PyLabRobot Tutorials BME590

Required software installs

Install Python=3.11
Install Git

Setting up the virtual environment and dependencies

First, set up a virtual environment to prevent conflicts with any other projects. From the terminal:

pip install virtualenv
virtualenv plr_env --python python3.11
source plr_env/bin/activate

Installing PyLabRobot

From the terminal:

git clone https://github.com/PyLabRobot/pylabrobot.git
cd pylabrobot
pip install -e '.[visualizer]'
pip install libusb_package
pip install websockets
cd ..

If you've previously installed PyLabRobot don't repeat the above, just runcd PyLabRobot and git pull.

Now, install jupyterlab and all the other dependencies. Make sure to pip install opentrons with --no-deps.

pip install jupyterlab
pip install pylibftdi
pip install aionotify==0.3.1
pip install pydantic==1.10.9
pip install ipykernel==6.29.3
pip install ipython==8.25.0
pip install pyserial
pip install numpy
pip install opentrons --no-deps
pip install opentrons_shared_data --no-deps

Download the tutorial notebook (do this once)

git clone https://github.com/stefangolas/PyLabRobot_Tutorials_BME590.git

Recommended development environment

It is recommended to use VSCode with the following extensions:

• Python
• Jupyter
• Browser Lite

Install VSCode here

To install extensions on VSCode, click the building block icon on the left side.

Do this every time before you start working

Open a new terminal in VSCode

Now you can start your virtual environment and run jupyter notebook. Open the notebook file from VSCode (File-> Open "PyLabRobot_Tutorials_BME590/...")

From the VSCode terminal:

cd ~
cd pylabrobot
git pull
cd ..
cd PyLabRobot_Tutorials_BME590
git pull
cd ..
source plr_env/bin/activate
jupyter lab

Now you need to connect to the Jupyter kernel.

• Press F1 to open the command search bar and select Notebook: Select Notebook Kernel.
• Select Existing Jupyter Server...
• From the terminal where you started Jupyter Notebook, copy and paste the URL that starts with "127.0.0.1..." into the search bar
• Press Enter through the rest of the options

If you want to view the visualizer in VSCode instead of switching between windows:

• Press F1 and select Browser Lite: Open Window
• Paste the visualizer URL into the Browser Lite window