diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile
index 56f6bdc9c904..2ca2822457a4 100644
--- a/biology/py-macs3/Makefile
+++ b/biology/py-macs3/Makefile
@@ -1,47 +1,46 @@
 PORTNAME=		MACS3
 DISTVERSIONPREFIX=	v
-DISTVERSION=		3.0.1
+DISTVERSION=		3.0.2
 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
 
 NOT_FOR_ARCHS=	i386
 NOT_FOR_ARCHS_REASON_i386=Requires _Float16
 
-BUILD_DEPENDS=	${PY_SETUPTOOLS} \
-		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \
+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}
+		${PYTHON_PKGNAMEPREFIX}hmmlearn>=0.3.2:math/py-hmmlearn@${PY_FLAVOR}
 RUN_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR}
+		${PYTHON_PKGNAMEPREFIX}hmmlearn>=0.3.2:math/py-hmmlearn@${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*
 
 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 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 b742493c53a1..bacae8bd911a 100644
--- a/biology/py-macs3/distinfo
+++ b/biology/py-macs3/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1713397031
-SHA256 (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 8a2f5b2dccfc255ea2fd5e54e0d6aa9c12f5ce83762b17b779ce2546ade860ce
-SIZE (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 197400439
+TIMESTAMP = 1725973815
+SHA256 (macs3-project-MACS-v3.0.2_GH0.tar.gz) = 33e877460f1b621ee85c78221b52d1e067b8f5aacdaf4d16bd887485bf636e08
+SIZE (macs3-project-MACS-v3.0.2_GH0.tar.gz) = 197484503
diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml
index 15f55a86a701..94a5699aa764 100644
--- a/biology/py-macs3/files/patch-pyproject.toml
+++ b/biology/py-macs3/files/patch-pyproject.toml
@@ -1,7 +1,7 @@
---- pyproject.toml.orig	2024-02-23 05:43:44 UTC
+--- pyproject.toml.orig	2024-09-07 16:11:35 UTC
 +++ pyproject.toml
 @@ -1,3 +1,3 @@
  [build-system]
--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']
+-requires=['setuptools>=68.0', 'numpy>=1.25,<2.0.0', 'scipy>=1.12', 'cykhash>=2.0,<3.0', 'Cython>=3.0,<3.1', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2']
++requires=['setuptools>=63.0', 'numpy>=1.25,<2.0.0', 'scipy>=1.11.1', 'cykhash>=2.0,<3.0', 'Cython>=0.29.37', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2']
  
diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt
index 81c9a1f75f88..ceac91b3141e 100644
--- a/biology/py-macs3/files/patch-requirements.txt
+++ b/biology/py-macs3/files/patch-requirements.txt
@@ -1,11 +1,14 @@
---- requirements.txt.orig	2024-02-23 05:43:44 UTC
+--- requirements.txt.orig	2024-09-07 16:11:35 UTC
 +++ requirements.txt
-@@ -1,6 +1,6 @@
--Cython~=3.0
-+Cython>=0
- numpy>=1.24.2
--scipy>=1.11.4
+@@ -1,8 +1,8 @@
+-Cython>=3.0,<3.1
++Cython>=0.29.37
+ numpy>=1.25,<2.0.0
+-scipy>=1.12
 +scipy>=1.11.1
- scikit-learn>=1.2.1
- hmmlearn>=0.3
+ scikit-learn>=1.3
+ hmmlearn>=0.3.2
  cykhash>=2.0,<3.0 
+ pytest>=7.0
+-setuptools>=68.0
++setuptools>=63.0
diff --git a/biology/py-macs3/files/patch-setup.py b/biology/py-macs3/files/patch-setup.py
deleted file mode 100644
index f309f3139736..000000000000
--- a/biology/py-macs3/files/patch-setup.py
+++ /dev/null
@@ -1,11 +0,0 @@
---- setup.py.orig	2024-02-24 14:39:02 UTC
-+++ setup.py
-@@ -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: