diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile
index d2cad2892df4..6ad3d9000471 100644
--- a/biology/py-macs3/Makefile
+++ b/biology/py-macs3/Makefile
@@ -1,49 +1,49 @@
 PORTNAME=		MACS3
 DISTVERSIONPREFIX=	v
-DISTVERSION=		3.0.0
+DISTVERSION=		3.0.1
 CATEGORIES=		biology python
 PKGNAMEPREFIX=		${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Peak caller aimed at transcription factor binding sites
 WWW=		https://github.com/taoliu/MACS
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \
 		${PYNUMPY} \
 		simde>0:devel/simde \
 		${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR}
 RUN_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \
 		bash:shells/bash
 
 USES=		localbase perl5 python shebangfix
 USE_GITHUB=	yes
 USE_PERL5=	test
 USE_PYTHON=	autoplist concurrent cython pep517
 
 GH_ACCOUNT=	macs3-project
 GH_PROJECT=	MACS
 SHEBANG_FILES=	test/cmdlinetest* test/prockreport test/*.py test/pyprofile*
 
 .include <bsd.port.options.mk>
 
 .if ${OPSYS} == FreeBSD && ${OSVERSION} < 1302509
 IGNORE=		does not run properly on FreeBSD 13.2 and earlier due to use of dynamically loaded libc by py-threadpoolctl.  Please upgrade to a newer FreeBSD or use py-macs2 instead.  See PR 276231
 .endif
 
 post-stage:
 	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS3/*/*.so
 
 # FIXME: Some tests fail due to a py-threadpoolctl issue
 # https://github.com/joblib/threadpoolctl/pull/148
-do-test: deinstall install
+do-test: deinstall reinstall
 	@${RM} -rf ${WRKSRC}/temp
 	@cd ${WRKSRC}/test && ./cmdlinetest tag
 
 .include <bsd.port.mk>
diff --git a/biology/py-macs3/distinfo b/biology/py-macs3/distinfo
index 757e9bbaf640..b06631987784 100644
--- a/biology/py-macs3/distinfo
+++ b/biology/py-macs3/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1703890666
-SHA256 (macs3-project-MACS-v3.0.0_GH0.tar.gz) = faa7ec2ea1f47b8c4cd747f00f2754d0e40051fe44d81d229d0111e3dad34a1d
-SIZE (macs3-project-MACS-v3.0.0_GH0.tar.gz) = 197389439
+TIMESTAMP = 1708785426
+SHA256 (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 8a2f5b2dccfc255ea2fd5e54e0d6aa9c12f5ce83762b17b779ce2546ade860ce
+SIZE (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 197400439
diff --git a/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c
index d66d83f33606..e385ca2fc010 100644
--- a/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c
+++ b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c
@@ -1,11 +1,11 @@
---- MACS3/fermi-lite/ksw.c.orig	2023-11-15 16:09:23 UTC
+--- MACS3/fermi-lite/ksw.c.orig	2024-02-24 15:09:33 UTC
 +++ MACS3/fermi-lite/ksw.c
 @@ -28,7 +28,7 @@
  
  /* I modified this according to https://github.com/lh3/bwa/pull/283/*/
  #ifdef USE_SIMDE
 -#include "lib/x86/sse2.h"
 +#include <simde/x86/sse2.h>
  #else
  #include <emmintrin.h>
  #endif
diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml
index cf54cae8892f..15f55a86a701 100644
--- a/biology/py-macs3/files/patch-pyproject.toml
+++ b/biology/py-macs3/files/patch-pyproject.toml
@@ -1,6 +1,7 @@
---- pyproject.toml.orig	2024-01-06 15:00:01 UTC
+--- pyproject.toml.orig	2024-02-23 05:43:44 UTC
 +++ pyproject.toml
-@@ -1,2 +1,2 @@
+@@ -1,3 +1,3 @@
  [build-system]
--requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'hmmlearn>=0.3']
-+requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython>=0', 'hmmlearn>=0.3']
+-requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.4', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3']
++requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.1', 'cykhash>=2.0,<3.0', 'Cython>=0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3']
+ 
diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt
index 0c8106f79680..81c9a1f75f88 100644
--- a/biology/py-macs3/files/patch-requirements.txt
+++ b/biology/py-macs3/files/patch-requirements.txt
@@ -1,8 +1,11 @@
---- requirements.txt.orig	2024-01-06 14:55:53 UTC
+--- requirements.txt.orig	2024-02-23 05:43:44 UTC
 +++ requirements.txt
-@@ -1,4 +1,4 @@
+@@ -1,6 +1,6 @@
 -Cython~=3.0
 +Cython>=0
- numpy>=1.19
+ numpy>=1.24.2
+-scipy>=1.11.4
++scipy>=1.11.1
+ scikit-learn>=1.2.1
  hmmlearn>=0.3
  cykhash>=2.0,<3.0 
diff --git a/biology/py-macs3/files/patch-setup.py b/biology/py-macs3/files/patch-setup.py
index 58dde13ba2c2..f309f3139736 100644
--- a/biology/py-macs3/files/patch-setup.py
+++ b/biology/py-macs3/files/patch-setup.py
@@ -1,20 +1,11 @@
---- setup.py.orig	2023-11-15 16:09:23 UTC
+--- setup.py.orig	2024-02-24 14:39:02 UTC
 +++ setup.py
-@@ -40,7 +40,7 @@ classifiers =[\
- install_requires = [ "numpy>=1.19",
-                      "hmmlearn>=0.3",
-                      "cykhash>=2.0,<3.0",
--                     "Cython~=3.0" ]
-+                     "Cython>=0" ]
- 
- tests_requires = [ 'pytest' ]
- 
 @@ -70,7 +70,7 @@ def main():
  
      if not clang:
          try:
 -            gcc_version_check = subprocess.check_output( ["gcc", "--version"], universal_newlines=True)
 +            gcc_version_check = subprocess.check_output( ["cc", "--version"], universal_newlines=True)
              if gcc_version_check.find("clang") != -1:
                  clang = True
              else: