ad_sdl.wei 0.5.1.dev0

The Rapid Prototyping Laboratory's Workcell Execution Interface.

wei

The Workcell Execution Interface (WEI) for Autonomous Discovery/Self Driving Laboratories (AD/SDLs)

For more details and specific examples of how to use wei, please see our documentation.

Table of Contents

• wei
  • Table of Contents
  • Installation
    • Bare-Metal Install
    • Docker Install
  • Usage
  • Development
  • Contributing
  • Acknowledgments
  • License

Installation

There are 2 options for installing WEI:

• A bare-metal install, which can be used in most contexts where python can run.
• A containerized install using docker and docker-compose

Bare-Metal Install

1. Clone the repository.
2. If using WEI as a library (for instance, as a dependency for a specific module), skip to step 5.
3. If you intend to run the WEI engine and server, install Redis
4. If you intend to run the examples, you'll need to install TMUX
5. Within the cloned repository, run the following:

sudo apt install redis
sudo apt install tmux
pip3 install --upgrade pip
git clone https://github.com/AD-SDL/wei/
cd wei
# For just WEI and its core dependencies
pip3 install -e .
# Or, with support for the examples:
pip3 install -e '.[examples]'

Docker Install

1. Install Docker for your platform of choice
2. Clone the repository.
3. Within the cloned repository, run the following:

docker/build_wei.sh

Usage

Running the Examples (Bare-Metal Install)

1. Run examples/run_examples.sh
2. In the corresponding TMUX session, you should see a number of windows corresponding to each component of WEI. Check each tab to ensure the servers are up and operating properly
3. In the last window, you should see a python command pre-populated. Press enter to run this example experiment script
4. If you have an attached webcam, you can change the SIMULATED flag in examples/experiment_example.py to False to test taking an actual picture.

Running the Examples (Docker Install)

1. Run docker/start_wei.sh
2. In your browser, navigate to localhost:8888
3. Enter wei as the token
4. Navigate to examples/experiment_example.ipynb and run the cells in the Jupyter Notebook to run an example WEI Experiment
5. If you have an attached webcam, you can change the SIMULATED flag to False to test taking an actual picture.

Development

1. First, install pdm.
2. Next, run the following in the cloned repo's directory:

pip install pre-commit ruff
pdm install
pre-commit install

Using Pre-commit

• To run pre-commit checks before committing, run pre-commit run --all-files
• NONE OF THE FOLLOWING SHOULD BE DONE REGULARLY, AND ALL CHECKS SHOULD BE PASSING BEFORE BRANCHES ARE MERGED
  • To skip linting during commits, use SKIP=ruff git commit ...
  • To skip formatting during commits, use SKIP=ruff-format git commit ...
  • To skip all pre-commit hooks, use git commit --no-verify ...
• See pre-commit documentation for more

Using pdm

• Managing Dependencies
• Build and Publish
• Running Using PDM
  • pdm run engine <args> to start the WEI engine
  • pdm run server <args> to start the WEI server
  • pdm run <arbitrary command> to run an arbitrary command inside the python environment

Contributing

Please report bugs, enhancement requests, or questions through the Issue Tracker.

If you are looking to contribute, please see CONTRIBUTING.md.

Citing

@Article{D3DD00142C,
author ="Vescovi, Rafael and Ginsburg, Tobias and Hippe, Kyle and Ozgulbas, Doga and Stone, Casey and Stroka, Abraham and Butler, Rory and Blaiszik, Ben and Brettin, Tom and Chard, Kyle and Hereld, Mark and Ramanathan, Arvind and Stevens, Rick and Vriza, Aikaterini and Xu, Jie and Zhang, Qingteng and Foster, Ian",
title  ="Towards a modular architecture for science factories",
journal  ="Digital Discovery",
year  ="2023",
pages  ="-",
publisher  ="RSC",
doi  ="10.1039/D3DD00142C",
url  ="http://dx.doi.org/10.1039/D3DD00142C",
abstract  ="Advances in robotic automation{,} high-performance computing (HPC){,} and artificial intelligence (AI) encourage us to conceive of science factories: large{,} general-purpose computation- and AI-enabled self-driving laboratories (SDLs) with the generality and scale needed both to tackle large discovery problems and to support thousands of scientists. Science factories require modular hardware and software that can be replicated for scale and (re)configured to support many applications. To this end{,} we propose a prototype modular science factory architecture in which reconfigurable modules encapsulating scientific instruments are linked with manipulators to form workcells{,} that can themselves be combined to form larger assemblages{,} and linked with distributed computing for simulation{,} AI model training and inference{,} and related tasks. Workflows that perform sets of actions on modules can be specified{,} and various applications{,} comprising workflows plus associated computational and data manipulation steps{,} can be run concurrently. We report on our experiences prototyping this architecture and applying it in experiments involving 15 different robotic apparatus{,} five applications (one in education{,} two in biology{,} two in materials){,} and a variety of workflows{,} across four laboratories. We describe the reuse of modules{,} workcells{,} and workflows in different applications{,} the migration of applications between workcells{,} and the use of digital twins{,} and suggest directions for future work aimed at yet more generality and scalability. Code and data are available at https://ad-sdl.github.io/wei2023 and in the ESI."}

License

WEI is MIT licensed, as seen in the LICENSE file.