diff options
Diffstat (limited to 'science')
333 files changed, 2755 insertions, 2300 deletions
diff --git a/science/Makefile b/science/Makefile index 9713030b534d..f14398a64291 100644 --- a/science/Makefile +++ b/science/Makefile @@ -64,6 +64,7 @@ SUBDIR += coordgenlibs SUBDIR += cp2k SUBDIR += cp2k-data + SUBDIR += cpcmx SUBDIR += csvtk SUBDIR += dakota SUBDIR += dalton @@ -210,6 +211,7 @@ SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nlcglib + SUBDIR += numsa SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += ocean @@ -313,8 +315,9 @@ 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 @@ -350,7 +353,7 @@ SUBDIR += py-h5netcdf SUBDIR += py-h5py SUBDIR += py-h5pyd - SUBDIR += py-hiphive + SUBDIR += py-hiPhive SUBDIR += py-hoomd-blue SUBDIR += py-icet SUBDIR += py-inequality @@ -415,6 +418,7 @@ SUBDIR += py-pyphot SUBDIR += py-pyprecice SUBDIR += py-pyqubo + SUBDIR += py-pysal SUBDIR += py-pyscf SUBDIR += py-pyteomics SUBDIR += py-qcelemental @@ -526,6 +530,5 @@ SUBDIR += xtb SUBDIR += yoda SUBDIR += zotero - SUBDIR += zx .include <bsd.port.subdir.mk> 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/afni/Makefile b/science/afni/Makefile index 60a9c6179d87..d9df14c3314c 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 25.2.18 +DISTVERSION= 25.3.00 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index 86a0070395b4..bbc262bd6adb 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1759213947 -SHA256 (afni-afni-AFNI_25.2.18_GH0.tar.gz) = 9f21faf0f8ed66eba8a2c1473a4c5c0421909e0f386fc699ed599bebced96003 -SIZE (afni-afni-AFNI_25.2.18_GH0.tar.gz) = 53390003 +TIMESTAMP = 1763655339 +SHA256 (afni-afni-AFNI_25.3.00_GH0.tar.gz) = 6122a5a48620d84c59ca076967ce53189dd1afb1e31d4cc04b6e4b2ad9598686 +SIZE (afni-afni-AFNI_25.3.00_GH0.tar.gz) = 53396071 diff --git a/science/agrum/Makefile b/science/agrum/Makefile index 761cac949744..d70ab19ce63e 100644 --- a/science/agrum/Makefile +++ b/science/agrum/Makefile @@ -1,5 +1,5 @@ PORTNAME= agrum -DISTVERSION= 2.2.1 +DISTVERSION= 2.3.0 CATEGORIES= science math MAINTAINER= yuri@FreeBSD.org @@ -20,7 +20,7 @@ LLD_UNSAFE= yes USE_GITLAB= yes GL_ACCOUNT= agrumery GL_PROJECT= aGrUM -GL_TAGNAME= 40993102 +GL_TAGNAME= 50ed291c SHEBANG_FILES= act @@ -60,6 +60,6 @@ do-test: @cd ${WRKSRC} && \ ${SETENV} ${MAKE_ENV} ./act test release agrum -t all -# tests as of 2.2.1: Failed 0 of 1485 tests +# tests as of 2.3.0: Failed 0 of 1486 tests .include <bsd.port.mk> diff --git a/science/agrum/distinfo b/science/agrum/distinfo index 03113cb380cc..966b46e198de 100644 --- a/science/agrum/distinfo +++ b/science/agrum/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1759029558 -SHA256 (aGrUM-40993102.tar.bz2) = f0a4174d7854ea4e045e79c9c6a85c40f2d017906beca221a95fba3a1f233e08 -SIZE (aGrUM-40993102.tar.bz2) = 21812219 +TIMESTAMP = 1762156368 +SHA256 (aGrUM-50ed291c.tar.bz2) = 3272acabc75dda0ebb5853aaa13553925642402a3a964811c766d6f5b75e8cb0 +SIZE (aGrUM-50ed291c.tar.bz2) = 21811308 diff --git a/science/agrum/pkg-plist b/science/agrum/pkg-plist index bdc68b53969c..cc509992e91b 100644 --- a/science/agrum/pkg-plist +++ b/science/agrum/pkg-plist @@ -1012,6 +1012,31 @@ lib/libagrumMRF.so.%%VERSION%% %%PYTHON_SITELIBDIR%%/pyagrum/ctbn/notebook.py %%PYTHON_SITELIBDIR%%/pyagrum/defaults.ini %%PYTHON_SITELIBDIR%%/pyagrum/deprecated.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ComputationCausal.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ComputationConditional.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ComputationMarginal.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_CustomShapleyCache.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_Explainer.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_Explanation.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_FIFOCache.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallCausalValues.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallConditionalValues.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallMarginalValues.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallValues.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShapCausalValues.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShapConditionalValues.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShapMarginalValues.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShapleyValues.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/__init__.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_explGeneralizedMarkovBlanket.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_explIndependenceListForPairs.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/_explInformationGraph.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/notebook/__init__.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/notebook/_bar.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/notebook/_beeswarm.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/notebook/_showShapValues.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/notebook/_waterfall.py +%%PYTHON_SITELIBDIR%%/pyagrum/explain/shapley.py %%PYTHON_SITELIBDIR%%/pyagrum/lib/__init__.py %%PYTHON_SITELIBDIR%%/pyagrum/lib/_colors.py %%PYTHON_SITELIBDIR%%/pyagrum/lib/bn2graph.py @@ -1030,7 +1055,6 @@ lib/libagrumMRF.so.%%VERSION%% %%PYTHON_SITELIBDIR%%/pyagrum/lib/mrf2graph.py %%PYTHON_SITELIBDIR%%/pyagrum/lib/notebook.py %%PYTHON_SITELIBDIR%%/pyagrum/lib/proba_histogram.py -%%PYTHON_SITELIBDIR%%/pyagrum/lib/shapley.py %%PYTHON_SITELIBDIR%%/pyagrum/lib/utils.py %%PYTHON_SITELIBDIR%%/pyagrum/pyagrum.py %%PYTHON_SITELIBDIR%%/pyagrum/skbn/_MBCalcul.py diff --git a/science/arbor/Makefile b/science/arbor/Makefile index d2d6e0cf6ef2..e507aab7bd79 100644 --- a/science/arbor/Makefile +++ b/science/arbor/Makefile @@ -1,7 +1,7 @@ PORTNAME= arbor DISTVERSIONPREFIX= v -DISTVERSION= 0.10.1 -PORTREVISION= 3 +DISTVERSION= 0.11.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -12,25 +12,26 @@ 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_armv7= compilation fails: unknown type name 'float64x2_t' BUILD_DEPENDS= bash:shells/bash \ libfmt>0:devel/libfmt \ nlohmann-json>0:devel/nlohmann-json \ random123>0:devel/random123 \ - ${PYTHON_PKGNAMEPREFIX}svgwrite>0:graphics/py-svgwrite@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}svgwrite>0:graphics/py-svgwrite@${PY_FLAVOR} \ + tinyopt>0:devel/tinyopt BUILD_DEPENDS+= ${LOCALBASE}/lib/cmake/GTest/GTestConfig.cmake:devel/googletest # https://github.com/arbor-sim/arbor/issues/2205 LIB_DEPENDS= libhwloc.so:devel/hwloc2 \ libpugixml.so:textproc/pugixml \ libunits.so:misc/units RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}svgwrite>0:graphics/py-svgwrite@${PY_FLAVOR} -TEST_DEPENDS= googletest>=0:devel/googletest +TEST_DEPENDS= googletest>0:devel/googletest -USES= cmake compiler:c++17-lang localbase python shebangfix +USES= cmake compiler:c++20-lang localbase pkgconfig python shebangfix USE_GITHUB= yes GH_ACCOUNT= arbor-sim +GH_TUPLE= cpm-cmake:CPM.cmake:v0.39.0:cpm SHEBANG_FILES= scripts/arbor-build-catalogue @@ -38,6 +39,8 @@ CMAKE_ON= BUILD_SHARED_LIBS CMAKE_OFF= ARB_USE_BUNDLED_UNITS CMAKE_ARGS= -DPython3_EXECUTABLE=${PYTHON_CMD} +CONFIGURE_ENV= CPM_REPO=${WRKSRC_cpm} +CXXFLAGS+= -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_NONE # prevent hardening issues with libc++, see https://github.com/arbor-sim/arbor/issues/2484 LDFLAGS+= -L${LOCALBASE}/lib -lunits OPTIONS_DEFINE= NATIVE @@ -45,9 +48,16 @@ OPTIONS_DEFINE= NATIVE NATIVE_CMAKE_ON= -DARB_ARCH=native NATIVE_CMAKE_OFF= -DARB_ARCH=none -TEST_TARGET= tests # tests fail to build, see https://github.com/arbor-sim/arbor/issues/2075 +TEST_TARGET= tests post-install: @${RMDIR} ${STAGEDIR}${DOCSDIR} +post-test: # run tests + @${BUILD_WRKSRC}/bin/unit + @${BUILD_WRKSRC}/bin/unit-local + @${BUILD_WRKSRC}/bin/unit-modcc + +# tests fail with LIBCPP assertion for invalid array element access, see https://github.com/arbor-sim/arbor/issues/2484 + .include <bsd.port.mk> diff --git a/science/arbor/distinfo b/science/arbor/distinfo index 895ebcc91640..ddd22577d041 100644 --- a/science/arbor/distinfo +++ b/science/arbor/distinfo @@ -1,3 +1,5 @@ -TIMESTAMP = 1724617928 -SHA256 (arbor-sim-arbor-v0.10.1_GH0.tar.gz) = 6a9a209dc20ab6edcf9847a70b0b4dbabf0c0d3c7e6e29b5bec7c00de9d7b8ae -SIZE (arbor-sim-arbor-v0.10.1_GH0.tar.gz) = 10159032 +TIMESTAMP = 1762075604 +SHA256 (arbor-sim-arbor-v0.11.0_GH0.tar.gz) = 6df68b308dd629df993eda40319676cd43407ae211d0846100b0cf42e8c9ad22 +SIZE (arbor-sim-arbor-v0.11.0_GH0.tar.gz) = 12511038 +SHA256 (cpm-cmake-CPM.cmake-v0.39.0_GH0.tar.gz) = 621cfca03a5a0fcf316f08aee37d775a71620879e768ebf74be8495773f6b578 +SIZE (cpm-cmake-CPM.cmake-v0.39.0_GH0.tar.gz) = 100981 diff --git a/science/arbor/files/patch-CMakeLists.txt b/science/arbor/files/patch-CMakeLists.txt index b813375ca016..9a056733f8ea 100644 --- a/science/arbor/files/patch-CMakeLists.txt +++ b/science/arbor/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2024-08-09 10:22:00 UTC +--- CMakeLists.txt.orig 2025-04-24 10:33:03 UTC +++ CMakeLists.txt -@@ -40,7 +40,7 @@ check_cxx_compiler_flag("-march=native" CXX_HAS_NATIVE +@@ -60,7 +60,7 @@ check_cxx_compiler_flag("-march=native" CXX_HAS_NATIVE # Specify target architecture. check_cxx_compiler_flag("-march=native" CXX_HAS_NATIVE) @@ -9,11 +9,16 @@ set(ARB_DEFAULT_ARCH "native") else() set(ARB_DEFAULT_ARCH "none") -@@ -307,7 +307,6 @@ install(TARGETS ext-units EXPORT arbor-targets) - install(TARGETS ext-random123 EXPORT arbor-targets) - target_link_libraries(arbor-public-deps INTERFACE ext-units) - install(TARGETS ext-units EXPORT arbor-targets) --install(TARGETS units compile_flags_target EXPORT arbor-targets) +@@ -302,11 +302,7 @@ install(TARGETS ext-hwloc EXPORT arbor-targets) + endif() + install(TARGETS ext-hwloc EXPORT arbor-targets) - # Keep track of packages we need to add to the generated CMake config - # file for arbor. +-CPMFindPackage(NAME json +- GITHUB_REPOSITORY nlohmann/json +- VERSION 3.12.0 +- OPTIONS "CMAKE_SUPPRESS_DEVELOPER_WARNINGS ON") +-install(TARGETS nlohmann_json EXPORT arbor-targets) ++find_package(nlohmann_json REQUIRED) + + add_library(ext-random123 INTERFACE) + CPMFindPackage(NAME random123 diff --git a/science/arbor/files/patch-cmake_CPM.cmake b/science/arbor/files/patch-cmake_CPM.cmake new file mode 100644 index 000000000000..5d3f5f935cac --- /dev/null +++ b/science/arbor/files/patch-cmake_CPM.cmake @@ -0,0 +1,12 @@ +--- cmake/CPM.cmake.orig 2025-04-24 10:33:03 UTC ++++ cmake/CPM.cmake +@@ -9,6 +9,9 @@ elseif(DEFINED ENV{CPM_SOURCE_CACHE}) + set(CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake") + elseif(DEFINED ENV{CPM_SOURCE_CACHE}) + set(CPM_DOWNLOAD_LOCATION "$ENV{CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake") ++elseif(DEFINED ENV{CPM_REPO}) ++ include("$ENV{CPM_REPO}/cmake/CPM.cmake") ++ return() + else() + set(CPM_DOWNLOAD_LOCATION "${CMAKE_BINARY_DIR}/cmake/CPM_${CPM_DOWNLOAD_VERSION}.cmake") + endif() diff --git a/science/arbor/files/patch-sup_CMakeLists.txt b/science/arbor/files/patch-sup_CMakeLists.txt index 95eac6c5f7eb..7fff28ceb029 100644 --- a/science/arbor/files/patch-sup_CMakeLists.txt +++ b/science/arbor/files/patch-sup_CMakeLists.txt @@ -1,4 +1,4 @@ ---- sup/CMakeLists.txt.orig 2024-08-09 10:22:00 UTC +--- sup/CMakeLists.txt.orig 2025-04-24 10:33:03 UTC +++ sup/CMakeLists.txt @@ -3,7 +3,7 @@ set(sup-sources json_meter.cpp @@ -7,5 +7,5 @@ -add_library(arbor-sup ${sup-sources}) +add_library(arbor-sup STATIC ${sup-sources}) - if (ARB_USE_BUNDLED_FMT) - target_include_directories(arbor-sup + target_link_libraries(arbor-sup PRIVATE fmt::fmt-header-only) + diff --git a/science/arbor/pkg-plist b/science/arbor/pkg-plist index f7844f35709c..e01333db8354 100644 --- a/science/arbor/pkg-plist +++ b/science/arbor/pkg-plist @@ -21,7 +21,6 @@ include/arbor/domdecexcept.hpp include/arbor/event_generator.hpp include/arbor/export.hpp include/arbor/fvm_types.hpp -include/arbor/generic_event.hpp include/arbor/gpu/cuda_api.hpp include/arbor/gpu/gpu_api.hpp include/arbor/gpu/gpu_common.hpp @@ -52,7 +51,6 @@ include/arbor/morph/segment_tree.hpp include/arbor/morph/stitch.hpp include/arbor/network.hpp include/arbor/network_generation.hpp -include/arbor/profile/clock.hpp include/arbor/profile/meter.hpp include/arbor/profile/meter_manager.hpp include/arbor/profile/profiler.hpp @@ -90,7 +88,6 @@ include/arbor/util/expected.hpp include/arbor/util/extra_traits.hpp include/arbor/util/handle_set.hpp include/arbor/util/hash_def.hpp -include/arbor/util/lexcmp_def.hpp include/arbor/util/pp_util.hpp include/arbor/util/scope_exit.hpp include/arbor/util/typed_map.hpp @@ -106,6 +103,7 @@ include/arborenv/gpu_env.hpp include/arborenv/with_mpi.hpp include/arborio/cableio.hpp include/arborio/cv_policy_parse.hpp +include/arborio/debug.hpp include/arborio/export.hpp include/arborio/json_serdes.hpp include/arborio/label_parse.hpp diff --git a/science/ascent/Makefile b/science/ascent/Makefile index a94aa81f952a..1687ea96d527 100644 --- a/science/ascent/Makefile +++ b/science/ascent/Makefile @@ -1,6 +1,7 @@ PORTNAME= ascent DISTVERSIONPREFIX= v -DISTVERSION= 0.9.3 +DISTVERSION= 0.9.5 +PORTREVISION= 1 CATEGORIES= science PKGNAMESUFFIX= -visualizer @@ -52,4 +53,6 @@ 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/axom/Makefile b/science/axom/Makefile index 58c94b7ba017..254bf8397995 100644 --- a/science/axom/Makefile +++ b/science/axom/Makefile @@ -1,7 +1,7 @@ PORTNAME= axom DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 -PORTREVISION= 1 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org 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/bout++/Makefile b/science/bout++/Makefile index 2e49f217994d..88dce44c18f9 100644 --- a/science/bout++/Makefile +++ b/science/bout++/Makefile @@ -1,7 +1,7 @@ PORTNAME= bout++ DISTVERSIONPREFIX= v DISTVERSION= 5.1.1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science math # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/cantera/Makefile b/science/cantera/Makefile index aea50ad6e4a7..bb99d1558988 100644 --- a/science/cantera/Makefile +++ b/science/cantera/Makefile @@ -1,7 +1,7 @@ PORTNAME= cantera DISTVERSIONPREFIX= v DISTVERSION= 3.1.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science # chemistry physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/checkmol/Makefile b/science/checkmol/Makefile index 84440a536957..8b92c6ffe802 100644 --- a/science/checkmol/Makefile +++ b/science/checkmol/Makefile @@ -1,6 +1,6 @@ PORTNAME= checkmol PORTVERSION= 0.5 -PORTREVISION= 17 +PORTREVISION= 18 CATEGORIES= science MASTER_SITES= https://homepage.univie.ac.at/norbert.haider/download/chemistry/checkmol/ DISTFILES= ${PORTNAME} diff --git a/science/chemicalfun/Makefile b/science/chemicalfun/Makefile index 9b3afed93586..482c69a62961 100644 --- a/science/chemicalfun/Makefile +++ b/science/chemicalfun/Makefile @@ -1,6 +1,6 @@ PORTNAME= chemicalfun DISTVERSION= 0.1.8 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science # chemistry MASTER_SITES= https://bitbucket.org/${BB_ACCOUNT}/${PORTNAME}/get/${BB_COMMIT}${EXTRACT_SUFX}?dummy=/:src DISTFILES= ${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}:src 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/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..5f2c3994456b 100644 --- a/science/conduit/Makefile +++ b/science/conduit/Makefile @@ -1,6 +1,7 @@ PORTNAME= conduit DISTVERSIONPREFIX= v -DISTVERSION= 0.9.3 +DISTVERSION= 0.9.5 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -45,6 +46,6 @@ 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/cpcmx/Makefile b/science/cpcmx/Makefile new file mode 100644 index 000000000000..d6d2b20459b5 --- /dev/null +++ b/science/cpcmx/Makefile @@ -0,0 +1,34 @@ +PORTNAME= cpcmx +DISTVERSION= 1.1.0 +CATEGORIES= science # chemistry +MASTER_SITES= https://github.com/grimme-lab/CPCM-X/releases/download/v${DISTVERSION}/ +DISTNAME= cpx-${DISTVERSION} + +MAINTAINER= alven@FreeBSD.org +COMMENT= Extended conductor-like polarizable continuum solvation model +WWW= https://github.com/grimme-lab/CPCM-X/ + +LICENSE= LGPL3+ +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libmctc-lib.so:science/mctc-lib \ + libnumsa.so:science/numsa \ + libtoml-f.so:textproc/toml-f +TEST_DEPENDS= test-drive>0:devel/test-drive + +USES= blaslapack cmake fortran tar:xz +USE_LDCONFIG= yes + +CMAKE_ON= BUILD_SHARED_LIBS + +TEST_TARGET= test + +# Remove bundled libraries +post-extract: + ${RM} -r ${WRKSRC}/subprojects + +post-patch: # same as https://github.com/grimme-lab/mctc-lib/pull/55 + @${REINPLACE_CMD} -e 's|$${CMAKE_Fortran_COMPILER_ID}-$${CMAKE_Fortran_COMPILER_VERSION}||' \ + ${WRKSRC}/config/CMakeLists.txt + +.include <bsd.port.mk> diff --git a/science/cpcmx/distinfo b/science/cpcmx/distinfo new file mode 100644 index 000000000000..ba586f9900e5 --- /dev/null +++ b/science/cpcmx/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1762129285 +SHA256 (cpx-1.1.0.tar.xz) = 255dfa9b70c41580163fa3636125a0103c3b553c52fc8558d3a63f4654cc41c1 +SIZE (cpx-1.1.0.tar.xz) = 13048668 diff --git a/science/cpcmx/files/patch-CMakeLists.txt b/science/cpcmx/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..cda652ab3ede --- /dev/null +++ b/science/cpcmx/files/patch-CMakeLists.txt @@ -0,0 +1,10 @@ +--- CMakeLists.txt.orig 2025-03-13 13:29:31 UTC ++++ CMakeLists.txt +@@ -120,5 +120,7 @@ install( + ) + + # add the testsuite ++if (BUILD_TESTING) + enable_testing() + add_subdirectory("test") ++endif() diff --git a/science/cpcmx/files/patch-config_CMakeLists.txt b/science/cpcmx/files/patch-config_CMakeLists.txt new file mode 100644 index 000000000000..fa284074452a --- /dev/null +++ b/science/cpcmx/files/patch-config_CMakeLists.txt @@ -0,0 +1,11 @@ +--- config/CMakeLists.txt.orig 2025-03-13 13:29:31 UTC ++++ config/CMakeLists.txt +@@ -14,7 +14,7 @@ + # You should have received a copy of the GNU Lesser General Public License + # along with CPCM-X. If not, see <https://www.gnu.org/licenses/>. + +-if(NOT DEFINED "${PROJECT_NAME}-dependeny-method") ++if(NOT DEFINED "${PROJECT_NAME}-dependency-method") + set( + "${PROJECT_NAME}-dependency-method" + "subproject" "cmake" "pkgconf" "fetch" diff --git a/science/cpcmx/pkg-descr b/science/cpcmx/pkg-descr new file mode 100644 index 000000000000..06664d3f7bb6 --- /dev/null +++ b/science/cpcmx/pkg-descr @@ -0,0 +1,10 @@ +This is an fully Free Software solvation model, based on the original conductor +like screening model for realistic solvation (COSMO-RS) model by Klamt et al. in +combination with the universal solvation model based on solute electron density +(SMD) by Marenich, Cramer and Truhlar. + +While there are also parameters in this repository, that are optimized for +running this library with ORCA and TURBOMOLE, the published version of this +model was built to be run with the semi-empirical GFN2-xTB method. However, the +final goal of this project is to deliver a robust Free Software solvation +framework, which can be reparametrized for the method of choice. diff --git a/science/cpcmx/pkg-plist b/science/cpcmx/pkg-plist new file mode 100644 index 000000000000..a8a105b1f20a --- /dev/null +++ b/science/cpcmx/pkg-plist @@ -0,0 +1,36 @@ +bin/cpx +include/cpcmx/bonding.mod +include/cpcmx/cpx.mod +include/cpcmx/cpx_c_api.mod +include/cpcmx/cpxcalc.mod +include/cpcmx/crs.mod +include/cpcmx/crs_broyden.mod +include/cpcmx/crs_lapack.mod +include/cpcmx/crs_timer.mod +include/cpcmx/data.mod +include/cpcmx/eledata_module.mod +include/cpcmx/element_dict.mod +include/cpcmx/globals.mod +include/cpcmx/initialize_cosmo.mod +include/cpcmx/internaldb.mod +include/cpcmx/isodens.mod +include/cpcmx/pr.mod +include/cpcmx/profile.mod +include/cpcmx/qc_calc.mod +include/cpcmx/sac_mod.mod +include/cpcmx/sdm.mod +include/cpcmx/sigma_av.mod +include/cpcmx/sort.mod +include/cpcmx/type.mod +lib/cmake/cpcmx/Findmctc-lib.cmake +lib/cmake/cpcmx/Findnumsa.cmake +lib/cmake/cpcmx/Findtest-drive.cmake +lib/cmake/cpcmx/Findtoml-f.cmake +lib/cmake/cpcmx/cpcm-x-utils.cmake +lib/cmake/cpcmx/cpcmx-config-version.cmake +lib/cmake/cpcmx/cpcmx-config.cmake +lib/cmake/cpcmx/cpcmx-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/cpcmx/cpcmx-targets.cmake +lib/libcpcmx.so +lib/libcpcmx.so.1 +lib/libcpcmx.so.1.1.0 diff --git a/science/csvtk/Makefile b/science/csvtk/Makefile index 3d2c9d80ac57..de62272c0764 100644 --- a/science/csvtk/Makefile +++ b/science/csvtk/Makefile @@ -1,7 +1,7 @@ PORTNAME= csvtk DISTVERSIONPREFIX= v -DISTVERSION= 0.34.0 -PORTREVISION= 3 +DISTVERSION= 0.35.