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
------------

.. code-block:: bash

   pip install pyglmGamPoi

Current release: **0.2.1** — see :doc:`changelog` and :doc:`evaluation`.

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

Editable install
----------------

.. code-block:: bash

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

Run tests
---------

.. code-block:: bash

   pytest tests/ -q

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

.. code-block:: bash

   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``):

.. code-block:: bash

   python scripts/export_theta_od_golden.py