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

For development, create a fresh Python environment; this should not contain the PyPI-published version of the package.

PyPI publishing

pip install hatch
pip install keyrings.alt

hatch build
hatch publish -r https://upload.pypi.org/legacy/

Username: __token__ Password: {API token for PyPI}

Running pytest tests

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

• Install pytest in 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=loadfile

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.