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= jwb@FreeBSD.org diff --git a/science/csvtk/distinfo b/science/csvtk/distinfo index 0dfce56d9fa9..f96f90ae121a 100644 --- a/science/csvtk/distinfo +++ b/science/csvtk/distinfo @@ -1,7 +1,7 @@ -TIMESTAMP = 1753550609 -SHA256 (go/science_csvtk/csvtk-v0.34.0/v0.34.0.mod) = 485d911da4192efc1aaf72df722990fb897f03cdac18aff77fee199a3dab507f -SIZE (go/science_csvtk/csvtk-v0.34.0/v0.34.0.mod) = 2607 -SHA256 (go/science_csvtk/csvtk-v0.34.0/v0.34.0.zip) = aa1a8825b1c69e507717b825c270d9849234ee21da04f0b58d9f064056f1c971 -SIZE (go/science_csvtk/csvtk-v0.34.0/v0.34.0.zip) = 2656260 -SHA256 (go/science_csvtk/csvtk-v0.34.0/golang-sys-v0.6.0_GH0.tar.gz) = b4f6d17c7a128f76169964b437cb66b3f2dbf9a33361928ec19dfecf7b03fc54 -SIZE (go/science_csvtk/csvtk-v0.34.0/golang-sys-v0.6.0_GH0.tar.gz) = 1434234 +TIMESTAMP = 1761745541 +SHA256 (go/science_csvtk/csvtk-v0.35.0/v0.35.0.mod) = eeb9915dc3bd2695d637683b3da2a00d5c2c24bf995b0476a7bfa44a35916d4a +SIZE (go/science_csvtk/csvtk-v0.35.0/v0.35.0.mod) = 2595 +SHA256 (go/science_csvtk/csvtk-v0.35.0/v0.35.0.zip) = bb258e5ac8ce551063cf8c818be75ab055458c34dacf2e911783c2040017e1e8 +SIZE (go/science_csvtk/csvtk-v0.35.0/v0.35.0.zip) = 2659159 +SHA256 (go/science_csvtk/csvtk-v0.35.0/golang-sys-v0.6.0_GH0.tar.gz) = b4f6d17c7a128f76169964b437cb66b3f2dbf9a33361928ec19dfecf7b03fc54 +SIZE (go/science_csvtk/csvtk-v0.35.0/golang-sys-v0.6.0_GH0.tar.gz) = 1434234 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/dftd4/Makefile b/science/dftd4/Makefile index 7a1fea532da5..aa8e5fc6d68f 100644 --- a/science/dftd4/Makefile +++ b/science/dftd4/Makefile @@ -1,12 +1,13 @@ PORTNAME= dftd4 DISTVERSIONPREFIX= v -DISTVERSION= 3.7.0 -PORTREVISION= 1 +DISTVERSION= 3.7.0-31 +DISTVERSIONSUFFIX= -g476e6be CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Atomic-charge dependent london dispersion correction computation -WWW= https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4/ +WWW= https://dftd4.readthedocs.io/en/latest/ \ + https://github.com/dftd4/dftd4 LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/science/dftd4/distinfo b/science/dftd4/distinfo index 3924901dc8cd..0274ee6407a9 100644 --- a/science/dftd4/distinfo +++ b/science/dftd4/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1725080870 -SHA256 (dftd4-dftd4-v3.7.0_GH0.tar.gz) = f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c -SIZE (dftd4-dftd4-v3.7.0_GH0.tar.gz) = 388657 +TIMESTAMP = 1762271663 +SHA256 (dftd4-dftd4-v3.7.0-31-g476e6be_GH0.tar.gz) = 6f70d17299963d51b59ae79372a7a01caf896a6103ccf636cfdc87465eb47971 +SIZE (dftd4-dftd4-v3.7.0-31-g476e6be_GH0.tar.gz) = 466471 diff --git a/science/dftd4/pkg-plist b/science/dftd4/pkg-plist index 5560af8233bf..35758c3ce35d 100644 --- a/science/dftd4/pkg-plist +++ b/science/dftd4/pkg-plist @@ -13,9 +13,14 @@ include/dftd4/dftd4_data_covrad.mod include/dftd4/dftd4_data_en.mod include/dftd4/dftd4_data_hardness.mod include/dftd4/dftd4_data_r4r2.mod +include/dftd4/dftd4_data_wfpair.mod include/dftd4/dftd4_data_zeff.mod include/dftd4/dftd4_disp.mod include/dftd4/dftd4_model.mod +include/dftd4/dftd4_model_d4.mod +include/dftd4/dftd4_model_d4s.mod +include/dftd4/dftd4_model_type.mod +include/dftd4/dftd4_model_utils.mod include/dftd4/dftd4_ncoord.mod include/dftd4/dftd4_numdiff.mod include/dftd4/dftd4_output.mod 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/gcp/pkg-descr b/science/gcp/pkg-descr index 2f382bc095d9..07b8e2ada95b 100644 --- a/science/gcp/pkg-descr +++ b/science/gcp/pkg-descr @@ -1,2 +1,9 @@ -Geometrical Counter-Poise Correction -for quantum chemistry. +The gCP (Geometrical Counter-Poise) correction method is a way to deal +with the basis set superposition error (BSSE) in quantum chemical +calculations. + +The BSSE is a fundamental error that occurs in all practical electronic +structure calculations that use finite basis sets. The gCP is a +semi-empirical method that is much more efficient than the standard +Boys-Bernardi counterpoise (BB-CP) correction, especially for geometry +optimizations. 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/gromacs/Makefile b/science/gromacs/Makefile index fe0f72f32e22..558eab81f1ba 100644 --- a/science/gromacs/Makefile +++ b/science/gromacs/Makefile @@ -1,5 +1,5 @@ PORTNAME= gromacs -DISTVERSION= 2025.0 +DISTVERSION= 2025.4 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://ftp.gromacs.org/pub/gromacs/ @@ -126,6 +126,7 @@ post-patch: @${REINPLACE_CMD} -e '/CMAKE_REQUIRED_LIBRARIES/d' \ ${WRKSRC}/cmake/gmxTestdlopen.cmake -# tests fail to compile, see https://gitlab.com/gromacs/gromacs/-/issues/5141 +# tests as of 2025.3: 100% tests passed, 0 tests failed out of 92 +# 2025.4: tests fail to compile: https://gitlab.com/gromacs/gromacs/-/issues?show=eyJpaWQiOiI1NTAxIiwiZnVsbF9wYXRoIjoiZ3JvbWFjcy9ncm9tYWNzIiwiaWQiOjE3NzU1MDUzMn0%3D .include <bsd.port.mk> diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo index 6b2c689e8b4b..4cf0d1f50a41 100644 --- a/science/gromacs/distinfo +++ b/science/gromacs/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1739341467 -SHA256 (gromacs-2025.0.tar.gz) = a27ad35a646295bbec129abe684d9d03d1e2e0bd76b0d625e9055746aaefae82 -SIZE (gromacs-2025.0.tar.gz) = 44417653 +TIMESTAMP = 1763922155 +SHA256 (gromacs-2025.4.tar.gz) = ca17720b4a260eb73649211e9f6a940ee7543452129844213c3accb0a927a5c3 +SIZE (gromacs-2025.4.tar.gz) = 44406127 diff --git a/science/healpix/Makefile b/science/healpix/Makefile index 92f6cbda719f..7505dc0033bc 100644 --- a/science/healpix/Makefile +++ b/science/healpix/Makefile @@ -1,14 +1,15 @@ PORTNAME= healpix DISTVERSION= 3.50 DISTVERSIONSUFFIX= _2018Dec10 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MASTER_SITES= SF/${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$/C/}/autotools diff --git a/science/helfem/Makefile b/science/helfem/Makefile index e468518af7f5..464b6053adcb 100644 --- a/science/helfem/Makefile +++ b/science/helfem/Makefile @@ -1,11 +1,7 @@ PORTNAME= helfem -DISTVERSION= g20210912 -PORTREVISION= 10 +DISTVERSION= g20251026 CATEGORIES= science # chemistry -PATCH_SITES= https://github.com/${GH_ACCOUNT}/${GH_PROJECT}/commit/ -PATCHFILES= 4c0196c3ef3f254a22030eda787105c8a48df919.patch:-p1 # https://github.com/susilehtola/HelFEM/pull/7 - MAINTAINER= yuri@FreeBSD.org COMMENT= Finite element methods for electronic structure calculations WWW= https://github.com/susilehtola/HelFEM @@ -20,11 +16,12 @@ LIB_DEPENDS= libarmadillo.so:math/armadillo \ libxc.so:science/libxc USES= cmake fortran +USE_CXXSTD= c++14 USE_GITHUB= yes GH_ACCOUNT= susilehtola GH_PROJECT= HelFEM -GH_TAGNAME= 21461e9 +GH_TAGNAME= ca3fa54 CMAKE_ON= HELFEM_FIND_DEPS BUILD_SHARED_LIBS diff --git a/science/helfem/distinfo b/science/helfem/distinfo index dced120724b0..2156b0c12092 100644 --- a/science/helfem/distinfo +++ b/science/helfem/distinfo @@ -1,5 +1,3 @@ -TIMESTAMP = 1656098405 -SHA256 (susilehtola-HelFEM-g20210912-21461e9_GH0.tar.gz) = 08dde1f20ff741ca0befbc0472b0264f48be82e083fb4dd34927ef9cd7bffca6 -SIZE (susilehtola-HelFEM-g20210912-21461e9_GH0.tar.gz) = 1020779 -SHA256 (4c0196c3ef3f254a22030eda787105c8a48df919.patch) = 349f730515667da1a85d8646d282208ee26dc3c93a5fd0468dab06ad727593fc -SIZE (4c0196c3ef3f254a22030eda787105c8a48df919.patch) = 573 +TIMESTAMP = 1762390738 +SHA256 (susilehtola-HelFEM-g20251026-ca3fa54_GH0.tar.gz) = 0cc795fc23df945eeb9ca284cdb8ac04a569093775721d47918f4808bb3e3269 +SIZE (susilehtola-HelFEM-g20251026-ca3fa54_GH0.tar.gz) = 1053211 diff --git a/science/helfem/files/patch-CMakeLists.txt b/science/helfem/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..0a3cbc833542 --- /dev/null +++ b/science/helfem/files/patch-CMakeLists.txt @@ -0,0 +1,11 @@ +--- CMakeLists.txt.orig 2025-11-06 01:10:35 UTC ++++ CMakeLists.txt +@@ -1,7 +1,7 @@ project (helfem CXX Fortran) + # CMake project file for HelFEM + cmake_minimum_required (VERSION 3.5) + project (helfem CXX Fortran) +-set(CMAKE_CXX_STANDARD 11) ++set(CMAKE_CXX_STANDARD 14) + + # Ensure we are building out-of-source so that the tests work (issue 120) + get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH) diff --git a/science/helfem/files/patch-src_general_dftfuncs.cpp b/science/helfem/files/patch-src_general_dftfuncs.cpp deleted file mode 100644 index 999399167b70..000000000000 --- a/science/helfem/files/patch-src_general_dftfuncs.cpp +++ /dev/null @@ -1,38 +0,0 @@ ---- src/general/dftfuncs.cpp.orig 2021-09-12 09:32:14 UTC -+++ src/general/dftfuncs.cpp -@@ -388,7 +388,7 @@ double exact_exchange(int func_id) { - throw std::runtime_error(oss.str()); - } - --#if XC_MAJOR_VERSION < 6 -+#if XC_MAJOR_VERSION < 7 - switch(func.info->family) - { - #ifdef XC_FAMILY_HYB_LDA -@@ -431,7 +431,7 @@ bool is_supported(int func_id) { - throw std::runtime_error(oss.str()); - } - // Get flag --#if XC_MAJOR_VERSION >= 6 -+#if XC_MAJOR_VERSION > 6 - switch(xc_hyb_type(&func)) { - case(XC_HYB_SEMILOCAL): - case(XC_HYB_HYBRID): -@@ -463,7 +463,7 @@ void is_range_separated(int func_id, bool & erf, bool - throw std::runtime_error(oss.str()); - } - // Get flag --#if XC_MAJOR_VERSION < 6 -+#if XC_MAJOR_VERSION < 7 - erf=(func.info->flags & XC_FLAGS_HYB_CAM) || (func.info->flags & XC_FLAGS_HYB_LC); - yukawa=(func.info->flags & XC_FLAGS_HYB_CAMY) || (func.info->flags & XC_FLAGS_HYB_LCY); - #else -@@ -507,7 +507,7 @@ void range_separation(int func_id, double & omega, dou - throw std::runtime_error(oss.str()); - } - --#if XC_MAJOR_VERSION >= 6 -+#if XC_MAJOR_VERSION > 6 - switch(xc_hyb_type(&func)) { - case(XC_HYB_SEMILOCAL): - break; diff --git a/science/helfem/pkg-plist b/science/helfem/pkg-plist index 115cfa74521a..aab99275cf9c 100644 --- a/science/helfem/pkg-plist +++ b/science/helfem/pkg-plist @@ -3,14 +3,15 @@ bin/diatomic bin/diatomic_cbasis bin/diatomic_cpl bin/gensap -bin/libhelfem-common.so -bin/liblegendre.so -include/helfem.h -include/helfem/GaussianNucleus.h -include/helfem/HollowNucleus.h -include/helfem/ModelPotential.h -include/helfem/PointNucleus.h -include/helfem/PolynomialBasis.h -include/helfem/RadialBasis.h -include/helfem/SphericalNucleus.h +include/FiniteElementBasis.h +include/GaussianNucleus.h +include/HollowNucleus.h +include/ModelPotential.h +include/PointNucleus.h +include/PolynomialBasis.h +include/RadialBasis.h +include/RegularizedNucleus.h +include/SphericalNucleus.h +lib/libhelfem-common.so lib/libhelfem.so +lib/liblegendre.so diff --git a/science/highfive/Makefile b/science/highfive/Makefile index b35fd3ff30ae..7eab1f11d288 100644 --- a/science/highfive/Makefile +++ b/science/highfive/Makefile @@ -1,24 +1,25 @@ 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 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 + 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/kalzium/distinfo b/science/kalzium/distinfo index 2ed98aa072cd..f93bc65bb23c 100644 --- a/science/kalzium/distinfo +++ b/science/kalzium/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1757410249 -SHA256 (KDE/release-service/25.08.1/kalzium-25.08.1.tar.xz) = 64ecba7f0cc8333ee528fc951e500e591d263380e72af59e36b37654a8e1ae8b -SIZE (KDE/release-service/25.08.1/kalzium-25.08.1.tar.xz) = 22661180 +TIMESTAMP = 1762264756 +SHA256 (KDE/release-service/25.08.3/kalzium-25.08.3.tar.xz) = 36e6c4f46e1a5daaace14ebb5b1f6dac3429ad5df3d4fc1f0adeaec3e28e420b +SIZE (KDE/release-service/25.08.3/kalzium-25.08.3.tar.xz) = 22663696 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/libgridxc/Makefile b/science/libgridxc/Makefile index 009dd21ccb1b..0d6de425b923 100644 --- a/science/libgridxc/Makefile +++ b/science/libgridxc/Makefile @@ -1,6 +1,5 @@ PORTNAME= libgridxc -DISTVERSION= 1.1.0 -PORTREVISION= 2 +DISTVERSION= 2.0.2 CATEGORIES= science MASTER_SITES= https://gitlab.com/siesta-project/libraries/${PORTNAME}/-/archive/${DISTVERSION}/ diff --git a/science/libgridxc/distinfo b/science/libgridxc/distinfo index 38361b759c64..afbbc475003f 100644 --- a/science/libgridxc/distinfo +++ b/science/libgridxc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1672867830 -SHA256 (libgridxc-1.1.0.tar.gz) = e7883e57a4db2438ee59437740291c06e0cfe1c8ae1901e4001f32312307e46a -SIZE (libgridxc-1.1.0.tar.gz) = 357558 +TIMESTAMP = 1762391721 +SHA256 (libgridxc-2.0.2.tar.gz) = ce7e3de5b1232e63bc953a994f549411edb90c22b22f9b7749d8f2a79d3c1a98 +SIZE (libgridxc-2.0.2.tar.gz) = 360208 diff --git a/science/libgridxc/pkg-plist b/science/libgridxc/pkg-plist index cdef24a1782d..27dcfaea375e 100644 --- a/science/libgridxc/pkg-plist +++ b/science/libgridxc/pkg-plist @@ -37,6 +37,6 @@ lib/cmake/libgridxc/libgridxc-config.cmake lib/cmake/libgridxc/libgridxc-targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/libgridxc/libgridxc-targets.cmake lib/libgridxc.so -lib/libgridxc.so.1 -lib/libgridxc.so.1.1.0 +lib/libgridxc.so.2 +lib/libgridxc.so.2.0.2 libdata/pkgconfig/libgridxc.pc diff --git a/science/libint2-psi4/Makefile b/science/libint2-psi4/Makefile index 3ac7e76bd463..dce366b9440e 100644 --- a/science/libint2-psi4/Makefile +++ b/science/libint2-psi4/Makefile @@ -1,6 +1,6 @@ PORTNAME= libint2-psi4 DISTVERSION= 0.1-${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/libxc/Makefile b/science/libxc/Makefile index b16e5f32333f..38fa9487e013 100644 --- a/science/libxc/Makefile +++ b/science/libxc/Makefile @@ -2,7 +2,7 @@ PORTNAME= libxc DISTVERSION= 6.2.2 CATEGORIES= science -MAINTAINER= ports@FreeBSD.org +MAINTAINER= yuri@FreeBSD.org COMMENT= Library of exchange-correlation functionals for DFT WWW= https://gitlab.com/libxc/libxc 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/mbdyn/files/patch-libraries_libmbwrap_umfpackwrap.h b/science/mbdyn/files/patch-libraries_libmbwrap_umfpackwrap.h new file mode 100644 index 000000000000..95e7aa4d791a --- /dev/null +++ b/science/mbdyn/files/patch-libraries_libmbwrap_umfpackwrap.h @@ -0,0 +1,19 @@ +-- +-- workaround for https://public.gitlab.polimi.it/DAER/mbdyn/-/issues/431 +-- ... 1.7.3 is very old and it fails to compile: error: templates must have C++ linkage: Please make a release +-- + +--- libraries/libmbwrap/umfpackwrap.h.orig 2025-11-18 16:35:30 UTC ++++ libraries/libmbwrap/umfpackwrap.h +@@ -72,9 +72,9 @@ + #include <iostream> + #include <vector> + +-extern "C" { ++//extern "C" { + #include <umfpack.h> +-} ++//} + + #include "myassert.h" + #include "mynewmem.h" diff --git a/science/mctc-lib/Makefile b/science/mctc-lib/Makefile index a776e8418ff4..882279cb0e33 100644 --- a/science/mctc-lib/Makefile +++ b/science/mctc-lib/Makefile @@ -1,11 +1,12 @@ PORTNAME= mctc-lib DISTVERSIONPREFIX= v -DISTVERSION= 0.4.0 +DISTVERSION= 0.5.0 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Computation tool chain library to work with molecular structure data -WWW= https://grimme-lab.github.io/mctc-lib/ +WWW= https://grimme-lab.github.io/mctc-lib/ \ + https://github.com/grimme-lab/mctc-lib/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE @@ -18,9 +19,14 @@ GH_ACCOUNT= grimme-lab CMAKE_ON= BUILD_SHARED_LIBS +TESTING_UNSAFE= yes + post-patch: # same as https://github.com/grimme-lab/mctc-lib/pull/55 - @${REINPLACE_CMD} -e 's|$${CMAKE_Fortran_COMPILER_ID}-$${CMAKE_Fortran_COMPILER_VERSION}||' ${WRKSRC}/config/CMakeLists.txt + @${REINPLACE_CMD} -e 's|$${CMAKE_Fortran_COMPILER_ID}-$${CMAKE_Fortran_COMPILER_VERSION}||' \ + ${WRKSRC}/config/CMakeLists.txt -# tests as of 0.4.0: 100% tests passed, 0 tests failed out of 28 +# tests as of 0.5.0: 97% tests passed, 1 tests failed out of 32 +# The following tests FAILED: +# 4 - mctc-lib/ncoord (Failed) .include <bsd.port.mk> diff --git a/science/mctc-lib/distinfo b/science/mctc-lib/distinfo index a4dbcd7fe8fe..66cbf479de1b 100644 --- a/science/mctc-lib/distinfo +++ b/science/mctc-lib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1743699981 -SHA256 (grimme-lab-mctc-lib-v0.4.0_GH0.tar.gz) = a3c2de289770d691534ff70556f5da4bfce4b184d89053b7a2c7ff2ca1c12b0a -SIZE (grimme-lab-mctc-lib-v0.4.0_GH0.tar.gz) = 173015 +TIMESTAMP = 1762020968 +SHA256 (grimme-lab-mctc-lib-v0.5.0_GH0.tar.gz) = ed0276618b9e1b41b5d228aedd4a1e07500472cfab5236179feb0cb55a0c8dc3 +SIZE (grimme-lab-mctc-lib-v0.5.0_GH0.tar.gz) = 189254 diff --git a/science/mctc-lib/pkg-plist b/science/mctc-lib/pkg-plist index 674cd9c8c3dc..e0f3a9c3afb5 100644 --- a/science/mctc-lib/pkg-plist +++ b/science/mctc-lib/pkg-plist @@ -22,7 +22,9 @@ include/mctc-lib/modules/mctc_io_read_cjson.mod include/mctc-lib/modules/mctc_io_read_ctfile.mod include/mctc-lib/modules/mctc_io_read_gaussian.mod include/mctc-lib/modules/mctc_io_read_genformat.mod +include/mctc-lib/modules/mctc_io_read_json.mod include/mctc-lib/modules/mctc_io_read_pdb.mod +include/mctc-lib/modules/mctc_io_read_pymatgen.mod include/mctc-lib/modules/mctc_io_read_qchem.mod include/mctc-lib/modules/mctc_io_read_qcschema.mod include/mctc-lib/modules/mctc_io_read_turbomole.mod @@ -40,6 +42,7 @@ include/mctc-lib/modules/mctc_io_write_ctfile.mod include/mctc-lib/modules/mctc_io_write_gaussian.mod include/mctc-lib/modules/mctc_io_write_genformat.mod include/mctc-lib/modules/mctc_io_write_pdb.mod +include/mctc-lib/modules/mctc_io_write_pymatgen.mod include/mctc-lib/modules/mctc_io_write_qchem.mod include/mctc-lib/modules/mctc_io_write_qcschema.mod include/mctc-lib/modules/mctc_io_write_turbomole.mod @@ -53,12 +56,14 @@ include/mctc-lib/modules/mctc_ncoord_erf_en.mod include/mctc-lib/modules/mctc_ncoord_exp.mod include/mctc-lib/modules/mctc_ncoord_type.mod include/mctc-lib/modules/mctc_version.mod -lib/cmake/mctc-lib/Findjsonfortran.cmake +lib/cmake/mctc-lib/Findjonquil.cmake +lib/cmake/mctc-lib/Findtoml-f.cmake lib/cmake/mctc-lib/mctc-lib-config-version.cmake lib/cmake/mctc-lib/mctc-lib-config.cmake lib/cmake/mctc-lib/mctc-lib-targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/mctc-lib/mctc-lib-targets.cmake +lib/cmake/mctc-lib/mctc-utils.cmake lib/libmctc-lib.so lib/libmctc-lib.so.0 -lib/libmctc-lib.so.0.4.0 +lib/libmctc-lib.so.0.5.0 libdata/pkgconfig/mctc-lib.pc 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/mmg/Makefile b/science/mmg/Makefile index a3bf8dc89a09..7c749c173ef0 100644 --- a/science/mmg/Makefile +++ b/science/mmg/Makefile @@ -1,27 +1,28 @@ PORTNAME= mmg DISTVERSIONPREFIX= v -DISTVERSION= 5.7.3 -PORTREVISION= 1 +DISTVERSION= 5.8.0 CATEGORIES= science -MAINTAINER= ports@FreeBSD.org +MAINTAINER= alven@FreeBSD.org COMMENT= Bidimensional and tridimensional remeshing -WWW= https://www.mmgtools.org/ +WWW= https://www.mmgtools.org/ \ + https://github.com/MmgTools/mmg/ -LICENSE= LGPL3 -LICENSE_FILE= ${WRKSRC}/LICENSE +LICENSE= LGPL3+ +LICENSE_FILE= ${WRKSRC}/COPYING.LESSER -LIB_DEPENDS= libscotch.so:cad/scotch \ - libElas.so:science/linearelasticity \ +BUILD_DEPENDS= bash:shells/bash +LIB_DEPENDS= libElas.so:science/linearelasticity \ + libscotch.so:cad/scotch \ libvtksys-${VTK_VER}.so:math/vtk${VTK_VER:R} USES= cmake perl5 shebangfix -USE_PERL5= build -SHEBANG_FILES= scripts/*.pl -USE_LDCONFIG= yes - USE_GITHUB= yes GH_ACCOUNT= MmgTools +USE_LDCONFIG= yes +USE_PERL5= build + +SHEBANG_FILES= scripts/*.pl scripts/*.sh CMAKE_ON= BUILD_SHARED_LIBS diff --git a/science/mmg/distinfo b/science/mmg/distinfo index 8b9062f46ae9..ff7418170732 100644 --- a/science/mmg/distinfo +++ b/science/mmg/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1718986408 -SHA256 (MmgTools-mmg-v5.7.3_GH0.tar.gz) = b0a9c5ad6789df369a68f94295df5b324b6348020b73bcc395d32fdd44abe706 -SIZE (MmgTools-mmg-v5.7.3_GH0.tar.gz) = 9645997 +TIMESTAMP = 1762284434 +SHA256 (MmgTools-mmg-v5.8.0_GH0.tar.gz) = 686eaab84de79c072f3aedf26cd11ced44c84b435d51ce34e016ad203172922f +SIZE (MmgTools-mmg-v5.8.0_GH0.tar.gz) = 9675000 diff --git a/science/mmg/files/patch-CMakeLists.txt b/science/mmg/files/patch-CMakeLists.txt deleted file mode 100644 index c7cb99ce1840..000000000000 --- a/science/mmg/files/patch-CMakeLists.txt +++ /dev/null @@ -1,14 +0,0 @@ ---- CMakeLists.txt.orig 2024-04-25 08:15:24 UTC -+++ CMakeLists.txt -@@ -124,10 +124,7 @@ IF (NOT WIN32 OR MINGW) - IF (NOT WIN32 OR MINGW) - - ADD_CUSTOM_TARGET(GenerateGitHashMmg -- COMMAND ./git_log_mmg.sh ${PROJECT_SOURCE_DIR} ${MMGCOMMON_BINARY_DIR} -- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/scripts/ -- COMMENT "Getting git commit hash" -- BYPRODUCTS ${MMGCOMMON_BINARY_DIR}/git_log_mmg.h -+ COMMAND cp ${PROJECT_SOURCE_DIR}/git_log_mmg.h ${MMGCOMMON_BINARY_DIR}/git_log_mmg.h - ) - ENDIF () - diff --git a/science/mmg/files/patch-git__log__mmg.h b/science/mmg/files/patch-git__log__mmg.h deleted file mode 100644 index 4a8ec0ac0b8a..000000000000 --- a/science/mmg/files/patch-git__log__mmg.h +++ /dev/null @@ -1,9 +0,0 @@ ---- git_log_mmg.h.orig 2024-06-23 16:47:08 UTC -+++ git_log_mmg.h -@@ -0,0 +1,6 @@ -+#ifndef _GIT_LOG_MMG_H -+#define _GIT_LOG_MMG_H -+#define MMG_GIT_BRANCH "No git branch found" -+#define MMG_GIT_COMMIT "No git commit found" -+#define MMG_GIT_DATE "No git commit found" -+#endif diff --git a/science/mmg/pkg-descr b/science/mmg/pkg-descr index 94c22fa37676..80e53e09c931 100644 --- a/science/mmg/pkg-descr +++ b/science/mmg/pkg-descr @@ -1,5 +1,5 @@ -Mmg is an open source software for simplicial remeshing. It provides 3 -applications and 4 libraries: +Mmg is a Free Software for bidimensional and tridimensional surface and volume +remeshing. It provides 3 applications and 4 libraries: - the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set diff --git a/science/mmg/pkg-plist b/science/mmg/pkg-plist index 80ad5b0c74ef..d298038769ca 100644 --- a/science/mmg/pkg-plist +++ b/science/mmg/pkg-plist @@ -26,16 +26,16 @@ lib/cmake/mmg/MmgTargets.cmake lib/cmake/mmg/mmgConfig.cmake lib/libmmg.so lib/libmmg.so.5 -lib/libmmg.so.5.7.0 +lib/libmmg.so.5.8.0 lib/libmmg2d.so lib/libmmg2d.so.5 -lib/libmmg2d.so.5.7.0 +lib/libmmg2d.so.5.8.0 lib/libmmg3d.so lib/libmmg3d.so.5 -lib/libmmg3d.so.5.7.0 +lib/libmmg3d.so.5.8.0 lib/libmmgs.so lib/libmmgs.so.5 -lib/libmmgs.so.5.7.0 +lib/libmmgs.so.5.8.0 share/man/man1/mmg2d.1.gz share/man/man1/mmg3d.1.gz share/man/man1/mmgs.1.gz diff --git a/science/mol2ps/Makefile b/science/mol2ps/Makefile index 218698f47061..55e4829e1500 100644 --- a/science/mol2ps/Makefile +++ b/science/mol2ps/Makefile @@ -1,6 +1,6 @@ PORTNAME= mol2ps PORTVERSION= 0.4c -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://homepage.univie.ac.at/norbert.haider/download/chemistry/mol2ps/ DISTNAME= ${PORTNAME} diff --git a/science/molgif/Makefile b/science/molgif/Makefile index af14421a80b8..5310cd883c17 100644 --- a/science/molgif/Makefile +++ b/science/molgif/Makefile @@ -1,6 +1,6 @@ PORTNAME= molgif DISTVERSION= g20180108 -PORTREVISION= 31 +PORTREVISION= 33 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/mopac/Makefile b/science/mopac/Makefile index 10f04cf9f3ba..4793323e925b 100644 --- a/science/mopac/Makefile +++ b/science/mopac/Makefile @@ -1,6 +1,6 @@ PORTNAME= mopac DISTVERSIONPREFIX= v -DISTVERSION= 23.1.2 +DISTVERSION= 23.2.2 PORTEPOCH= 1 CATEGORIES= science # chemistry @@ -32,5 +32,6 @@ PLIST_FILES= bin/mopac \ lib/libmopac.so.2 # tests as of 23.1.2: 100% tests passed, 0 tests failed out of 125 +# tests as of 23.2.2: 99% tests passed, 1 tests failed out of 125, see https://github.com/openmopac/mopac/issues/302 .include <bsd.port.mk> diff --git a/science/mopac/distinfo b/science/mopac/distinfo index 461a54e74626..0d3ab5cfdb3d 100644 --- a/science/mopac/distinfo +++ b/science/mopac/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1739870708 -SHA256 (openmopac-mopac-v23.1.2_GH0.tar.gz) = 60436bbf62045f06f17b4604bf241c8c6359a70a89c41d00913833bf32ea0121 -SIZE (openmopac-mopac-v23.1.2_GH0.tar.gz) = 