Install

This tutorial is for MacOS users. For Windows/Linux, take a look at this section.

Install Poetry and Python 3.12

brew install poetry
brew install python@3.12

Clone the repo
```
git clone ...
cd digilut
```
The project makes use of PyFAST for slide processing. Follow this tutorial. For MacOS users, here is the command to run
```
brew install openslide libomp
```
Create a virtual environment
```
poetry install --with docs,dev
```

Test your installation

source $(poetry env info --path)/bin/activate 
digilut --help

You should be prompted something like:

Usage: digilut [OPTIONS] COMMAND [ARGS]...                                                                                                        

Entrypoint of Digilut's main CLI.                                                                                                                 

╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --install-completion          Install completion for the current shell.                                                                         │
│ --show-completion             Show completion for the current shell, to copy it or customize the installation.                                  │
│ --help                        Show this message and exit.                                                                                       │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ clean-bbox    Remove obvious labelling mistakes from the input bounding box csv and save a new cleaned dataset csv.                             │
│ credits       Print credits with style.                                                                                                         │
│ pyfast        Pyfast processing commands to patchify .tif WSI images.                                                                           │
│ tiles         Commands for tiles.                                                                                                               │
│ undersample   Undersample patches to solve class imbalance                                                                                      │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