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-rw-r--r--science/chrono/Makefile2
-rw-r--r--science/gramps/Makefile2
-rw-r--r--science/gramps/distinfo6
-rw-r--r--science/highfive/Makefile11
-rw-r--r--science/highfive/distinfo8
-rw-r--r--science/highfive/files/patch-CMakeLists.txt12
-rw-r--r--science/highfive/pkg-plist25
-rw-r--r--science/nwchem-data/Makefile2
-rw-r--r--science/nwchem-data/distinfo6
-rw-r--r--science/nwchem/Makefile4
-rw-r--r--science/nwchem/distinfo14
-rw-r--r--science/py-geometer/Makefile2
-rw-r--r--science/py-geometer/distinfo6
-rw-r--r--science/py-libpysal/Makefile11
-rw-r--r--science/qmcpack/Makefile3
-rw-r--r--science/qmcpack/distinfo6
-rw-r--r--science/tblite/Makefile1
17 files changed, 78 insertions, 43 deletions
diff --git a/science/chrono/Makefile b/science/chrono/Makefile
index c54abe30bb4d..4904d3e9bb73 100644
--- a/science/chrono/Makefile
+++ b/science/chrono/Makefile
@@ -1,6 +1,6 @@
PORTNAME= chrono
DISTVERSION= 9.0.1
-PORTREVISION= 2
+PORTREVISION= 3
CATEGORIES= science devel
PKGNAMESUFFIX= -physics-simulation-engine
diff --git a/science/gramps/Makefile b/science/gramps/Makefile
index be05bc98c53f..3e73bcd1d1cb 100644
--- a/science/gramps/Makefile
+++ b/science/gramps/Makefile
@@ -1,5 +1,5 @@
PORTNAME= gramps
-DISTVERSION= 6.0.5
+DISTVERSION= 6.0.6
CATEGORIES= science gnome python
MASTER_SITES= PYPI
diff --git a/science/gramps/distinfo b/science/gramps/distinfo
index 3e0a307bfe15..bb94a14bcaf8 100644
--- a/science/gramps/distinfo
+++ b/science/gramps/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1757244514
-SHA256 (gramps-6.0.5.tar.gz) = 2160e04ec7033838e48fe3c68cfd4f383bec4e6f5398e207250b76687923e2dc
-SIZE (gramps-6.0.5.tar.gz) = 22268263
+TIMESTAMP = 1762683414
+SHA256 (gramps-6.0.6.tar.gz) = 01ac3f4d00dec92398f3d3fbc64ad9f76f5c670037aa220da4c091192d4f1c97
+SIZE (gramps-6.0.6.tar.gz) = 22442896
diff --git a/science/highfive/Makefile b/science/highfive/Makefile
index 2dcc0c740d0c..7eab1f11d288 100644
--- a/science/highfive/Makefile
+++ b/science/highfive/Makefile
@@ -1,11 +1,12 @@
PORTNAME= highfive
DISTVERSIONPREFIX= v
-DISTVERSION= 2.10.1
+DISTVERSION= 3.2.0
CATEGORIES= science devel
MAINTAINER= yuri@FreeBSD.org
COMMENT= Header-only C++ HDF5 interface
-WWW= https://github.com/BlueBrain/HighFive
+WWW= https://highfive-devs.github.io/highfive/ \
+ https://github.com/highfive-devs/highfive
LICENSE= BSL
LICENSE_FILE= ${WRKSRC}/LICENSE
@@ -16,9 +17,9 @@ RUN_DEPENDS= ${LOCALBASE}/include/boost/multi_array.hpp:devel/boost-libs \
TEST_DEPENDS= catch2>0:devel/catch2
USES= cmake eigen:3,run
+
USE_GITHUB= yes
-GH_ACCOUNT= BlueBrain
-GH_PROJECT= HighFive
+GH_ACCOUNT= highfive-devs
CMAKE_OFF= HIGHFIVE_USE_BOOST HIGHFIVE_UNIT_TESTS HIGHFIVE_EXAMPLES
@@ -31,4 +32,6 @@ do-test: # one test fails, see https://github.com/BlueBrain/HighFive/issues/634
${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \
${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test
+# tests as of 3.2.0: 99% tests passed, 3 tests failed out of 278, skipped tests are reported as failed, see https://github.com/highfive-devs/highfive/issues/88
+
.include <bsd.port.mk>
diff --git a/science/highfive/distinfo b/science/highfive/distinfo
index f65f182a8eae..b7311dead1bf 100644
--- a/science/highfive/distinfo
+++ b/science/highfive/distinfo
