diff options
Diffstat (limited to '')
94 files changed, 280 insertions, 176 deletions
diff --git a/science/Makefile b/science/Makefile index 9713030b534d..9141575c630d 100644 --- a/science/Makefile +++ b/science/Makefile @@ -313,8 +313,9 @@ SUBDIR += py-cirq-google SUBDIR += py-cirq-ionq SUBDIR += py-cirq-pasqal - SUBDIR += py-cirq-rigetti + SUBDIR += py-cirq-web SUBDIR += py-coards + SUBDIR += py-corner SUBDIR += py-dftbplus SUBDIR += py-dftd4 SUBDIR += py-dimod diff --git a/science/R-cran-Epi/Makefile b/science/R-cran-Epi/Makefile index 371fe4129bcb..8c784e4d3808 100644 --- a/science/R-cran-Epi/Makefile +++ b/science/R-cran-Epi/Makefile @@ -1,5 +1,5 @@ PORTNAME= Epi -PORTVERSION= 2.60 +PORTVERSION= 2.61 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/science/R-cran-Epi/distinfo b/science/R-cran-Epi/distinfo index ec0e369f065d..a39deb708e63 100644 --- a/science/R-cran-Epi/distinfo +++ b/science/R-cran-Epi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1752227410 -SHA256 (Epi_2.60.tar.gz) = 29d6d91a7a0f04369852738fce009b3aefa59c65380174b6eec24ba7046aec57 -SIZE (Epi_2.60.tar.gz) = 3976720 +TIMESTAMP = 1760064085 +SHA256 (Epi_2.61.tar.gz) = 66b10d8737b079ed13de874c6023a23256ebabb91f160ae8b916ae5c1002eca3 +SIZE (Epi_2.61.tar.gz) = 5974357 diff --git a/science/arbor/Makefile b/science/arbor/Makefile index d2d6e0cf6ef2..2251d579cd4b 100644 --- a/science/arbor/Makefile +++ b/science/arbor/Makefile @@ -12,8 +12,8 @@ WWW= https://arbor-sim.org/ \ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_FreeBSD_15= compilation fails with clang-19, see https://github.com/arbor-sim/arbor/issues/2424 -BROKEN_armv7= compilation fails: unknown type name 'float64x2_t' +BROKEN= compilation fails with clang-19, see https://github.com/arbor-sim/arbor/issues/2424 +#BROKEN_armv7= compilation fails: unknown type name 'float64x2_t' BUILD_DEPENDS= bash:shells/bash \ libfmt>0:devel/libfmt \ diff --git a/science/ascent/Makefile b/science/ascent/Makefile index a94aa81f952a..700c3175eeba 100644 --- a/science/ascent/Makefile +++ b/science/ascent/Makefile @@ -1,6 +1,6 @@ PORTNAME= ascent DISTVERSIONPREFIX= v -DISTVERSION= 0.9.3 +DISTVERSION= 0.9.5 CATEGORIES= science PKGNAMESUFFIX= -visualizer @@ -52,4 +52,6 @@ OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_BROKEN= still chooses mpich, see https://github.com/Alpine-DAV/ascent/issues/1091 +# tests as of 0.9.5: 100% tests passed, 0 tests failed out of 97 + .include <bsd.port.mk> diff --git a/science/ascent/distinfo b/science/ascent/distinfo index aeca2259461c..a8a71257682d 100644 --- a/science/ascent/distinfo +++ b/science/ascent/distinfo @@ -1,6 +1,6 @@ -TIMESTAMP = 1725897564 -SHA256 (Alpine-DAV-ascent-v0.9.3_GH0.tar.gz) = 69b2129380a89c6dd84ea9deaf4321d2b99cdd33c334c509998b796637f51025 -SIZE (Alpine-DAV-ascent-v0.9.3_GH0.tar.gz) = 148193922 +TIMESTAMP = 1760809604 +SHA256 (Alpine-DAV-ascent-v0.9.5_GH0.tar.gz) = 590ea90c5210af57a01399ac535332823207d78cfc9dc68bdaf42d2bcf12891f +SIZE (Alpine-DAV-ascent-v0.9.5_GH0.tar.gz) = 162734403 SHA256 (Alpine-DAV-spack_configs-26ea412_GH0.tar.gz) = 2d92cf6fa0f0b541f9fb70e897e96230b820c3d93e01e345653cb541a089e1e1 SIZE (Alpine-DAV-spack_configs-26ea412_GH0.tar.gz) = 14097 SHA256 (LLNL-blt-9ff7734_GH0.tar.gz) = 4ab173f8c82c33f31dc066bced2bcf15fe96345a252c59c647ed1940f6426d68 diff --git a/science/ascent/pkg-plist b/science/ascent/pkg-plist index 74e9d3fe74f9..b869941ba019 100644 --- a/science/ascent/pkg-plist +++ b/science/ascent/pkg-plist @@ -41,6 +41,10 @@ include/ascent/ascent_jit_kernel.hpp include/ascent/ascent_jit_math.hpp include/ascent/ascent_jit_topology.hpp include/ascent/ascent_logging.hpp +include/ascent/ascent_logging_config.h +include/ascent/ascent_logging_exports.h +include/ascent/ascent_logging_old.hpp +include/ascent/ascent_logging_timer.hpp include/ascent/ascent_main_runtime.hpp include/ascent/ascent_math.hpp include/ascent/ascent_memory_manager.hpp @@ -58,6 +62,7 @@ include/ascent/ascent_runtime_htg_filters.hpp include/ascent/ascent_runtime_param_check.hpp include/ascent/ascent_runtime_query_filters.hpp include/ascent/ascent_runtime_relay_filters.hpp +include/ascent/ascent_runtime_steering_filters.hpp include/ascent/ascent_runtime_trigger_filters.hpp include/ascent/ascent_runtime_utils.hpp include/ascent/ascent_runtime_vtkh_utils.hpp @@ -92,6 +97,7 @@ lib/cmake/ascent/thirdparty/BLTSetupMPI.cmake lib/libascent.so lib/libascent_flow.so lib/libascent_lodepng.so +lib/libascent_logging.so %%NO_NOMPI%%lib/libascent_mpi.so %%DATADIR%%/ascent_config.mk %%DATADIR%%/web_clients/ascent/index.html diff --git a/science/bagel/Makefile b/science/bagel/Makefile index 16f1638f3987..eba1ca2b2705 100644 --- a/science/bagel/Makefile +++ b/science/bagel/Makefile @@ -1,7 +1,7 @@ PORTNAME= bagel DISTVERSIONPREFIX= v DISTVERSION= 1.2.2-132 -PORTREVISION= 16 +PORTREVISION= 17 DISTVERSIONSUFFIX= -g2955e4d1a CATEGORIES= science diff --git a/science/bddsolve/Makefile b/science/bddsolve/Makefile index 697130a1f5fd..49e5392248d3 100644 --- a/science/bddsolve/Makefile +++ b/science/bddsolve/Makefile @@ -1,6 +1,6 @@ PORTNAME= bddsolve PORTVERSION= 1.04 -PORTREVISION= 19 +PORTREVISION= 20 CATEGORIES= science MASTER_SITES= http://www.win.tue.nl/~wieger/bddsolve/_downloads/ DISTNAME= ${PORTNAME}-source-${PORTVERSION} diff --git a/science/cif-tools/Makefile b/science/cif-tools/Makefile index 401eae02834e..297be4c78553 100644 --- a/science/cif-tools/Makefile +++ b/science/cif-tools/Makefile @@ -1,7 +1,7 @@ PORTNAME= cif-tools DISTVERSIONPREFIX= v DISTVERSION= 1.0.12 # chemistry -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/conduit/Makefile b/science/conduit/Makefile index 782cddcf23f2..fe04ba696b7a 100644 --- a/science/conduit/Makefile +++ b/science/conduit/Makefile @@ -1,6 +1,6 @@ PORTNAME= conduit DISTVERSIONPREFIX= v -DISTVERSION= 0.9.3 +DISTVERSION= 0.9.5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -45,6 +45,6 @@ MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON -# 100% tests passed, 0 tests failed out of 3 +# tests as of 0.9.5: 100% tests passed, 0 tests failed out of 3 .include <bsd.port.mk> diff --git a/science/conduit/distinfo b/science/conduit/distinfo index 6494006efe0a..959302ee4603 100644 --- a/science/conduit/distinfo +++ b/science/conduit/distinfo @@ -1,6 +1,6 @@ -TIMESTAMP = 1738037667 -SHA256 (LLNL-conduit-v0.9.3_GH0.tar.gz) = 7315813bcdbf8701d2060dd776ac16a79bfd5fe436d802a46e3f89a223f7bf8f -SIZE (LLNL-conduit-v0.9.3_GH0.tar.gz) = 24469438 +TIMESTAMP = 1760810723 +SHA256 (LLNL-conduit-v0.9.5_GH0.tar.gz) = 1a635050670644ffd3ef55351f96ac0f6bb15789b23643557e7ddacbcbf5460f +SIZE (LLNL-conduit-v0.9.5_GH0.tar.gz) = 107725385 SHA256 (LLNL-blt-058b312_GH0.tar.gz) = 93dd61bf6c52c17ce6a383687ccc7e589c250ab5997608e37623695a772d7e3d SIZE (LLNL-blt-058b312_GH0.tar.gz) = 1281374 SHA256 (Alpine-DAV-spack_configs-26a5d10_GH0.tar.gz) = 16e382c4054a21ddc6acd4319ec14e3f3c68921fe879ee470d011cc96e6a98b1 diff --git a/science/csvtk/Makefile b/science/csvtk/Makefile index 3d2c9d80ac57..6b140beda671 100644 --- a/science/csvtk/Makefile +++ b/science/csvtk/Makefile @@ -1,7 +1,7 @@ PORTNAME= csvtk DISTVERSIONPREFIX= v DISTVERSION= 0.34.