Histopathology BIM-DES integration demo

Maintainer: Yin-Chi Chan, Institute for Manufacturing, University of Cambridge

Authors:

• Yin-Chi Chan, University of Cambridge (BIM-DES integration, simulation modules)
• Nicola Moretti, University College London (BIM-DES integration)

Developer Setup

VSCode and WSL2 (for Windows users)

It is recommended to work on this project using Visual Studio Code with WSL2, which provides a Linux environment on Windows. See this tutorial on how to set up VSCode and WSL2.

Cloning the repository

git clone https://github.com/yinchi/histopath-bim-des.git
cd histopath-bim-des

# Open the newly cloned repo in VS Code
code .

Installing the project and its dependencies

This project uses the Poetry package manager. To set up the project on your local computer, run:

# Installs poetry system-wide 
sudo apt install python3-poetry
# optional
poetry config virtualenvs.in-project true

poetry install

Other useful Poetry commands include add, remove, and run. As this project is not meant to be used as a library, the build and publish commands are not recommended.

scripts.sh

scripts.sh contains functions for Sphinx documentation. To use these, run the following in bash:

poetry shell

# in the new bash subshell:

source scripts.sh
clean-docs  # reset the /docs directory
build-docs
serve-docs  # defaulting to port 8000

# use CTRL+D to exit to the base shell.

scripts.sh also provides projroot() for quickly changing to the root of the project directory, as well as adding script/ to the PATH environment variable.