Changelog
=========

Version 0.2.1
-------------

* **Shrinkage parity fix:** cross-gene ``overdispersion_shrinkage`` now uses
  ``gene_means = rowMeans(Mu)`` from the first-pass beta with rough dispersion
  (R ``glm_gp``), not the post-OD intercept. Intercept med |Δ| vs R on
  GSE288946 step-1 drops from ~10\ :sup:`-4` to ~10\ :sup:`-9` (100% within
  0.01).
* **Evaluation docs:** benchmark tables and :doc:`evaluation` narrative updated
  to reflect shrinkage-aligned intercept parity.

Version 0.2.0
-------------

* **OpenMP parallel fitting**: per-gene C++ loop uses ``schedule(dynamic, 16)``;
  ~**7×** faster than R on GSE288946 SCT step-1 (2000×2000, 8 threads) with
  unchanged ``theta`` / ``Intercept`` parity.
* **Native CSR sparse path**: scipy CSR matrices are fitted in place (no
  ``toarray()``); implicit zero cells still contribute to the likelihood.
  ``sort_indices()`` is applied so gene/cell slicing preserves R parity.
* **Evaluation documentation**: paper-style :doc:`evaluation` page with
  synthetic and real-data benchmark tables (regenerate via
  ``python scripts/run_all_benchmarks.py``).
* **Release automation**: GitHub Actions ``auto-release.yml`` publishes to PyPI
  on ``v*`` tags; Read the Docs builds from ``.readthedocs.yaml``.
* **Fix RTD build**: set Sphinx ``version`` in ``conf.py`` (inventory dump).

Version 0.1.0
-------------

* Initial release: C++ reimplementation of ``sctransform::fit_glmGamPoi_offset``
  with Cox–Reid overdispersion MLE, ``allow_inf_theta``, cross-gene shrinkage,
  and trackcell-compatible ``fit_offset_model`` API.