Popari is a versatile framework for joint analysis and investigation of complex spatial transcriptomics datasets. Read the documentation (including installation instructions) here.
Popari requires CUDA-capable GPU hardware as a prerequisite. At least ~10 GB of GPU memory - for example, as provided by an NVIDIA GeForce RTX 2080 Ti chip - is necessary for most applications.
Click to expand dev instructions!
For development, create a fresh Python environment; this should not contain the PyPI-published version of the package.
pip install hatch
pip install keyrings.alt
hatch build
hatch publish -r https://upload.pypi.org/legacy/
Username: __token__
Password: {API token for PyPI}
To run the provided tests and ensure that Popari can run on your platform, follow the instructions below:
- Install
pytestin your environment.
pip install pytest- Navigate to the root directory of this repo, and run all tests with
python -m pytest -s- Alternatively, run a single test suite as below:
python -m pytest -s tests/test_popari_shared.py- To run tests in parallel, try
python -m pytest -n 4 --dist=loadfileAssuming 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.