git: 9997daa47946 - main - biology/py-PySCeS: update 1.1.1 → 1.2.1

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=9997daa4794629faced65dbd8f0b1d49ab7bcdfa

commit 9997daa4794629faced65dbd8f0b1d49ab7bcdfa
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-05-26 19:35:31 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2024-05-26 21:57:06 +0000

    biology/py-PySCeS: update 1.1.1 → 1.2.1
    
    Reported by:    portscout
---
 biology/py-PySCeS/Makefile                   | 26 +++++++++++++-------------
 biology/py-PySCeS/distinfo                   |  6 +++---
 biology/py-PySCeS/files/patch-pyproject.toml | 12 ++++++++++++
 3 files changed, 28 insertions(+), 16 deletions(-)

diff --git a/biology/py-PySCeS/Makefile b/biology/py-PySCeS/Makefile
index 5ca807f6ded2..d50bb3ccd733 100644
--- a/biology/py-PySCeS/Makefile
+++ b/biology/py-PySCeS/Makefile
@@ -1,5 +1,5 @@
-PORTNAME=	PySCeS
-DISTVERSION=	1.1.1
+PORTNAME=	pysces
+DISTVERSION=	1.2.1
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -7,25 +7,25 @@ DISTNAME=	${PORTNAME:tl}-${DISTVERSION}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Python Simulator for Cellular Systems
-WWW=		https://pysces.sourceforge.net/
+WWW=		https://pysces.github.io/
 
 LICENSE=	BSD3CLAUSE
-LICENSE_FILE=	${WRKSRC}/LICENCE.txt
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-PY_DEPENDS=	${PYNUMPY} \
-		${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR}
+BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}meson-python>0:devel/meson-python@${PY_FLAVOR} \
+		${PYNUMPY}
 PY_EXTRA=	${PYTHON_PKGNAMEPREFIX}python-libsbml>0:biology/py-python-libsbml@${PY_FLAVOR}
-BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}scikit-build>0:devel/py-scikit-build@${PY_FLAVOR} \
-		cmake:devel/cmake-core \
-		${PY_DEPENDS}
-RUN_DEPENDS=	${PY_DEPENDS} \
+RUN_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \
 		${PY_EXTRA}
 
 USES=		fortran localbase:ldflags python
-USE_PYTHON=	distutils autoplist pytest
+USE_PYTHON=	pep517 autoplist pytest
+
+LDFLAGS+=	-lpython${PYTHON_VER}
 
-LDFLAGS+=	-lpython${PYTHON_VER} -shared # see https://github.com/PySCeS/pysces/issues/29
+BINARY_ALIAS=	python3=${PYTHON_CMD}
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 
diff --git a/biology/py-PySCeS/distinfo b/biology/py-PySCeS/distinfo
index 070c6e317ddf..2d91e6fed642 100644
--- a/biology/py-PySCeS/distinfo
+++ b/biology/py-PySCeS/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1690346893
-SHA256 (pysces-1.1.1.tar.gz) = 170f9ccdcd3ff0336d144f3891c54ee5dfb9b61b1e7129f48e96ff02d6c9b6e5
-SIZE (pysces-1.1.1.tar.gz) = 1036708
+TIMESTAMP = 1716746850
+SHA256 (pysces-1.2.1.tar.gz) = 5dbde64cf398c599f5303d9ce084a50e047080c0899951529774a822a549fc20
+SIZE (pysces-1.2.1.tar.gz) = 2753986
diff --git a/biology/py-PySCeS/files/patch-pyproject.toml b/biology/py-PySCeS/files/patch-pyproject.toml
new file mode 100644
index 000000000000..334fd0cf97b2
--- /dev/null
+++ b/biology/py-PySCeS/files/patch-pyproject.toml
@@ -0,0 +1,12 @@
+--- pyproject.toml.orig	2024-04-05 22:51:04 UTC
++++ pyproject.toml
+@@ -3,8 +3,7 @@ requires = [
+ requires = [
+   'meson-python',
+   'meson>=1.2.3',
+-	'ninja',
+-	'numpy>=1.26.0,<1.27',
++	'numpy',
+ ]
+ 
+ [tool.meson-python.args]