scatrans 0.9.8.dev6__tar.gz → 0.9.9.dev1__tar.gz

{scatrans-0.9.8.dev6 → scatrans-0.9.9.dev1}/CHANGELOG.md

@@ -5,6 +5,31 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.9.9] - 2026-07-04
+
+### Added
+- **`scat.pl.volcano_plot(style=...)`**: ggVolcano-inspired styles from
+  [BioSenior/ggVolcano](https://github.com/BioSenior/ggVolcano) — ``style="ggvolcano"``
+  (teal/grey/orange Up-Down-Normal, theme_bw, FDR labels) and ``style="gradual"``
+  (gradient by ``-log10 FDR``). Default ``style="auto"`` keeps the previous look.
+  Documented in README §3.4 and API reference.
+
+### Fixed
+- **PyDESeq2 pseudobulk tests**: use ``pb_x_layer="counts"`` + ``pb_use_total_for_x=False``
+  (``spliced+unspliced`` sums are non-integer and correctly fail ``strict_pydeseq2_counts``).
+- **MixedLM edge-case test**: design meets ≥4 samples/group after stricter mixed-model gates.
+- **Small-sample edge tests** (`tests/test_small_sample_edges.py`): 1–2 cells/group, all-zero genes.
+- **Regression tests**: ``max_avoid_points`` volcano subsampling, numpy ``raw_gene_list`` enrichment
+  universe, and ``recommend_workflow`` auto-disabling ``use_permutation`` on small pseudobulk designs.
+- **README**: mixed-model small-sample guidance (≥4 samples/group); documented ``paired_replicates``
+  and ``filter_active_genes(preset='significant')``.
+- **`run_enrichment` / `run_kegg` DataFrame `gene_list`**: gene symbols read from index
+  (or ``gene`` / ``names`` columns), not column names.
+- **`run_gsea` DataFrame `ranked_genes`**: index-based ``all_results`` support.
+- **MixedLM**: NaN neutral-fill on degenerate fits; composite ``condition::sample``
+  random-effect groups when replicate labels are reused across conditions (``paired_replicates=True``
+  for paired designs).
+
 ## [0.9.8 bugfix 2026-07-04]
 
 ### Fixed

{scatrans-0.9.8.dev6 → scatrans-0.9.9.dev1}/CITATION.cff

@@ -8,7 +8,7 @@ authors:
 repository-code: "https://github.com/scATrans/scatrans"
 url: "https://github.com/scATrans/scatrans"
 license: Apache-2.0
-version: 0.9.8
+version: 0.9.9
 keywords:
   - single-cell
   - RNA-seq