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= jwb@FreeBSD.org diff --git a/science/dakota/Makefile b/science/dakota/Makefile index 059d349e1323..4eaabc3a1754 100644 --- a/science/dakota/Makefile +++ b/science/dakota/Makefile @@ -1,5 +1,6 @@ PORTNAME= dakota DISTVERSION= 6.22.0 +PORTREVISION= 1 PORTEVISION= 1 CATEGORIES= science MASTER_SITES= https://github.com/snl-dakota/dakota/releases/download/v${DISTVERSION}/ diff --git a/science/dssp/Makefile b/science/dssp/Makefile index 2b65378d1409..87eaec6066d4 100644 --- a/science/dssp/Makefile +++ b/science/dssp/Makefile @@ -1,7 +1,7 @@ PORTNAME= dssp DISTVERSIONPREFIX= v DISTVERSION= 4.4.11 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/eccodes/Makefile b/science/eccodes/Makefile index 9d4fac3000af..b9dc2c6e4f68 100644 --- a/science/eccodes/Makefile +++ b/science/eccodes/Makefile @@ -1,5 +1,5 @@ PORTNAME= eccodes -PORTVERSION= 2.42.0 +PORTVERSION= 2.44.0 DISTVERSIONSUFFIX= -Source CATEGORIES= science MASTER_SITES= https://confluence.ecmwf.int/download/attachments/45757960/ \ diff --git a/science/eccodes/distinfo b/science/eccodes/distinfo index 4347e3129fb3..979a7f4d7fbb 100644 --- a/science/eccodes/distinfo +++ b/science/eccodes/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1751375037 -SHA256 (eccodes-2.42.0-Source.tar.gz) = 60371b357cb011dee546db2eabace5b7e27f0f87d3ea4a5adde7891371b3c128 -SIZE (eccodes-2.42.0-Source.tar.gz) = 12279749 +TIMESTAMP = 1759774559 +SHA256 (eccodes-2.44.0-Source.tar.gz) = c75fb1f91b765b6b8b4774632a8a6fbcec96934db015fb63c2ad2560aedd443b +SIZE (eccodes-2.44.0-Source.tar.gz) = 12374133 diff --git a/science/eccodes/pkg-plist b/science/eccodes/pkg-plist index 52d540fa23dd..e4d27d1155ba 100644 --- a/science/eccodes/pkg-plist +++ b/science/eccodes/pkg-plist @@ -15930,6 +15930,10 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/localConcepts/ecmf/marsLevtypeConcept.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelNameConcept.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.IFS.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-compo-ens-crps.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-compo-ens.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-compo-single-mse.def +%%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-compo-single.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-ens-crps.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-ens-diff.def %%DATADIR%%/definitions/grib2/localConcepts/ecmf/modelVersionConcept.aifs-ens.def @@ -15998,6 +16002,7 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/localConcepts/era6/name.def %%DATADIR%%/definitions/grib2/localConcepts/era6/paramId.def %%DATADIR%%/definitions/grib2/localConcepts/era6/shortName.def +%%DATADIR%%/definitions/grib2/localConcepts/era6/timespanConcept.def %%DATADIR%%/definitions/grib2/localConcepts/era6/typeOfLevelConcept.def %%DATADIR%%/definitions/grib2/localConcepts/era6/units.def %%DATADIR%%/definitions/grib2/localConcepts/eswi/name.def @@ -16097,12 +16102,14 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/paramtypeConcept.def %%DATADIR%%/definitions/grib2/postProcessingConcept.def %%DATADIR%%/definitions/grib2/post_meta_data.hook.products_12.def +%%DATADIR%%/definitions/grib2/post_meta_data.hook.products_13.def %%DATADIR%%/definitions/grib2/productDefinitionTemplateConcept.def %%DATADIR%%/definitions/grib2/products_0.def %%DATADIR%%/definitions/grib2/products_1.def %%DATADIR%%/definitions/grib2/products_10.def %%DATADIR%%/definitions/grib2/products_11.def %%DATADIR%%/definitions/grib2/products_12.def +%%DATADIR%%/definitions/grib2/products_13.def %%DATADIR%%/definitions/grib2/products_2.def %%DATADIR%%/definitions/grib2/products_3.def %%DATADIR%%/definitions/grib2/products_4.def @@ -16130,6 +16137,7 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/shortName.def %%DATADIR%%/definitions/grib2/shortName.legacy.def %%DATADIR%%/definitions/grib2/shortName.lte33.def +%%DATADIR%%/definitions/grib2/stattypeConcept.def %%DATADIR%%/definitions/grib2/stepUnits.def %%DATADIR%%/definitions/grib2/tables/0.0.table %%DATADIR%%/definitions/grib2/tables/1.0.table @@ -19886,7 +19894,6 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/tables/34/5.6.table %%DATADIR%%/definitions/grib2/tables/34/5.7.table %%DATADIR%%/definitions/grib2/tables/34/6.0.table -%%DATADIR%%/definitions/grib2/tables/35/5.40.table %%DATADIR%%/definitions/grib2/tables/35/0.0.table %%DATADIR%%/definitions/grib2/tables/35/1.0.table %%DATADIR%%/definitions/grib2/tables/35/1.1.table @@ -20064,6 +20071,7 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/tables/35/5.26.table %%DATADIR%%/definitions/grib2/tables/35/5.3.table %%DATADIR%%/definitions/grib2/tables/35/5.4.table +%%DATADIR%%/definitions/grib2/tables/35/5.40.table %%DATADIR%%/definitions/grib2/tables/35/5.5.table %%DATADIR%%/definitions/grib2/tables/35/5.6.table %%DATADIR%%/definitions/grib2/tables/35/5.7.table @@ -20747,7 +20755,6 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/tables/local/ecmf/1/4.233.table %%DATADIR%%/definitions/grib2/tables/local/ecmf/1/4.238.table %%DATADIR%%/definitions/grib2/tables/local/ecmf/1/4.5.table -%%DATADIR%%/definitions/grib2/tables/local/ecmf/4/1.2.table %%DATADIR%%/definitions/grib2/tables/local/ecmf/obstat.1.0.table %%DATADIR%%/definitions/grib2/tables/local/ecmf/obstat.10.0.table %%DATADIR%%/definitions/grib2/tables/local/ecmf/obstat.11.0.table @@ -21880,6 +21887,12 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/mars/grib.sfmm.fcstdev.def %%DATADIR%%/definitions/mars/grib.smma.em.def %%DATADIR%%/definitions/mars/grib.smma.fcmean.def +%%DATADIR%%/definitions/mars/grib.sttd.an.def +%%DATADIR%%/definitions/mars/grib.sttd.fc.def +%%DATADIR%%/definitions/mars/grib.stte.an.def +%%DATADIR%%/definitions/mars/grib.stte.em.def +%%DATADIR%%/definitions/mars/grib.stte.es.def +%%DATADIR%%/definitions/mars/grib.stte.fc.def %%DATADIR%%/definitions/mars/grib.supd.an.def %%DATADIR%%/definitions/mars/grib.swmm.fcmax.def %%DATADIR%%/definitions/mars/grib.swmm.fcmean.def @@ -21954,6 +21967,7 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/mars/grib.wmfm.fcmin.def %%DATADIR%%/definitions/mars/grib.wmfm.fcstdev.def %%DATADIR%%/definitions/mars/mars.quantile.def +%%DATADIR%%/definitions/mars/mars.wavelength.def %%DATADIR%%/definitions/mars/marsTypeConcept.def %%DATADIR%%/definitions/mars/model.96.table %%DATADIR%%/definitions/mars/stream.table diff --git a/science/healpix/Makefile b/science/healpix/Makefile index 92f6cbda719f..7505dc0033bc 100644 --- a/science/healpix/Makefile +++ b/science/healpix/Makefile @@ -1,14 +1,15 @@ PORTNAME= healpix DISTVERSION= 3.50 DISTVERSIONSUFFIX= _2018Dec10 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MASTER_SITES= SF/${PORTNAME}/Healpix_${DISTVERSION}/ DISTNAME= Healpix_${DISTVERSIONFULL} MAINTAINER= yuri@FreeBSD.org COMMENT= Software for pixelization, visualization, etc of data on the sphere -WWW= https://healpix.jpl.nasa.gov/ +WWW= https://healpix.sourceforge.io/ + #https://healpix.jpl.nasa.gov/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING @@ -23,9 +24,12 @@ cxx_PLIST= ${.CURDIR}/pkg-plist-cxx c_PLIST= ${.CURDIR}/pkg-plist-c USES= autoreconf compiler:c++11-lang gmake libtool pkgconfig +USE_LDCONFIG= yes + GNU_CONFIGURE= yes CONFIGURE_ARGS= --disable-static -USE_LDCONFIG= yes + +LDFLAGS+= -lomp WRKSRC= ${WRKDIR}/Healpix_${DISTVERSION} AUTORECONF_WRKSRC= ${WRKSRC}/src/${FLAVOR:S/^c$/C/}/autotools diff --git a/science/highfive/Makefile b/science/highfive/Makefile index b35fd3ff30ae..2dcc0c740d0c 100644 --- a/science/highfive/Makefile +++ b/science/highfive/Makefile @@ -12,7 +12,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libhdf5.so:science/hdf5 RUN_DEPENDS= ${LOCALBASE}/include/boost/multi_array.hpp:devel/boost-libs \ - ${LOCALBASE}/include/xtensor/xtensor.hpp:math/xtensor + ${LOCALBASE}/include/xtensor.hpp:math/xtensor TEST_DEPENDS= catch2>0:devel/catch2 USES= cmake eigen:3,run diff --git a/science/libcifpp/Makefile b/science/libcifpp/Makefile index 08680c8e05d4..96e945f88975 100644 --- a/science/libcifpp/Makefile +++ b/science/libcifpp/Makefile @@ -1,7 +1,7 @@ PORTNAME= libcifpp DISTVERSIONPREFIX= v DISTVERSION= 7.0.8 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= https://files.wwpdb.org/pub/pdb/data/monomers/:components DISTFILES= components.cif.gz:components diff --git a/science/libint2-psi4/Makefile b/science/libint2-psi4/Makefile index 3ac7e76bd463..dce366b9440e 100644 --- a/science/libint2-psi4/Makefile +++ b/science/libint2-psi4/Makefile @@ -1,6 +1,6 @@ PORTNAME= libint2-psi4 DISTVERSION= 0.1-${VERSION} -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MASTER_SITES= https://github.com/loriab/libint/releases/download/v${DISTVERSION:C/-.*//}/ DISTFILES= libint-${VERSION}-post1-5-4-3-6-5-4_mm4f12ob2_1.tgz @@ -16,7 +16,7 @@ BROKEN_aarch64= compilation fails: runaway processes and out-of-memory condition BROKEN_i386= compilation fails: clang runs out of memory BROKEN_armv7= compilation fails: clang runs out of memory -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libgmpxx.so:math/gmp USES= cmake:testing eigen:3 python:build diff --git a/science/libint2/Makefile b/science/libint2/Makefile index 49d12c0e9529..9bbda009de5b 100644 --- a/science/libint2/Makefile +++ b/science/libint2/Makefile @@ -1,7 +1,7 @@ PORTNAME= libint DISTVERSIONPREFIX= v DISTVERSION= 2.11.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science PKGNAMESUFFIX= 2 @@ -12,7 +12,7 @@ WWW= https://github.com/evaleev/libint LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libgmpxx.so:math/gmp USES= autoreconf:build compiler:c++11-lang gmake libtool localbase:ldflags diff --git a/science/libkml/Makefile b/science/libkml/Makefile index 7a1d72729c2a..4f393b67245b 100644 --- a/science/libkml/Makefile +++ b/science/libkml/Makefile @@ -1,6 +1,6 @@ PORTNAME= libkml PORTVERSION= 1.3.0 -PORTREVISION= 30 +PORTREVISION= 31 CATEGORIES= science MAINTAINER= sunpoet@FreeBSD.org diff --git a/science/maeparser/Makefile b/science/maeparser/Makefile index 20538a1eac85..77813610f5b7 100644 --- a/science/maeparser/Makefile +++ b/science/maeparser/Makefile @@ -1,6 +1,7 @@ PORTNAME= maeparser DISTVERSIONPREFIX= v DISTVERSION= 1.3.3 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/mdynamix/Makefile b/science/mdynamix/Makefile index 7227c210b3f0..fe71bb4d552c 100644 --- a/science/mdynamix/Makefile +++ b/science/mdynamix/Makefile @@ -18,7 +18,7 @@ WRKSRC= ${WRKDIR}/mdynamix ALL_TARGET= default mpi MAKE_ARGS= FFLAGS="${FFLAGS} -ffast-math" LDFLAGS="${LDFLAGS}" -BINARY_ALIAS= make=gmake gfortran=gfortran${GCC_DEFAULT} +BINARY_ALIAS= make=gmake gfortran=${FC} PLIST_FILES= bin/md bin/mdp @@ -28,7 +28,7 @@ do-install: .include <bsd.port.pre.mk> -.if ${GCC_DEFAULT} >= 10 +.if ${FORTRAN_DEFAULT} == gfortran && ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/REAL(4)). # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch diff --git a/science/molgif/Makefile b/science/molgif/Makefile index af14421a80b8..1f15ede46747 100644 --- a/science/molgif/Makefile +++ b/science/molgif/Makefile @@ -1,6 +1,6 @@ PORTNAME= molgif DISTVERSION= g20180108 -PORTREVISION= 31 +PORTREVISION= 32 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/nest/Makefile b/science/nest/Makefile index 49b9c6090721..c4eafdc4790a 100644 --- a/science/nest/Makefile +++ b/science/nest/Makefile @@ -1,7 +1,7 @@ PORTNAME= nest DISTVERSIONPREFIX= v DISTVERSION= 3.8 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science biology # NEST is used in neuroscience MAINTAINER= yuri@FreeBSD.org @@ -14,7 +14,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= compilation fails: error: expected identifier before '__is_convertible' BROKEN_i386= https://github.com/nest/nest-simulator/issues/1205 -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libgsl.so:math/gsl \ libltdl.so:devel/libltdl RUN_DEPENDS= bash:shells/bash diff --git a/science/openbabel/Makefile b/science/openbabel/Makefile index b14fb8f12ff0..0dc26cebd570 100644 --- a/science/openbabel/Makefile +++ b/science/openbabel/Makefile @@ -1,6 +1,6 @@ PORTNAME= openbabel DISTVERSION= 3-1-1-178 -PORTREVISION= 5 +PORTREVISION= 6 #DISTVERSIONSUFFIX= -source DISTVERSIONSUFFIX= -g2b211d6ac CATEGORIES= science diff --git a/science/openems/Makefile b/science/openems/Makefile index 04c0f0305e74..9a1862a1ca80 100644 --- a/science/openems/Makefile +++ b/science/openems/Makefile @@ -1,7 +1,7 @@ PORTNAME= openems DISTVERSIONPREFIX= v DISTVERSION= 0.0.36 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -14,7 +14,7 @@ LICENSE_FILE= ${WRKSRC}/COPYING ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le ONLY_FOR_ARCHS_REASON= upstream only supports amd64 and powerpc64 -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libCSXCAD.so:cad/csxcad \ libfparser-4.5.so:math/fparser \ libhdf5.so:science/hdf5 \ diff --git a/science/openmodelica/Makefile b/science/openmodelica/Makefile index 20193cb276c9..bfb448159694 100644 --- a/science/openmodelica/Makefile +++ b/science/openmodelica/Makefile @@ -1,6 +1,7 @@ PORTNAME= openmodelica DISTVERSIONPREFIX= v DISTVERSION= 1.25.4 +PORTREVISION= 1 CATEGORIES= science cad java DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} diff --git a/science/orthanc-dicomweb/Makefile b/science/orthanc-dicomweb/Makefile index 9c049433aab3..4621c2660c8a 100644 --- a/science/orthanc-dicomweb/Makefile +++ b/science/orthanc-dicomweb/Makefile @@ -1,6 +1,6 @@ PORTNAME= orthanc-dicomweb DISTVERSION= 1.8 -PORTREVISION= 14 +PORTREVISION= 15 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-dicom-web/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ diff --git a/science/orthanc-mysql/Makefile