From 0a3e92e3ca693e786e12e3afcf2526923c436f34 Mon Sep 17 00:00:00 2001
From: Starlitnightly <41826060@xs.ustb.edu.cn>
Date: Thu, 30 Nov 2023 15:56:21 +0800
Subject: [PATCH] Fixed an error in `pyDEG.deg_analysis` when `n_cpus` can not
 be set in `pyDeseq2(v0.4.3)`

---
 omicverse/bulk/_Deseq2.py             | 12 +++++++++++-
 omicverse_guide/docs/Release_notes.md |  3 +++
 pyproject.toml                        |  2 +-
 3 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/omicverse/bulk/_Deseq2.py b/omicverse/bulk/_Deseq2.py
index 4d9425ac..cd706ad2 100644
--- a/omicverse/bulk/_Deseq2.py
+++ b/omicverse/bulk/_Deseq2.py
@@ -492,7 +492,7 @@ def deg_analysis(self,group1:list,group2:list,
                     refit_cooks=True,
                     n_cpus=n_cpus,
                 )
-            else:
+            elif pydeseq2.__version__<='0.4.1':
                 dds = DeseqDataSet(
                     counts=counts_df,
                     metadata=clinical_df,
@@ -502,6 +502,16 @@ def deg_analysis(self,group1:list,group2:list,
                     refit_cooks=True,
                     n_cpus=n_cpus,
                 )
+            else:
+                from pydeseq2.default_inference import DefaultInference
+                inference = DefaultInference(n_cpus=n_cpus)
+                dds = DeseqDataSet(
+                    counts=counts_df,
+                    metadata=clinical_df,
+                    design_factors="condition",  # compare samples based on the "condition"
+                    refit_cooks=True,
+                    inference=inference,
+                )
 
             
             dds.fit_size_factors()
diff --git a/omicverse_guide/docs/Release_notes.md b/omicverse_guide/docs/Release_notes.md
index 7a3e28b6..ee3b7b92 100644
--- a/omicverse_guide/docs/Release_notes.md
+++ b/omicverse_guide/docs/Release_notes.md
@@ -259,3 +259,6 @@
 ### pp Module:
 - Added `doublets` argument of `ov.pp.qc` to control doublets('Default'=True)
 
+## v 1.5.4
+### bulk Module:
+- Fixed an error in `pyDEG.deg_analysis` when `n_cpus` can not be set in `pyDeseq2(v0.4.3)`
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index f0ab65c1..894a9b05 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "omicverse"
-version = "1.5.3"
+version = "1.5.4"
 description = "OmicVerse: A single pipeline for exploring the entire transcriptome universe"
 readme = "README.md"
 requires-python = ">=3.8"