git: fdebc5b7b2eb - main - biology/py-PySCeS: Update 1.0.2 -> 1.0.3

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=fdebc5b7b2eb21430f474c42198869e82faf059e

commit fdebc5b7b2eb21430f474c42198869e82faf059e
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-09-26 08:17:38 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-09-26 08:18:31 +0000

    biology/py-PySCeS: Update 1.0.2 -> 1.0.3
    
    Reported by:    portscout
---
 biology/py-PySCeS/Makefile             | 18 ++++++++++--------
 biology/py-PySCeS/distinfo             |  6 +++---
 biology/py-PySCeS/files/patch-setup.py | 15 ---------------
 3 files changed, 13 insertions(+), 26 deletions(-)

diff --git a/biology/py-PySCeS/Makefile b/biology/py-PySCeS/Makefile
index 22d55f31307b..e9648cf6acfc 100644
--- a/biology/py-PySCeS/Makefile
+++ b/biology/py-PySCeS/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	PySCeS
-DISTVERSION=	1.0.2
+DISTVERSION=	1.0.3
 CATEGORIES=	biology python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -13,25 +13,27 @@ LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENCE.txt
 
 PY_DEPENDS=	${PYNUMPY} \
-		${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}nose>0:devel/py-nose@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}python-libsbml>0:biology/py-python-libsbml@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR}
-BUILD_DEPENDS=	${PY_DEPENDS}
-RUN_DEPENDS=	${PY_DEPENDS}
+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} ${PY_EXTRA}
 
 USES=		fortran python
 USE_PYTHON=	distutils autoplist
 
 LDFLAGS+=	-lpython${PYTHON_VER} -shared # see https://github.com/PySCeS/pysces/issues/29
 
+TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
+
 post-install:
 	@${STRIP_CMD} \
 		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysces/pitcon/pitcon.cpython-${PYTHON_SUFFIX}.so \
 		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysces/nleq2/nleq2.cpython-${PYTHON_SUFFIX}.so
 
-do-test: install # from section 2.1 Loading PySCeS in http://pysces.sourceforge.net/pdf/userguide.pdf
-	@${PYTHON_CMD} -c "import pysces; pysces.test();"
+do-test: # from section 2.1 Loading PySCeS in http://pysces.sourceforge.net/pdf/userguide.pdf
+	@${SETENV} ${TEST_ENV} ${PYTHON_CMD} -c "import pysces; pysces.test();"
 
 .include <bsd.port.mk>
diff --git a/biology/py-PySCeS/distinfo b/biology/py-PySCeS/distinfo
index 90859705afa6..431efae39ed0 100644
--- a/biology/py-PySCeS/distinfo
+++ b/biology/py-PySCeS/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1653078460
-SHA256 (pysces-1.0.2.tar.gz) = da49a292c50152890c8359a0e0b3b6e8204f161fc45960318dbee9798436562f
-SIZE (pysces-1.0.2.tar.gz) = 1606306
+TIMESTAMP = 1664176747
+SHA256 (pysces-1.0.3.tar.gz) = 19bb2da5a02b9e5b3e4ef77924d4eaa62505e6ac8c4373f9f3704f2118db0059
+SIZE (pysces-1.0.3.tar.gz) = 1014531
diff --git a/biology/py-PySCeS/files/patch-setup.py b/biology/py-PySCeS/files/patch-setup.py
deleted file mode 100644
index c7f868849c6b..000000000000
--- a/biology/py-PySCeS/files/patch-setup.py
+++ /dev/null
@@ -1,15 +0,0 @@
---- setup.py.orig	2021-09-14 08:51:28 UTC
-+++ setup.py
-@@ -284,9 +284,9 @@ mydata_files.append((os.path.join('pysces'), [os.path.
- mydata_files.append(('', [os.path.join('pysces', 'pysces.pth')]))
- 
- # JR 2021-08 userguide.pdf included as a symlink to built docs in submodule
--mydata_files.append(
--    (os.path.join("pysces", "docs"), [os.path.join("pysces", "docs", "userguide.pdf")])
--)
-+#mydata_files.append(
-+#    (os.path.join("pysces", "docs"), [os.path.join("pysces", "docs", "userguide.pdf")])
-+#)
- mydata_files.append(
-     (
-         os.path.join('pysces', 'examples'),