@@ -1,3 +1,5 @@
-TIMESTAMP = 1733388367
-SHA256 (BlueBrain-HighFive-v2.10.1_GH0.tar.gz) = 60d66ba1315730494470afaf402bb40300a39eb6ef3b9d67263335a236069cce
-SIZE (BlueBrain-HighFive-v2.10.1_GH0.tar.gz) = 559344
+TIMESTAMP = 1762679687
+SHA256 (highfive-devs-highfive-v3.2.0_GH0.tar.gz) = 01ea2eed7dbce1cf5dfff59476cfa113a7822b641aecbd99c674592fe7a4e630
+SIZE (highfive-devs-highfive-v3.2.0_GH0.tar.gz) = 216218
+SHA256 (catchorg-catch2-fa43b77_GH0.tar.gz) = ec3b3ca270338c35dfed8673050c159476b85c6f788776cbdbde281adb682d04
+SIZE (catchorg-catch2-fa43b77_GH0.tar.gz) = 1193121
diff --git a/science/highfive/files/patch-CMakeLists.txt b/science/highfive/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..e93ed5c9bef1
--- /dev/null
+++ b/science/highfive/files/patch-CMakeLists.txt
@@ -0,0 +1,12 @@
+--- CMakeLists.txt.orig 2025-11-09 09:21:35 UTC
++++ CMakeLists.txt
+@@ -180,7 +180,8 @@ if(HIGHFIVE_UNIT_TESTS)
+ endif()
+
+ if(HIGHFIVE_UNIT_TESTS)
+- add_subdirectory(deps/catch2 EXCLUDE_FROM_ALL)
++ #add_subdirectory(deps/catch2 EXCLUDE_FROM_ALL)
++ find_package(Catch2 REQUIRED)
+ list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/deps/catch2/contrib)
+ enable_testing()
+ add_subdirectory(tests/unit)
diff --git a/science/highfive/pkg-plist b/science/highfive/pkg-plist
index 648733c11d9b..f13fd6b2bdc2 100644
--- a/science/highfive/pkg-plist
+++ b/science/highfive/pkg-plist
@@ -5,7 +5,6 @@ include/highfive/H5DataType.hpp
include/highfive/H5Easy.hpp
include/highfive/H5Exception.hpp
include/highfive/H5File.hpp
-include/highfive/H5FileDriver.hpp
include/highfive/H5Group.hpp
include/highfive/H5Object.hpp
include/highfive/H5PropertyList.hpp
@@ -21,7 +20,6 @@ include/highfive/bits/H5DataSet_misc.hpp
include/highfive/bits/H5DataType_misc.hpp
include/highfive/bits/H5Dataspace_misc.hpp
include/highfive/bits/H5Exception_misc.hpp
-include/highfive/bits/H5FileDriver_misc.hpp
include/highfive/bits/H5File_misc.hpp
include/highfive/bits/H5Friends.hpp
include/highfive/bits/H5Inspector_decl.hpp
@@ -40,6 +38,9 @@ include/highfive/bits/H5Slice_traits.hpp
include/highfive/bits/H5Slice_traits_misc.hpp
include/highfive/bits/H5Utils.hpp
include/highfive/bits/H5_definitions.hpp
+include/highfive/bits/assert_compatible_spaces.hpp
+include/highfive/bits/compute_total_size.hpp
+include/highfive/bits/convert_size_vector.hpp
include/highfive/bits/h5_wrapper.hpp
include/highfive/bits/h5a_wrapper.hpp
include/highfive/bits/h5d_wrapper.hpp
@@ -53,19 +54,25 @@ include/highfive/bits/h5p_wrapper.hpp
include/highfive/bits/h5r_wrapper.hpp
include/highfive/bits/h5s_wrapper.hpp
include/highfive/bits/h5t_wrapper.hpp
+include/highfive/bits/inspector_stl_span_misc.hpp
+include/highfive/bits/squeeze.hpp
include/highfive/bits/string_padding.hpp
+include/highfive/bits/xtensor_header_version.hpp
include/highfive/boost.hpp
+include/highfive/boost_multi_array.hpp
+include/highfive/boost_span.hpp
+include/highfive/boost_ublas.hpp
include/highfive/eigen.hpp
+include/highfive/experimental/opencv.hpp
include/highfive/h5easy_bits/H5Easy_Eigen.hpp
include/highfive/h5easy_bits/H5Easy_misc.hpp
-include/highfive/h5easy_bits/H5Easy_opencv.hpp
include/highfive/h5easy_bits/H5Easy_public.hpp
include/highfive/h5easy_bits/H5Easy_scalar.hpp
-include/highfive/h5easy_bits/H5Easy_vector.hpp
