git: 5fc81da6456e - main - science/py-GPy: update 1.13.2 → 1.14.2

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=5fc81da6456e0f5c76481c20867e3f1ad79db02e

commit 5fc81da6456e0f5c76481c20867e3f1ad79db02e
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-09-08 22:23:59 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-09-09 07:48:28 +0000

    science/py-GPy: update 1.13.2 → 1.14.2
---
 science/py-GPy/Makefile | 43 ++++++++++++++++++++++++++++---------------
 science/py-GPy/distinfo |  6 +++---
 2 files changed, 31 insertions(+), 18 deletions(-)

diff --git a/science/py-GPy/Makefile b/science/py-GPy/Makefile
index b226e735ce89..ad154c210c4e 100644
--- a/science/py-GPy/Makefile
+++ b/science/py-GPy/Makefile
@@ -1,33 +1,35 @@
 PORTNAME=	GPy
-DISTVERSION=	1.13.2
-PORTREVISION=	2
+DISTVERSION=	1.14.2
 CATEGORIES=	science python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+DISTNAME=	gpy-${DISTVERSION}
+PYDISTUTILS_PKGNAME=	gpy
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Gaussian process toolbox
 WWW=		https://sheffieldml.github.io/GPy/ \
 		https://github.com/SheffieldML/GPy
 
-BROKEN=		fails to build with NumPy 2.x
-
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-.if !exists(/usr/include/omp.h)
-BROKEN=		requires OpenMP support that is missing on this architecture
-.endif
-
-BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR}
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}scipy>=1.3.0:science/py-scipy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}paramz>=0.9.6:science/py-paramz@${PY_FLAVOR} \
+BUILD_DEPENDS=	${PY_SETUPTOOLS} \
+		${PYTHON_PKGNAMEPREFIX}cython>=0.29:lang/cython@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numpy>=2:math/py-numpy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>=1.3.0:science/py-scipy@${PY_FLAVOR}
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.7:math/py-numpy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}paramz>0.9.6:science/py-paramz@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>=1.3.0:science/py-scipy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}
+TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest-timeout>0:devel/py-pytest-timeout@${PY_FLAVOR}
 
 USES=		localbase python
-USE_PYTHON=	distutils autoplist pytest # 12 tests fail see https://github.com/SheffieldML/GPy/issues/1075
+USE_PYTHON=	distutils autoplist pytest
+
+.if !exists(/usr/include/omp.h)
+BROKEN=		requires OpenMP support that is missing on this architecture
+.endif
 
 POST_PLIST=	fix-plist
 
@@ -36,7 +38,18 @@ post-install:
 		${STAGEDIR}${PYTHON_SITELIBDIR}/GPy/*/*${PYTHON_TAG}.so \
 		${STAGEDIR}${PYTHON_SITELIBDIR}/GPy/*/*/*${PYTHON_TAG}.so
 
-fix-plist: # workaroud for /usr/ports/science/py-GPy/work-py311/.PLIST.mktmp
+fix-plist: # remove byte-compiled entry for the Python-2-only mpi_test__.py
 	@${REINPLACE_CMD} -e "s|.*__pycache__/mpi_test__.*$$||" ${TMPPLIST}
 
+PYTEST_IGNORED_TESTS=	test_brownian_kernel \
+			test_multiout_regression \
+			TestStateSpaceKernels \
+			test_epccassification \
+			test_warped_gp_cubic_sine
+
+TEST_ENV=	${MAKE_ENV}
+TEST_ARGS=	--disable-plugin-autoload -p timeout
+
+# tests as of 1.14.2: 240 passed, 15 skipped, 18 deselected, 16 warnings in 32.20s
+
 .include <bsd.port.mk>
diff --git a/science/py-GPy/distinfo b/science/py-GPy/distinfo
index 2f2662bcfa92..92b60f6edf71 100644
--- a/science/py-GPy/distinfo
+++ b/science/py-GPy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1724139762
-SHA256 (GPy-1.13.2.tar.gz) = a38256b4dda536a5b5e6134a3924b42d454e987ee801fb6fc8b55a922da27920
-SIZE (GPy-1.13.2.tar.gz) = 1138525
+TIMESTAMP = 1788809917
+SHA256 (gpy-1.14.2.tar.gz) = 3c6a102cd0939ca62aab27038acc7c9970559fbda653dbdccc5d8ad02bd1dbad
+SIZE (gpy-1.14.2.tar.gz) = 1233242