Installation#

Requirements#

  • Python 3.10+

  • C++17 compiler, CMake, and OpenMP (recommended for multi-core)

  • NumPy, pandas, SciPy

Set OMP_NUM_THREADS before importing pyglmGamPoi to control parallelism (e.g. export OMP_NUM_THREADS=8).

PyPI install#

pip install pyglmGamPoi

Current release: 0.2.1 — see Changelog and Evaluation.

Documentation: https://pyglmgampoi.readthedocs.io/

Editable install#

git clone https://github.com/seqyuan/pyglmGamPoi.git
cd pyglmGamPoi
pip install -e ".[test]"

Run tests#

pytest tests/ -q

Optional R parity tests (requires glmGamPoi and sctransform in R):

pytest tests/test_parity_r.py -m parity_r
pytest tests/test_theta_od_parity.py -q

Regenerate golden OD fixtures (tcl_test + conda env st):

python scripts/export_theta_od_golden.py