-include/highfive/h5easy_bits/H5Easy_xtensor.hpp
+include/highfive/h5easy_bits/default_io_impl.hpp
include/highfive/half_float.hpp
include/highfive/highfive.hpp
-share/HighFive/CMake/HighFiveConfig.cmake
-share/HighFive/CMake/HighFiveConfigVersion.cmake
-share/HighFive/CMake/HighFiveTargetDeps.cmake
-share/HighFive/CMake/HighFiveTargets.cmake
+include/highfive/span.hpp
+include/highfive/xtensor.hpp
+lib/cmake/HighFive/HighFiveConfig.cmake
+lib/cmake/HighFive/HighFiveConfigVersion.cmake
+lib/cmake/HighFive/HighFiveTargets.cmake
diff --git a/science/nwchem-data/Makefile b/science/nwchem-data/Makefile
index e52c446ec9df..e119e3dfd9ca 100644
--- a/science/nwchem-data/Makefile
+++ b/science/nwchem-data/Makefile
@@ -1,6 +1,6 @@
PORTNAME= nwchem-data
DISTVERSIONPREFIX= v
-DISTVERSION= 7.3.0
+DISTVERSION= 7.3.1
DISTVERSIONSUFFIX= -release
CATEGORIES= science
diff --git a/science/nwchem-data/distinfo b/science/nwchem-data/distinfo
index 1e12361d7a92..fd9ca5e51be4 100644
--- a/science/nwchem-data/distinfo
+++ b/science/nwchem-data/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1762147577
-SHA256 (nwchemgit-nwchem-v7.3.0-release_GH0.tar.gz) = 42148e705956113bf6082d5e5520927a09f51a4309e19b6bde69d65c01a6367d
-SIZE (nwchemgit-nwchem-v7.3.0-release_GH0.tar.gz) = 216145612
+TIMESTAMP = 1762669902
+SHA256 (nwchemgit-nwchem-v7.3.1-release_GH0.tar.gz) = 394d1cef35350896ef16e365b073055239b1294cc21b4cc6bae27b401cc8f1d4
+SIZE (nwchemgit-nwchem-v7.3.1-release_GH0.tar.gz) = 216407355
diff --git a/science/nwchem/Makefile b/science/nwchem/Makefile
index bcf73b0c428a..ea8db7bb6730 100644
--- a/science/nwchem/Makefile
+++ b/science/nwchem/Makefile
@@ -1,7 +1,7 @@
PORTNAME= nwchem
#DISTVERSIONPREFIX= v
-DISTVERSION= 7.3.0
-DISTVERSIONSUFFIX= -release.revision-e60d3d90-src.2025-10-24
+DISTVERSION= 7.3.1
+DISTVERSIONSUFFIX= -release.revision-23c3b41b-src.2025-11-06
CATEGORIES= science
MASTER_SITES= https://github.com/nwchemgit/nwchem/releases/download/v${DISTVERSION}-release/ \
https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3/:dft3 \
diff --git a/science/nwchem/distinfo b/science/nwchem/distinfo
index 7f2e16ed88e6..ade23a4c4149 100644
--- a/science/nwchem/distinfo
+++ b/science/nwchem/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1762156432
-SHA256 (nwchem-7.3.0/nwchem-7.3.0-release.revision-e60d3d90-src.2025-10-24.tar.gz) = e462db097bb6abb155603219adb55bacaa6ba220e5afdba9d0a91a8d9a60418d
-SIZE (nwchem-7.3.0/nwchem-7.3.0-release.revision-e60d3d90-src.2025-10-24.tar.gz) = 236380823
-SHA256 (nwchem-7.3.0/dftd3.tgz) = d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59
-SIZE (nwchem-7.3.0/dftd3.tgz) = 555804
-SHA256 (nwchem-7.3.0/libxc-7.0.0.tar.gz) = 8d4e343041c9cd869833822f57744872076ae709a613c118d70605539fb13a77
-SIZE (nwchem-7.3.0/libxc-7.0.0.tar.gz) = 67985837
+TIMESTAMP = 1762671036
+SHA256 (nwchem-7.3.1/nwchem-7.3.1-release.revision-23c3b41b-src.2025-11-06.tar.gz) = 2dc7d715615ac9f3fc1ddc5c464f77db56bb53473a029d993c900153bae8a1ab
+SIZE (nwchem-7.3.1/nwchem-7.3.1-release.revision-23c3b41b-src.2025-11-06.tar.gz) = 236375450
+SHA256 (nwchem-7.3.1/dftd3.tgz) = d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59
+SIZE (nwchem-7.3.1/dftd3.tgz) = 555804
+SHA256 (nwchem-7.3.1/libxc-7.0.0.tar.gz) = 8d4e343041c9cd869833822f57744872076ae709a613c118d70605539fb13a77
