alam-shahul / popari

Popari

Popari is a versatile framework for joint analysis and investigation of complex spatial transcriptomics datasets. Read the documentation (including installation instructions) here.

⚠️ Popari is still under active development. Check back in a bit for a more complete user experience!

Dev Instructions

Install

pip install popari

Publishing

pip install hatch
pip install keyrings.alt

hatch build
hatch publish

Username: __token__ Password: {API token for PyPI}

Tests

To run the provided tests and ensure that SpiceMix can run on your platform, follow the instructions below:

• Download this repo.

git clone https://github.com/alam-shahul/SpiceMixPlus.git

• Install pytest in your environment.

pip install pytest

• Navigate to the root directory of this repo.
• Run the following command. With GPU resources, this test should execute without errors in ~2.5 minutes:

python -m pytest -s tests/test_popari_shared.py

Building Documentation

Assuming you have CMake:

1. Navigate to docs/.

cd docs/

2. Install Sphinx requirements.

pip install -r requirements.txt

3. Clean and build.

make clean
make html

4. Push to GitHub, and documentation will automatically build.