b/science/orthanc-mysql/Makefile index f963cfd53313..c5bbe0d89ec5 100644 --- a/science/orthanc-mysql/Makefile +++ b/science/orthanc-mysql/Makefile @@ -1,6 +1,6 @@ PORTNAME= orthanc-mysql DISTVERSION= 4.3 -PORTREVISION= 11 +PORTREVISION= 12 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-mysql/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ diff --git a/science/orthanc-postgresql/Makefile b/science/orthanc-postgresql/Makefile index 044e5ef0a822..3479520ad2ed 100644 --- a/science/orthanc-postgresql/Makefile +++ b/science/orthanc-postgresql/Makefile @@ -1,6 +1,6 @@ PORTNAME= orthanc-postgresql DISTVERSION= 4.0 -PORTREVISION= 11 +PORTREVISION= 12 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-postgresql/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ diff --git a/science/orthanc-webviewer/Makefile b/science/orthanc-webviewer/Makefile index 71b7598926a0..f05e3a9795cb 100644 --- a/science/orthanc-webviewer/Makefile +++ b/science/orthanc-webviewer/Makefile @@ -1,6 +1,6 @@ PORTNAME= orthanc-webviewer DISTVERSION= 2.9 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-webviewer/:main \ https://orthanc.uclouvain.be/downloads/sources/orthanc/:framework \ diff --git a/science/orthanc/Makefile b/science/orthanc/Makefile index 515e49a5a4fb..e2760ebdd218 100644 --- a/science/orthanc/Makefile +++ b/science/orthanc/Makefile @@ -1,6 +1,6 @@ PORTNAME= orthanc DISTVERSION= 1.12.6 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc/ DISTNAME= Orthanc-${PORTVERSION} diff --git a/science/p5-Chemistry-Mol/Makefile b/science/p5-Chemistry-Mol/Makefile index 4f4c2e70ec69..9aed9a34acf7 100644 --- a/science/p5-Chemistry-Mol/Makefile +++ b/science/p5-Chemistry-Mol/Makefile @@ -1,5 +1,5 @@ PORTNAME= Chemistry-Mol -PORTVERSION= 0.39 +PORTVERSION= 0.40 CATEGORIES= science perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- diff --git a/science/p5-Chemistry-Mol/distinfo b/science/p5-Chemistry-Mol/distinfo index fec03561553b..71c6d905887c 100644 --- a/science/p5-Chemistry-Mol/distinfo +++ b/science/p5-Chemistry-Mol/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1657835607 -SHA256 (Chemistry-Mol-0.39.tar.gz) = 1fc7b65e3ee0e77410c55e12493018a0722e14df6e4ed553fdef68144feaeba4 -SIZE (Chemistry-Mol-0.39.tar.gz) = 44747 +TIMESTAMP = 1760370250 +SHA256 (Chemistry-Mol-0.40.tar.gz) = ac357b5034a60f2db6b674c77e682e5b93efb0a37d19fd63cf95ea5965402530 +SIZE (Chemistry-Mol-0.40.tar.gz) = 45518 diff --git a/science/p5-Geo-BUFR/Makefile b/science/p5-Geo-BUFR/Makefile index 5b338ed15a8c..869ac524584f 100644 --- a/science/p5-Geo-BUFR/Makefile +++ b/science/p5-Geo-BUFR/Makefile @@ -1,5 +1,5 @@ PORTNAME= Geo-BUFR -PORTVERSION= 1.39 +PORTVERSION= 1.40 CATEGORIES= science perl5 geography MASTER_SITES= CPAN PKGNAMEPREFIX= p5- diff --git a/science/p5-Geo-BUFR/distinfo b/science/p5-Geo-BUFR/distinfo index 4ac5244e2358..dfa464bd79fd 100644 --- a/science/p5-Geo-BUFR/distinfo +++ b/science/p5-Geo-BUFR/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1677771143 -SHA256 (Geo-BUFR-1.39.tar.gz) = ae3a7e88e5ae101d6babcb1d5c8743e586506da47c074c8746e6b363931af28b -SIZE (Geo-BUFR-1.39.tar.gz) = 326318 +TIMESTAMP = 1759816612 +SHA256 (Geo-BUFR-1.40.tar.gz) = 73f53bb6d5fa59d4e285931d764c8d286e18bdaaf83c727874902d9f6ddc39ab +SIZE (Geo-BUFR-1.40.tar.gz) = 322793 diff --git a/science/pagmo2/Makefile b/science/pagmo2/Makefile index dd0ecbe367c2..f589d88affc4 100644 --- a/science/pagmo2/Makefile +++ b/science/pagmo2/Makefile @@ -1,7 +1,7 @@ PORTNAME= pagmo2 DISTVERSIONPREFIX= v DISTVERSION= 2.19.1 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/paraview/Makefile b/science/paraview/Makefile index e657e04d7f84..550b2e39fe73 100644 --- a/science/paraview/Makefile +++ b/science/paraview/Makefile @@ -1,6 +1,6 @@ PORTNAME= paraview DISTVERSION= ${PARAVIEW_VER}.3 -PORTREVISION= 5 +PORTREVISION= 7 CATEGORIES= science graphics MASTER_SITES= http://www.paraview.org/files/v${PARAVIEW_VER}/ DISTNAME= ParaView-v${PORTVERSION} diff --git a/science/pcmsolver/Makefile b/science/pcmsolver/Makefile index ff137c88f6ef..0b234b6f90d9 100644 --- a/science/pcmsolver/Makefile +++ b/science/pcmsolver/Makefile @@ -1,7 +1,7 @@ PORTNAME= pcmsolver DISTVERSIONPREFIX= v DISTVERSION= 1.3.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -11,9 +11,7 @@ WWW= https://github.com/PCMSolver/pcmsolver LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_FreeBSD_15= compilation is broken with clang-19, see https://github.com/PCMSolver/pcmsolver/issues/208 - -USES= cmake compiler:c11 fortran python +USES= cmake compiler:c++14-lang fortran python:build USE_LDCONFIG= yes USE_GITHUB= yes diff --git a/science/pcmsolver/files/patch-cmake_custom_compilers_CXXFlags.cmake b/science/pcmsolver/files/patch-cmake_custom_compilers_CXXFlags.cmake new file mode 100644 index 000000000000..a9bf3aef3f64 --- /dev/null +++ b/science/pcmsolver/files/patch-cmake_custom_compilers_CXXFlags.cmake @@ -0,0 +1,8 @@ +--- cmake/custom/compilers/CXXFlags.cmake.orig 2025-10-15 01:10:00 UTC ++++ cmake/custom/compilers/CXXFlags.cmake +@@ -1,4 +1,4 @@ +-set(CMAKE_CXX_STANDARD 11) ++set(CMAKE_CXX_STANDARD 14) + set(CMAKE_CXX_STANDARD_REQUIRED TRUE) + set(CMAKE_CXX_EXTENSIONS FALSE) + diff --git a/science/pcmsolver/files/patch-external_eigen3_include_eigen3_Eigen_src_Core_Transpositions.h b/science/pcmsolver/files/patch-external_eigen3_include_eigen3_Eigen_src_Core_Transpositions.h new file mode 100644 index 000000000000..ada24c1f6175 --- /dev/null +++ b/science/pcmsolver/files/patch-external_eigen3_include_eigen3_Eigen_src_Core_Transpositions.h @@ -0,0 +1,14 @@ +- fix build error with Eigen 3.3.2 + + +--- external/eigen3/include/eigen3/Eigen/src/Core/Transpositions.h.orig 2025-10-15 01:10:00 UTC ++++ external/eigen3/include/eigen3/Eigen/src/Core/Transpositions.h +@@ -384,7 +384,7 @@ class Transpose<TranspositionsBase<TranspositionsDeri + const Product<OtherDerived, Transpose, AliasFreeProduct> + operator*(const MatrixBase<OtherDerived>& matrix, const Transpose& trt) + { +- return Product<OtherDerived, Transpose, AliasFreeProduct>(matrix.derived(), trt.derived()); ++ return Product<OtherDerived, Transpose, AliasFreeProduct>(matrix.derived(), trt); + } + + /** \returns the \a matrix with the inverse transpositions applied to the rows. diff --git a/science/precice/Makefile b/science/precice/Makefile index 7f6315a778c2..419d8e0cccc3 100644 --- a/science/precice/Makefile +++ b/science/precice/Makefile @@ -1,7 +1,7 @@ PORTNAME= precice DISTVERSIONPREFIX= v DISTVERSION= 3.1.