+SIZE (nwchem-7.3.1/libxc-7.0.0.tar.gz) = 67985837
diff --git a/science/py-geometer/Makefile b/science/py-geometer/Makefile
index e4d0aaf184a2..2a6c6aa18abb 100644
--- a/science/py-geometer/Makefile
+++ b/science/py-geometer/Makefile
@@ -1,5 +1,5 @@
PORTNAME= geometer
-PORTVERSION= 0.4.1
+PORTVERSION= 0.4.2
CATEGORIES= science python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/science/py-geometer/distinfo b/science/py-geometer/distinfo
index 911086479111..6dc94e117697 100644
--- a/science/py-geometer/distinfo
+++ b/science/py-geometer/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1749813104
-SHA256 (geometer-0.4.1.tar.gz) = 1701124dea9f748f00b50adad91a1a471af96571ae8d5ff9b73858a1cbdb9822
-SIZE (geometer-0.4.1.tar.gz) = 114402
+TIMESTAMP = 1762586872
+SHA256 (geometer-0.4.2.tar.gz) = 0df63113a74d7a8c97886d9788299947215fed5badd01acf2da08db85487193a
+SIZE (geometer-0.4.2.tar.gz) = 46142
diff --git a/science/py-libpysal/Makefile b/science/py-libpysal/Makefile
index 9ad512eb6589..51a39b19aa7a 100644
--- a/science/py-libpysal/Makefile
+++ b/science/py-libpysal/Makefile
@@ -31,4 +31,15 @@ USE_PYTHON= autoplist concurrent pep517
NO_ARCH= yes
+OPTIONS_DEFINE= PLUS
+PLUS_DESC= Extra features
+
+PLUS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}joblib>=1.2:devel/py-joblib@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}networkx>=2.7:math/py-networkx@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}numba>=0.55:devel/py-numba@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}pyarrow>=7.0:databases/py-pyarrow@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}sqlalchemy20>=2.0:databases/py-sqlalchemy20@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}xarray>=2022.3:devel/py-xarray@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}zstd>=0:archivers/py-zstd@${PY_FLAVOR}
+
.include <bsd.port.mk>
diff --git a/science/qmcpack/Makefile b/science/qmcpack/Makefile
index cf5db3ae4960..7bec4719c90a 100644
--- a/science/qmcpack/Makefile
+++ b/science/qmcpack/Makefile
@@ -1,7 +1,6 @@
PORTNAME= qmcpack
DISTVERSIONPREFIX= v
-DISTVERSION= 4.0.0
-PORTREVISION= 4
+DISTVERSION= 4.1.0
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/qmcpack/distinfo b/science/qmcpack/distinfo
index 62793ebf274f..90ac21de2d82 100644
--- a/science/qmcpack/distinfo
+++ b/science/qmcpack/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1738829052
-SHA256 (QMCPACK-qmcpack-v4.0.0_GH0.tar.gz) = 26dd4276fb8442d241e437a79ec4b6d7d11507b0f9f1e3c4708660c74690b6ea
-SIZE (QMCPACK-qmcpack-v4.0.0_GH0.tar.gz) = 122843366
+TIMESTAMP = 1762712021
+SHA256 (QMCPACK-qmcpack-v4.1.0_GH0.tar.gz) = a9295e10b11aa2fa1b0f8342d214e9070b93ad5b8824fff061f00576f825dbaf
+SIZE (QMCPACK-qmcpack-v4.1.0_GH0.tar.gz) = 123194248
diff --git a/science/tblite/Makefile b/science/tblite/Makefile
index f968a9897145..c1314fe73bb0 100644
--- a/science/tblite/Makefile
+++ b/science/tblite/Makefile
@@ -11,6 +11,7 @@ WWW= https://tblite.readthedocs.io/ \
LICENSE= LGPL3+
LICENSE_FILE= ${WRKSRC}/COPYING.LESSER
+BROKEN= compilation fails after science/dftd4 update, see https://github.com/tblite/tblite/issues/296
.if !exists(/usr/include/omp.h)
BROKEN= requires OpenMP support that is missing on this architecture
.endif
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-10 11:15:55 +0000