16972367 +TIMESTAMP = 1761900683 +SHA256 (openmopac-mopac-v23.2.2_GH0.tar.gz) = d64525fa4ae709b214ecbd5981b7e8a2928e2f1a91d85a253e8dbd04616e14cd +SIZE (openmopac-mopac-v23.2.2_GH0.tar.gz) = 16947337 diff --git a/science/mpqc/files/patch-configure b/science/mpqc/files/patch-configure index 692451d6e025..d75a082b072d 100644 --- a/science/mpqc/files/patch-configure +++ b/science/mpqc/files/patch-configure @@ -1,6 +1,6 @@ --- configure.orig 2006-03-22 19:13:52 UTC +++ configure -@@ -2268,14 +2268,12 @@ echo Using FORTRAN runtime libraries: $withval +@@ -2268,14 +2268,12 @@ fi; fi; @@ -15,7 +15,7 @@ echo Using extra library directories: $withval fi; -@@ -2290,7 +2288,7 @@ if test "${with_cca_chem_config+set}" = set; then +@@ -2290,7 +2288,7 @@ else else @@ -24,7 +24,7 @@ # Extract the first word of "cca-chem-config", so it can be a program name with args. set dummy cca-chem-config; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 -@@ -5207,7 +5205,7 @@ case $target_cpu in +@@ -5207,7 +5205,7 @@ esac ;; esac @@ -33,7 +33,7 @@ echo "$as_me:$LINENO: checking for C++ cpu tuning flag" >&5 echo $ECHO_N "checking for C++ cpu tuning flag... $ECHO_C" >&6 -@@ -5265,7 +5263,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu +@@ -5265,7 +5263,7 @@ fi echo "${ECHO_T}$cxx_tuneflag" >&6 fi @@ -42,6 +42,15 @@ echo "$as_me:$LINENO: checking for C cpu tuning flag" >&5 echo $ECHO_N "checking for C cpu tuning flag... $ECHO_C" >&6 CFLAGS_SAV=$CFLAGS +@@ -12444,7 +12442,7 @@ if test -n "$F77" -a "$F77" != no ; then + echo " return" >> ffunc.f + echo " end" >> ffunc.f + $F77 -c ffunc.f 1>/dev/null 2>/dev/null +- echo "main(){ FF(); return 0; }" > flink.c ++ echo "int FF(void); int main(){ FF(); return 0; }" > flink.c + if $CC -o flink -DFF=ffunc flink.c ffunc.o $LDFLAGS $LIBS 1>/dev/null 2>/dev/null; then + echo "$as_me:$LINENO: result: same as C" >&5 + echo "${ECHO_T}same as C" >&6 @@ -28629,10 +28627,10 @@ ENABLESHARED=$enable_shared diff --git a/science/multicharge/Makefile b/science/multicharge/Makefile index 13da7abc8c2c..db7c0f26fa03 100644 --- a/science/multicharge/Makefile +++ b/science/multicharge/Makefile @@ -1,12 +1,11 @@ PORTNAME= multicharge DISTVERSIONPREFIX= v -DISTVERSION= 0.3.0 -PORTREVISION= 1 +DISTVERSION= 0.4.0 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Electronegativity equilibration model for atomic partial charges -WWW= https://github.com/grimme-lab/mstore +WWW= https://github.com/grimme-lab/multicharge/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE @@ -16,14 +15,14 @@ LIB_DEPENDS= libmctc-lib.so:science/mctc-lib \ libopenblas.so:math/openblas USES= cmake:testing fortran -USE_LDCONFIG= yes - USE_GITHUB= yes GH_ACCOUNT= grimme-lab +USE_LDCONFIG= yes CMAKE_ON= BUILD_SHARED_LIBS post-patch: # see https://github.com/toml-f/toml-f/issues/51 - @${REINPLACE_CMD} -e 's|$${CMAKE_Fortran_COMPILER_ID}-$${CMAKE_Fortran_COMPILER_VERSION}||' ${WRKSRC}/config/CMakeLists.txt + @${REINPLACE_CMD} -e 's|$${CMAKE_Fortran_COMPILER_ID}-$${CMAKE_Fortran_COMPILER_VERSION}||' \ + ${WRKSRC}/config/CMakeLists.txt .include <bsd.port.mk> diff --git a/science/multicharge/distinfo b/science/multicharge/distinfo index aa8b280dd362..3d4353fa8267 100644 --- a/science/multicharge/distinfo +++ b/science/multicharge/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1725080939 -SHA256 (grimme-lab-multicharge-v0.3.0_GH0.tar.gz) = 2fcc1f80871f404f005e9db458ffaec95bb28a19516a0245278cd3175b63a6b2 -SIZE (grimme-lab-multicharge-v0.3.0_GH0.tar.gz) = 45784 +TIMESTAMP = 1762045153 +SHA256 (grimme-lab-multicharge-v0.4.0_GH0.tar.gz) = 7dadf50db5449bfcd8b08cfda5e89021242a7d58fa28b28865ef9421e59227fb +SIZE (grimme-lab-multicharge-v0.4.0_GH0.tar.gz) = 42763 diff --git a/science/multicharge/pkg-descr b/science/multicharge/pkg-descr index 253281c855d0..0c318a1fe4b5 100644 --- a/science/multicharge/pkg-descr +++ b/science/multicharge/pkg-descr @@ -1,4 +1 @@ -mstore is molecular structure store for testing. - -It allows to store molecular structures in computational chemistry -software. +Electronegativity equilibration models for atomic partial charges. diff --git a/science/multicharge/pkg-plist b/science/multicharge/pkg-plist index 9cc7a9af065c..4288d56145a6 100644 --- a/science/multicharge/pkg-plist +++ b/science/multicharge/pkg-plist @@ -2,12 +2,9 @@ bin/multicharge include/multicharge/multicharge.mod include/multicharge/multicharge_blas.mod include/multicharge/multicharge_cutoff.mod -include/multicharge/multicharge_data.mod -include/multicharge/multicharge_data_covrad.mod include/multicharge/multicharge_ewald.mod include/multicharge/multicharge_lapack.mod include/multicharge/multicharge_model.mod -include/multicharge/multicharge_ncoord.mod include/multicharge/multicharge_output.mod include/multicharge/multicharge_param.mod include/multicharge/multicharge_param_eeq2019.mod @@ -24,5 +21,5 @@ lib/cmake/multicharge/multicharge-targets.cmake lib/cmake/multicharge/multicharge-utils.cmake lib/libmulticharge.so lib/libmulticharge.so.0 -lib/libmulticharge.so.0.3.0 +lib/libmulticharge.so.0.4.0 libdata/pkgconfig/multicharge.pc 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= ${WRKSRC}/LICENSE BROKEN_armv7= compilation fails: error: expected identifier before '__is_convertible' BROKEN_i386= https://github.com/nest/nest-simulator/issues/1205 -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libgsl.so:math/gsl \ libltdl.so:devel/libltdl RUN_DEPENDS= bash:shells/bash diff --git a/science/numsa/Makefile b/science/numsa/Makefile new file mode 100644 index 000000000000..1252edc60c82 --- /dev/null +++ b/science/numsa/Makefile @@ -0,0 +1,27 @@ +PORTNAME= numsa +DISTVERSION= 0.2.0 +CATEGORIES= science # chemistry +MASTER_SITES= https://github.com/grimme-lab/${PORTNAME}/releases/download/v${DISTVERSION}/ + +MAINTAINER= alven@FreeBSD.org +COMMENT= Solvent accessible surface area calculation +WWW= https://github.com/grimme-lab/numsa/ + +LICENSE= LGPL3+ +LICENSE_FILE= ${WRKSRC}/COPYING.LESSER + +LIB_DEPENDS= libmctc-lib.so:science/mctc-lib +TEST_DEPENDS= test-drive>0:devel/test-drive + +USES= blaslapack cmake fortran tar:xz +USE_LDCONFIG= yes + +CMAKE_ON= BUILD_SHARED_LIBS + +TEST_TARGET= test + +post-patch: # same as https://github.com/grimme-lab/mctc-lib/pull/55 + @${REINPLACE_CMD} -e 's|$${CMAKE_Fortran_COMPILER_ID}-$${CMAKE_Fortran_COMPILER_VERSION}||' \ + ${WRKSRC}/config/CMakeLists.txt + +.include <bsd.port.mk> diff --git a/science/numsa/distinfo b/science/numsa/distinfo new file mode 100644 index 000000000000..d4ce95de9de8 --- /dev/null +++ b/science/numsa/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1762114720 +SHA256 (numsa-0.2.0.tar.xz) = 3e20cefb3747627876cc6c6750bf74692e35b81c059580dd3bd75333f9b7c089 +SIZE (numsa-0.2.0.tar.xz) = 1516116 diff --git a/science/numsa/files/patch-config_CMakeLists.txt b/science/numsa/files/patch-config_CMakeLists.txt new file mode 100644 index 000000000000..918f631e94d1 --- /dev/null +++ b/science/numsa/files/patch-config_CMakeLists.txt @@ -0,0 +1,11 @@ +--- config/CMakeLists.txt.orig 2025-11-02 00:19:55 UTC ++++ config/CMakeLists.txt +@@ -14,7 +14,7 @@ + # You should have received a copy of the GNU Lesser General Public License + # along with numsa. If not, see <https://www.gnu.org/licenses/>. + +-if(NOT DEFINED "${PROJECT_NAME}-dependeny-method") ++if(NOT DEFINED "${PROJECT_NAME}-dependency-method") + set( + "${PROJECT_NAME}-dependency-method" + "subproject" "cmake" "pkgconf" "fetch" diff --git a/science/numsa/files/patch-src_numsa_version.f90 b/science/numsa/files/patch-src_numsa_version.f90 new file mode 100644 index 000000000000..a9771fa34606 --- /dev/null +++ b/science/numsa/files/patch-src_numsa_version.f90 @@ -0,0 +1,15 @@ +--- src/numsa/version.f90.orig 2025-03-12 09:02:29 UTC ++++ src/numsa/version.f90 +@@ -24,10 +24,10 @@ module numsa_version + + + !> String representation of the numsa version +- character(len=*), parameter :: numsa_version_string = "0.1.0" ++ character(len=*), parameter :: numsa_version_string = "0.2.0" + + !> Numeric representation of the numsa version +- integer, parameter :: numsa_version_compact(3) = [0, 1, 0] ++ integer, parameter :: numsa_version_compact(3) = [0, 2, 0] + + + contains diff --git a/science/numsa/pkg-descr b/science/numsa/pkg-descr new file mode 100644 index 000000000000..17b22e21e2f4 --- /dev/null +++ b/science/numsa/pkg-descr @@ -0,0 +1,2 @@ +Numerical surface area integrator for molecular inputs. This project is based on +routines from xtb and dftb+. diff --git a/science/numsa/pkg-plist b/science/numsa/pkg-plist new file mode 100644 index 000000000000..7fa7c1cc3c2a --- /dev/null +++ b/science/numsa/pkg-plist @@ -0,0 +1,24 @@ +bin/numsa-exe +include/numsa/numsa.mod +include/numsa/numsa_data.mod +include/numsa/numsa_lebedev.mod +include/numsa/numsa_output.mod +include/numsa/numsa_search.mod +include/numsa/numsa_surface.mod +include/numsa/numsa_version.mod +include/numsa/smd.mod +include/numsa/smd_cds.mod +include/numsa/smd_init.mod +include/numsa/smd_io.mod +include/numsa/smd_output.mod +include/numsa/smd_sigma.mod +lib/cmake/numsa/Findmctc-lib.cmake +lib/cmake/numsa/Findtest-drive.cmake +lib/cmake/numsa/numsa-config-version.cmake +lib/cmake/numsa/numsa-config.cmake +lib/cmake/numsa/numsa-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/numsa/numsa-targets.cmake +lib/cmake/numsa/numsa-utils.cmake +lib/libnumsa.so +lib/libnumsa.so.0 +lib/libnumsa.so.0.2.0 diff --git a/science/nwchem-data/Makefile b/science/nwchem-data/Makefile index c35a040a29e8..e119e3dfd9ca 100644 --- a/science/nwchem-data/Makefile +++ b/science/nwchem-data/Makefile @@ -1,6 +1,6 @@ PORTNAME= nwchem-data DISTVERSIONPREFIX= v -DISTVERSION= 7.2.3 +DISTVERSION= 7.3.1 DISTVERSIONSUFFIX= -release CATEGORIES= science diff --git a/science/nwchem-data/distinfo b/science/nwchem-data/distinfo index 480ac53a0703..fd9ca5e51be4 100644 --- a/science/nwchem-data/distinfo +++ b/science/nwchem-data/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1725044418 -SHA256 (nwchemgit-nwchem-v7.2.3-release_GH0.tar.gz) = fec76fbe650cdab8b00c8c1d7a5671554313e04a8e9e2fb300a7aad486910e6f -SIZE (nwchemgit-nwchem-v7.2.3-release_GH0.tar.gz) = 213226695 +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 1d58b0dd7435..ea8db7bb6730 100644 --- a/science/nwchem/Makefile +++ b/science/nwchem/Makefile @@ -1,8 +1,7 @@ PORTNAME= nwchem #DISTVERSIONPREFIX= v -DISTVERSION= 7.2.3 -DISTVERSIONSUFFIX= -release.revision-d690e065-src.2024-08-27 -PORTREVISION= 2 +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 \ @@ -15,7 +14,8 @@ EXTRACT_ONLY= ${DISTNAME}.tar.gz MAINTAINER= yuri@FreeBSD.org COMMENT= High-performance computational chemistry software -WWW= https://nwchemgit.github.io/ +WWW= https://nwchemgit.github.io/ \ + https://github.com/nwchemgit/nwchem LICENSE= ECL20 LICENSE_NAME= Educational Community License (ECL) 2.0 @@ -27,7 +27,8 @@ BROKEN_aarch64= fails to build: gfortran10: error: unrecognized command-line opt BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libblas.so:math/blas \ libga.so:devel/ga \ - libhwloc.so:devel/hwloc2 + libhwloc.so:devel/hwloc2 \ + libscalapack.so:math/scalapack RUN_DEPENDS= nwchem-data>0:science/nwchem-data TEST_DEPENDS= bash:shells/bash @@ -53,7 +54,10 @@ BINARY_ALIAS+= make=${GMAKE} # only for LIBXC PLIST_FILES= bin/nwchem etc/nwchemrc -LIBXC_VERSION= 6.1.0 # from src/libext/libxc/build_libxc.sh +LIBXC_VERSION= 7.0.0 # from src/libext/libxc/build_libxc.sh + +MAKE_ENV+= SCALAPACK_LIB=${PREFIX}/lib/libscalapack.so \ + SCALAPACK_SIZE=8 OPTIONS_DEFINE= LIBXC PYTHON # more potential optional dependencies are listed in src/libext/GNUmakefile OPTIONS_DEFAULT= LIBXC PYTHON BLAS_SIZE_4 MPICH # the MPI default should be the same as for the MPI option in math/scalapack and devel/ga diff --git a/science/nwchem/distinfo b/science/nwchem/distinfo index 3cfba638d886..ade23a4c4149 100644 --- a/science/nwchem/distinfo +++ b/science/nwchem/distinfo @@ -1,7 +1,7 @@ -TIMESTAMP = 1725406261 -SHA256 (nwchem-7.2.3/nwchem-7.2.3-release.revision-d690e065-src.2024-08-27.tar.gz) = a0f76f12ae2f634d33e76409cd389787e6c458cc2cf05ed453538de2d47a23a5 -SIZE (nwchem-7.2.3/nwchem-7.2.3-release.revision-d690e065-src.2024-08-27.tar.gz) = 234392394 -SHA256 (nwchem-7.2.3/dftd3.tgz) = d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59 -SIZE (nwchem-7.2.3/dftd3.tgz) = 555804 -SHA256 (nwchem-7.2.3/libxc-6.1.0.tar.gz) = 9baf23501dca21b05fa22d8e2ffeb56f294abe19ba12584cb3f9b421ae719c5f -SIZE (nwchem-7.2.3/libxc-6.1.0.tar.gz) = 64588321 +TIMESTAMP = 1762671036 +SHA256 (nwchem-7.3.1/nwchem-7.3.1-release.revision-23c3b41b-src.2025-11-06.tar.gz) = 2dc7d715615ac9f3fc1ddc5c464f77db56bb53473a029d993c900153bae8a1ab +SIZE (nwchem-7.3.1/nwchem-7.3.1-release.revision-23c3b41b-src.2025-11-06.tar.gz) = 236375450 +SHA256 (nwchem-7.3.1/dftd3.tgz) = d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59 +SIZE (nwchem-7.3.1/dftd3.tgz) = 555804 +SHA256 (nwchem-7.3.1/libxc-7.0.0.tar.gz) = 8d4e343041c9cd869833822f57744872076ae709a613c118d70605539fb13a77 +SIZE (nwchem-7.3.1/libxc-7.0.0.tar.gz) = 67985837 diff --git a/science/octopus/Makefile b/science/octopus/Makefile index 0045115f1a80..21935ea92ee8 100644 --- a/science/octopus/Makefile +++ b/science/octopus/Makefile @@ -1,6 +1,5 @@ PORTNAME= octopus -DISTVERSION= 15.1 -PORTREVISION= 2 +DISTVERSION= 16.0 CATEGORIES= science # chemistry MASTER_SITES= https://octopus-code.org/download/${DISTVERSION}/ @@ -30,8 +29,7 @@ LIB_DEPENDS= libarpack.so:math/arpack-ng \ libxc.so:science/libxc \ libyaml.so:textproc/libyaml -USES= compiler:c++14-lang fortran gmake jpeg libtool localbase:ldflags perl5 python shebangfix -USE_CXXSTD= c++14 +USES= compiler:c++14-lang fortran gmake jpeg libtool localbase:ldflags perl5 pkgconfig python shebangfix USE_LDCONFIG= yes SHEBANG_FILES= src/fdep/fortran_dependencies.pl testsuite/performance/create_combinations.py diff --git a/science/octopus/distinfo b/science/octopus/distinfo index 67b1584339cd..a87cb3bc7d71 100644 --- a/science/octopus/distinfo +++ b/science/octopus/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737081048 -SHA256 (octopus-15.1.tar.gz) = 6c4deb535ddfcdcdf6f26764b38fb1ad05faa9b418ec18d5d93f8d1040165bda -SIZE (octopus-15.1.tar.gz) = 42705145 +TIMESTAMP = 1762369025 +SHA256 (octopus-16.0.tar.gz) = 528f9d8625c16284b4e01756b349c6d39fff5e11eaef9da3590cf822960ab3d2 +SIZE (octopus-16.0.tar.gz) = 49798903 diff --git a/science/octopus/pkg-plist b/science/octopus/pkg-plist index 0a4eabda5277..863a5d10958f 100644 --- a/science/octopus/pkg-plist +++ b/science/octopus/pkg-plist @@ -199,6 +199,7 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/HGH/lda/Y.hgh %%DATADIR%%/pseudopotentials/HGH/lda/Zn.hgh %%DATADIR%%/pseudopotentials/HGH/lda/Zr.hgh +%%DATADIR%%/pseudopotentials/HGH/lda/elements_map.dat %%DATADIR%%/pseudopotentials/HGH/lda_sc/Ag_sc.hgh %%DATADIR%%/pseudopotentials/HGH/lda_sc/Au_sc.hgh %%DATADIR%%/pseudopotentials/HGH/lda_sc/Ba_sc.hgh @@ -256,6 +257,7 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/HGH/lda_sc/Yb_sc.hgh %%DATADIR%%/pseudopotentials/HGH/lda_sc/Zn_sc.hgh %%DATADIR%%/pseudopotentials/HGH/lda_sc/Zr_sc.hgh +%%DATADIR%%/pseudopotentials/HGH/lda_sc/elements_map.dat %%DATADIR%%/pseudopotentials/PSF/C.psf %%DATADIR%%/pseudopotentials/PSF/Cd.psf %%DATADIR%%/pseudopotentials/PSF/D.psf @@ -269,44 +271,104 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/PSF/Si.psf %%DATADIR%%/pseudopotentials/PSF/T.psf %%DATADIR%%/pseudopotentials/PSF/Ti.psf +%%DATADIR%%/pseudopotentials/PSF/elements_map.dat %%DATADIR%%/pseudopotentials/PSF/set_defaults %%DATADIR%%/pseudopotentials/elements.dat +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ag.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Al.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ar.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/As.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Au.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/B.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ba.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Be.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Bi.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Br.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/C.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ca.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Cd.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Cl.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Co.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Cr.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Cs.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Cu.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/F.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Fe.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ga.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ge.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/H.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/He.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Hf.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Hg.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/I.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/In.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ir.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/K.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Kr.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Li.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Mg.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Mn.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Mo.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/N.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Na.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Nb.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ne.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ni.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/O.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Os.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/P.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Pb.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Pd.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Po.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Pt.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Rb.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Re.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Rh.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Rn.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ru.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/S.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Sb.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Sc.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Se.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Si.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Sn.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Sr.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ta.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Tc.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Te.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Ti.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Tl.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/V.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/W.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Xe.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Y.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Zn.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-fr-04_pbe_standard/Zr.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ag.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Al.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Al.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ar.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ar.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/As.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Au.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/B.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/B.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ba.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Be.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Be.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Bi.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Br.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/C.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/C.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ca.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Cd.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Cl.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Cl.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Co.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Cr.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Cs.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Cu.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/D.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/D.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/F.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/F.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Fe.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ga.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ga.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ge.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/H.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/H.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/He.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/He.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Hf.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Hg.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/I.upf @@ -316,21 +378,16 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Kr.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/La.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Li.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Li.