stLearn-tutorials

Tutorials used for stLearn documentation.

Setup

• Make sure you have git lfs installed and inited as there are some large files in annotations.

Conda Environment

Create

conda create --prefix [some-directory]/conda/stlearn python=3.12 --y
conda activate [some-directory]/conda/stlearn

Install stlearn:

pip install -e "/path/to/stlearn/directory[jupyter]"

OR

python -m pip install --use-pep517 stlearn==1.4.1

python -m pip install --use-pep517 papermill harmonypy==0.2.0

Running

Witht the stlearn conda enviroment activate run:

process.sh

The upload expects a zip file called "tutorials.zip" with notebooks in the tutorials directory.

Remove

conda env remove --prefix [some-directory]/conda/stlearn --y