git: 8cd5ea075a8d - main - biology/py-macs3: Update to 3.0.5

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=8cd5ea075a8d7d286cd3f94b3239443f7fc47dfc

commit 8cd5ea075a8d7d286cd3f94b3239443f7fc47dfc
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-09-26 20:43:03 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-09-26 20:43:03 +0000

    biology/py-macs3: Update to 3.0.5
    
    A few fixes and enhancements
    Changes: https://github.com/macs3-project/MACS/releases
    
    Reported by:    portscout
---
 biology/py-macs3/Makefile                     |  7 +++----
 biology/py-macs3/distinfo                     |  6 +++---
 biology/py-macs3/files/patch-pyproject.toml   | 10 +++++-----
 biology/py-macs3/files/patch-requirements.txt | 11 ++++++-----
 4 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile
index 61e5deb79d3e..27bf458886b4 100644
--- a/biology/py-macs3/Makefile
+++ b/biology/py-macs3/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		MACS3
 DISTVERSIONPREFIX=	v
-DISTVERSION=		3.0.4
-PORTREVISION=	1
+DISTVERSION=		3.0.5
 CATEGORIES=		biology python
 PKGNAMEPREFIX=		${PYTHON_PKGNAMEPREFIX}
 
@@ -15,7 +14,7 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 NOT_FOR_ARCHS=	i386
 NOT_FOR_ARCHS_REASON_i386=Requires _Float16
 
-COMMON_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
+COMMON_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}scipy>1.11.1:science/py-scipy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}cykhash>=2.0,<3.0:devel/py-cykhash@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.3:science/py-scikit-learn@${PY_FLAVOR} \
@@ -31,7 +30,7 @@ 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 cython pep517
 
 GH_ACCOUNT=	macs3-project
 GH_PROJECT=	MACS
diff --git a/biology/py-macs3/distinfo b/biology/py-macs3/distinfo
index 643ab3644b4e..15ee14ad7253 100644
--- a/biology/py-macs3/distinfo
+++ b/biology/py-macs3/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1772212991
-SHA256 (macs3-project-MACS-v3.0.4_GH0.tar.gz) = e74ac701dbff16ea8dddc82d7431e8e6648a9fb2d99b8b7cd4fe6577f53692c8
-SIZE (macs3-project-MACS-v3.0.4_GH0.tar.gz) = 200470087
+TIMESTAMP = 1790423408
+SHA256 (macs3-project-MACS-v3.0.5_GH0.tar.gz) = 44482073ea59c80a79722e399cf6df7752c1801f76c4711c673abb240c3bbb9a
+SIZE (macs3-project-MACS-v3.0.5_GH0.tar.gz) = 200703018
diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml
index 40c429df69a5..6d8e8dbd37d4 100644
--- a/biology/py-macs3/files/patch-pyproject.toml
+++ b/biology/py-macs3/files/patch-pyproject.toml
@@ -1,16 +1,16 @@
---- pyproject.toml.orig	2026-02-22 22:11:36 UTC
+--- pyproject.toml.orig	2026-09-25 16:23:47 UTC
 +++ pyproject.toml
 @@ -1,5 +1,5 @@
  [build-system]
--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']
+-requires=['setuptools>=80.0', 'numpy>=1.25', 'Cython>=3.0']
++requires=['setuptools>=63.0', 'numpy>=1.25', 'Cython>=3.0']
  build-backend = "setuptools.build_meta"
  
  [project]
-@@ -10,7 +10,6 @@ requires-python = ">=3.9"
+@@ -10,7 +10,6 @@ requires-python = ">=3.12"
  	   {name = "Philippa Doherty", email = "Philippa.Doherty@RoswellPark.org"}]
  readme = "README.md"
- requires-python = ">=3.9"
+ requires-python = ">=3.12"
 -license = "BSD-3-Clause"
  classifiers =['Development Status :: 5 - Production/Stable',
                'Environment :: Console',
diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt
index 4350e4b71051..0a6dd173c80d 100644
--- a/biology/py-macs3/files/patch-requirements.txt
+++ b/biology/py-macs3/files/patch-requirements.txt
@@ -1,14 +1,15 @@
---- requirements.txt.orig	2026-02-22 22:11:36 UTC
+--- requirements.txt.orig	2026-09-25 16:23:47 UTC
 +++ requirements.txt
-@@ -1,8 +1,8 @@
+@@ -1,10 +1,10 @@
 -Cython>=3.0,<3.1
 +Cython>=3.0
  numpy>=1.25
--scipy>=1.12
-+scipy>=1.11.1
+ scipy>=1.12
  scikit-learn>=1.3
  hmmlearn>=0.3.2
- cykhash>=2.0,<3.0 
  pytest>=7.0
 -setuptools>=68.0
 +setuptools>=63.0
+ pandas
+ anndata
+ ncls