Popari: a probabilistic graphical model for integrated spatial transcriptomics analysis
Project description
Popari
Popari is a versatile framework for joint analysis and investigation of complex spatial transcriptomics datasets. Read the documentation (including installation instructions) here.
:warning: 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:
- Navigate to
docs/
.
cd docs/
- Install Sphinx requirements.
pip install -r requirements.txt
- Clean and build.
make clean
make html
- Push to GitHub, and documentation will automatically build.
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Source Distribution
popari-0.0.72.tar.gz
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