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Lu.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Mg.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Mn.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Mo.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/N.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/N.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Na.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Na.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Nb.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ne.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ne.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ni.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/O.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/O.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Os.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/P.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Pb.upf @@ -343,16 +400,13 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Rn.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ru.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/S.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/S.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Sb.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Sc.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Se.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Si.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Si.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Sn.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Sr.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/T.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/T.upf.spacing %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Ta.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Tc.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Te.upf @@ -364,6 +418,7 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Y.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Zn.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/Zr.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbe_standard/elements_map.dat %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbesol_standard/Ag.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbesol_standard/Al.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbesol_standard/Ar.upf @@ -438,6 +493,7 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbesol_standard/Y.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbesol_standard/Zn.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbesol_standard/Zr.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pbesol_standard/elements_map.dat %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Ag.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Al.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Ar.upf @@ -456,7 +512,6 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Cr.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Cs.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Cu.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/D.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/F.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Fe.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Ga.upf @@ -498,7 +553,6 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Si.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Sn.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Sr.upf -%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/T.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Ta.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Tc.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Te.upf @@ -510,6 +564,7 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Y.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Zn.upf %%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/Zr.upf +%%DATADIR%%/pseudopotentials/pseudo-dojo.org/nc-sr-04_pw_standard/elements_map.dat %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/lda/Ac_HSCV_LDA-1.0.xml %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/lda/Ag_HSCV_LDA-1.0.xml %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/lda/Al_HSCV_LDA-1.0.xml @@ -605,6 +660,7 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/lda/Yb_HSCV_LDA-1.0.xml %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/lda/Zn_HSCV_LDA-1.0.xml %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/lda/Zr_HSCV_LDA-1.1.xml +%%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/lda/elements_map.dat %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/pbe/Ac_HSCV_PBE-1.0.xml %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/pbe/Ag_HSCV_PBE-1.0.xml %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/pbe/Al_HSCV_PBE-1.0.xml @@ -700,6 +756,7 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/pbe/Yb_HSCV_PBE-1.0.xml %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/pbe/Zn_HSCV_PBE-1.0.xml %%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/pbe/Zr_HSCV_PBE-1.1.xml +%%DATADIR%%/pseudopotentials/quantum-simulation.org/hscv/pbe/elements_map.dat %%DATADIR%%/pseudopotentials/quantum-simulation.org/sg15/Ag_ONCV_PBE-1.2.upf %%DATADIR%%/pseudopotentials/quantum-simulation.org/sg15/Al_ONCV_PBE-1.2.upf %%DATADIR%%/pseudopotentials/quantum-simulation.org/sg15/Ar_ONCV_PBE-1.2.upf @@ -771,6 +828,7 @@ share/man/man1/octopus.1.gz %%DATADIR%%/pseudopotentials/quantum-simulation.org/sg15/Y_ONCV_PBE-1.2.upf %%DATADIR%%/pseudopotentials/quantum-simulation.org/sg15/Zn_ONCV_PBE-1.2.upf %%DATADIR%%/pseudopotentials/quantum-simulation.org/sg15/Zr_ONCV_PBE-1.2.upf +%%DATADIR%%/pseudopotentials/quantum-simulation.org/sg15/elements_map.dat %%DATADIR%%/recipes/da/octopus_gallega.txt %%DATADIR%%/recipes/da/sugo_zucchini.txt %%DATADIR%%/recipes/de/oktopus_gallega.txt @@ -855,6 +913,8 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/components/12-hartree_direct_3d.test %%DATADIR%%/testsuite/components/13-hartree_3d_mg.01-multigrid.inp %%DATADIR%%/testsuite/components/13-hartree_3d_mg.02-curvilinear.inp +%%DATADIR%%/testsuite/components/13-hartree_3d_mg.03-w_shape.inp +%%DATADIR%%/testsuite/components/13-hartree_3d_mg.04-curvilinear_gauss_seidel.inp %%DATADIR%%/testsuite/components/13-hartree_3d_mg.test %%DATADIR%%/testsuite/components/14-center-geom.01-run.inp %%DATADIR%%/testsuite/components/14-center-geom.test @@ -880,6 +940,10 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/components/20-dft_u.06-real_submesh_unpacked.inp %%DATADIR%%/testsuite/components/20-dft_u.07-complex_mesh_unpacked.inp %%DATADIR%%/testsuite/components/20-dft_u.08-complex_submesh_unpacked.inp +%%DATADIR%%/testsuite/components/20-dft_u.09-spinor_mesh.inp +%%DATADIR%%/testsuite/components/20-dft_u.10-spinor_submesh.inp +%%DATADIR%%/testsuite/components/20-dft_u.11-spinor_mesh_unpacked.inp +%%DATADIR%%/testsuite/components/20-dft_u.12-spinor_submesh_unpacked.inp %%DATADIR%%/testsuite/components/20-dft_u.test %%DATADIR%%/testsuite/components/21-hamiltonian_apply.01-Si.inp %%DATADIR%%/testsuite/components/21-hamiltonian_apply.test @@ -926,6 +990,8 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/components/34-regridding.12-curvilinear.inp %%DATADIR%%/testsuite/components/34-regridding.13-noncommensurate.inp %%DATADIR%%/testsuite/components/34-regridding.14-noncommensurate-nearestneighbor.inp +%%DATADIR%%/testsuite/components/34-regridding.15-order3.inp +%%DATADIR%%/testsuite/components/34-regridding.16-curvilinear-order3.inp %%DATADIR%%/testsuite/components/34-regridding.test %%DATADIR%%/testsuite/components/35-helmholtz_decom.01-large_box_no_surf_corr.inp %%DATADIR%%/testsuite/components/35-helmholtz_decom.02-small_box_no_surf_corr.inp @@ -941,6 +1007,19 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/components/38-mixing.02_linear.inp %%DATADIR%%/testsuite/components/38-mixing.03_diis.inp %%DATADIR%%/testsuite/components/38-mixing.test +%%DATADIR%%/testsuite/components/39-optimizers.inp +%%DATADIR%%/testsuite/components/39-optimizers.test +%%DATADIR%%/testsuite/components/40-weighted-kmeans-finitebc.01.inp +%%DATADIR%%/testsuite/components/40-weighted-kmeans.test +%%DATADIR%%/testsuite/components/41-csv_input.01-1d.inp +%%DATADIR%%/testsuite/components/41-csv_input.02-2d.inp +%%DATADIR%%/testsuite/components/41-csv_input.03-3d.inp +%%DATADIR%%/testsuite/components/41-csv_input.1d.csv +%%DATADIR%%/testsuite/components/41-csv_input.2d.csv +%%DATADIR%%/testsuite/components/41-csv_input.3d.csv +%%DATADIR%%/testsuite/components/41-csv_input.test +%%DATADIR%%/testsuite/components/42-composition_chebyshev.01.inp +%%DATADIR%%/testsuite/components/42-composition_chebyshev.test %%DATADIR%%/testsuite/errors/01-run_mode.01-one_shot.inp %%DATADIR%%/testsuite/errors/01-run_mode.test %%DATADIR%%/testsuite/errors/02-scf_errors.01-rdmft.inp @@ -958,11 +1037,18 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/finite_systems_1d/03-He-Hartree-Fock.test %%DATADIR%%/testsuite/finite_systems_1d/04-lithium.01-ground_state.inp %%DATADIR%%/testsuite/finite_systems_1d/04-lithium.02-absorbing_boundaries.inp +%%DATADIR%%/testsuite/finite_systems_1d/04-lithium.03-convergence_with_extra_states.inp %%DATADIR%%/testsuite/finite_systems_1d/04-lithium.test %%DATADIR%%/testsuite/finite_systems_1d/09-morse.01-gs.inp %%DATADIR%%/testsuite/finite_systems_1d/09-morse.02-unocc.inp %%DATADIR%%/testsuite/finite_systems_1d/09-morse.03-td.inp %%DATADIR%%/testsuite/finite_systems_1d/09-morse.test +%%DATADIR%%/testsuite/finite_systems_1d/10-file_input.01-gs.inp +%%DATADIR%%/testsuite/finite_systems_1d/10-file_input.02-td-csv.inp +%%DATADIR%%/testsuite/finite_systems_1d/10-file_input.03-td-obf.inp +%%DATADIR%%/testsuite/finite_systems_1d/10-file_input.shifted-gaussian.csv +%%DATADIR%%/testsuite/finite_systems_1d/10-file_input.shifted-gaussian.obf +%%DATADIR%%/testsuite/finite_systems_1d/10-file_input.test %%DATADIR%%/testsuite/finite_systems_2d/01-quadratic_box.01-ground_state.inp %%DATADIR%%/testsuite/finite_systems_2d/01-quadratic_box.02-hartree.inp %%DATADIR%%/testsuite/finite_systems_2d/01-quadratic_box.03-hartree+xc.inp @@ -993,6 +1079,14 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/finite_systems_2d/09-magnetic_2d.02-gs_gauge_xy.inp %%DATADIR%%/testsuite/finite_systems_2d/09-magnetic_2d.03-gs_gauge_y.inp %%DATADIR%%/testsuite/finite_systems_2d/09-magnetic_2d.test +%%DATADIR%%/testsuite/finite_systems_2d/10-file_input.01-gs.inp +%%DATADIR%%/testsuite/finite_systems_2d/10-file_input.02-td-csv.inp +%%DATADIR%%/testsuite/finite_systems_2d/10-file_input.03-td-obf.inp +%%DATADIR%%/testsuite/finite_systems_2d/10-file_input.04-td-ncdf.inp +%%DATADIR%%/testsuite/finite_systems_2d/10-file_input.shifted-gaussian.csv +%%DATADIR%%/testsuite/finite_systems_2d/10-file_input.shifted-gaussian.ncdf +%%DATADIR%%/testsuite/finite_systems_2d/10-file_input.shifted-gaussian.obf +%%DATADIR%%/testsuite/finite_systems_2d/10-file_input.test %%DATADIR%%/testsuite/finite_systems_3d/01-carbon_atom.01-psf_l0.inp %%DATADIR%%/testsuite/finite_systems_3d/01-carbon_atom.02-psf_l1.inp %%DATADIR%%/testsuite/finite_systems_3d/01-carbon_atom.03-static_field.inp @@ -1090,6 +1184,9 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/finite_systems_3d/30-local_multipoles.03-multipoles_restart.inp %%DATADIR%%/testsuite/finite_systems_3d/30-local_multipoles.test %%DATADIR%%/testsuite/finite_systems_3d/31-acetylene_b3lyp.01-gs.inp +%%DATADIR%%/testsuite/finite_systems_3d/31-acetylene_b3lyp.02-noACE.inp +%%DATADIR%%/testsuite/finite_systems_3d/31-acetylene_b3lyp.03-parstates.inp +%%DATADIR%%/testsuite/finite_systems_3d/31-acetylene_b3lyp.04-noACE_parstates.inp %%DATADIR%%/testsuite/finite_systems_3d/31-acetylene_b3lyp.test %%DATADIR%%/testsuite/finite_systems_3d/32-tdpcm_methane.01-ground_state.inp %%DATADIR%%/testsuite/finite_systems_3d/32-tdpcm_methane.02-td_prop_neq.inp @@ -1274,7 +1371,22 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/functionals/18-mgga.04-ncbr.inp %%DATADIR%%/testsuite/functionals/18-mgga.05-ncbr_oep.inp %%DATADIR%%/testsuite/functionals/18-mgga.06_nccs.inp +%%DATADIR%%/testsuite/functionals/18-mgga.07-ncbr_explicit.inp %%DATADIR%%/testsuite/functionals/18-mgga.test +%%DATADIR%%/testsuite/functionals/19-qedft-breit-1d.01-etac-px.inp +%%DATADIR%%/testsuite/functionals/19-qedft-breit-1d.02-pxlda.inp +%%DATADIR%%/testsuite/functionals/19-qedft-breit-1d.test +%%DATADIR%%/testsuite/functionals/20-qedft-breit-2d.01-etac-px.inp +%%DATADIR%%/testsuite/functionals/20-qedft-breit-2d.02-pxlda-weak.inp +%%DATADIR%%/testsuite/functionals/20-qedft-breit-2d.03-pxlda-strong.inp +%%DATADIR%%/testsuite/functionals/20-qedft-breit-2d.test +%%DATADIR%%/testsuite/functionals/21-qedft-breit-3d.01-pxlda-hydrogen.inp +%%DATADIR%%/testsuite/functionals/21-qedft-breit-3d.02-pxlda-helium.inp +%%DATADIR%%/testsuite/functionals/21-qedft-breit-3d.test +%%DATADIR%%/testsuite/functionals/22-vdw_d3_stress.01-Be_hpc.inp +%%DATADIR%%/testsuite/functionals/22-vdw_d3_stress.test +%%DATADIR%%/testsuite/functionals/23-xc_lrx.inp +%%DATADIR%%/testsuite/functionals/23-xc_lrx.test %%DATADIR%%/testsuite/lda_u/01-nio.01-U5-gs.inp %%DATADIR%%/testsuite/lda_u/01-nio.02-unocc.inp %%DATADIR%%/testsuite/lda_u/01-nio.test @@ -1315,6 +1427,10 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/lda_u/12-intersite_spinors.01-Na2_gs.inp %%DATADIR%%/testsuite/lda_u/12-intersite_spinors.02-Na2_td.inp %%DATADIR%%/testsuite/lda_u/12-intersite_spinors.test +%%DATADIR%%/testsuite/lda_u/13-j_dependent.01_O2.inp +%%DATADIR%%/testsuite/lda_u/13-j_dependent.02_combined_j_orbs.inp +%%DATADIR%%/testsuite/lda_u/13-j_dependent.O_fr.UPF +%%DATADIR%%/testsuite/lda_u/13-j_dependent.test %%DATADIR%%/testsuite/linear_response/01-casida.01-gs.inp %%DATADIR%%/testsuite/linear_response/01-casida.02-vib_modes.inp %%DATADIR%%/testsuite/linear_response/01-casida.03-unocc.inp @@ -1429,6 +1545,8 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/multisystem/01-nested_systems.01-two_levels.inp %%DATADIR%%/testsuite/multisystem/01-nested_systems.02-three_levels.inp %%DATADIR%%/testsuite/multisystem/01-nested_systems.03-four_levels.inp +%%DATADIR%%/testsuite/multisystem/01-nested_systems.04-three_levels-different-timesteps.inp +%%DATADIR%%/testsuite/multisystem/01-nested_systems.05-three_levels-different-timesteps-fail.inp %%DATADIR%%/testsuite/multisystem/01-nested_systems.test %%DATADIR%%/testsuite/multisystem/02-interaction_graph.01-three_body.inp %%DATADIR%%/testsuite/multisystem/02-interaction_graph.test @@ -1441,6 +1559,7 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/multisystem/04-propagation_verlet.02-three_body.inp %%DATADIR%%/testsuite/multisystem/04-propagation_verlet.03-two_body_different_time_steps.inp %%DATADIR%%/testsuite/multisystem/04-propagation_verlet.04-three_body_different_time_steps.inp +%%DATADIR%%/testsuite/multisystem/04-propagation_verlet.05-three_body_different_time_steps-fail.inp %%DATADIR%%/testsuite/multisystem/04-propagation_verlet.test %%DATADIR%%/testsuite/multisystem/05-propagation_beeman.01-two_body.inp %%DATADIR%%/testsuite/multisystem/05-propagation_beeman.02-three_body.inp @@ -1489,6 +1608,12 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/multisystem/17-lasers.test %%DATADIR%%/testsuite/multisystem/18-incompatible_timing.01-run.inp %%DATADIR%%/testsuite/multisystem/18-incompatible_timing.test +%%DATADIR%%/testsuite/multisystem/19-intra_interaction.01-ions.inp +%%DATADIR%%/testsuite/multisystem/19-intra_interaction.test +%%DATADIR%%/testsuite/multisystem/20-ensemble.01-solar-system.inp +%%DATADIR%%/testsuite/multisystem/20-ensemble.test +%%DATADIR%%/testsuite/multisystem/21-electronic_gs.01-gs.inp +%%DATADIR%%/testsuite/multisystem/21-electronic_gs.test %%DATADIR%%/testsuite/multisystem/99-carbon_hydrogen.01-gs.inp %%DATADIR%%/testsuite/multisystem/99-carbon_hydrogen.02-td.inp %%DATADIR%%/testsuite/multisystem/99-carbon_hydrogen.03-td_restart.inp @@ -1670,6 +1795,9 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/periodic_systems/23-hybrids.04-parstates.inp %%DATADIR%%/testsuite/periodic_systems/23-hybrids.test %%DATADIR%%/testsuite/periodic_systems/24-hartree_fock_1D.01-gs.inp +%%DATADIR%%/testsuite/periodic_systems/24-hartree_fock_1D.02-noACE.inp +%%DATADIR%%/testsuite/periodic_systems/24-hartree_fock_1D.03-polarized.inp +%%DATADIR%%/testsuite/periodic_systems/24-hartree_fock_1D.04-noACE_polarized.inp %%DATADIR%%/testsuite/periodic_systems/24-hartree_fock_1D.test %%DATADIR%%/testsuite/periodic_systems/25-Fe_polarized.01-gs.inp %%DATADIR%%/testsuite/periodic_systems/25-Fe_polarized.02-setup.inp @@ -1702,9 +1830,12 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/periodic_systems/33-go_shape.02-Si_cell_only.inp %%DATADIR%%/testsuite/periodic_systems/33-go_shape.03-Si_par_domains.inp %%DATADIR%%/testsuite/periodic_systems/33-go_shape.04_monolayerBN.inp +%%DATADIR%%/testsuite/periodic_systems/33-go_shape.05-pressure.inp %%DATADIR%%/testsuite/periodic_systems/33-go_shape.test -%%DATADIR%%/testsuite/periodic_systems/34-zora.01-gs.inp -%%DATADIR%%/testsuite/periodic_systems/34-zora.test +%%DATADIR%%/testsuite/periodic_systems/34-jellium_slab.01-gs.inp +%%DATADIR%%/testsuite/periodic_systems/34-jellium_slab.test +%%DATADIR%%/testsuite/periodic_systems/35-zora.01-gs.inp +%%DATADIR%%/testsuite/periodic_systems/35-zora.test %%DATADIR%%/testsuite/photo_electron/01-h1d_lin.01-mask.inp %%DATADIR%%/testsuite/photo_electron/01-h1d_lin.02-ba.inp %%DATADIR%%/testsuite/photo_electron/01-h1d_lin.test @@ -1790,6 +1921,8 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/pseudopotentials/17-hgh_occupations.03-W_sc.inp %%DATADIR%%/testsuite/pseudopotentials/17-hgh_occupations.04-Au_sc.inp %%DATADIR%%/testsuite/pseudopotentials/17-hgh_occupations.test +%%DATADIR%%/testsuite/pseudopotentials/18-Bi_pseudodojo_fr.01-gs.inp +%%DATADIR%%/testsuite/pseudopotentials/18-Bi_pseudodojo_fr.test %%DATADIR%%/testsuite/pseudopotentials/T_ONCV_PBE-1.2.upf %%DATADIR%%/testsuite/real_time/01-propagators.01-gs.inp %%DATADIR%%/testsuite/real_time/01-propagators.02-expmid.inp @@ -1909,6 +2042,9 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/real_time/25-nondipolesfa.01-gs.inp %%DATADIR%%/testsuite/real_time/25-nondipolesfa.02-td.inp %%DATADIR%%/testsuite/real_time/25-nondipolesfa.test +%%DATADIR%%/testsuite/real_time/26-bomd_solids.01-gs.inp +%%DATADIR%%/testsuite/real_time/26-bomd_solids.02-td.inp +%%DATADIR%%/testsuite/real_time/26-bomd_solids.test %%DATADIR%%/testsuite/symmetries/01-triclinic.01-spg1.inp %%DATADIR%%/testsuite/symmetries/01-triclinic.02-spg2.inp %%DATADIR%%/testsuite/symmetries/01-triclinic.test @@ -2161,8 +2297,8 @@ share/man/man1/octopus.1.gz %%DATADIR%%/testsuite/tutorials/01-octopus_basics-getting_started.03-H_atom_independent.inp %%DATADIR%%/testsuite/tutorials/01-octopus_basics-getting_started.test %%DATADIR%%/testsuite/tutorials/02-octopus_basics-basic_input_options.01-N_atom.inp +%%DATADIR%%/testsuite/tutorials/02-octopus_basics-basic_input_options.02-N_atom_chebyshev.inp %%DATADIR%%/testsuite/tutorials/02-octopus_basics-basic_input_options.test -%%DATADIR%%/testsuite/tutorials/03-octopus_basics-total_energy_convergence.01-N_atom.inp %%DATADIR%%/testsuite/tutorials/03-octopus_basics-total_energy_convergence.02-methane.inp %%DATADIR%%/testsuite/tutorials/03-octopus_basics-total_energy_convergence.test %%DATADIR%%/testsuite/tutorials/04-octopus_basics-visualization.01-benzene.inp 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/openmc/Makefile b/science/openmc/Makefile index dd31d577e3d7..6e025f6c4f36 100644 --- a/science/openmc/Makefile +++ b/science/openmc/Makefile @@ -1,7 +1,7 @@ PORTNAME= openmc DISTVERSIONPREFIX= v DISTVERSION= 0.15.