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org @@ -14,7 +14,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN= fails to build with Boost>=1.87 BUILD_DEPENDS= ${PYNUMPY} -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libmpicxx.so:net/mpich RUN_DEPENDS= ${PYNUMPY} diff --git a/science/pulseview/Makefile b/science/pulseview/Makefile index 3caf31619525..76cce2ea8df2 100644 --- a/science/pulseview/Makefile +++ b/science/pulseview/Makefile @@ -1,6 +1,6 @@ PORTNAME= pulseview PORTVERSION= 0.4.2 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= science cad MASTER_SITES= http://sigrok.org/download/source/pulseview/ diff --git a/science/py-abipy/Makefile b/science/py-abipy/Makefile index 06e725dae361..17fc7722db8c 100644 --- a/science/py-abipy/Makefile +++ b/science/py-abipy/Makefile @@ -6,7 +6,8 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library for analyzing the results produced by ABINIT -WWW= https://abinit.github.io/abipy/ +WWW= https://abinit.github.io/abipy/ \ + https://github.com/abinit/abipy LICENSE= GPLv2 diff --git a/science/py-asdf/Makefile b/science/py-asdf/Makefile index 5a7e1522c875..76f131028c90 100644 --- a/science/py-asdf/Makefile +++ b/science/py-asdf/Makefile @@ -1,5 +1,5 @@ PORTNAME= asdf -PORTVERSION= 4.5.0 +PORTVERSION= 5.0.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-asdf/distinfo b/science/py-asdf/distinfo index cf61646370fe..39f1bfcd99c2 100644 --- a/science/py-asdf/distinfo +++ b/science/py-asdf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1757436539 -SHA256 (asdf-4.5.0.tar.gz) = 1f37979263cac53b8f7b078c521fda8aa9a08cd5d2badb9aacec34d6badd2dc1 -SIZE (asdf-4.5.0.tar.gz) = 900039 +TIMESTAMP = 1759816708 +SHA256 (asdf-5.0.0.tar.gz) = a7c37703db1b99dc29b686978c2d43fcd4b99019dc499b48cabd210776750590 +SIZE (asdf-5.0.0.tar.gz) = 894440 diff --git a/science/py-cfgrib/Makefile b/science/py-cfgrib/Makefile index f5481f4e9c04..0d1d3856f1df 100644 --- a/science/py-cfgrib/Makefile +++ b/science/py-cfgrib/Makefile @@ -1,5 +1,5 @@ PORTNAME= cfgrib -PORTVERSION= 0.9.15.0 +PORTVERSION= 0.9.15.1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,7 +11,8 @@ WWW= https://github.com/ecmwf/cfgrib LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=61:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}setuptools-scm>=8:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}attrs>=19.2:devel/py-attrs@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} \ diff --git a/science/py-cfgrib/distinfo b/science/py-cfgrib/distinfo index 7f15c79eb0da..eb140f13f1e7 100644 --- a/science/py-cfgrib/distinfo +++ b/science/py-cfgrib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1735227962 -SHA256 (cfgrib-0.9.15.0.tar.gz) = d455034e19b9560a75d008ba9d09b2d4e65762adfb2e911f28b841f4b9c6b47f -SIZE (cfgrib-0.9.15.0.tar.gz) = 6511752 +TIMESTAMP = 1759774703 +SHA256 (cfgrib-0.9.15.1.tar.gz) = d959d8b97e55a63646fa86686b297905ff7f2918a91e3a11d6292dab09598e4d +SIZE (cfgrib-0.9.15.1.tar.gz) = 9746591 diff --git a/science/py-cirq-aqt/Makefile b/science/py-cirq-aqt/Makefile index e283bf48ecdf..fb3104f62315 100644 --- a/science/py-cirq-aqt/Makefile +++ b/science/py-cirq-aqt/Makefile @@ -1,6 +1,6 @@ PORTNAME= cirq-aqt DISTVERSIONPREFIX= v -DISTVERSION= 1.5.0 +DISTVERSION= 1.6.1 PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-aqt/distinfo b/science/py-cirq-aqt/distinfo index 90789b1d2df1..bea87b2b10aa 100644 --- a/science/py-cirq-aqt/distinfo +++ b/science/py-cirq-aqt/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1744354009 -SHA256 (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = ff1622dea7de12e58fc47458e30d576c9a5a4faba5fd85bc6849150d1da3fc7f -SIZE (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = 8126107 +TIMESTAMP = 1760339430 +SHA256 (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 65da567eea507b5a2b2609fea8cb5e6a2b4e92a6622fad9c2a5c406761b09475 +SIZE (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 7898333 diff --git a/science/py-cirq-core/Makefile b/science/py-cirq-core/Makefile index 61e40b03c471..4a52814ebfbf 100644 --- a/science/py-cirq-core/Makefile +++ b/science/py-cirq-core/Makefile @@ -1,6 +1,6 @@ PORTNAME= cirq-core DISTVERSIONPREFIX= v -DISTVERSION= 1.5.0 +DISTVERSION= 1.6.1 PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-core/distinfo b/science/py-cirq-core/distinfo index 90789b1d2df1..0ca224a1899c 100644 --- a/science/py-cirq-core/distinfo +++ b/science/py-cirq-core/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1744354009 -SHA256 (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = ff1622dea7de12e58fc47458e30d576c9a5a4faba5fd85bc6849150d1da3fc7f -SIZE (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = 8126107 +TIMESTAMP = 1760339431 +SHA256 (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 65da567eea507b5a2b2609fea8cb5e6a2b4e92a6622fad9c2a5c406761b09475 +SIZE (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 7898333 diff --git a/science/py-cirq-google/Makefile b/science/py-cirq-google/Makefile index 4ea483157b29..d82b59c678b5 100644 --- a/science/py-cirq-google/Makefile +++ b/science/py-cirq-google/Makefile @@ -1,6 +1,6 @@ PORTNAME= cirq-google DISTVERSIONPREFIX= v -DISTVERSION= 1.5.0 +DISTVERSION= 1.6.1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-google/distinfo b/science/py-cirq-google/distinfo index 4fbbd69035e7..c05992b52a67 100644 --- a/science/py-cirq-google/distinfo +++ b/science/py-cirq-google/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1744354010 -SHA256 (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = ff1622dea7de12e58fc47458e30d576c9a5a4faba5fd85bc6849150d1da3fc7f -SIZE (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = 8126107 +TIMESTAMP = 1760339432 +SHA256 (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 65da567eea507b5a2b2609fea8cb5e6a2b4e92a6622fad9c2a5c406761b09475 +SIZE (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 7898333 diff --git a/science/py-cirq-ionq/Makefile b/science/py-cirq-ionq/Makefile index ea3fc7ffc5c6..c0d8482d6e69 100644 --- a/science/py-cirq-ionq/Makefile +++ b/science/py-cirq-ionq/Makefile @@ -1,6 +1,6 @@ PORTNAME= cirq-ionq DISTVERSIONPREFIX= v -DISTVERSION= 1.5.0 +DISTVERSION= 1.6.1 PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-ionq/distinfo b/science/py-cirq-ionq/distinfo index 4fbbd69035e7..0ca224a1899c 100644 --- a/science/py-cirq-ionq/distinfo +++ b/science/py-cirq-ionq/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1744354010 -SHA256 (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = ff1622dea7de12e58fc47458e30d576c9a5a4faba5fd85bc6849150d1da3fc7f -SIZE (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = 8126107 +TIMESTAMP = 1760339431 +SHA256 (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 65da567eea507b5a2b2609fea8cb5e6a2b4e92a6622fad9c2a5c406761b09475 +SIZE (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 7898333 diff --git a/science/py-cirq-pasqal/Makefile b/science/py-cirq-pasqal/Makefile index c279a6440d3f..0a49c04f2af5 100644 --- a/science/py-cirq-pasqal/Makefile +++ b/science/py-cirq-pasqal/Makefile @@ -1,6 +1,6 @@ PORTNAME= cirq-pasqal DISTVERSIONPREFIX= v -DISTVERSION= 1.5.0 +DISTVERSION= 1.6.1 PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-pasqal/distinfo b/science/py-cirq-pasqal/distinfo index 1ee12b3cfff6..bea87b2b10aa 100644 --- a/science/py-cirq-pasqal/distinfo +++ b/science/py-cirq-pasqal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1744354008 -SHA256 (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = ff1622dea7de12e58fc47458e30d576c9a5a4faba5fd85bc6849150d1da3fc7f -SIZE (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = 8126107 +TIMESTAMP = 1760339430 +SHA256 (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 65da567eea507b5a2b2609fea8cb5e6a2b4e92a6622fad9c2a5c406761b09475 +SIZE (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 7898333 diff --git a/science/py-cirq-rigetti/distinfo b/science/py-cirq-rigetti/distinfo deleted file mode 100644 index 4fbbd69035e7..000000000000 --- a/science/py-cirq-rigetti/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1744354010 -SHA256 (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = ff1622dea7de12e58fc47458e30d576c9a5a4faba5fd85bc6849150d1da3fc7f -SIZE (quantumlib-Cirq-v1.5.0_GH0.tar.gz) = 8126107 diff --git a/science/py-cirq-rigetti/pkg-descr b/science/py-cirq-rigetti/pkg-descr deleted file mode 100644 index f42a2725c284..000000000000 --- a/science/py-cirq-rigetti/pkg-descr +++ /dev/null @@ -1,2 +0,0 @@ -cirq-ionq provides everything you'll need to run Cirq quantum algorithms -on Rigetti quantum computers. diff --git a/science/py-cirq-rigetti/Makefile b/science/py-cirq-web/Makefile index 9f32d20ceff5..d537afc2c21d 100644 --- a/science/py-cirq-rigetti/Makefile +++ b/science/py-cirq-web/Makefile @@ -1,20 +1,16 @@ -PORTNAME= cirq-rigetti +PORTNAME= cirq-web DISTVERSIONPREFIX= v -DISTVERSION= 1.5.0 -PORTREVISION= 1 +DISTVERSION= 1.6.1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org -COMMENT= Cirq module to run on Rigetti quantum computers +COMMENT= Cirq module to visualize quantum circuits in 3D in a web browser WWW= https://github.com/quantumlib/cirq LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cirq-core>0:science/py-cirq-core@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pyquil>=3.0.0:devel/py-pyquil@${PY_FLAVOR} - USES= python USE_PYTHON= distutils autoplist @@ -22,7 +18,7 @@ USE_GITHUB= yes GH_ACCOUNT= quantumlib GH_PROJECT= Cirq -WRKSRC_SUBDIR= cirq-rigetti +WRKSRC_SUBDIR= cirq-web NO_ARCH= yes diff --git a/science/py-cirq-web/distinfo b/science/py-cirq-web/distinfo new file mode 100644 index 000000000000..bea87b2b10aa --- /dev/null +++ b/science/py-cirq-web/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1760339430 +SHA256 (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 65da567eea507b5a2b2609fea8cb5e6a2b4e92a6622fad9c2a5c406761b09475 +SIZE (quantumlib-Cirq-v1.6.1_GH0.tar.gz) = 7898333 diff --git a/science/py-cirq-web/files/example.py b/science/py-cirq-web/files/example.py new file mode 100644 index 000000000000..d93432d5d3bf --- /dev/null +++ b/science/py-cirq-web/files/example.py @@ -0,0 +1,18 @@ +import cirq + +# Pick a qubit. +qubit = cirq.GridQubit(0, 0) + +# Create a circuit +circuit = cirq.Circuit( + cirq.X(qubit)**0.5, # Square root of NOT. + cirq.measure(qubit, key='m') # Measurement. +) +print("Circuit:") +print(circuit) + +# Simulate the circuit several times. +simulator = cirq.Simulator() +result = simulator.run(circuit, repetitions=20) +print("Results:") +print(result) diff --git a/science/py-cirq-web/pkg-descr b/science/py-cirq-web/pkg-descr new file mode 100644 index 000000000000..22e7e20a4ae9 --- /dev/null +++ b/science/py-cirq-web/pkg-descr @@ -0,0 +1,4 @@ +Cirq-web is a Python library that provides browser-based 3D visualization +tools for quantum circuits created with the Cirq framework. It allows users +to inspect and understand the structure of their quantum circuits in a visual +way. diff --git a/science/py-corner/Makefile b/science/py-corner/Makefile new file mode 100644 index 000000000000..fc69061b3a5b --- /dev/null +++ b/science/py-corner/Makefile @@ -0,0 +1,31 @@ +PORTNAME= corner +DISTVERSION= 2.2.3 +CATEGORIES= science graphics python +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Make some beautiful corner plots +WWW= https://github.com/dfm/corner.py + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}hatchling>0:devel/py-hatchling@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}hatch-vcs>0:devel/py-hatch-vcs@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.1:math/py-matplotlib@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}arviz>=0.9:math/py-arviz@${PY_FLAVOR} \ + nox>0:devel/nox \ + ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} + +USES= python +USE_PYTHON= autoplist concurrent pep517 pytest + +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +TEST_WRKSRC= ${WRKSRC}/tests + +NO_ARCH= yes + +# tests as of 2.2.3: 12 failed, 49 passed in 174.75s (0:02:54) + +.include <bsd.port.mk> diff --git a/science/py-corner/distinfo b/science/py-corner/distinfo new file mode 100644 index 000000000000..8e19b029a15f --- /dev/null +++ b/science/py-corner/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1760469512 +SHA256 (corner-2.2.3.tar.gz) = 471b7b63395d8f1dee176bb779348ade38d56abd23404a48802a593607745e1c +SIZE (corner-2.2.3.tar.gz) = 5932840 diff --git a/science/py-corner/pkg-descr b/science/py-corner/pkg-descr new file mode 100644 index 000000000000..3ba0d780bc59 --- /dev/null +++ b/science/py-corner/pkg-descr @@ -0,0 +1,11 @@ +py-corner is a Python library designed to create "corner plots" (also known as +triangle plots or scatterplot matrices) for visualizing high-dimensional data. + +These plots are particularly useful in scientific fields such as astrophysics, +cosmology, and statistics for displaying the marginalized distributions of +parameters from a multi-dimensional sample (e.g., from Markov Chain Monte Carlo +simulations). + +The library generates 1D histograms for individual parameters and 2D histograms +(or scatter plots) for all pairs of parameters, providing a comprehensive +overview of their distributions and correlations. diff --git a/science/py-eccodes/Makefile b/science/py-eccodes/Makefile index 044eb813edc2..0c08fc46cba2 100644 --- a/science/py-eccodes/Makefile +++ b/science/py-eccodes/Makefile @@ -1,5 +1,5 @@ PORTNAME= eccodes -PORTVERSION= 2.43.0 +PORTVERSION= 2.44.