-to-SBOL** is an open source python library that converts [Excel Templates](https://github.com/SynBioDex/Excel-to-SBOL/tree/master/excel2sbol/resources/templates) to [SBOL](https://sbolstandard.org/) documents.\n\nA similar utility developed for SBOL3 support (developed by Jake Beal) is [SBOL-utilities](https://github.com/SynBioDex/SBOL-utilities).\n\nFor further depth and information on Excel-to-SBOL, including how to contribute to the project, visit the [Excel-to-SBOL wiki on github](https://github.com/SynBioDex/Excel-to-SBOL/wiki)\n\n\n\n# Table of Contents\n- [Installation \u0026 How to Use](#installation--how-to-use)\n    - [Installation](#installation)\n    - [How to Use](#how-to-use)\n- [Example Conversion](#example-conversion)\n- [Architecture](#architecture)\n- [Publishing](#publishing)\n\n\u003c!-- # Interface\n\n![VisBOL Example Visualization](./images/example.png) --\u003e\n\n# Excel-to-SBOL: Installation \u0026 How to use\n\n## Installation\n\nExcel-to-SBOL can be installed using `pip install excel2sbol`\n\nTo get the latest version you can use `git clone https://github.com/SynBioDex/Excel-to-SBOL` followed by `cd .\\excel2sbol` and `python setup.py install`\n\n## How to use\n\n**1) Choose an Excel Template**\nChoose an excel template from the [templates folder](https://github.com/SynBioDex/Excel-to-SBOL/tree/master/excel2sbol/resources/templates).\nWe suggest choosing the latest version (dates are given at the end of the file names in the form yyyymmdd). Fill out the template as the instructions indicate.\n\n**2) Install the Converter**\nThere are several ways to install the converter. The easiest is via pip: `pip install excel2sbol` but it can also be done by [cloning the repository](https://github.com/SynBioDex/Excel-to-SBOL/wiki/2.-Cloning-From-GitHub).\n\n**3) Run the Converter**\nUse the code below substituting {things in curly brackets} with the appropriate values.\n\n```\nimport excel2sbol.converter_function as conf\n\nconf.converter({template_name}, {file_path_in}, {file_path_out})\n```\n\nAn example:\n\n```\nimport excel2sbol.converter_function as conf\n\nconf.converter(\"excel2bol_darpa_template_blank_v005_20220222.xlsx\",\n               \"C:/Users/Test_User/Downloads/Filled_Template.xlsx\",\n               \"C:/Users/Test_User/Downloads/Output_SBOL.xml\")\n```\nTip: the use of `os.getcwd()` and `os.path.join` is reccommended for the creation of the file paths. This is safer from a cybersecurity stand point and provide better operating system interoperability.\n\n**4) Use the output file**\nThe SBOL file that is output can then be used by further [SBOL tools](https://sbolstandard.org/applications/) or uploaded to an SBOL repository like [SynBioHub](https://synbiohub.org/).\n\n# Example Conversion\n\nA data-filled [spreadsheet](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/excel2sbol/tests/test_files/pichia_toolkit_KWK_v002.xlsx) was converted to an [SBOL file](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/excel2sbol/tests/test_files/pichia_toolkit_KWK_v002.xml) and subsequently [uploaded to SynBioHub](https://synbioks.org/public/pichia_toolkit_KWK/pichia_toolkit_KWK_collection/1).\n\n**Example Spreadsheet**\n![Example Spreadsheet](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/images/excel2sbol_spreadsheet.PNG)\n\n**Example SBOL**\n![Example SBOL](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/images/excel2sbol_xml.PNG)\n\n**Example SynBioHub Upload**\n![Example SynBioHub](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/images/excel2sbol_synbiohub.PNG)\n\n# Architecture\n\nThe [repository architecture and module architecture](https://github.com/SynBioDex/Excel-to-SBOL/wiki/4.-Excel2SBOL-Module-and-Repository-Architecture) are described in the wiki.\n\n# Publishing\n\nA new version of the python package is automatically published via [the python-publish GitHub action](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/.github/workflows/python-publish.yml) whenever a new release is created.\n\nAlternatively you can also make changes to the package and then use it locally:\n1. 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