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/openmodelica/Makefile b/science/openmodelica/Makefile index 20193cb276c9..eeb9e6e84e73 100644 --- a/science/openmodelica/Makefile +++ b/science/openmodelica/Makefile @@ -1,6 +1,6 @@ PORTNAME= openmodelica DISTVERSIONPREFIX= v -DISTVERSION= 1.25.4 +DISTVERSION= 1.25.7 CATEGORIES= science cad java DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} @@ -37,11 +37,9 @@ RUN_DEPENDS= bash:shells/bash \ gmake:devel/gmake USES= cmake compiler:c++14-lang iconv fortran gettext-runtime gl \ - gnome blaslapack localbase:ldflags qt:5 readline pkgconfig \ + gnome blaslapack localbase:ldflags qt:6 readline pkgconfig \ python:build shebangfix java -USE_QT= concurrent core declarative gui location network opengl \ - printsupport svg webchannel webengine widgets xml xmlpatterns \ - buildtools:build linguisttools:build qmake:build +USE_QT= 5compat base declarative positioning webchannel webengine svg tools:build USE_GL= gl opengl USE_GNOME= libxml2 USE_LDCONFIG= ${PREFIX}/lib/omc ${PREFIX}/lib/omc/OMSimulator ${PREFIX}/lib/omc/cpp ${PREFIX}/lib/omc/ffi # https://github.com/OpenModelica/OpenModelica/issues/9925 @@ -54,28 +52,31 @@ SHEBANG_GLOB= *.sh *.in *.ac GH_TUPLE= \ OpenModelica:OMOptim:d53288b:OpenModelica_OMOptim/OMOptim \ + OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMOptim/common \ OpenModelica:OMSimulator:e3a3aeb:OpenModelica_OMSimulator/OMSimulator \ - OpenModelica:OMSimulator-3rdParty:5c10de1648d1134a577d9284b58580a72383d89f:OpenModelica_OMSimulator_3rdParty/OMSimulator/3rdParty \ - OpenModelica:OMCompiler-3rdParty:520663f:OpenModelica_OMCompiler_3rdParty/OMCompiler/3rdParty \ - OpenModelica:OMSens:093ad11:OpenModelica_OMSens/OMSens \ - OpenModelica:OMSens_Qt:bab329a:OpenModelica_OMSens_Qt/OMSens_Qt \ - OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMOptim/common \ - OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMSens_Qt/common + OpenModelica:OMSimulator-3rdParty:5c10de1648d1134a577d9284b58580a72383d89f:OpenModelica_OMSimulator_3rdParty/OMSimulator/3rdParty \ + OpenModelica:OMCompiler-3rdParty:3d2d50d:OpenModelica_OMCompiler_3rdParty/OMCompiler/3rdParty \ + OpenModelica:OMSens_Qt:9c5dfb2:OpenModelica_OMSens_Qt/OMSens_Qt \ + OpenModelica:OpenModelica-common:6e6d4fd:OpenModelica_OpenModelica_common/OMSens_Qt/common GH_TUPLE+= OpenModelica:OMBootstrapping:04d16f7461e5401321f0f72613daf466ae2f76be:bootstrapping/OMCompiler/Compiler/boot/bomc # downloaded by cmake # this should change make program everywhere, but it doesn't, # hence the patches in OMCompiler/Compiler/runtime/CMakeLists.txt, OMEdit/OMEditLIB/Simulation/SimulationOutputWidget.cpp -CMAKE_ARGS= -DCMAKE_MAKE_PROGRAM=gmake \ +CMAKE_ARGS= -DOM_QT_MAJOR_VERSION=6 \ + -DCMAKE_MAKE_PROGRAM=gmake \ -DPython_EXECUTABLE=${PYTHON_CMD} CMAKE_ARGS+= -DOM_USE_CCACHE:BOOL=${CCACHE_ENABLED:S/yes/ON/:S/no/OFF/} # if refuses to build w/out ccache by default #CMAKE_ARGS+= -DOM_QT_MAJOR_VERSION=6 # broken, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=287596 CMAKE_ON= OM_OMEDIT_ENABLE_QTWEBENGINE +CMAKE_OFF= OM_OMC_ENABLE_IPOPT # broken: omc::3rd::ipopt isn't found, see https://github.com/OpenModelica/OpenModelica/issues/14702 LDFLAGS+= -lexecinfo -lintl -pthread BINARY_ALIAS= make=${GMAKE} +CONFLICTS_INSTALL= cminpack # see https://github.com/OpenModelica/OpenModelica/issues/14701 + post-extract: # remove stray *.orig files @${FIND} ${WRKSRC} -name "*.orig" -delete diff --git a/science/openmodelica/distinfo b/science/openmodelica/distinfo index 2597c4be9261..2ad0980ff458 100644 --- a/science/openmodelica/distinfo +++ b/science/openmodelica/distinfo @@ -1,19 +1,17 @@ -TIMESTAMP = 1757658835 -SHA256 (openmodelica-1.25.4/OpenModelica-OpenModelica-v1.25.4_GH0.tar.gz) = b9d50f8321f4537735d70368b2ca105e35ad118797d71b0107b24eb660387ad4 -SIZE (openmodelica-1.25.4/OpenModelica-OpenModelica-v1.25.4_GH0.tar.gz) = 148278628 -SHA256 (openmodelica-1.25.4/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = d5012951f43e90dce03d7866d221278ee11ddfbdac4db20fe43d93adbc3748e7 -SIZE (openmodelica-1.25.4/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = 4024177 -SHA256 (openmodelica-1.25.4/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 6192d933c258950fb0171f5d0ddac0353632d17ee99f6974ba53dd654f547e49 -SIZE (openmodelica-1.25.4/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 95557541 -SHA256 (openmodelica-1.25.4/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d -SIZE (openmodelica-1.25.4/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 -SHA256 (openmodelica-1.25.4/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 37c82357fc1e862eb13d79cf1ff2d143f263502472db9bb2c350c0c551022954 -SIZE (openmodelica-1.25.4/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 50256095 -SHA256 (openmodelica-1.25.4/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 335512c08f94902bb07e75278cea791370a551336272f7bebef8c707ef5e5e2b -SIZE (openmodelica-1.25.4/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 8871049 -SHA256 (openmodelica-1.25.4/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 2f2dcba4defd7f13e9fd5e0c26bb4951b9f1fcc7da64960a6ad1cee32a628efa -SIZE (openmodelica-1.25.4/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 211270 -SHA256 (openmodelica-1.25.4/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = fdb5bb442da0375373ef221cf26195114bf149511c1c2be051caad6301c21c9a -SIZE (openmodelica-1.25.4/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = 36148 -SHA256 (openmodelica-1.25.4/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 9ac6d28be6a331dfb61a57b033f2bcf984448cd63bc1a4cd140d60c2f5c64a79 -SIZE (openmodelica-1.25.4/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 3346859 +TIMESTAMP = 1764143142 +SHA256 (openmodelica-1.25.7/OpenModelica-OpenModelica-v1.25.7_GH0.tar.gz) = c51a0a3e48c469924469fed14a1d722d15d494673cb20b6f64f38da3540102ae +SIZE (openmodelica-1.25.7/OpenModelica-OpenModelica-v1.25.7_GH0.tar.gz) = 148281929 +SHA256 (openmodelica-1.25.7/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = d5012951f43e90dce03d7866d221278ee11ddfbdac4db20fe43d93adbc3748e7 +SIZE (openmodelica-1.25.7/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = 4024177 +SHA256 (openmodelica-1.25.7/OpenModelica-OpenModelica-common-6e6d4fd_GH0.tar.gz) = bff17b6705ef5fe7c1ebae9ca42c1b29d414d7dec59535e1376499f6a5afac54 +SIZE (openmodelica-1.25.7/OpenModelica-OpenModelica-common-6e6d4fd_GH0.tar.gz) = 36187 +SHA256 (openmodelica-1.25.7/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 6192d933c258950fb0171f5d0ddac0353632d17ee99f6974ba53dd654f547e49 +SIZE (openmodelica-1.25.7/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 95557541 +SHA256 (openmodelica-1.25.7/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d +SIZE (openmodelica-1.25.7/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 +SHA256 (openmodelica-1.25.7/OpenModelica-OMCompiler-3rdParty-3d2d50d_GH0.tar.gz) = 5f154453c2018a64e8a8a6e58fea59db7def74b937fafbfbaec73154f00cc96f +SIZE (openmodelica-1.25.7/OpenModelica-OMCompiler-3rdParty-3d2d50d_GH0.tar.gz) = 61466733 +SHA256 (openmodelica-1.25.7/OpenModelica-OMSens_Qt-9c5dfb2_GH0.tar.gz) = 552e96f327678672dfe0d2e9c364deb625651333245613e92e5eea57f50e34c0 +SIZE (openmodelica-1.25.7/OpenModelica-OMSens_Qt-9c5dfb2_GH0.tar.gz) = 210958 +SHA256 (openmodelica-1.25.7/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 9ac6d28be6a331dfb61a57b033f2bcf984448cd63bc1a4cd140d60c2f5c64a79 +SIZE (openmodelica-1.25.7/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 3346859 diff --git a/science/openmodelica/files/patch-OMCompiler_Compiler_runtime_systemimpl.c b/science/openmodelica/files/patch-OMCompiler_Compiler_runtime_systemimpl.c index 9492fab582b3..e76992e3d19e 100644 --- a/science/openmodelica/files/patch-OMCompiler_Compiler_runtime_systemimpl.c +++ b/science/openmodelica/files/patch-OMCompiler_Compiler_runtime_systemimpl.c @@ -1,8 +1,8 @@ - make it single-threaded as a workaround for https://github.com/OpenModelica/OpenModelica/issues/9922 ---- OMCompiler/Compiler/runtime/systemimpl.c.orig 2023-04-14 14:33:28 UTC +--- OMCompiler/Compiler/runtime/systemimpl.c.orig 2025-11-24 16:18:03 UTC +++ OMCompiler/Compiler/runtime/systemimpl.c -@@ -772,6 +772,7 @@ char* System_popen(threadData_t *threadData, const cha +@@ -779,6 +779,7 @@ int System_numProcessors(void) int System_numProcessors(void) { @@ -10,7 +10,7 @@ #if WITH_HWLOC==1 hwloc_topology_t topology; if (0==hwloc_topology_init(&topology) && 0==hwloc_topology_load(topology)) { -@@ -790,6 +791,8 @@ int System_numProcessors(void) +@@ -797,6 +798,8 @@ int System_numProcessors(void) #else return intMax(sysconf(_SC_NPROCESSORS_ONLN), 1); #endif diff --git a/science/openmodelica/files/patch-OMSens__Qt_OMSensPlugin.h b/science/openmodelica/files/patch-OMSens__Qt_OMSensPlugin.h new file mode 100644 index 000000000000..81ab7c6f6374 --- /dev/null +++ b/science/openmodelica/files/patch-OMSens__Qt_OMSensPlugin.h @@ -0,0 +1,13 @@ +--- OMSens_Qt/OMSensPlugin.h.orig 2025-11-26 07:56:10 UTC ++++ OMSens_Qt/OMSensPlugin.h +@@ -24,8 +24,8 @@ class OMSensPlugin: public QObject, public Information + public: + virtual void setOpenModelicaHome(const QString &omhome) override; + virtual void setTempPath(const QString &path) override; +- virtual void setOMSensPath(const QString &path) override; +- virtual void setPython(const QString &path) override; ++ virtual void setOMSensPath(const QString &path); ++ virtual void setPython(const QString &path); + + // ModelInterface interface + public: diff --git a/science/openmodelica/pkg-plist b/science/openmodelica/pkg-plist index 9c08ba4f8e0a..c2d8884127a1 100644 --- a/science/openmodelica/pkg-plist +++ b/science/openmodelica/pkg-plist @@ -7,6 +7,8 @@ bin/OMSimulator bin/OMSimulatorPython3 bin/omc bin/omc-diff +include/cminpack-1/cminpack.h +include/cminpack-1/minpack.h include/omc/FMI/fmi_import_context.h include/omc/FMI/fmi_import_util.h include/omc/FMI/fmi_util.h @@ -42,73 +44,6 @@ include/omc/FMI2/fmi2_import_variable.h include/omc/FMI2/fmi2_import_variable_list.h include/omc/FMI2/fmi2_types.h include/omc/FMI2/fmi2_xml_callbacks.h -include/omc/Ipopt/IpAlgBuilder.hpp -include/omc/Ipopt/IpAlgStrategy.hpp -include/omc/Ipopt/IpAlgTypes.hpp -include/omc/Ipopt/IpAugSystemSolver.hpp -include/omc/Ipopt/IpBlas.hpp -include/omc/Ipopt/IpCachedResults.hpp -include/omc/Ipopt/IpCompoundMatrix.hpp -include/omc/Ipopt/IpCompoundSymMatrix.hpp -include/omc/Ipopt/IpCompoundVector.hpp -include/omc/Ipopt/IpConvCheck.hpp -include/omc/Ipopt/IpDebug.hpp -include/omc/Ipopt/IpDenseVector.hpp -include/omc/Ipopt/IpDiagMatrix.hpp -include/omc/Ipopt/IpEqMultCalculator.hpp -include/omc/Ipopt/IpException.hpp -include/omc/Ipopt/IpExpansionMatrix.hpp -include/omc/Ipopt/IpGenTMatrix.hpp -include/omc/Ipopt/IpHessianUpdater.hpp -include/omc/Ipopt/IpIdentityMatrix.hpp -include/omc/Ipopt/IpIpoptAlg.hpp -include/omc/Ipopt/IpIpoptApplication.hpp -include/omc/Ipopt/IpIpoptCalculatedQuantities.hpp -include/omc/Ipopt/IpIpoptData.hpp -include/omc/Ipopt/IpIpoptNLP.hpp -include/omc/Ipopt/IpIterateInitializer.hpp -include/omc/Ipopt/IpIteratesVector.hpp -include/omc/Ipopt/IpIterationOutput.hpp -include/omc/Ipopt/IpJournalist.hpp -include/omc/Ipopt/IpLapack.hpp -include/omc/Ipopt/IpLineSearch.hpp -include/omc/Ipopt/IpMatrix.hpp -include/omc/Ipopt/IpMuUpdate.hpp -include/omc/Ipopt/IpNLP.hpp -include/omc/Ipopt/IpNLPScaling.hpp -include/omc/Ipopt/IpObserver.hpp -include/omc/Ipopt/IpOptionsList.hpp -include/omc/Ipopt/IpOrigIpoptNLP.hpp -include/omc/Ipopt/IpPDSystemSolver.hpp -include/omc/Ipopt/IpReferenced.hpp -include/omc/Ipopt/IpRegOptions.hpp -include/omc/Ipopt/IpReturnCodes.h -include/omc/Ipopt/IpReturnCodes.hpp -include/omc/Ipopt/IpReturnCodes.inc -include/omc/Ipopt/IpReturnCodes_inc.h -include/omc/Ipopt/IpScaledMatrix.hpp -include/omc/Ipopt/IpSearchDirCalculator.hpp -include/omc/Ipopt/IpSmartPtr.hpp -include/omc/Ipopt/IpSolveStatistics.hpp -include/omc/Ipopt/IpStdCInterface.h -include/omc/Ipopt/IpSumSymMatrix.hpp -include/omc/Ipopt/IpSymLinearSolver.hpp -include/omc/Ipopt/IpSymMatrix.hpp -include/omc/Ipopt/IpSymScaledMatrix.hpp -include/omc/Ipopt/IpSymTMatrix.hpp -include/omc/Ipopt/IpTNLP.hpp -include/omc/Ipopt/IpTNLPAdapter.hpp -include/omc/Ipopt/IpTNLPReducer.hpp -include/omc/Ipopt/IpTaggedObject.hpp -include/omc/Ipopt/IpTimedTask.hpp -include/omc/Ipopt/IpTimingStatistics.hpp -include/omc/Ipopt/IpTripletHelper.hpp -include/omc/Ipopt/IpTypes.hpp -include/omc/Ipopt/IpUtils.hpp -include/omc/Ipopt/IpVector.hpp -include/omc/Ipopt/IpZeroSymMatrix.hpp -include/omc/Ipopt/IpoptConfig.h -include/omc/Ipopt/config_ipopt_default.h include/omc/JM/jm_callbacks.h include/omc/JM/jm_named_ptr.h include/omc/JM/jm_portability.h @@ -117,6 +52,16 @@ include/omc/JM/jm_string_set.h include/omc/JM/jm_types.h include/omc/JM/jm_vector.h include/omc/JM/jm_vector_template.h +include/omc/ModelicaExternalC/ModelicaIO.c +include/omc/ModelicaExternalC/ModelicaIO.h +include/omc/ModelicaExternalC/ModelicaMatIO.c +include/omc/ModelicaExternalC/ModelicaMatIO.h +include/omc/ModelicaExternalC/ModelicaStandardTables.c +include/omc/ModelicaExternalC/ModelicaStandardTables.h +include/omc/ModelicaExternalC/ModelicaStandardTablesDummyUsertab.c +include/omc/ModelicaExternalC/read_data_impl.h +include/omc/ModelicaExternalC/safe-math.h +include/omc/ModelicaExternalC/snprintf.c include/omc/OMSimulator/OMSimulator.h include/omc/OMSimulator/Types.h include/omc/ParModelica/auto/om_pm_interface.hpp @@ -261,8 +206,6 @@ include/omc/c/util/utility.h include/omc/c/util/varinfo.h include/omc/c/util/write_csv.h include/omc/c/util/write_matlab4.h -include/omc/cminpack-1/cminpack.h -include/omc/cminpack-1/minpack.h include/omc/cpp/Core/DataExchange/DefaultContainerManager.h include/omc/cpp/Core/DataExchange/FactoryExport.h include/omc/cpp/Core/DataExchange/FactoryPolicy.h @@ -717,12 +660,12 @@ lib/omc/libamd.a lib/omc/libbtf.a lib/omc/libcdaskr.a lib/omc/libcminpack.a -lib/omc/libcoinmumps.a +lib/omc/libcminpackld.a +lib/omc/libcminpacks.a lib/omc/libcolamd.a lib/omc/libexpat.a lib/omc/libffi.a lib/omc/libfmilib.a -lib/omc/libipopt.a lib/omc/libklu.a lib/omc/liblis.a lib/omc/libmetis.a @@ -761,8 +704,9 @@ lib/omc/libumfpack.a lib/omc/libzlib.a lib/omc/libzmq.a lib/omc/pkgconfig/cminpack.pc +lib/omc/pkgconfig/cminpackld.pc +lib/omc/pkgconfig/cminpacks.pc lib/omc/pkgconfig/expat.pc -lib/omc/pkgconfig/ipopt.pc lib/omc/pkgconfig/libzmq.pc share/OMSimulator/schema/fmi2/fmi2Annotation.xsd share/OMSimulator/schema/fmi2/fmi2AttributeGroups.xsd @@ -793,6 +737,8 @@ share/cmake/ZeroMQ/ZeroMQConfigVersion.cmake share/cmake/ZeroMQ/ZeroMQTargets-%%CMAKE_BUILD_TYPE%%.cmake share/cmake/ZeroMQ/ZeroMQTargets.cmake share/cmake/tbb/TBBConfigVersion.cmake +share/cminpack/CMinpackConfig-%%CMAKE_BUILD_TYPE%%.cmake +share/cminpack/CMinpackConfig.cmake share/omc/runtime/c/fmi/buildproject/CMakeLists.txt.in share/omc/runtime/c/fmi/buildproject/config.guess share/omc/runtime/c/fmi/buildproject/config.sub @@ -808,16 +754,19 @@ share/omc/scripts/replace-startValue.bat share/omc/scripts/replace-startValue.sh share/omc/scripts/replace-startValue.xsl share/omc/scripts/simcodedump.xsl +share/omc/sources/c/external_solvers/F77_aloc.c share/omc/sources/c/external_solvers/blaswrap.h share/omc/sources/c/external_solvers/clapack.h share/omc/sources/c/external_solvers/cminpack.h share/omc/sources/c/external_solvers/dgemm.c +share/omc/sources/c/external_solvers/dgemv.c share/omc/sources/c/external_solvers/dger.c share/omc/sources/c/external_solvers/dgesc2.c share/omc/sources/c/external_solvers/dgesv.c share/omc/sources/c/external_solvers/dgetc2.c share/omc/sources/c/external_solvers/dgetf2.c share/omc/sources/c/external_solvers/dgetrf.c +share/omc/sources/c/external_solvers/dgetri.c share/omc/sources/c/external_solvers/dgetrs.c share/omc/sources/c/external_solvers/dlabad.c share/omc/sources/c/external_solvers/dlamch.c @@ -826,8 +775,13 @@ share/omc/sources/c/external_solvers/dogleg_.c share/omc/sources/c/external_solvers/dpmpar_.c share/omc/sources/c/external_solvers/dscal.c share/omc/sources/c/external_solvers/dswap.c +share/omc/sources/c/external_solvers/dtrmm.c +share/omc/sources/c/external_solvers/dtrmv.c share/omc/sources/c/external_solvers/dtrsm.c +share/omc/sources/c/external_solvers/dtrti2.c +share/omc/sources/c/external_solvers/dtrtri.c share/omc/sources/c/external_solvers/enorm_.c +share/omc/sources/c/external_solvers/exit_.c share/omc/sources/c/external_solvers/f2c.h share/omc/sources/c/external_solvers/hybrj_.c share/omc/sources/c/external_solvers/i_nint.c @@ -837,11 +791,13 @@ share/omc/sources/c/external_solvers/ilaenv.c share/omc/sources/c/external_solvers/iparmq.c share/omc/sources/c/external_solvers/lsame.c share/omc/sources/c/external_solvers/minpack.h +share/omc/sources/c/external_solvers/minpackP.h share/omc/sources/c/external_solvers/pow_di.c share/omc/sources/c/external_solvers/qform_.c share/omc/sources/c/external_solvers/qrfac_.c share/omc/sources/c/external_solvers/r1mpyq_.c share/omc/sources/c/external_solvers/r1updt_.c +share/omc/sources/c/external_solvers/s_cat.c share/omc/sources/c/external_solvers/s_cmp.c share/omc/sources/c/external_solvers/s_copy.c share/omc/sources/c/external_solvers/xerbla.c diff --git a/science/openmolcas/Makefile b/science/openmolcas/Makefile index 6f986684c0b0..0843133371ad 100644 --- a/science/openmolcas/Makefile +++ b/science/openmolcas/Makefile @@ -1,5 +1,5 @@ PORTNAME= openmolcas -DISTVERSION= 24.06 +DISTVERSION= 25.10 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org diff --git a/science/opensph/Makefile b/science/opensph/Makefile index 8550bb4472b0..1818a335107c 100644 --- a/science/opensph/Makefile +++ b/science/opensph/Makefile @@ -1,6 +1,6 @@ PORTNAME= OpenSPH DISTVERSION= 0.4.1 -PORTREVISION= 9 +PORTREVISION= 10 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/orthanc-dicomweb/Makefile b/science/orthanc-dicomweb/Makefile index 9c049433aab3..cf8110adbcb9 100644 --- a/science/orthanc-dicomweb/Makefile +++ b/science/orthanc-dicomweb/Makefile @@ -1,47 +1,42 @@ PORTNAME= orthanc-dicomweb -DISTVERSION= 1.8 -PORTREVISION= 14 +DISTVERSION= 1.21 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 \ - https://orthanc.osimis.io/ThirdPartyDownloads/:thirdparty \ - https://orthanc.osimis.io/ThirdPartyDownloads/dicom-web/:thirdpartydicomweb -DISTFILES= OrthancDicomWeb-${PORTVERSION}.tar.gz:main -EXTRADISTFILES= Orthanc-1.11.0.tar.gz:framework \ +MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-dicomweb/:dicomweb \ + https://orthanc.uclouvain.be/downloads/third-party-downloads/:thirdparty \ + https://orthanc.uclouvain.be/downloads/third-party-downloads/dicom-web/:thirdpartyweb \ + https://orthanc.uclouvain.be/downloads/sources/orthanc/:orthanc +DISTFILES= OrthancDicomWeb-${PORTVERSION}.tar.gz:dicomweb +EXTRADISTFILES= Orthanc-${ORTHANC_VER}.tar.gz:orthanc \ e2fsprogs-1.44.5.tar.gz:thirdparty \ - bootstrap-4.3.1.zip:thirdpartydicomweb \ - vuejs-2.6.10.tar.gz:thirdpartydicomweb \ - axios-0.19.0.tar.gz:thirdpartydicomweb \ - Font-Awesome-4.7.0.tar.gz:thirdpartydicomweb \ - bootstrap-vue-2.0.0-rc.24-dist.tar.gz:thirdpartydicomweb \ - babel-polyfill-6.26.0.min.js.gz:thirdpartydicomweb + bootstrap-5.3.3.zip:thirdparty \ + babel-polyfill-6.26.0.min.js.gz:thirdpartyweb \ + vuejs-2.6.10.tar.gz:thirdpartyweb \ + axios-0.19.0.tar.gz:thirdpartyweb \ + Font-Awesome-4.7.0.tar.gz:thirdpartyweb DISTFILES+= ${EXTRADISTFILES} DIST_SUBDIR= orthanc EXTRACT_ONLY= OrthancDicomWeb-${PORTVERSION}.tar.gz -MAINTAINER= maintainer.freebsd@xpoundit.com -COMMENT= Orthanc plugin to bring support of the DICOMweb standard into Orthanc +MAINTAINER= jwb@FreeBSD.org +COMMENT= Orthanc DICOMWeb plugin WWW= https://www.orthanc-server.com/static.php?page=dicomweb LICENSE= AGPLv3 LICENSE_FILE= ${WRKSRC}/COPYING -BROKEN= fails to build with boost-1.86+ - -BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCPlugin.h:science/orthanc +BUILD_DEPENDS= orthanc>=${ORTHANC_VER}:science/orthanc \ + googletest>0:devel/googletest LIB_DEPENDS= libboost_atomic.so:devel/boost-libs \ - libexpat.so:textproc/expat2 \ - libgdcmCommon.so:devel/gdcm \ - libicudata.so:devel/icu \ libjsoncpp.so:devel/jsoncpp \ - libopenjp2.so:graphics/openjpeg \ libpugixml.so:textproc/pugixml -RUN_DEPENDS= Orthanc:science/orthanc +RUN_DEPENDS= orthanc>=${ORTHANC_VER}:science/orthanc USES= cmake localbase python:build -USE_LDCONFIG= yes +# FIXME: Should plugins be moved to lib? +USE_LDCONFIG= ${DATADIR}/plugins -CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/ThirdPartyDownloads/Orthanc-1.11.0/OrthancFramework/Sources \ +ORTHANC_VER= 1.12.9 +CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/ThirdPartyDownloads/Orthanc-${ORTHANC_VER}/OrthancFramework/Sources \ -DORTHANC_FRAMEWORK_SOURCE=path CMAKE_OFF= USE_SYSTEM_UUID @@ -57,7 +52,7 @@ post-extract: .for f in ${EXTRADISTFILES:C/:[^:]*//} ${CP} ${DISTDIR}/${DIST_SUBDIR}/${f} ${WRKSRC}/ThirdPartyDownloads .endfor - ${TAR} -C ${WRKSRC}/ThirdPartyDownloads -xf ${WRKSRC}/ThirdPartyDownloads/Orthanc-1.11.0.tar.gz + ${TAR} -C ${WRKSRC}/ThirdPartyDownloads -xf ${WRKSRC}/ThirdPartyDownloads/Orthanc-${ORTHANC_VER}.tar.gz do-test: @cd ${BUILD_WRKSRC} && ./UnitTests diff --git a/science/orthanc-dicomweb/distinfo b/science/orthanc-dicomweb/distinfo index 2d9a67378d22..97b550726de8 100644 --- a/science/orthanc-dicomweb/distinfo +++ b/science/orthanc-dicomweb/distinfo @@ -1,19 +1,17 @@ -TIMESTAMP = 1652283828 -SHA256 (orthanc/OrthancDicomWeb-1.8.tar.gz) = e32a02914ceec019f70c56988939d7f7b16d7fce75895cb756d2a91fd2fe4f9c -SIZE (orthanc/OrthancDicomWeb-1.8.tar.gz) = 203789 -SHA256 (orthanc/Orthanc-1.11.0.tar.gz) = 23949a70562487fd6e79d6f3f13c71a0fc90aa25e492fb3a99575fee0722c5af -SIZE (orthanc/Orthanc-1.11.0.tar.gz) = 1899829 +TIMESTAMP = 1761569002 +SHA256 (orthanc/OrthancDicomWeb-1.21.tar.gz) = 30b7b1c7e710b78f378fd1e46e09be3ece33111331acb0227f80bfebf7d1417c +SIZE (orthanc/OrthancDicomWeb-1.21.tar.gz) = 296207 +SHA256 (orthanc/Orthanc-1.12.9.tar.gz) = 7a7cbc5f3663939fbef31ded021b36fcd52420337911ed43491bb663bcb5a4b2 +SIZE (orthanc/Orthanc-1.12.9.tar.gz) = 2165182 SHA256 (orthanc/e2fsprogs-1.44.5.tar.gz) = 2e211fae27ef74d5af4a4e40b10b8df7f87c655933bd171aab4889bfc4e6d1cc SIZE (orthanc/e2fsprogs-1.44.5.tar.gz) = 7619237 -SHA256 (orthanc/bootstrap-4.3.1.zip) = c7fcae50c070250e4e1ae36a670e5ee8fe9d529eb3f1a03c527f8223ce3f61bc -SIZE (orthanc/bootstrap-4.3.1.zip) = 2705432 +SHA256 (orthanc/bootstrap-5.3.3.zip) = 55d7f1ce795040afb8311df09d29d0d34648400c1eaabb2d0a2ed2216b3db05d +SIZE (orthanc/bootstrap-5.3.3.zip) = 8594807 +SHA256 (orthanc/babel-polyfill-6.26.0.min.js.gz) = 087d3d2d6212afb418f50491858f7f055cb54defb6351d6c5d008f662a2a95c2 +SIZE (orthanc/babel-polyfill-6.26.0.min.js.gz) = 34718 SHA256 (orthanc/vuejs-2.6.10.tar.gz) = e3d900cd9266b5bed9bb6d575fc9ab6787e79e7ad21c01ee1277bff5453121f2 SIZE (orthanc/vuejs-2.6.10.tar.gz) = 1576461 SHA256 (orthanc/axios-0.19.0.tar.gz) = 29577c6085b090b4e4a99392fcdd582fb6bbcb49b2aaf2cc7b7fa3874529b380 SIZE (orthanc/axios-0.19.0.tar.gz) = 125193 SHA256 (orthanc/Font-Awesome-4.7.0.tar.gz) = de512ba0e1dead382bbfce372cde74b3f18971d876fffb635ee9333f0db05d43 SIZE (orthanc/Font-Awesome-4.7.0.tar.gz) = 2672776 -SHA256 (orthanc/bootstrap-vue-2.0.0-rc.24-dist.tar.gz) = bc62cc91c2c3c24ddd29321d91be629e72db6129413ab6b8111ce13c2a57775b -SIZE (orthanc/bootstrap-vue-2.0.0-rc.24-dist.tar.gz) = 2448005 -SHA256 (orthanc/babel-polyfill-6.26.0.min.js.gz) = 087d3d2d6212afb418f50491858f7f055cb54defb6351d6c5d008f662a2a95c2 -SIZE (orthanc/babel-polyfill-6.26.0.min.js.gz) = 34718 diff --git a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancFramework_Sources_OrthancFramework.h b/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancFramework_Sources_OrthancFramework.h deleted file mode 100644 index 7e2d22ba1503..000000000000 --- a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancFramework_Sources_OrthancFramework.h +++ /dev/null @@ -1,10 +0,0 @@ ---- ThirdPartyDownloads/Orthanc-1.11.0/OrthancFramework/Sources/OrthancFramework.h.orig 2022-05-09 09:19:44 UTC -+++ ThirdPartyDownloads/Orthanc-1.11.0/OrthancFramework/Sources/OrthancFramework.h -@@ -70,6 +70,7 @@ - - - #include <string> -+#include <cassert> - - namespace Orthanc - { diff --git a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancFramework_Sources_SystemToolbox.cpp b/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancFramework_Sources_SystemToolbox.cpp deleted file mode 100644 index be3a52257299..000000000000 --- a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancFramework_Sources_SystemToolbox.