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-eccodes/distinfo b/science/py-eccodes/distinfo index e37fc89abc25..a98818fea0d8 100644 --- a/science/py-eccodes/distinfo +++ b/science/py-eccodes/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753796092 -SHA256 (eccodes-2.43.0.tar.gz) = b99c41aaa64b20291452297a3d513e0b08cc96bcedfe364d8f58348159c48faa -SIZE (eccodes-2.43.0.tar.gz) = 2269307 +TIMESTAMP = 1759774561 +SHA256 (eccodes-2.44.0.tar.gz) = 8aba9316749349e64db7d075100bff8e24a892814e3529132ec97b6d787eb8f4 +SIZE (eccodes-2.44.0.tar.gz) = 2310714 diff --git a/science/py-fresnel/Makefile b/science/py-fresnel/Makefile index 3133b2c1777e..89973e8ef4a6 100644 --- a/science/py-fresnel/Makefile +++ b/science/py-fresnel/Makefile @@ -1,8 +1,6 @@ PORTNAME= fresnel DISTVERSIONPREFIX= v -DISTVERSION= 0.13.4-4 -DISTVERSIONSUFFIX= -g3ba217f -PORTREVISION= 9 +DISTVERSION= 0.13.8 CATEGORIES= science # physics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,7 +12,7 @@ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= pybind11>0:devel/pybind11 -LIB_DEPENDS= libembree3.so:graphics/embree3 \ +LIB_DEPENDS= libembree4.so:graphics/embree \ libqhull_r.so:math/qhull \ libtbb.so:devel/onetbb TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pillow>0:graphics/py-pillow@${PY_FLAVOR} @@ -25,7 +23,7 @@ USE_GITHUB= yes GH_ACCOUNT= glotzerlab GH_TUPLE= glotzerlab:random123:7f2371b8c597a486cd33fb421a196d78efe08043:glotzerlab_random123/extern/random123 \ - glotzerlab:fresnel-examples:dad005682fc3b5d167861ce7eda23a157baf2ce7:glotzerlab_fresnel_examples/doc/examples \ + glotzerlab:fresnel-examples:edae193:glotzerlab_fresnel_examples/doc/examples \ glotzerlab:qhull:613debeaea72ee66626dace9ba1a2eff11b5d37d:glotzerlab_qhull/extern/qhull do-test: install diff --git a/science/py-fresnel/distinfo b/science/py-fresnel/distinfo index e9eab2d2039d..8c3c9eb135d2 100644 --- a/science/py-fresnel/distinfo +++ b/science/py-fresnel/distinfo @@ -1,9 +1,9 @@ -TIMESTAMP = 1642820220 -SHA256 (glotzerlab-fresnel-v0.13.4-4-g3ba217f_GH0.tar.gz) = ac0b4f0e26050cdb4c1f5aa65cca66462127f2e6f2d6e0c97138d510fe5356e6 -SIZE (glotzerlab-fresnel-v0.13.4-4-g3ba217f_GH0.tar.gz) = 11009467 +TIMESTAMP = 1760712135 +SHA256 (glotzerlab-fresnel-v0.13.8_GH0.tar.gz) = b64b5aac2836bb3c30d8e7c8256e5726ff680b52674dcb0286a291f05e9c2241 +SIZE (glotzerlab-fresnel-v0.13.8_GH0.tar.gz) = 11065739 SHA256 (glotzerlab-random123-7f2371b8c597a486cd33fb421a196d78efe08043_GH0.tar.gz) = c96b9240953197387977244858d624c81bef15d74c5badd77a07c8d29cb30a8e SIZE (glotzerlab-random123-7f2371b8c597a486cd33fb421a196d78efe08043_GH0.tar.gz) = 648611 -SHA256 (glotzerlab-fresnel-examples-dad005682fc3b5d167861ce7eda23a157baf2ce7_GH0.tar.gz) = c603a5a48b7b559ae091d11f4a1ccdae2628929ccef721d9da1bd17bb8928e5a -SIZE (glotzerlab-fresnel-examples-dad005682fc3b5d167861ce7eda23a157baf2ce7_GH0.tar.gz) = 8110548 +SHA256 (glotzerlab-fresnel-examples-edae193_GH0.tar.gz) = e6b89dd8a4d15283f645aa206b91b139d0c89feb47e379c25dd37f0a42b8d73a +SIZE (glotzerlab-fresnel-examples-edae193_GH0.tar.gz) = 8109210 SHA256 (glotzerlab-qhull-613debeaea72ee66626dace9ba1a2eff11b5d37d_GH0.tar.gz) = b4504a190dc15c3ae932b998a2eed3cba8c7bdda1ab2a886e7e09d0526ee8143 SIZE (glotzerlab-qhull-613debeaea72ee66626dace9ba1a2eff11b5d37d_GH0.tar.gz) = 1308230 diff --git a/science/py-openpiv/Makefile b/science/py-openpiv/Makefile index 4243feff9291..98b63217ff89 100644 --- a/science/py-openpiv/Makefile +++ b/science/py-openpiv/Makefile @@ -1,35 +1,28 @@ PORTNAME= openpiv -PORTVERSION= 0.23.8 -PORTREVISION= 4 -DISTVERSIONPREFIX= v +PORTVERSION= 0.25.3 CATEGORIES= science python +MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= makc@FreeBSD.org COMMENT= Python module for Particle Image Velocimetry -WWW= http://www.openpiv.net/ +WWW= https://github.com/OpenPIV LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt -BUILD_DEPENDS= ${PYNUMPY} +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}poetry-core>0:devel/py-poetry-core@${PY_FLAVOR} RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=0:science/py-scipy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scikit-image>=0.12.0:graphics/py-scikit-image@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}imageio>0:graphics/py-imageio@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}importlib-resources>0:devel/py-importlib-resources@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}natsort>0:devel/py-natsort@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scikit-image>0:graphics/py-scikit-image@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist distutils -USE_GITHUB= yes -GH_ACCOUNT= OpenPIV -GH_PROJECT= openpiv-python - +USE_PYTHON= autoplist pep517 NO_ARCH= yes -OPTIONS_DEFINE= EXTRA -EXTRA_DESC= Install additional Python packages (for tutorial/examples) - -EXTRA_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}natsort>=0:devel/py-natsort@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}imageio>=0:graphics/py-imageio@${PY_FLAVOR} - .include <bsd.port.mk> diff --git a/science/py-openpiv/distinfo b/science/py-openpiv/distinfo index 6d100e8e2475..e36cb9f13e6e 100644 --- a/science/py-openpiv/distinfo +++ b/science/py-openpiv/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1636128772 -SHA256 (OpenPIV-openpiv-python-v0.23.8_GH0.tar.gz) = ea5121593b0e718af082c22bb2afedd888e32998b4f9a526d65286b2e547028c -SIZE (OpenPIV-openpiv-python-v0.23.8_GH0.tar.gz) = 23930754 +TIMESTAMP = 1758658302 +SHA256 (openpiv-0.25.3.tar.gz) = 94e7588e897c6a5d64831aa9b906d4a9ed2d37a3ec71d668ba917783ddf1947d +SIZE (openpiv-0.25.3.tar.gz) = 37915252 diff --git a/science/py-pygmo2/Makefile b/science/py-pygmo2/Makefile index 869cc90d53f7..b86ea2682ff5 100644 --- a/science/py-pygmo2/Makefile +++ b/science/py-pygmo2/Makefile @@ -1,7 +1,7 @@ PORTNAME= pygmo2 DISTVERSIONPREFIX= v DISTVERSION= 2.19.7 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= science graphics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pymatgen/Makefile b/science/py-pymatgen/Makefile index 666ba10e005f..9a43fc7b1005 100644 --- a/science/py-pymatgen/Makefile +++ b/science/py-pymatgen/Makefile @@ -1,7 +1,6 @@ PORTNAME= pymatgen DISTVERSIONPREFIX= v -DISTVERSION= 2025.6.14 -PORTREVISION= 1 +DISTVERSION= 2025.10.7 CATEGORIES= science python #MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -27,8 +26,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}bibtexparser>=1.4.0:textproc/py-bibtexparser ${PYTHON_PKGNAMEPREFIX}palettable>=3.3.3:misc/py-palettable@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=2:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plotly>=5.0.0:graphics/py-plotly@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pybtex>=0.24.0:textproc/py-pybtex@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}requests>=2.32:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>=2.30:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ruamel.yaml>=0.17.0:devel/py-ruamel.yaml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.13.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spglib>=2.5:science/py-spglib@${PY_FLAVOR} \ @@ -57,7 +55,6 @@ TEST_WRKSRC= ${WRKSRC}/tests post-install: # strip binaries @cd ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/${PORTNAME} && ${STRIP_CMD} \ - optimization/linear_assignment*.so \ optimization/neighbors*.so \ util/coord_cython*.so diff --git a/science/py-pymatgen/distinfo b/science/py-pymatgen/distinfo index 8258c6d8ccd7..065d8cf9cafe 100644 --- a/science/py-pymatgen/distinfo +++ b/science/py-pymatgen/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1750130703 -SHA256 (materialsproject-pymatgen-v2025.6.14_GH0.tar.gz) = 5fb34d91889816240e93888a64bdf0b8d17ae23c51b9f6f9dcd5c940a90f47a6 -SIZE (materialsproject-pymatgen-v2025.6.14_GH0.tar.gz) = 272204087 +TIMESTAMP = 1760667421 +SHA256 (materialsproject-pymatgen-v2025.10.7_GH0.tar.gz) = e60338fdd70a3b944737a5379769f9bc892b6b6b7ba91336f01efb9799654624 +SIZE (materialsproject-pymatgen-v2025.10.7_GH0.tar.gz) = 271966495 diff --git a/science/qmcpack/Makefile b/science/qmcpack/Makefile index e53ffec135e8..cf5db3ae4960 100644 --- a/science/qmcpack/Makefile +++ b/science/qmcpack/Makefile @@ -1,7 +1,7 @@ PORTNAME= qmcpack DISTVERSIONPREFIX= v DISTVERSION= 4.0.