Pigeon

Pigeon is a tool that generates SBOL compliant visualizations from text scripts. This readme provides instructions on how to install and use Pigeon.

Installation

Make sure you have the following dependency installed:

graphviz Detailed Instructions

From source

Clone the repository.
Install the project and dependencies by running pip install -e . or poetry install (if you want to actively edit the project).
If using Poetry, activate the shell with poetry shell, then run pigeon <your_pigeon_script>.txt to generate the SVGs.

If you only want to install and use the project without any development, simply run pip install ..

Command Line Interface

To run Pigeon from the command line, use the following command:

pigeon <your_pigeon_script>.txt

If you have installed the project, a softlink for pigeon should be added. If you encounter any issues, you can use python cmdline.py instead.

By default, Pigeon generates an SVG with the same name as the pigeon script passed in and saves it in the project repository. For example, if you run:

pigeon pigeon_script.txt

Pigeon will generate and save an image called pigeon_script.svg in the same folder.

You can also specify additional configuration options when using Pigeon, including:

Image name
Image format (png, pdf, or svg)
Image location

For example:

python cmdline.py -name=my_image -format=png -location=/path/to/myFolder pigeon_script.txt

This will generate an image named my_image.png and save it in the /myFolder directory.

Code Integration (see cmdline.py for example)

To integrate Pigeon into your code, follow these steps:

Check pyproject.toml to ensure all required dependencies are installed.
Import Pigeon (see class specifications in Pigeon.py).
Create a parser, generate and save the image using the following code:

parser = Pigeon.Pigeon(image_format) # If no format is specified, the default is SVG.
parser.parseAndGenerateImage(script_string) # The script is passed as a string to the parsing function.
parser.save(image_location, image_name) # Saves the image with the name 'image_name' in the folder specified by 'image_location'.

Web Setup (To be updated)

To set up Pigeon with Flask, follow these steps:

Set Flask variables:

export FLASK_ENV=development
export FLASK_APP=server.py

Run the application:

flask run