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- ThirdPartyDownloads/Orthanc-1.11.0/OrthancFramework/Sources/SystemToolbox.cpp.orig 2022-05-09 09:19:44 UTC -+++ ThirdPartyDownloads/Orthanc-1.11.0/OrthancFramework/Sources/SystemToolbox.cpp -@@ -728,7 +728,7 @@ namespace Orthanc - - MimeType SystemToolbox::AutodetectMimeType(const std::string& path) - { -- std::string extension = boost::filesystem::extension(path); -+ std::string extension = boost::filesystem::path(path).extension().string(); - Toolbox::ToLowerCase(extension); - - // http://en.wikipedia.org/wiki/Mime_types diff --git a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancServer_Plugins_Engine_PluginsManager.cpp b/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancServer_Plugins_Engine_PluginsManager.cpp deleted file mode 100644 index 7e84c746faa1..000000000000 --- a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancServer_Plugins_Engine_PluginsManager.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- ThirdPartyDownloads/Orthanc-1.11.0/OrthancServer/Plugins/Engine/PluginsManager.cpp.orig 2022-05-09 09:19:44 UTC -+++ ThirdPartyDownloads/Orthanc-1.11.0/OrthancServer/Plugins/Engine/PluginsManager.cpp -@@ -292,7 +292,7 @@ namespace Orthanc - } - else - { -- std::string extension = boost::filesystem::extension(it->path()); -+ std::string extension = it->path().extension().string(); - Toolbox::ToLowerCase(extension); - - if (extension == PLUGIN_EXTENSION) diff --git a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancServer_Plugins_Samples_ModalityWorklists_Plugin.cpp b/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancServer_Plugins_Samples_ModalityWorklists_Plugin.cpp deleted file mode 100644 index dad50da54856..000000000000 --- a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancServer_Plugins_Samples_ModalityWorklists_Plugin.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- ThirdPartyDownloads/Orthanc-1.11.0/OrthancServer/Plugins/Samples/ModalityWorklists/Plugin.cpp.orig 2022-05-09 09:19:44 UTC -+++ ThirdPartyDownloads/Orthanc-1.11.0/OrthancServer/Plugins/Samples/ModalityWorklists/Plugin.cpp -@@ -163,7 +163,7 @@ OrthancPluginErrorCode Callback(OrthancPluginWorklistA - if (type == fs::regular_file || - type == fs::reparse_file) // cf. BitBucket issue #11 - { -- std::string extension = fs::extension(it->path()); -+ std::string extension = it->path().extension().string(); - std::transform(extension.begin(), extension.end(), extension.begin(), tolower); // Convert to lowercase - - if (extension == ".wl") diff --git a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancServer_Sources_OrthancConfiguration.cpp b/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancServer_Sources_OrthancConfiguration.cpp deleted file mode 100644 index 9df1a25a54a7..000000000000 --- a/science/orthanc-dicomweb/files/patch-ThirdPartyDownloads_Orthanc-1.11.0_OrthancServer_Sources_OrthancConfiguration.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- ThirdPartyDownloads/Orthanc-1.11.0/OrthancServer/Sources/OrthancConfiguration.cpp.orig 2022-05-09 09:19:44 UTC -+++ ThirdPartyDownloads/Orthanc-1.11.0/OrthancServer/Sources/OrthancConfiguration.cpp -@@ -113,7 +113,7 @@ namespace Orthanc - { - if (!is_directory(it->status())) - { -- std::string extension = boost::filesystem::extension(it->path()); -+ std::string extension = it->path().extension().string(); - Toolbox::ToLowerCase(extension); - - if (extension == ".json") diff --git a/science/orthanc-mysql/Makefile b/science/orthanc-mysql/Makefile index f963cfd53313..37620e7c7b54 100644 --- a/science/orthanc-mysql/Makefile +++ b/science/orthanc-mysql/Makefile @@ -1,40 +1,36 @@ PORTNAME= orthanc-mysql -DISTVERSION= 4.3 -PORTREVISION= 11 +DISTVERSION= 5.2 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 \ - https://orthanc.osimis.io/ThirdPartyDownloads/:thirdparty -DISTFILES= OrthancMySQL-${PORTVERSION}.tar.gz:main \ - Orthanc-1.9.3.tar.gz:framework \ +MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-mysql/:mysql \ + https://orthanc.uclouvain.be/downloads/sources/orthanc/:orthanc \ + https://orthanc.uclouvain.be/downloads/third-party-downloads/:thirdparty +DISTFILES= OrthancMySQL-${PORTVERSION}.tar.gz:mysql \ + Orthanc-${ORTHANC_VER}.tar.gz:orthanc \ e2fsprogs-1.44.5.tar.gz:thirdparty DIST_SUBDIR= orthanc EXTRACT_ONLY= OrthancMySQL-${PORTVERSION}.tar.gz -MAINTAINER= maintainer.freebsd@xpoundit.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Orthanc plugin to use MySQL/MariaDB for indexing or storage WWW= https://www.orthanc-server.com/static.php?page=mysql LICENSE= AGPLv3 LICENSE_FILE= ${WRKSRC}/COPYING -BROKEN= fails to build with boost-1.86+ - -BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCDatabasePlugin.h:science/orthanc +BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCDatabasePlugin.h:science/orthanc \ + googletest>0:devel/googletest LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ libcurl.so:ftp/curl \ - libgdcmCommon.so:devel/gdcm \ libjsoncpp.so:devel/jsoncpp \ - libpugixml.so:textproc/pugixml + libprotobuf.so:devel/protobuf RUN_DEPENDS= Orthanc:science/orthanc USES= cmake localbase mysql:client python:build ssl -USE_CXXSTD= c++14 # googletest 1.13 -USE_LDCONFIG= yes +USE_LDCONFIG= ${DATADIR}/plugins WRKSRC= ${WRKDIR}/OrthancMySQL-${PORTVERSION} -CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancFramework/Sources \ +CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/MySQL/ThirdPartyDownloads/Orthanc-${ORTHANC_VER}/OrthancFramework/Sources \ -DORTHANC_FRAMEWORK_SOURCE=path CMAKE_OFF= DBUILD_UNIT_TESTS USE_SYSTEM_ORTHANC_SDK USE_SYSTEM_UUID CMAKE_SOURCE_PATH= ${WRKSRC}/MySQL @@ -44,10 +40,12 @@ CXXFLAGS+= -I${LOCALBASE}/include -DNDEBUG PLIST_SUB= DISTVERSION=${DISTVERSION} +ORTHANC_VER= 1.12.9 + post-extract: ${MKDIR} ${WRKSRC}/MySQL/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/e2fsprogs-1.44.5.tar.gz ${WRKSRC}/MySQL/ThirdPartyDownloads - ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-1.9.3.tar.gz ${WRKSRC}/MySQL/ThirdPartyDownloads - ${TAR} -C ${WRKSRC}/MySQL/ThirdPartyDownloads -xf ${WRKSRC}/MySQL/ThirdPartyDownloads/Orthanc-1.9.3.tar.gz + ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-${ORTHANC_VER}.tar.gz ${WRKSRC}/MySQL/ThirdPartyDownloads + ${TAR} -C ${WRKSRC}/MySQL/ThirdPartyDownloads -xf ${WRKSRC}/MySQL/ThirdPartyDownloads/Orthanc-${ORTHANC_VER}.tar.gz .include <bsd.port.mk> diff --git a/science/orthanc-mysql/distinfo b/science/orthanc-mysql/distinfo index f73c567cbf40..7b57fb02015e 100644 --- a/science/orthanc-mysql/distinfo +++ b/science/orthanc-mysql/distinfo @@ -1,7 +1,7 @@ -TIMESTAMP = 1629969268 -SHA256 (orthanc/OrthancMySQL-4.3.tar.gz) = 7a22cbb482809bc1f6732e3e582cbbf4449e9205f297453ad4c7b7792956efba -SIZE (orthanc/OrthancMySQL-4.3.tar.gz) = 321585 -SHA256 (orthanc/Orthanc-1.9.3.tar.gz) = 41cc35a3d15ecb0d7b834e8e28a740cc4ffa1f333c019a764228d60e96608960 -SIZE (orthanc/Orthanc-1.9.3.tar.gz) = 1818313 +TIMESTAMP = 1761521650 +SHA256 (orthanc/OrthancMySQL-5.2.tar.gz) = 0d446b53c3fdaa66d9f2365864f1ac54d133fe3760d7d3bb52c850ca67ce9fbb +SIZE (orthanc/OrthancMySQL-5.2.tar.gz) = 603876 +SHA256 (orthanc/Orthanc-1.12.9.tar.gz) = 7a7cbc5f3663939fbef31ded021b36fcd52420337911ed43491bb663bcb5a4b2 +SIZE (orthanc/Orthanc-1.12.9.tar.gz) = 2165182 SHA256 (orthanc/e2fsprogs-1.44.5.tar.gz) = 2e211fae27ef74d5af4a4e40b10b8df7f87c655933bd171aab4889bfc4e6d1cc SIZE (orthanc/e2fsprogs-1.44.5.tar.gz) = 7619237 diff --git a/science/orthanc-mysql/files/patch-MySQL_Plugins_IndexPlugin.cpp b/science/orthanc-mysql/files/patch-MySQL_Plugins_IndexPlugin.cpp new file mode 100644 index 000000000000..af34bb427ab3 --- /dev/null +++ b/science/orthanc-mysql/files/patch-MySQL_Plugins_IndexPlugin.cpp @@ -0,0 +1,10 @@ +--- MySQL/Plugins/IndexPlugin.cpp.orig 2025-10-27 11:52:57 UTC ++++ MySQL/Plugins/IndexPlugin.cpp +@@ -30,6 +30,7 @@ + #include <Toolbox.h> + + #include <google/protobuf/any.h> ++#include <google/protobuf/stubs/common.h> + + #define ORTHANC_PLUGIN_NAME "mysql-index" + diff --git a/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancFramework_Sources_SystemToolbox.cpp b/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancFramework_Sources_SystemToolbox.cpp deleted file mode 100644 index 338388756a00..000000000000 --- a/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancFramework_Sources_SystemToolbox.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancFramework/Sources/SystemToolbox.cpp.orig 2021-05-07 07:22:38 UTC -+++ MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancFramework/Sources/SystemToolbox.cpp -@@ -727,7 +727,7 @@ namespace Orthanc - - MimeType SystemToolbox::AutodetectMimeType(const std::string& path) - { -- std::string extension = boost::filesystem::extension(path); -+ std::string extension = boost::filesystem::path(path).extension().string(); - Toolbox::ToLowerCase(extension); - - // http://en.wikipedia.org/wiki/Mime_types diff --git a/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Engine_PluginsManager.cpp b/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Engine_PluginsManager.cpp deleted file mode 100644 index c739fd182701..000000000000 --- a/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Engine_PluginsManager.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Plugins/Engine/PluginsManager.cpp.orig 2021-05-07 07:22:38 UTC -+++ MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Plugins/Engine/PluginsManager.cpp -@@ -303,7 +303,7 @@ namespace Orthanc - } - else - { -- std::string extension = boost::filesystem::extension(it->path()); -+ std::string extension = it->path().extension().string(); - Toolbox::ToLowerCase(extension); - - if (extension == PLUGIN_EXTENSION) diff --git a/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Samples_ModalityWorklists_Plugin.cpp b/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Samples_ModalityWorklists_Plugin.cpp deleted file mode 100644 index 2c45326a9e12..000000000000 --- a/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Samples_ModalityWorklists_Plugin.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Plugins/Samples/ModalityWorklists/Plugin.cpp.orig 2021-05-07 07:22:38 UTC -+++ MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Plugins/Samples/ModalityWorklists/Plugin.cpp -@@ -162,7 +162,7 @@ OrthancPluginErrorCode Callback(OrthancPluginWorklistA - if (type == fs::regular_file || - type == fs::reparse_file) // cf. BitBucket issue #11 - { -- std::string extension = fs::extension(it->path()); -+ std::string extension = it->path().extension().string(); - std::transform(extension.begin(), extension.end(), extension.begin(), tolower); // Convert to lowercase - - if (extension == ".wl") diff --git a/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Sources_OrthancConfiguration.cpp b/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Sources_OrthancConfiguration.cpp deleted file mode 100644 index 6ed1b2fd66f7..000000000000 --- a/science/orthanc-mysql/files/patch-MySQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Sources_OrthancConfiguration.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Sources/OrthancConfiguration.cpp.orig 2021-05-07 07:22:38 UTC -+++ MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Sources/OrthancConfiguration.cpp -@@ -123,7 +123,7 @@ namespace Orthanc - { - if (!is_directory(it->status())) - { -- std::string extension = boost::filesystem::extension(it->path()); -+ std::string extension = it->path().extension().string(); - Toolbox::ToLowerCase(extension); - - if (extension == ".json") diff --git a/science/orthanc-mysql/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake b/science/orthanc-mysql/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake new file mode 100644 index 000000000000..e4826a677166 --- /dev/null +++ b/science/orthanc-mysql/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake @@ -0,0 +1,47 @@ +--- MySQL/ThirdPartyDownloads/Orthanc-1.12.9/OrthancFramework/Resources/CMake/ProtobufConfiguration.cmake.orig 2025-08-11 16:02:50 UTC ++++ MySQL/ThirdPartyDownloads/Orthanc-1.12.9/OrthancFramework/Resources/CMake/ProtobufConfiguration.cmake +@@ -60,27 +60,31 @@ else() + add_custom_target(ProtobufCompiler) + endif() + +- check_include_file_cxx(google/protobuf/any.h HAVE_PROTOBUF_H) +- if (NOT HAVE_PROTOBUF_H) +- message(FATAL_ERROR "Please install the libprotobuf-dev package") +- endif() ++ if (${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") ++ find_package(Protobuf REQUIRED) ++ else() ++ check_include_file_cxx(google/protobuf/any.h HAVE_PROTOBUF_H) ++ if (NOT HAVE_PROTOBUF_H) ++ message(FATAL_ERROR "Please install the libprotobuf-dev package") ++ endif() + +- set(CMAKE_REQUIRED_LIBRARIES "protobuf") ++ set(CMAKE_REQUIRED_LIBRARIES "protobuf") + +- include(CheckCXXSourceCompiles) +- check_cxx_source_compiles( +- " ++ include(CheckCXXSourceCompiles) ++ check_cxx_source_compiles( ++ " + #include <google/protobuf/descriptor.h> + int main() + { + google::protobuf::FieldDescriptor::TypeName(google::protobuf::FieldDescriptor::TYPE_FLOAT); + } +-" HAVE_PROTOBUF_LIB) +- if (NOT HAVE_PROTOBUF_LIB) +- message(FATAL_ERROR "Cannot find the protobuf library") +- endif() ++ " HAVE_PROTOBUF_LIB) ++ if (NOT HAVE_PROTOBUF_LIB) ++ message(FATAL_ERROR "Cannot find the protobuf library") ++ endif() + +- unset(CMAKE_REQUIRED_LIBRARIES) ++ unset(CMAKE_REQUIRED_LIBRARIES) ++ endif() + + link_libraries(protobuf) + endif() diff --git a/science/orthanc-mysql/files/patch-Resources_Orthanc_Databases_ISqlLookupFormatter.cpp b/science/orthanc-mysql/files/patch-Resources_Orthanc_Databases_ISqlLookupFormatter.cpp deleted file mode 100644 index e48c152f1165..000000000000 --- a/science/orthanc-mysql/files/patch-Resources_Orthanc_Databases_ISqlLookupFormatter.cpp +++ /dev/null @@ -1,10 +0,0 @@ ---- Resources/Orthanc/Databases/ISqlLookupFormatter.cpp.orig 2021-07-22 18:16:30 UTC -+++ Resources/Orthanc/Databases/ISqlLookupFormatter.cpp -@@ -37,6 +37,7 @@ - - #include "DatabaseConstraint.h" - -+#include <cassert> - #include <boost/lexical_cast.hpp> - - diff --git a/science/orthanc-postgresql/Makefile b/science/orthanc-postgresql/Makefile index 044e5ef0a822..8b89f3124aee 100644 --- a/science/orthanc-postgresql/Makefile +++ b/science/orthanc-postgresql/Makefile @@ -1,40 +1,38 @@ PORTNAME= orthanc-postgresql -DISTVERSION= 4.0 -PORTREVISION= 11 +DISTVERSION= 9.0 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 \ - https://orthanc.osimis.io/ThirdPartyDownloads/:thirdparty -DISTFILES= OrthancPostgreSQL-${PORTVERSION}.tar.gz:main \ - Orthanc-1.9.3.tar.gz:framework \ +MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-postgresql/:pgsql \ + https://orthanc.uclouvain.be/downloads/sources/orthanc/:orthanc \ + https://orthanc.uclouvain.be/downloads/third-party-downloads/:thirdparty +DISTFILES= OrthancPostgreSQL-${PORTVERSION}.tar.gz:pgsql \ + Orthanc-${ORTHANC_VER}.tar.gz:orthanc \ e2fsprogs-1.44.5.tar.gz:thirdparty DIST_SUBDIR= orthanc EXTRACT_ONLY= OrthancPostgreSQL-${PORTVERSION}.tar.gz -MAINTAINER= maintainer.freebsd@xpoundit.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Orthanc plugin to use PostgreSQL for indexing or storage WWW= https://www.orthanc-server.com/static.php?page=postgresql LICENSE= AGPLv3 LICENSE_FILE= ${WRKSRC}/COPYING -BROKEN= fails to build with boost-1.86+ - -BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCDatabasePlugin.h:science/orthanc +BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCDatabasePlugin.h:science/orthanc \ + googletest>0:devel/googletest LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ libgdcmCommon.so:devel/gdcm \ libjsoncpp.so:devel/jsoncpp \ libpugixml.so:textproc/pugixml RUN_DEPENDS= Orthanc:science/orthanc -USES= cmake compiler:c11 localbase pgsql:11+ python:build ssl -USE_LDCONFIG= yes +USES= cmake localbase pgsql:11+ python:build ssl +USE_LDCONFIG= ${DATADIR}/plugins WRKSRC= ${WRKDIR}/OrthancPostgreSQL-${PORTVERSION} CMAKE_SOURCE_PATH= ${WRKSRC}/PostgreSQL CMAKE_OFF= BUILD_UNIT_TESTS USE_SYSTEM_ORTHANC_SDK USE_SYSTEM_UUID -CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancFramework/Sources \ +CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/PostgreSQL/ThirdPartyDownloads/Orthanc-${ORTHANC_VER}/OrthancFramework/Sources \ -DORTHANC_FRAMEWORK_SOURCE=path CXXFLAGS+= -I${LOCALBASE}/include -DNDEBUG LDFLAGS+= -L${LOCALBASE}/lib @@ -42,10 +40,12 @@ CFLAGS+= -DORTHANC_ENABLE_LOGGING_PLUGIN -DNDEBUG PLIST_SUB= DISTVERSION=${DISTVERSION} +ORTHANC_VER= 1.12.9 + post-extract: ${MKDIR} ${WRKSRC}/PostgreSQL/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/e2fsprogs-1.44.5.tar.gz ${WRKSRC}/PostgreSQL/ThirdPartyDownloads - ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-1.9.3.tar.gz ${WRKSRC}/PostgreSQL/ThirdPartyDownloads - ${TAR} -C ${WRKSRC}/PostgreSQL/ThirdPartyDownloads -xf ${WRKSRC}/PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3.tar.gz + ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-${ORTHANC_VER}.tar.gz ${WRKSRC}/PostgreSQL/ThirdPartyDownloads + ${TAR} -C ${WRKSRC}/PostgreSQL/ThirdPartyDownloads -xf ${WRKSRC}/PostgreSQL/ThirdPartyDownloads/Orthanc-${ORTHANC_VER}.tar.gz .include <bsd.port.mk> diff --git a/science/orthanc-postgresql/distinfo b/science/orthanc-postgresql/distinfo index a438656c3e1d..c68e74661ed6 100644 --- a/science/orthanc-postgresql/distinfo +++ b/science/orthanc-postgresql/distinfo @@ -1,7 +1,7 @@ -TIMESTAMP = 1620906912 -SHA256 (orthanc/OrthancPostgreSQL-4.0.tar.gz) = a5049ed8a5d6bb8b6529636cf1d9f631d1b61f6e0bbfdc6accae45aded42bac5 -SIZE (orthanc/OrthancPostgreSQL-4.0.tar.gz) = 318047 -SHA256 (orthanc/Orthanc-1.9.3.tar.gz) = 41cc35a3d15ecb0d7b834e8e28a740cc4ffa1f333c019a764228d60e96608960 -SIZE (orthanc/Orthanc-1.9.3.tar.gz) = 1818313 +TIMESTAMP = 1761533913 +SHA256 (orthanc/OrthancPostgreSQL-9.0.tar.gz) = 92c3fde9c3baad343a4de7090759274a733ac28af06037538dbf70f0ee50cd75 +SIZE (orthanc/OrthancPostgreSQL-9.0.tar.gz) = 790691 +SHA256 (orthanc/Orthanc-1.12.9.tar.gz) = 7a7cbc5f3663939fbef31ded021b36fcd52420337911ed43491bb663bcb5a4b2 +SIZE (orthanc/Orthanc-1.12.9.tar.gz) = 2165182 SHA256 (orthanc/e2fsprogs-1.44.5.tar.gz) = 2e211fae27ef74d5af4a4e40b10b8df7f87c655933bd171aab4889bfc4e6d1cc SIZE (orthanc/e2fsprogs-1.44.5.tar.gz) = 7619237 diff --git a/science/orthanc-postgresql/files/patch-PostgreSQL_CMakeLists.txt b/science/orthanc-postgresql/files/patch-PostgreSQL_CMakeLists.txt deleted file mode 100644 index 389ee26f4b28..000000000000 --- a/science/orthanc-postgresql/files/patch-PostgreSQL_CMakeLists.txt +++ /dev/null @@ -1,12 +0,0 @@ ---- PostgreSQL/CMakeLists.txt.orig 2021-05-17 12:24:06 UTC -+++ PostgreSQL/CMakeLists.txt -@@ -23,6 +23,9 @@ set(OPENSSL_STATIC_VERSION "1.1.1" CACHE STRING "Force - - include(${CMAKE_SOURCE_DIR}/../Resources/CMake/DatabasesPluginConfiguration.cmake) - -+set(CMAKE_CXX_STANDARD 11) -+set(CMAKE_CXX_STANDARD_REQUIRED ON) -+set(CMAKE_CXX_EXTENSIONS OFF) - - if (${CMAKE_SYSTEM_NAME} STREQUAL "Windows") - execute_process( diff --git a/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancFramework_Sources_SystemToolbox.cpp b/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancFramework_Sources_SystemToolbox.cpp deleted file mode 100644 index b7291c206db2..000000000000 --- a/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancFramework_Sources_SystemToolbox.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancFramework/Sources/SystemToolbox.cpp.orig 2021-05-07 07:22:38 UTC -+++ PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancFramework/Sources/SystemToolbox.cpp -@@ -727,7 +727,7 @@ namespace Orthanc - - MimeType SystemToolbox::AutodetectMimeType(const std::string& path) - { -- std::string extension = boost::filesystem::extension(path); -+ std::string extension = boost::filesystem::path(path).extension().string(); - Toolbox::ToLowerCase(extension); - - // http://en.wikipedia.org/wiki/Mime_types diff --git a/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Engine_PluginsManager.cpp b/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Engine_PluginsManager.cpp deleted file mode 100644 index 6211b49b37a1..000000000000 --- a/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Engine_PluginsManager.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Plugins/Engine/PluginsManager.cpp.orig 2021-05-07 07:22:38 UTC -+++ PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Plugins/Engine/PluginsManager.cpp -@@ -303,7 +303,7 @@ namespace Orthanc - } - else - { -- std::string extension = boost::filesystem::extension(it->path()); -+ std::string extension = it->path().extension().string(); - Toolbox::ToLowerCase(extension); - - if (extension == PLUGIN_EXTENSION) diff --git a/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Samples_ModalityWorklists_Plugin.cpp b/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Samples_ModalityWorklists_Plugin.cpp deleted file mode 100644 index cd1e7aed264f..000000000000 --- a/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Plugins_Samples_ModalityWorklists_Plugin.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Plugins/Samples/ModalityWorklists/Plugin.cpp.orig 2021-05-07 07:22:38 UTC -+++ PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Plugins/Samples/ModalityWorklists/Plugin.cpp -@@ -162,7 +162,7 @@ OrthancPluginErrorCode Callback(OrthancPluginWorklistA - if (type == fs::regular_file || - type == fs::reparse_file) // cf. BitBucket issue #11 - { -- std::string extension = fs::extension(it->path()); -+ std::string extension = it->path().extension().string(); - std::transform(extension.begin(), extension.end(), extension.begin(), tolower); // Convert to lowercase - - if (extension == ".wl") diff --git a/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Sources_OrthancConfiguration.cpp b/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Sources_OrthancConfiguration.cpp deleted file mode 100644 index d41857168ca7..000000000000 --- a/science/orthanc-postgresql/files/patch-PostgreSQL_ThirdPartyDownloads_Orthanc-1.9.3_OrthancServer_Sources_OrthancConfiguration.