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -17,7 +17,7 @@ BROKEN_i386= undefined reference to `__atomic_load' BROKEN= requires OpenMP support that is missing on this architecture .endif -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libfftw3.so:math/fftw3 \ libhdf5.so:science/hdf5 \ libmpich.so:net/mpich \ diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index dd2255f3a900..6f80768ea090 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ DISTVERSION= 2025_03_1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font DISTFILES= ComicNeue-Regular.ttf:font @@ -19,11 +19,12 @@ LICENSE_FILE= ${WRKSRC}/license.txt BROKEN_FreeBSD_15_aarch64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 BROKEN_FreeBSD_15_amd64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 BROKEN_FreeBSD_15_i386= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 +BROKEN_FreeBSD_16_amd64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 BUILD_DEPENDS= catch>0:devel/catch \ flex:textproc/flex \ rapidjson>=0:devel/rapidjson -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libcoordgen.so:science/coordgenlibs \ libfreetype.so:print/freetype2 \ libmaeparser.so:science/maeparser diff --git a/science/rmf/Makefile b/science/rmf/Makefile index 9a1b1c673a5d..c8519329efa7 100644 --- a/science/rmf/Makefile +++ b/science/rmf/Makefile @@ -1,6 +1,6 @@ PORTNAME= rmf DISTVERSION= 1.7.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science graphics MAINTAINER= yuri@FreeBSD.org @@ -11,7 +11,7 @@ WWW= https://integrativemodeling.org/rmf/ \ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libhdf5.so:science/hdf5 USES= compiler:c++17-lang cmake:testing localbase:ldflags python:build shebangfix diff --git a/science/salome-kernel/Makefile b/science/salome-kernel/Makefile index 11413201242a..f2a8ad47c3ef 100644 --- a/science/salome-kernel/Makefile +++ b/science/salome-kernel/Makefile @@ -1,7 +1,7 @@ PORTNAME= salome-kernel DISTVERSIONPREFIX= V DISTVERSION= 9_11_0 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/simgrid/Makefile b/science/simgrid/Makefile index 5c1bb1e17497..db9fa7d63319 100644 --- a/science/simgrid/Makefile +++ b/science/simgrid/Makefile @@ -1,7 +1,7 @@ PORTNAME= SimGrid DISTVERSIONPREFIX= v DISTVERSION= 3.35 -PORTREVISION= 5 +PORTREVISION= 7 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/sirius/Makefile b/science/sirius/Makefile index 91683901767c..32d06b9b319e 100644 --- a/science/sirius/Makefile +++ b/science/sirius/Makefile @@ -12,6 +12,7 @@ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_FreeBSD_15= clang crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=276196 +BROKEN_FreeBSD_16= clang crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=276196 LIB_DEPENDS= libcosta.so:math/costa \ libgsl.so:math/gsl \ diff --git a/science/spheral/Makefile b/science/spheral/Makefile index 7365b12d8edd..c6c14ef6c84b 100644 --- a/science/spheral/Makefile +++ b/science/spheral/Makefile @@ -1,7 +1,7 @@ PORTNAME= spheral DISTVERSIONPREFIX= v DISTVERSION= 2024.06.1 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/tfel-edf/Makefile b/science/tfel-edf/Makefile index 5115a36f59d8..4c48fa3ba758 100644 --- a/science/tfel-edf/Makefile +++ b/science/tfel-edf/Makefile @@ -1,6 +1,6 @@ PORTNAME= tfel DISTVERSION= 3.2.1-1 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= science PKGNAMESUFFIX= -mfront-edf diff --git a/science/tfel/Makefile b/science/tfel/Makefile index 5fa523762c10..87805fdc1d76 100644 --- a/science/tfel/Makefile +++ b/science/tfel/Makefile @@ -1,6 +1,6 @@ PORTNAME= tfel PORTVERSION= 4.0.0 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= science MASTER_SITES= SF/${PORTNAME}/ PKGNAMESUFFIX= -mfront diff --git a/science/ttk/Makefile b/science/ttk/Makefile index 1b1d123f5933..fa46ea465c0b 100644 --- a/science/ttk/Makefile +++ b/science/ttk/Makefile @@ -1,6 +1,6 @@ PORTNAME= ttk DISTVERSION= 1.3.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/v_sim/Makefile b/science/v_sim/Makefile index 5108a9903564..d14c5625f2cb 100644 --- a/science/v_sim/Makefile +++ b/science/v_sim/Makefile @@ -1,6 +1,5 @@ PORTNAME= v_sim -DISTVERSION= 3.8.0 -PORTREVISION= 14 +DISTVERSION= 3.9.0 CATEGORIES= science MAINTAINER= thierry@FreeBSD.org @@ -16,7 +15,8 @@ BUILD_DEPENDS= p5-XML-LibXML>0:textproc/p5-XML-LibXML \ libarchive>0:archivers/libarchive \ xcrysden:science/xcrysden \ bash:shells/bash -LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ +LIB_DEPENDS= libgdkglext-x11-1.0.so:x11-toolkits/gtkglext \ + libfontconfig.so:x11-fonts/fontconfig \ libopenbabel.so:science/openbabel \ libfreetype.so:print/freetype2 \ libharfbuzz.so:print/harfbuzz \ diff --git a/science/v_sim/pkg-plist b/science/v_sim/pkg-plist index e34e27c4ef1e..1d1299811155 100644 --- a/science/v_sim/pkg-plist +++ b/science/v_sim/pkg-plist @@ -7,6 +7,7 @@ lib/libv_sim-3.so.8 lib/libv_sim-3.so.8.0.0 %%PYTHON_SITELIBDIR%%/gi/overrides/__pycache__/v_sim.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc %%PYTHON_SITELIBDIR%%/gi/overrides/__pycache__/v_sim.cpython-%%PYTHON_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/gi/overrides/__pycache__/v_sim%%PYTHON_TAG%%.opt-2.pyc %%PYTHON_SITELIBDIR%%/gi/overrides/v_sim.py %%AB%%lib/v_sim/plug-ins/libabinit.a %%AB%%lib/v_sim/plug-ins/libabinit.la diff --git a/science/votca/Makefile b/science/votca/Makefile index 07f97264f4bb..64dd6876295e 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -1,7 +1,7 @@ PORTNAME= votca DISTVERSIONPREFIX= v -DISTVERSION= 2025 -PORTREVISION= 4 +DISTVERSION= 2025.1 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -73,6 +73,6 @@ do-test: # several tests fail, see https://github.com/votca/votca/issues/1098 ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test -# tests as of 2025: 100% tests passed, 0 tests failed out of 250 +# tests as of 2025.1: 100% tests passed, 0 tests failed out of 249 .include <bsd.port.mk> diff --git a/science/votca/distinfo b/science/votca/distinfo index 500ff40eff82..2c2f89fe0252 100644 --- a/science/votca/distinfo +++ b/science/votca/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1743227786 -SHA256 (votca-votca-v2025_GH0.tar.gz) = ee2ac59c858ee41ef3ecf636b263464cac5895c0ee9c8f97b1aafca4b8b76350 -SIZE (votca-votca-v2025_GH0.tar.gz) = 41334705 +TIMESTAMP = 1760182463 +SHA256 (votca-votca-v2025.1_GH0.tar.gz) = 85b487d2b2a31f26869be422c98f816b95c88a4ab112ea4650cccd4c2706bdbf +SIZE (votca-votca-v2025.1_GH0.tar.gz) = 41332679 |