Skip site navigation (1)Skip section navigation (2) 
Date:      Thu, 05 Mar 2026 13:31:19 +0000
From:      Jason W. Bacon <jwb@FreeBSD.org>
To:        ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org
Subject:   git: 9c59e8acfec3 - main - biology/py-macs3: Update to 3.0.4
Message-ID:  <69a985a7.1eac3.48a1ee0c@gitrepo.freebsd.org>
index | next in thread | raw e-mail 

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=9c59e8acfec3e87d6ddf912d0f25a27571427f23

commit 9c59e8acfec3e87d6ddf912d0f25a27571427f23
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-03-05 13:29:48 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-03-05 13:31:18 +0000

    biology/py-macs3: Update to 3.0.4
    
    A few fixes and enhancements
    Changes: https://github.com/macs3-project/MACS/releases
    
    Reported by:    portscout
---
 biology/py-macs3/Makefile                     |  6 ++++--
 biology/py-macs3/distinfo                     |  6 +++---
 biology/py-macs3/files/patch-pyproject.toml   | 14 +++++++++++---
 biology/py-macs3/files/patch-requirements.txt |  4 ++--
 4 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile
index 9e80cf787df6..697cda306f9b 100644
--- a/biology/py-macs3/Makefile
+++ b/biology/py-macs3/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		MACS3
 DISTVERSIONPREFIX=	v
-DISTVERSION=		3.0.3
+DISTVERSION=		3.0.4
 CATEGORIES=		biology python
 PKGNAMEPREFIX=		${PYTHON_PKGNAMEPREFIX}
 
@@ -20,7 +20,9 @@ COMMON_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.3:science/py-scikit-learn@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}hmmlearn>=0.3.2:math/py-hmmlearn@${PY_FLAVOR}
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \
 		simde>0:devel/simde \
+		${PYTHON_PKGNAMEPREFIX}cython>0:lang/cython \
 		${COMMON_DEPENDS}
 RUN_DEPENDS=	${COMMON_DEPENDS}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \
@@ -29,7 +31,7 @@ TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \
 USES=		localbase perl5 python shebangfix
 USE_GITHUB=	yes
 USE_PERL5=	test
-USE_PYTHON=	autoplist concurrent cython distutils
+USE_PYTHON=	autoplist concurrent distutils
 
 GH_ACCOUNT=	macs3-project
 GH_PROJECT=	MACS
diff --git a/biology/py-macs3/distinfo b/biology/py-macs3/distinfo
index f02adff90730..643ab3644b4e 100644
--- a/biology/py-macs3/distinfo
+++ b/biology/py-macs3/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1740145847
-SHA256 (macs3-project-MACS-v3.0.3_GH0.tar.gz) = fb5cfe3d8189662b79df7c96f7782bc8327f1aafa61815a2ac86a8337917a558
-SIZE (macs3-project-MACS-v3.0.3_GH0.tar.gz) = 198064648
+TIMESTAMP = 1772212991
+SHA256 (macs3-project-MACS-v3.0.4_GH0.tar.gz) = e74ac701dbff16ea8dddc82d7431e8e6648a9fb2d99b8b7cd4fe6577f53692c8
+SIZE (macs3-project-MACS-v3.0.4_GH0.tar.gz) = 200470087
diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml
index 262eb251f817..40c429df69a5 100644
--- a/biology/py-macs3/files/patch-pyproject.toml
+++ b/biology/py-macs3/files/patch-pyproject.toml
@@ -1,9 +1,17 @@
---- pyproject.toml.orig	2025-02-20 03:43:04 UTC
+--- pyproject.toml.orig	2026-02-22 22:11:36 UTC
 +++ pyproject.toml
 @@ -1,5 +1,5 @@
  [build-system]
--requires=['setuptools>=68.0', 'numpy>=1.25', 'scipy>=1.12', 'cykhash>=2.0', 'Cython>=3.0', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2']
-+requires=['setuptools>=63.0', 'numpy>=1.25', 'scipy>=1.11.1', 'cykhash>=2.0', 'Cython>=0.29.37', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2']
+-requires=['setuptools>=80.0', 'numpy>=1.25', 'scipy>=1.12', 'cykhash>=2.0', 'Cython>=3.0', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2']
++requires=['setuptools>=63.0', 'numpy>=1.25', 'scipy>=1.11.1', 'cykhash>=2.0', 'Cython>=3.0', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2']
  build-backend = "setuptools.build_meta"
  
  [project]
+@@ -10,7 +10,6 @@ requires-python = ">=3.9"
+ 	   {name = "Philippa Doherty", email = "Philippa.Doherty@RoswellPark.org"}]
+ readme = "README.md"
+ requires-python = ">=3.9"
+-license = "BSD-3-Clause"
+ classifiers =['Development Status :: 5 - Production/Stable',
+               'Environment :: Console',
+               'Intended Audience :: Developers',
diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt
index 474854166d3c..4350e4b71051 100644
--- a/biology/py-macs3/files/patch-requirements.txt
+++ b/biology/py-macs3/files/patch-requirements.txt
@@ -1,8 +1,8 @@
---- requirements.txt.orig	2025-02-20 03:43:04 UTC
+--- requirements.txt.orig	2026-02-22 22:11:36 UTC
 +++ requirements.txt
 @@ -1,8 +1,8 @@
 -Cython>=3.0,<3.1
-+Cython>=0.29.37
++Cython>=3.0
  numpy>=1.25
 -scipy>=1.12
 +scipy>=1.11.1
home | help

Want to link to this message? Use this
URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?69a985a7.1eac3.48a1ee0c>