Installation

Installing under VS Code

You will need three things for this extension

  1. VS Code

  2. Anaconda python

  3. PyBioNetGen

First, download and install VS Code. The suggested way to install this VS Code extension is from the VS Code marketplace. Simply open the Extensions tab (or press CTRL/CMD + SHIFT + X) after openinng VS Code and search for Bionetgen. This package will show up, click install. If this step doesn’t work, please make sure you have the latest version.

Next you will need Python installed and you need to have your terminal environment set correctly. We recommend anaconda python since the rest of the workshop will make use of libraries that come with this distribution. Download and install anaconda python. In VS Code, open a new terminal (CTRL/CMD + ` or under Terminal -> New Terminal) and test if you have access to Python package manager pip. If you don’t, you need to setup your environment so that the terminal has access to pip, this is OS dependent and there are various guides you can find online.

Finally once you have access to pip, run pip install bionetgen. Once complete, make sure it’s installed correctly by running bionetgen -h. You can find more information on installation here.

Debug mode

Please note that this section is only if you can’t use the method above or are a developer working on the extension. There are two other ways to use the extension:

To use the extension in debug mode:

  1. Download and install VS Code from https://code.visualstudio.com

  2. Open VS Code and open a new terminal

    • Terminal -> New Terminal, or

    • CTRL/CMD + `

  3. In the terminal, run this line: git clone https://github.com/RuleWorld/BNG_vscode_extension.git to clone the repository in the desired directory

  4. File -> Open to open the repository folder (BNG_vscode_extension)

  5. To open up a new window running the extension

    • Run -> Start Debugging, or

    • F5

  6. Open an existing .bngl file or create a new file with .bngl extension