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Sources/OrthancConfiguration.cpp.orig 2021-05-07 07:22:38 UTC -+++ PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancServer/Sources/OrthancConfiguration.cpp -@@ -123,7 +123,7 @@ namespace Orthanc - { - if (!is_directory(it->status())) - { -- std::string extension = boost::filesystem::extension(it->path()); -+ std::string extension = it->path().extension().string(); - Toolbox::ToLowerCase(extension); - - if (extension == ".json") diff --git a/science/orthanc-postgresql/files/patch-Resources_Orthanc_Databases_ISqlLookupFormatter.cpp b/science/orthanc-postgresql/files/patch-Resources_Orthanc_Databases_ISqlLookupFormatter.cpp deleted file mode 100644 index c1b15d836a28..000000000000 --- a/science/orthanc-postgresql/files/patch-Resources_Orthanc_Databases_ISqlLookupFormatter.cpp +++ /dev/null @@ -1,10 +0,0 @@ ---- Resources/Orthanc/Databases/ISqlLookupFormatter.cpp.orig 2021-04-22 15:22:26 UTC -+++ Resources/Orthanc/Databases/ISqlLookupFormatter.cpp -@@ -49,6 +49,7 @@ - - #include "DatabaseConstraint.h" - -+#include <cassert> - #include <boost/lexical_cast.hpp> - - diff --git a/science/orthanc-webviewer/Makefile b/science/orthanc-webviewer/Makefile index 71b7598926a0..c88b6e69e403 100644 --- a/science/orthanc-webviewer/Makefile +++ b/science/orthanc-webviewer/Makefile @@ -1,43 +1,39 @@ PORTNAME= orthanc-webviewer -DISTVERSION= 2.9 -PORTREVISION= 1 +DISTVERSION= 2.10 CATEGORIES= science -MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-webviewer/:main \ - https://orthanc.uclouvain.be/downloads/sources/orthanc/:framework \ - http://orthanc.osimis.io/ThirdPartyDownloads/WebViewer/:thirdpartywebviewer \ - http://orthanc.osimis.io/ThirdPartyDownloads/:thirdparty -DISTFILES= OrthancWebViewer-${PORTVERSION}.tar.gz:main \ - jsPanel-2.3.3-fixed.zip:thirdpartywebviewer \ - cornerstone-0.11.0.zip:thirdpartywebviewer \ - jquery-ui-1.11.3.zip:thirdpartywebviewer \ - pako-0.2.5.zip:thirdpartywebviewer \ - js-url-1.8.6.zip:thirdpartywebviewer \ - Orthanc-${ORTHANC_FRAMEWORK_VERSION}.tar.gz:framework \ +MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-webviewer/:webviewer \ + https://orthanc.uclouvain.be/downloads/sources/orthanc/:orthanc \ + https://orthanc.uclouvain.be/downloads/third-party-downloads/web-viewer/:thirdpartyweb \ + https://orthanc.uclouvain.be/downloads/third-party-downloads/:thirdparty +DISTFILES= OrthancWebViewer-${PORTVERSION}.tar.gz:webviewer \ + jsPanel-2.3.3-fixed.zip:thirdpartyweb \ + cornerstone-0.11.0.zip:thirdpartyweb \ + jquery-ui-1.11.3.zip:thirdpartyweb \ + pako-0.2.5.zip:thirdpartyweb \ + js-url-1.8.6.zip:thirdpartyweb \ + Orthanc-${ORTHANC_VER}.tar.gz:orthanc \ e2fsprogs-1.44.5.tar.gz:thirdparty DIST_SUBDIR= orthanc EXTRACT_ONLY= OrthancWebViewer-${PORTVERSION}.tar.gz -MAINTAINER= maintainer.freebsd@xpoundit.com -COMMENT= Orthanc plugin to extend Orthanc with a Web viewer of medical images +MAINTAINER= jwb@FreeBSD.org +COMMENT= Orthanc web viewer plugin WWW= https://www.orthanc-server.com/static.php?page=web-viewer LICENSE= AGPLv3 LICENSE_FILE= ${WRKSRC}/COPYING -BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCPlugin.h:science/orthanc +BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCPlugin.h:science/orthanc \ + googletest>0:devel/googletest LIB_DEPENDS= libboost_atomic.so:devel/boost-libs \ - libexpat.so:textproc/expat2 \ - libgdcmCommon.so:devel/gdcm \ - libicudata.so:devel/icu \ libjsoncpp.so:devel/jsoncpp \ - libopenjp2.so:graphics/openjpeg \ libsqlite3.so:databases/sqlite3 RUN_DEPENDS= Orthanc:science/orthanc USES= cmake localbase python:build -USE_LDCONFIG= yes +USE_LDCONFIG= ${DATADIR}/plugins -CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/ThirdPartyDownloads/Orthanc-${ORTHANC_FRAMEWORK_VERSION}/OrthancFramework/Sources \ +CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/ThirdPartyDownloads/Orthanc-${ORTHANC_VER}/OrthancFramework/Sources \ -DORTHANC_FRAMEWORK_SOURCE=path CMAKE_OFF= USE_SYSTEM_UUID @@ -48,7 +44,8 @@ WRKSRC= ${WRKDIR}/OrthancWebViewer-${PORTVERSION} PLIST_SUB= DISTVERSION=${DISTVERSION} -ORTHANC_FRAMEWORK_VERSION= 1.12.6 +# Build fails with 1.12.8 and 1.12.9 +ORTHANC_VER= 1.12.7 post-extract: ${MKDIR} ${WRKSRC}/ThirdPartyDownloads @@ -58,8 +55,8 @@ post-extract: ${CP} ${DISTDIR}/${DIST_SUBDIR}/pako-0.2.5.zip ${WRKSRC}/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/js-url-1.8.6.zip ${WRKSRC}/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/e2fsprogs-1.44.5.tar.gz ${WRKSRC}/ThirdPartyDownloads - ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-${ORTHANC_FRAMEWORK_VERSION}.tar.gz ${WRKSRC}/ThirdPartyDownloads - ${TAR} -C ${WRKSRC}/ThirdPartyDownloads -xf ${WRKSRC}/ThirdPartyDownloads/Orthanc-${ORTHANC_FRAMEWORK_VERSION}.tar.gz + ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-${ORTHANC_VER}.tar.gz ${WRKSRC}/ThirdPartyDownloads + ${TAR} -C ${WRKSRC}/ThirdPartyDownloads -xf ${WRKSRC}/ThirdPartyDownloads/Orthanc-${ORTHANC_VER}.tar.gz post-build: @cd ${BUILD_WRKSRC} && ./UnitTests diff --git a/science/orthanc-webviewer/distinfo b/science/orthanc-webviewer/distinfo index beff3cb36584..e2e02d554be4 100644 --- a/science/orthanc-webviewer/distinfo +++ b/science/orthanc-webviewer/distinfo @@ -1,6 +1,6 @@ -TIMESTAMP = 1739140790 -SHA256 (orthanc/OrthancWebViewer-2.9.tar.gz) = 2f2cee66f908f6c5a6f0ebd69341f42fa94aa6179904ea540adeb21ac69c05fe -SIZE (orthanc/OrthancWebViewer-2.9.tar.gz) = 132935 +TIMESTAMP = 1761581265 +SHA256 (orthanc/OrthancWebViewer-2.10.tar.gz) = b01df44e17ee4efe4575bc544b4bb0767eb1423dc586b0c3b6457156c7501fa1 +SIZE (orthanc/OrthancWebViewer-2.10.tar.gz) = 135662 SHA256 (orthanc/jsPanel-2.3.3-fixed.zip) = 958a15c7009efbb865da62b5850a3a39661c62696e38b151c7f988f4ac445595 SIZE (orthanc/jsPanel-2.3.3-fixed.zip) = 826542 SHA256 (orthanc/cornerstone-0.11.0.zip) = 1bada9f1f2981968f72daa352e712abea5cac3e0417fe59176f70a23261f1da9 @@ -11,7 +11,7 @@ SHA256 (orthanc/pako-0.2.5.zip) = e493010e1b1af5c149631994365ed31e15722eed2d17cc SIZE (orthanc/pako-0.2.5.zip) = 704378 SHA256 (orthanc/js-url-1.8.6.zip) = ef2c7f50921ba64ac434eacf025669f1e6f39b5584100ffa8194a3edc08d43d3 SIZE (orthanc/js-url-1.8.6.zip) = 54717 -SHA256 (orthanc/Orthanc-1.12.6.tar.gz) = aa5b6d6309965ed360625b5572e79068e6c501b603163e330629f2f0a56a0fe9 -SIZE (orthanc/Orthanc-1.12.6.tar.gz) = 2089779 +SHA256 (orthanc/Orthanc-1.12.7.tar.gz) = f4349971c9e12f74599ba036c37ce7fe7fe8078b08dddbb83e08cf7b13e53adb +SIZE (orthanc/Orthanc-1.12.7.tar.gz) = 2097270 SHA256 (orthanc/e2fsprogs-1.44.5.tar.gz) = 2e211fae27ef74d5af4a4e40b10b8df7f87c655933bd171aab4889bfc4e6d1cc SIZE (orthanc/e2fsprogs-1.44.5.tar.gz) = 7619237 diff --git a/science/orthanc-webviewer/files/patch-CMakeLists.txt b/science/orthanc-webviewer/files/patch-CMakeLists.txt deleted file mode 100644 index 5ac2ba18ecbc..000000000000 --- a/science/orthanc-webviewer/files/patch-CMakeLists.txt +++ /dev/null @@ -1,11 +0,0 @@ ---- CMakeLists.txt.orig 2025-02-09 22:38:16 UTC -+++ CMakeLists.txt -@@ -28,7 +28,7 @@ else() - set(ORTHANC_FRAMEWORK_DEFAULT_VERSION "mainline") - set(ORTHANC_FRAMEWORK_DEFAULT_SOURCE "hg") - else() -- set(ORTHANC_FRAMEWORK_DEFAULT_VERSION "1.12.3") -+ set(ORTHANC_FRAMEWORK_DEFAULT_VERSION "1.12.6") - set(ORTHANC_FRAMEWORK_DEFAULT_SOURCE "web") - endif() - diff --git a/science/orthanc/Makefile b/science/orthanc/Makefile index 515e49a5a4fb..69612bbb386b 100644 --- a/science/orthanc/Makefile +++ b/science/orthanc/Makefile @@ -1,35 +1,29 @@ PORTNAME= orthanc -DISTVERSION= 1.12.6 -PORTREVISION= 3 +DISTVERSION= 1.12.9 CATEGORIES= science MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc/ DISTNAME= Orthanc-${PORTVERSION} -MAINTAINER= maintainer.freebsd@xpoundit.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Lightweight DICOM server for healthcare and medical research WWW= https://www.orthanc-server.com/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING -BUILD_DEPENDS= protoc:devel/protobuf - +BUILD_DEPENDS= protoc:devel/protobuf \ + googletest>0:devel/googletest LIB_DEPENDS= libboost_atomic.so:devel/boost-libs \ libcivetweb.so:www/civetweb \ libcurl.so:ftp/curl \ libdcmtkcharls.so:graphics/dcmtk \ - libgtest.so:devel/googletest \ - libicuuc.so:devel/icu \ libjsoncpp.so:devel/jsoncpp \ libpng16.so:graphics/png \ libprotobuf.so:devel/protobuf \ libpugixml.so:textproc/pugixml \ - libtiff.so:graphics/tiff \ libuuid.so:misc/libuuid USES= cmake gnome iconv jpeg lua python:build sqlite ssl -USE_GNOME= libxml2 -USE_LDCONFIG= yes USE_RC_SUBR= orthanc diff --git a/science/orthanc/distinfo b/science/orthanc/distinfo index 2498469be620..d57475212b4a 100644 --- a/science/orthanc/distinfo +++ b/science/orthanc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1739138261 -SHA256 (Orthanc-1.12.6.tar.gz) = aa5b6d6309965ed360625b5572e79068e6c501b603163e330629f2f0a56a0fe9 -SIZE (Orthanc-1.12.6.tar.gz) = 2089779 +TIMESTAMP = 1761178767 +SHA256 (Orthanc-1.12.9.tar.gz) = 7a7cbc5f3663939fbef31ded021b36fcd52420337911ed43491bb663bcb5a4b2 +SIZE (Orthanc-1.12.9.tar.gz) = 2165182 diff --git a/science/orthanc/files/orthanc.in b/science/orthanc/files/orthanc.in index 85d6af45d8a1..9cbe3d1cd321 100644 --- a/science/orthanc/files/orthanc.in +++ b/science/orthanc/files/orthanc.in @@ -23,13 +23,13 @@ desc="Lightweight DICOM server for healthcare and medical research" load_rc_config $name : ${orthanc_enable:=NO} -: ${orthanc_flags="%%ETCDIR%%/orthanc.json"} +: ${orthanc_config="%%ETCDIR%%/orthanc.json"} start_precmd=orthanc_prestart pidfile=/var/run/orthanc.pid procname=%%PREFIX%%/sbin/Orthanc command=/usr/sbin/daemon -command_args=" -f -p ${pidfile} -u orthanc ${procname} ${orthanc_flags}" +command_args=" --output-file /var/log/orthanc --sighup --child-pidfile ${pidfile} --user orthanc ${procname} ${orthanc_flags} ${orthanc_config}" orthanc_prestart() { diff --git a/science/orthanc/files/patch-OrthancFramework_Sources_Images_JpegWriter.cpp b/science/orthanc/files/patch-OrthancFramework_Sources_Images_JpegWriter.cpp deleted file mode 100644 index 59b845085092..000000000000 --- a/science/orthanc/files/patch-OrthancFramework_Sources_Images_JpegWriter.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- OrthancFramework/Sources/Images/JpegWriter.cpp.orig 2024-12-17 16:33:40 UTC -+++ OrthancFramework/Sources/Images/JpegWriter.cpp -@@ -187,7 +187,7 @@ namespace Orthanc - **/ - unsigned long size; - #else -- size_t size; -+ unsigned long size; - #endif - - if (setjmp(jerr.GetJumpBuffer())) diff --git a/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json b/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json index f6b4af632e2e..212fadfde386 100644 --- a/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json +++ b/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json @@ -5,13 +5,13 @@ // raw DICOM instances). Backslashes must be either escaped by // doubling them, or replaced by forward slashes "/". - "StorageDirectory" : "OrthancStorage", -+ "StorageDirectory" : "/var/db/orthanc/db-v5", ++ "StorageDirectory" : "/var/db/orthanc/db/db-v5", // Path to the directory that holds the SQLite index (if unset, the // value of StorageDirectory is used). This index could be stored on // a RAM-drive or a SSD device for performance reasons. - "IndexDirectory" : "OrthancStorage", -+ "IndexDirectory" : "/var/db/orthanc/db-v5", ++ "IndexDirectory" : "/var/db/orthanc/db/db-v5", // Path to the directory where Orthanc stores its large temporary // files. The content of this folder can be safely deleted once diff --git a/science/orthanc/files/patch-OrthancServer_Sources_Database_PrepareDatabase.sql b/science/orthanc/files/patch-OrthancServer_Sources_Database_PrepareDatabase.sql new file mode 100644 index 000000000000..ffe19920c2b0 --- /dev/null +++ b/science/orthanc/files/patch-OrthancServer_Sources_Database_PrepareDatabase.sql @@ -0,0 +1,13 @@ +--- OrthancServer/Sources/Database/PrepareDatabase.sql.orig 2025-08-11 16:02:50 UTC ++++ OrthancServer/Sources/Database/PrepareDatabase.sql +@@ -160,4 +160,9 @@ -- The "1" corresponds to the "GlobalProperty_Database + + -- Set the version of the database schema + -- The "1" corresponds to the "GlobalProperty_DatabaseSchemaVersion" enumeration +-INSERT INTO GlobalProperties VALUES (1, "6"); ++-- Upstream code has (1, "6"), which causes startup to fail on FreeBSD ++-- E1023 08:43:05.328003 MAIN Connection.cpp:169] SQLite execute error: no such column: "6" - should this be a string literal in single-quotes? (1) ++-- Apparently due to sqlite 3.41+ being stricter about string literals ++-- Debian packages currently uses 3.34 ++-- https://orthanc.uclouvain.be/bugs/show_bug.cgi?id=227 ++INSERT INTO GlobalProperties VALUES (1, 6); 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/packmol/Makefile b/science/packmol/Makefile index 5f2d5ae0c487..aa9368fabd48 100644 --- a/science/packmol/Makefile +++ b/science/packmol/Makefile @@ -1,6 +1,6 @@ PORTNAME= packmol DISTVERSIONPREFIX= v -DISTVERSION= 21.1.1 +DISTVERSION= 21.1.3 CATEGORIES= science MAINTAINER= eduardo@FreeBSD.org diff --git a/science/packmol/distinfo b/science/packmol/distinfo index a48cfe0d0a3d..04a34d95fab4 100644 --- a/science/packmol/distinfo +++ b/science/packmol/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1759409929 -SHA256 (m3g-packmol-v21.1.1_GH0.tar.gz) = 4bad785e6e1b91d8b80934eeebf91013e940c577693bbecd7ec56eb563f5d97f -SIZE (m3g-packmol-v21.1.1_GH0.tar.gz) = 634943 +TIMESTAMP = 1763590917 +SHA256 (m3g-packmol-v21.1.3_GH0.tar.gz) = 21a22e4e3f183e2c594c2e1d85cd7c16a95a8c609b36fc28d653f6c2c2d54c0c +SIZE (m3g-packmol-v21.1.3_GH0.tar.gz) = 637489 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..d512d062c0a6 100644 --- a/science/paraview/Makefile +++ b/science/paraview/Makefile @@ -1,6 +1,6 @@ PORTNAME= paraview DISTVERSION= ${PARAVIEW_VER}.3 -PORTREVISION= 5 +PORTREVISION= 8 CATEGORIES= science graphics MASTER_SITES= http://www.paraview.org/files/v${PARAVIEW_VER}/ DISTNAME= ParaView-v${PORTVERSION} diff --git a/science/parthenon/Makefile b/science/parthenon/Makefile index 98f08b45d7b7..b09ecf9ad2ee 100644 --- a/science/parthenon/Makefile +++ b/science/parthenon/Makefile @@ -1,7 +1,7 @@ PORTNAME= parthenon DISTVERSIONPREFIX= v DISTVERSION= 24.08 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org 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/polytope/Makefile b/science/polytope/Makefile index 2afc875ea600..51d29d283c38 100644 --- a/science/polytope/Makefile +++ b/science/polytope/Makefile @@ -1,10 +1,11 @@ PORTNAME= polytope -DISTVERSION= 0.7.3 +DISTVERSION= 0.7.4 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Library for generating Voronoi and Voronoi-like tessellations -WWW= https://github.com/pbtoast/polytope +WWW= https://github.com/LLNL/polytope LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE @@ -16,11 +17,13 @@ USES= cmake:testing USE_LDCONFIG= yes USE_GITHUB= yes -GH_ACCOUNT= pbtoast +GH_ACCOUNT= LLNL + +CXXFLAGS+= -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_NONE # prevent hardening issues with libc++, see https://github.com/LLNL/polytope/issues/24 CMAKE_ON= BUILD_SHARED_LIBS CMAKE_OFF= TESTING -CMAKE_TESTING_ON= TESTING # 1 test is known to fail, see https://github.com/pbtoast/polytope/issues/18 +CMAKE_TESTING_ON= TESTING OPTIONS_DEFINE= SILO OPTIONS_DEFAULT= SILO @@ -29,4 +32,6 @@ SILO_DESC= Use SILO reader/writer SILO_CMAKE_BOOL= USE_SILO SILO_LIB_DEPENDS= libsiloh5.so:science/silo +# tests as of 0.7.4: 96% tests passed, 1 tests failed out of 28 + .include <bsd.port.mk> diff --git a/science/polytope/distinfo b/science/polytope/distinfo index 26dcd6cce169..f546123336ae 100644 --- a/science/polytope/distinfo +++ b/science/polytope/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1686150327 -SHA256 (pbtoast-polytope-0.7.3_GH0.tar.gz) = f32817b44d2a3b98407531980b89d0a31b0c14b8b30de37a6a7bc6ec91e48bf1 -SIZE (pbtoast-polytope-0.7.3_GH0.tar.gz) = 6854100 +TIMESTAMP = 1762944488 +SHA256 (LLNL-polytope-0.7.4_GH0.tar.gz) = a1901b0feaf3c4d3660766e8a6c325c0fe1fcaeb236b5ae95c8d139c386147c8 +SIZE (LLNL-polytope-0.7.4_GH0.tar.gz) = 6854579 diff --git a/science/polytope/files/patch-src_CMakeLists.txt b/science/polytope/files/patch-src_CMakeLists.txt index 731eabaac985..311c5e49463a 100644 --- a/science/polytope/files/patch-src_CMakeLists.txt +++ b/science/polytope/files/patch-src_CMakeLists.txt @@ -1,8 +1,8 @@ - uses std::integer_sequence C++14 feature ---- src/CMakeLists.txt.orig 2022-12-03 08:18:04 UTC +--- src/CMakeLists.txt.orig 2025-10-29 23:24:46 UTC +++ src/CMakeLists.txt -@@ -17,7 +17,7 @@ endif() +@@ -17,7 +17,7 @@ if (HAVE_TRIANGLE) # TriangleTessellator and triangle source if (HAVE_TRIANGLE) list(APPEND TESSELLATOR_SOURCES TriangleTessellator.cc) @@ -11,12 +11,3 @@ #set(TRIANGLE_LIB triangle PARENT_SCOPE) set(TRIANGLE_LIB triangle) set_target_properties(triangle PROPERTIES -@@ -49,7 +49,7 @@ endif() - file(GLOB HEADERS *.hh) - list(APPEND HEADERS "${PROJECT_BINARY_DIR}/polytope.hh") - --add_library(polytope STATIC -+add_library(polytope - ${TESSELLATOR_SOURCES} ${IO_SOURCES} ErrorHandler.cc - polytope_internal_abort.cc) - diff --git a/science/polytope/pkg-plist b/science/polytope/pkg-plist index 1a3ad063500d..b31319b1417f 100644 --- a/science/polytope/pkg-plist +++ b/science/polytope/pkg-plist @@ -42,4 +42,7 @@ include/polytope/polytope_write_OOGL.hh include/polytope/removeElements.hh include/polytope/simplifyPLCfacets.hh include/polytope/snapToBoundary.hh +lib/cmake/polytope-config.cmake +lib/cmake/polytope-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/polytope-targets.cmake lib/libpolytope.so 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-arbor/Makefile b/science/py-arbor/Makefile index c7bf63b0a7b6..bd106edf2ffd 100644 --- a/science/py-arbor/Makefile +++ b/science/py-arbor/Makefile @@ -1,6 +1,6 @@ PORTNAME= arbor DISTVERSIONPREFIX= v -DISTVERSION= 0.10.1 +DISTVERSION= 0.11.0 CATEGORIES= science PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -16,9 +16,10 @@ BUILD_DEPENDS= gmake:devel/gmake \ pybind11>0:devel/pybind11 \ nlohmann-json>0:devel/nlohmann-json LIB_DEPENDS= libarbor.so:science/arbor +RUN_DEPENDS= ${PYNUMPY} USES= cmake compiler:c++17-lang localbase:ldflags python -USE_PYTHON= flavors pytest # tests fail to run, see https://github.com/arbor-sim/arbor/issues/2395 +USE_PYTHON= flavors unittest # tests fail to run, see https://github.com/arbor-sim/arbor/issues/2395 USE_GITHUB= yes GH_ACCOUNT= arbor-sim @@ -29,9 +30,11 @@ CMAKE_ARGS= -DPython3_EXECUTABLE=${PYTHON_CMD} \ -DARB_PYTHON_LIB_PATH=${PYTHONPREFIX_SITELIBDIR} CXXFLAGS+= -fPIC +CXXFLAGS+= -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_NONE # prevent hardening issues with libc++, see https://github.com/arbor-sim/arbor/issues/2484 TEST_WRKSRC= ${WRKSRC}/test/unit_distributed -TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +TEST_ENV= ${MAKE_ENV} \ + PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} BINARY_ALIAS= make=${GMAKE} @@ -41,7 +44,7 @@ post-patch: post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/arbor/_arbor${PYTHON_TAG}.so -do-test: # some tests fail with 'make'-related errors +do-test: # tests fail to run due to a bug with nadling complex CXXFLAGS in the test runner, see https://github.com/arbor-sim/arbor/issues/2395 @cd ${BUILD_WRKSRC} && \ ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -munittest discover -v -s ${WRKSRC} diff --git a/science/py-arbor/distinfo b/science/py-arbor/distinfo index 4e401f03e334..a707d5b502e0 100644 --- a/science/py-arbor/distinfo +++ b/science/py-arbor/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1724740903 -SHA256 (arbor-sim-arbor-v0.10.1_GH0.tar.gz) = 6a9a209dc20ab6edcf9847a70b0b4dbabf0c0d3c7e6e29b5bec7c00de9d7b8ae -SIZE (arbor-sim-arbor-v0.10.1_GH0.tar.gz) = 10159032 +TIMESTAMP = 1762102979 +SHA256 (arbor-sim-arbor-v0.11.0_GH0.tar.gz) = 6df68b308dd629df993eda40319676cd43407ae211d0846100b0cf42e8c9ad22 +SIZE (arbor-sim-arbor-v0.11.0_GH0.tar.gz) = 12511038 diff --git a/science/py-arbor/files/patch-CMakeLists.txt b/science/py-arbor/files/patch-CMakeLists.txt index b8d189dbb2b4..e8b0d0cf39e4 100644 --- a/science/py-arbor/files/patch-CMakeLists.txt +++ b/science/py-arbor/files/patch-CMakeLists.txt @@ -1,14 +1,20 @@ ---- CMakeLists.txt.orig 2024-08-09 10:22:00 UTC +--- CMakeLists.txt.orig 2025-04-24 10:33:03 UTC +++ CMakeLists.txt -@@ -1,3 +1,7 @@ +@@ -1,3 +1,13 @@ +cmake_minimum_required(VERSION 3.19) + +find_package(Python3 ${arb_py_version} COMPONENTS Interpreter Development REQUIRED) ++find_package(pybind11 REQUIRED) ++ ++set(CMAKE_CXX_STANDARD 20) ++set(CMAKE_CUDA_STANDARD 20) ++set(CMAKE_CXX_STANDARD_REQUIRED ON) ++set(CMAKE_CXX_EXTENSIONS OFF) + include(GNUInstallDirs) - set(PYBIND11_CPP_STANDARD -std=c++17) -@@ -84,14 +88,14 @@ endif() + set(pyarb_source +@@ -73,14 +83,14 @@ endif() endif() # For unit tests on C++ side of Python wrappers @@ -26,10 +32,9 @@ # Set the installation path -@@ -121,5 +125,4 @@ install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/__init__.py +@@ -122,4 +132,4 @@ install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/__init__.py install(TARGETS pyarb DESTINATION ${_python_module_install_path}) install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/__init__.py DESTINATION ${_python_module_install_path}) --install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/stubs/arbor/ DESTINATION ${_python_module_install_path}) -install(FILES ${PROJECT_SOURCE_DIR}/VERSION ${PROJECT_SOURCE_DIR}/README.md ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${_python_module_install_path}) -+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../VERSION DESTINATION ${_python_module_install_path}) ++install(FILES ${PROJECT_SOURCE_DIR}/../VERSION DESTINATION ${_python_module_install_path}) diff --git a/science/py-arbor/files/patch-pyarb.hpp b/science/py-arbor/files/patch-pyarb.hpp new file mode 100644 index 000000000000..ab3bb94cf316 --- /dev/null +++ b/science/py-arbor/files/patch-pyarb.hpp @@ -0,0 +1,11 @@ +--- pyarb.hpp.orig 2025-11-02 17:35:26 UTC ++++ pyarb.hpp +@@ -19,7 +19,7 @@ static_assert((PYBIND11_VERSION_HEX >= 0x02080100) + #define PB11_ERR(M, m, p) "Required version of pybind11 is 2.8.1 <= version < 3.0.0 Found " mk_ver(M, m, p) + static_assert((PYBIND11_VERSION_HEX >= 0x02080100) + && +- (PYBIND11_VERSION_HEX < 0x03000000), ++ (PYBIND11_VERSION_HEX < 0x04000000), + PB11_ERR(PYBIND11_VERSION_MAJOR, PYBIND11_VERSION_MINOR, PYBIND11_VERSION_PATCH)); + #undef PB11_ERR + #undef mk_ver 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-chempy/Makefile b/science/py-chempy/Makefile index f8038dcc66d8..c305778ba14d 100644 --- a/science/py-chempy/Makefile +++ b/science/py-chempy/Makefile @@ -1,6 +1,5 @@ PORTNAME= chempy -DISTVERSION= 0.9.0 -PORTREVISION= 3 +DISTVERSION= 0.10.1 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -16,13 +15,14 @@ PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dot2tex>=2.11.3:print/dot2tex@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.3:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}PuLP>=1.6.8:math/py-PuLP@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pyneqsys>=0.5.5:math/py-pyneqsys@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pyneqsys>=0.5.7:math/py-pyneqsys@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyodesys>=0.14.1:math/py-pyodesys@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyparsing>=2.0.3:devel/py-pyparsing@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}quantities>=0.12.1:science/py-quantities@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.0.1:science/py-scipy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}sym>=0.3.4:math/py-sym@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}sympy>=1.1.1:math/py-sympy@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}sym>=0.3.7:math/py-sym@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}sympy>=1.1.1:math/py-sympy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tabulate>0:devel/py-tabulate@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}black>0:devel/py-black@${PY_FLAVOR} \ @@ -40,7 +40,7 @@ CONFLICTS_INSTALL= ${PYTHON_PKGNAMEPREFIX}pymol # https://github.com/schrodinger OPTIONS_DEFINE= EXTRAS OPTIONS_DEFAULT= EXTRAS -EXTRAS_DESC= Install optional dependencies for additional functionality +EXTRAS_DESC= Install optional dependencies for additional functionality # this seems to be a copy of what extras pyodesys requires, see https://github.com/bjodah/chempy/issues/241 EXTRAS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}appdirs>0:devel/py-appdirs@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}bokeh>=0.13.0:www/py-bokeh@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipywidgets>0:devel/py-ipywidgets@${PY_FLAVOR} \ diff --git a/science/py-chempy/distinfo b/science/py-chempy/distinfo index 1ac919ccffb9..0cd0f9b75f33 100644 --- a/science/py-chempy/distinfo +++ b/science/py-chempy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1714020842 -SHA256 (chempy-0.9.0.tar.gz) = 3ba07d597fef672f3dea4c3ce81e64683f90afd263a7962a6d0db2ab8d9a0204 -SIZE (chempy-0.9.0.tar.gz) = 184714 +TIMESTAMP = 1761714393 +SHA256 (chempy-0.10.1.tar.gz) = 7112a2fe6cfe49730870de19e6061ff7f174a7d626a64244ab0505afa591cba0 +SIZE (chempy-0.10.1.tar.gz) = 428230 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-dwave-hybrid/Makefile b/science/py-dwave-hybrid/Makefile index e4f3e04da77e..9b248e914cc8 100644 --- a/science/py-dwave-hybrid/Makefile +++ b/science/py-dwave-hybrid/Makefile @@ -24,7 +24,7 @@ PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>5:devel/py-click@${PY_FLAVOR} \ BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} -USES= python:3.9+ +USES= python USE_PYTHON= distutils autoplist unittest # several tests fail, see https://github.com/dwavesystems/dwave-hybrid/issues/276 USE_GITHUB= yes diff --git a/science/py-dwave-inspector/Makefile b/science/py-dwave-inspector/Makefile index b583ab95b573..cb10191752ba 100644 --- a/science/py-dwave-inspector/Makefile +++ b/science/py-dwave-inspector/Makefile @@ -19,7 +19,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.10.0:science/py-dimod@${PY_FLAVOR} ${PYTHON_PKGNAMEPREFIX}werkzeug>0:www/py-werkzeug@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}vcrpy>0:devel/py-vcrpy@${PY_FLAVOR} -USES= python:3.9+ +USES= python USE_PYTHON= distutils cython unittest # few tests fail, see https://github.com/dwavesystems/dwave-inspector/issues/151 USE_GITHUB= yes diff --git a/science/py-dwavebinarycsp/Makefile b/science/py-dwavebinarycsp/Makefile index d32f01053748..b4c36dc582a3 100644 --- a/science/py-dwavebinarycsp/Makefile +++ b/science/py-dwavebinarycsp/Makefile @@ -18,7 +18,7 @@ BUILD_DEPENDS= ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} -USES= python:3.9+ +USES= python USE_PYTHON= distutils autoplist unittest USE_GITHUB= yes 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-esda/Makefile b/science/py-esda/Makefile index 7313b4b95a3c..8272b9cb7d24 100644 --- a/science/py-esda/Makefile +++ b/science/py-esda/Makefile @@ -1,5 +1,5 @@ PORTNAME= esda -PORTVERSION= 2.5.1 +PORTVERSION= 2.8.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,14 +15,25 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=61.0:devel/py-setuptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}setuptools-scm>=6.2:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}libpysal>=0:science/py-libpysal@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pandas>=1.4,1:math/py-pandas@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.0:science/py-scikit-learn@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=1.9:science/py-scipy@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geopandas>=0.14:graphics/py-geopandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}libpysal>=4.12:science/py-libpysal@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.26,1:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=2.1,1:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.4:science/py-scikit-learn@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.12:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}shapely>=2.1:devel/py-shapely@${PY_FLAVOR} -USES= python +USES= python:3.11+ USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes +OPTIONS_DEFINE= PLUS +PLUS_DESC= Extra features + +PLUS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.8:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numba>=0.58:devel/py-numba@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}rtree>=1.1:devel/py-rtree@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}seaborn>=0.12:math/py-seaborn@${PY_FLAVOR} + .include <bsd.port.mk> diff --git a/science/py-esda/distinfo b/science/py-esda/distinfo index 1100a1c0265a..1e82a6736485 100644 --- a/science/py-esda/distinfo +++ b/science/py-esda/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1698341073 -SHA256 (esda-2.5.1.tar.gz) = b1f0ac023b3a55dbdbad34a98eae6af2c7d2b3cc7a14ea884dfef51819c04c28 -SIZE (esda-2.5.1.tar.gz) = 44173327 +TIMESTAMP = 1759774725 +SHA256 (esda-2.8.0.tar.gz) = e86da2985d75bff31f351749491373411dc87fd97549006111c105173d25425c +SIZE (esda-2.8.0.tar.gz) = 26452351 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-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-h5py/Makefile b/science/py-h5py/Makefile index bd765b3986bd..64ce1e01a6f5 100644 --- a/science/py-h5py/Makefile +++ b/science/py-h5py/Makefile @@ -1,5 +1,5 @@ PORTNAME= h5py -PORTVERSION= 3.13.0 +PORTVERSION= 3.15.1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,17 +12,17 @@ WWW= https://www.h5py.org/ \ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/licenses/license.txt -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pkgconfig>=0,1:devel/py-pkgconfig@${PY_FLAVOR} \ +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.25.0,1<3,1:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pkgconfig>=1.5.5,1:devel/py-pkgconfig@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}setuptools>=61:devel/py-setuptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} LIB_DEPENDS= libhdf5.so:science/hdf5 -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.19.3,1:math/py-numpy@${PY_FLAVOR} -TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mpi4py>=3.1.1:net/py-mpi4py@${PY_FLAVOR} \ +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.21.2,1:math/py-numpy@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mpi4py>=3.1.2:net/py-mpi4py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tables>=3.4.4:devel/py-tables@${PY_FLAVOR} -USES= localbase pkgconfig python:3.9+ -USE_PYTHON= autoplist concurrent cython pep517 pytest +USES= localbase pkgconfig python +USE_PYTHON= autoplist concurrent cython3 pep517 pytest TEST_ENV= PYTHONPATH=${STAGEDIR}${PYTHON_SITELIBDIR} TEST_WRKSRC= ${STAGEDIR}${PYTHON_SITELIBDIR} diff --git a/science/py-h5py/distinfo b/science/py-h5py/distinfo index 5f1c739655f7..2a710069543b 100644 --- a/science/py-h5py/distinfo +++ b/science/py-h5py/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1739962484 -SHA256 (h5py-3.13.0.tar.gz) = 1870e46518720023da85d0895a1960ff2ce398c5671eac3b1a41ec696b7105c3 -SIZE (h5py-3.13.0.tar.gz) = 414876 +TIMESTAMP = 1761446742 +SHA256 (h5py-3.15.1.tar.gz) = c86e3ed45c4473564de55aa83b6fc9e5ead86578773dfbd93047380042e26b69 +SIZE (h5py-3.15.1.tar.gz) = 426236 diff --git a/science/py-h5py/files/patch-pyproject.toml b/science/py-h5py/files/patch-pyproject.toml index 3651460fab6a..5ab8a3db7945 100644 --- a/science/py-h5py/files/patch-pyproject.toml +++ b/science/py-h5py/files/patch-pyproject.toml @@ -1,11 +1,21 @@ ---- pyproject.toml.orig 2024-08-21 14:35:26 UTC +--- pyproject.toml.orig 2025-10-13 12:03:55 UTC +++ pyproject.toml -@@ -1,7 +1,7 @@ requires = [ - [build-system] - requires = [ - "Cython >=0.29.31,<4", -- "numpy >=2.0.0, <3", -+ "numpy", - "pkgconfig", - "setuptools >=61", +@@ -5,7 +5,7 @@ requires = [ + "Cython >=3.0.0, <4", + "numpy >=1.25.0, <3", + "pkgconfig >=1.5.5", +- "setuptools >=77.0.1", ++ "setuptools >=61", ] + # use an in-tree build backend, extending setuptools.build_meta + build-backend = "backend" +@@ -22,8 +22,7 @@ maintainers = [ + {name = "Thomas Kluyver", email = "thomas@kluyver.me.uk"}, + {name = "Thomas A Caswell", email = "tcaswell@bnl.gov"}, + ] +-license = "BSD-3-Clause" +-license-files = ["LICENSE", "lzf/LICENSE.txt", "licenses/*"] ++license = {text = "BSD-3-Clause"} + classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers", diff --git a/science/py-h5py/pkg-plist b/science/py-h5py/pkg-plist index bd294d4fe60b..515203f360eb 100644 --- a/science/py-h5py/pkg-plist +++ b/science/py-h5py/pkg-plist @@ -22,6 +22,7 @@ %%PORTDOCS%%%%DOCSDIR%%/special.rst %%PORTDOCS%%%%DOCSDIR%%/strings.rst %%PORTDOCS%%%%DOCSDIR%%/swmr.rst +%%PORTDOCS%%%%DOCSDIR%%/threads.rst %%PORTDOCS%%%%DOCSDIR%%/vds.rst %%PORTDOCS%%%%DOCSDIR%%/whatsnew/2.0.rst %%PORTDOCS%%%%DOCSDIR%%/whatsnew/2.1.rst @@ -41,6 +42,8 @@ %%PORTDOCS%%%%DOCSDIR%%/whatsnew/3.11.rst %%PORTDOCS%%%%DOCSDIR%%/whatsnew/3.12.rst %%PORTDOCS%%%%DOCSDIR%%/whatsnew/3.13.rst +%%PORTDOCS%%%%DOCSDIR%%/whatsnew/3.14.rst +%%PORTDOCS%%%%DOCSDIR%%/whatsnew/3.15.rst %%PORTDOCS%%%%DOCSDIR%%/whatsnew/3.2.rst %%PORTDOCS%%%%DOCSDIR%%/whatsnew/3.3.rst %%PORTDOCS%%%%DOCSDIR%%/whatsnew/3.4.rst diff --git a/science/py-hiphive/Makefile b/science/py-hiPhive/Makefile index f81c2e5085a0..32e729c27d4c 100644 --- a/science/py-hiphive/Makefile +++ b/science/py-hiPhive/Makefile @@ -1,17 +1,20 @@ -PORTNAME= hiphive -DISTVERSION= 1.2 -PORTREVISION= 2 +PORTNAME= hiPhive +DISTVERSION= 1.5 CATEGORIES= science python -MASTER_SITES= PYPI +#MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +#DISTNAME= ${PORTNAME:tl}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= High-order force constants for the masses -WWW= https://hiphive.materialsmodeling.org/ +WWW= https://hiphive.materialsmodeling.org/ \ + https://gitlab.com/materials-modeling/hiphive/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numba>=0.55:devel/py-numba@${PY_FLAVOR} \ @@ -24,8 +27,17 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}trainstation>=0.2:science/py-trainstation@${PY_FLAVOR} USES= python -USE_PYTHON= distutils autoplist pytest # tests fail due to the numba bug: https://github.com/numba/numba/issues/9130 +USE_PYTHON= pep517 autoplist pytest # tests fail due to the numba bug: https://github.com/numba/numba/issues/9130 + +USE_GITLAB= yes +GL_ACCOUNT= materials-modeling +GL_PROJECT= ${PORTNAME:tl} + +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +TEST_WRKSRC= ${WRKSRC}/tests NO_ARCH= yes +# tests as of 1.5: 102 passed, 4 warnings, 1 error in 90.96s (0:01:30), see https://gitlab.com/materials-modeling/hiphive/-/issues/578 + .include <bsd.port.mk> diff --git a/science/py-hiPhive/distinfo b/science/py-hiPhive/distinfo new file mode 100644 index 000000000000..94bbbd25b014 --- /dev/null +++ b/science/py-hiPhive/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1761708372 +SHA256 (hiphive-1.5.tar.bz2) = d621600f453f0172db938bb22124ed9128d8bce6ebcfff24345928371e72e466 +SIZE (hiphive-1.5.tar.bz2) = 1892547 diff --git a/science/py-hiphive/pkg-descr b/science/py-hiPhive/pkg-descr index 34337fd0cef4..34337fd0cef4 100644 --- a/science/py-hiphive/pkg-descr +++ b/science/py-hiPhive/pkg-descr diff --git a/science/py-hiphive/distinfo b/science/py-hiphive/distinfo deleted file mode 100644 index 70ba8046568e..000000000000 --- a/science/py-hiphive/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1691814711 -SHA256 (hiphive-1.2.tar.gz) = af1be045131e0d2ccfae58d513d2b6c7f3369dbe56c916e31c36d15c7c9394eb -SIZE (hiphive-1.2.tar.gz) = 1472541 diff --git a/science/py-hoomd-blue/Makefile b/science/py-hoomd-blue/Makefile index ae4a5b71af2e..5fb3d5f92d35 100644 --- a/science/py-hoomd-blue/Makefile +++ b/science/py-hoomd-blue/Makefile @@ -1,6 +1,6 @@ PORTNAME= hoomd-blue DISTVERSIONPREFIX= v -DISTVERSION= 5.1.0 +DISTVERSION= 6.0.0 CATEGORIES= science # physics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -20,14 +20,14 @@ USE_GITHUB= yes GH_ACCOUNT= glotzerlab GH_TUPLE= glotzerlab:upp11:0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360:glotzerlab_upp11/hoomd/extern/upp11 \ - glotzerlab:nano-signal-slot:34223a4a7e97f8e114ef007e5360cf7a71265da3:glotzerlab_nano_signal_slot/hoomd/extern/nano-signal-slot \ + glotzerlab:nano-signal-slot:8d13689:glotzerlab_nano_signal_slot/hoomd/extern/nano-signal-slot \ glotzerlab:quickhull:1ffbc6f884ea1da89e104a5996cf8a726db673d5:glotzerlab_quickhull/hoomd/extern/quickhull \ - glotzerlab:HIP:d211f99eebb3637b6840f310f8797abb25012c18:glotzerlab_HIP/hoomd/extern/HIP \ - glotzerlab:hipCUB:c70e19332a8402049b3359b409e50220a759c42d:glotzerlab_hipCUB/hoomd/extern/hipCUB \ + glotzerlab:HIP:db753e4:glotzerlab_HIP/hoomd/extern/HIP \ + glotzerlab:hipCUB:64d8adf:glotzerlab_hipCUB/hoomd/extern/hipCUB \ mphowardlab:neighbor:ba0f06869b766066a7068852fa3b8c5fa746f71f:mphowardlab_neighbor/hoomd/extern/neighbor \ - mphowardlab:hipper:b6da049a516ada03e4e1b66ca6b4c2c7c9668595:mphowardlab_hipper/hoomd/extern/hipper \ + mphowardlab:hipper:076059b:mphowardlab_hipper/hoomd/extern/hipper \ glotzerlab:hoomd-examples:94a5b52d159bc7c07e2650e31b429cef55384542:glotzerlab_hoomd_examples/sphinx-doc/tutorial \ - glotzerlab:OpenRAND:92dc12a23dff2d0aa3545f749d1c013677b9a87e:glotzerlab_OpenRAND/hoomd/extern/OpenRAND \ + glotzerlab:OpenRAND:92dc12a:glotzerlab_OpenRAND/hoomd/extern/OpenRAND \ mphowardlab:hipper:b6da049a516ada03e4e1b66ca6b4c2c7c9668595:mphowardlab_hipper/hoomd/extern/hipper SHEBANG_GLOB= *.sh @@ -58,7 +58,10 @@ TBB_DESC= Enable support for Threading Building Blocks (TBB) TBB_CMAKE_BOOL= ENABLE_TBB TBB_LIB_DEPENDS= libtbb.so:devel/onetbb -# the test mpi-test_communication requires excessive resources, see https://github.com/glotzerlab/hoomd-blue/issues/1396 +# tests as of 6.0.0: 97% tests passed, 2 tests failed out of 67 +# The following tests FAILED: +# 18 - mpi-test_load_balancer (Failed) +# 35 - mpi-test_communication (Failed) .include <bsd.port.pre.mk> diff --git a/science/py-hoomd-blue/distinfo b/science/py-hoomd-blue/distinfo index 3348d53d200c..6931b40814ac 100644 --- a/science/py-hoomd-blue/distinfo +++ b/science/py-hoomd-blue/distinfo @@ -1,21 +1,21 @@ -TIMESTAMP = 1740212206 -SHA256 (glotzerlab-hoomd-blue-v5.1.0_GH0.tar.gz) = 292d0297c41eeeaf7b7933bffd9dcd1469ca0c009929a257dac396ecd2bad899 -SIZE (glotzerlab-hoomd-blue-v5.1.0_GH0.tar.gz) = 2780980 +TIMESTAMP = 1763921144 +SHA256 (glotzerlab-hoomd-blue-v6.0.0_GH0.tar.gz) = 10e0c681dbd4195aeba66f6873e273b7859e61e647523d2fb2c1fcd1e635b696 +SIZE (glotzerlab-hoomd-blue-v6.0.0_GH0.tar.gz) = 2789144 SHA256 (glotzerlab-upp11-0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360_GH0.tar.gz) = 759695139bddae1d8a7cd52c967b856d6debf28fb37ea177f78c4434e2b210a8 SIZE (glotzerlab-upp11-0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360_GH0.tar.gz) = 21058 -SHA256 (glotzerlab-nano-signal-slot-34223a4a7e97f8e114ef007e5360cf7a71265da3_GH0.tar.gz) = d15030482c82d9e4a99c2f67d8ef23b33cc318dd48ac0f8e804c6d4750f27ff4 -SIZE (glotzerlab-nano-signal-slot-34223a4a7e97f8e114ef007e5360cf7a71265da3_GH0.tar.gz) = 4748 +SHA256 (glotzerlab-nano-signal-slot-8d13689_GH0.tar.gz) = 1f29012e0c211fe5c25714fbec858b8f29c3070b75bac893332b65ed46e3cfaa +SIZE (glotzerlab-nano-signal-slot-8d13689_GH0.tar.gz) = 4752 SHA256 (glotzerlab-quickhull-1ffbc6f884ea1da89e104a5996cf8a726db673d5_GH0.tar.gz) = 55c87e78bf990509ff35e3e039213ca6e3890ce988c2891647d65079696ae3a9 SIZE (glotzerlab-quickhull-1ffbc6f884ea1da89e104a5996cf8a726db673d5_GH0.tar.gz) = 16242 -SHA256 (glotzerlab-HIP-d211f99eebb3637b6840f310f8797abb25012c18_GH0.tar.gz) = badcb27eb7d540a668877dd193aba529755d5f69c8e6411ee495668984640e5c -SIZE (glotzerlab-HIP-d211f99eebb3637b6840f310f8797abb25012c18_GH0.tar.gz) = 898870 -SHA256 (glotzerlab-hipCUB-c70e19332a8402049b3359b409e50220a759c42d_GH0.tar.gz) = f3dbd921ea8c5fe9068d6d9e6e9112c11c7e18488169ce48423d9fdb014536c6 -SIZE (glotzerlab-hipCUB-c70e19332a8402049b3359b409e50220a759c42d_GH0.tar.gz) = 110500 +SHA256 (glotzerlab-HIP-db753e4_GH0.tar.gz) = a9cfe87ef06019891506e633d9ac0b8f52414ac1e5e4342d061963cbecdd1d7c +SIZE (glotzerlab-HIP-db753e4_GH0.tar.gz) = 897698 +SHA256 (glotzerlab-hipCUB-64d8adf_GH0.tar.gz) = 0709bc19af69bfed5c711833138bdede78e4e162e3462c7a60985f1555e0d155 +SIZE (glotzerlab-hipCUB-64d8adf_GH0.tar.gz) = 110322 SHA256 (mphowardlab-neighbor-ba0f06869b766066a7068852fa3b8c5fa746f71f_GH0.tar.gz) = 089129a1539d8e993f725017f1aadc60f9e40116e8a65dfbe70b0df9ac2d7cf3 SIZE (mphowardlab-neighbor-ba0f06869b766066a7068852fa3b8c5fa746f71f_GH0.tar.gz) = 49039 SHA256 (mphowardlab-hipper-b6da049a516ada03e4e1b66ca6b4c2c7c9668595_GH0.tar.gz) = c64a484884eaab3eb9fd8f7b27b144a7bfadfeab101e95d82bc2a6f7e4fb7cec SIZE (mphowardlab-hipper-b6da049a516ada03e4e1b66ca6b4c2c7c9668595_GH0.tar.gz) = 20228 SHA256 (glotzerlab-hoomd-examples-94a5b52d159bc7c07e2650e31b429cef55384542_GH0.tar.gz) = f685da65a32566036476a33740b45884bce58798e857d53689d3da20e928436c SIZE (glotzerlab-hoomd-examples-94a5b52d159bc7c07e2650e31b429cef55384542_GH0.tar.gz) = 5969001 -SHA256 (glotzerlab-OpenRAND-92dc12a23dff2d0aa3545f749d1c013677b9a87e_GH0.tar.gz) = a84657d9ac24083c1aef3d883927d5993270697af69a04f616227f9077eb8e19 -SIZE (glotzerlab-OpenRAND-92dc12a23dff2d0aa3545f749d1c013677b9a87e_GH0.tar.gz) = 298040 +SHA256 (glotzerlab-OpenRAND-92dc12a_GH0.tar.gz) = f760eefd9027ee69a5976954a539a28b9ceb581ba089014cec56f6e72c0f6a7d +SIZE (glotzerlab-OpenRAND-92dc12a_GH0.tar.gz) = 298000 diff --git a/science/py-hoomd-blue/files/patch-hoomd_extern_nano-signal-slot_nano__signal__slot.hpp b/science/py-hoomd-blue/files/patch-hoomd_extern_nano-signal-slot_nano__signal__slot.hpp deleted file mode 100644 index cd3fce241f6d..000000000000 --- a/science/py-hoomd-blue/files/patch-hoomd_extern_nano-signal-slot_nano__signal__slot.hpp +++ /dev/null @@ -1,30 +0,0 @@ -Fix build with LLVM 19 - -/wrkdirs/usr/ports/science/py-hoomd-blue/work/hoomd-blue-4.9.0/hoomd/extern/nano-signal-slot/nano_signal_slot.hpp:46:45: -error: a template argument list is expected after a name prefixed by the template keyword [-Wmissing-template-arg-list-after-template-kw] - 46 | Observer::insert(Delegate::template bind (instance), this); - | ^ -/wrkdirs/usr/ports/science/py-hoomd-blue/work/hoomd-blue-4.9.0/hoomd/extern/nano-signal-slot/nano_signal_slot.hpp:87:45: -error: a template argument list is expected after a name prefixed by the template keyword [-Wmissing-template-arg-list-after-template-kw] - 87 | Observer::remove(Delegate::template bind (instance), this); - ---- hoomd/extern/nano-signal-slot/nano_signal_slot.hpp.orig 2016-07-13 20:06:52 UTC -+++ hoomd/extern/nano-signal-slot/nano_signal_slot.hpp -@@ -43,7 +43,7 @@ class Signal<RT(Args...)> : private Observer - template <typename L> - void connect(L* instance) - { -- Observer::insert(Delegate::template bind (instance), this); -+ Observer::insert(Delegate::bind (instance), this); - } - template <typename L> - void connect(L& instance) -@@ -84,7 +84,7 @@ class Signal<RT(Args...)> : private Observer - template <typename L> - void disconnect(L* instance) - { -- Observer::remove(Delegate::template bind (instance), this); -+ Observer::remove(Delegate::bind (instance), this); - } - template <typename L> - void disconnect(L& instance) diff --git a/science/py-hoomd-blue/pkg-plist b/science/py-hoomd-blue/pkg-plist index 004601c86f0c..6f2f97246186 100644 --- a/science/py-hoomd-blue/pkg-plist +++ b/science/py-hoomd-blue/pkg-plist @@ -57,6 +57,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/pair.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/step.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/union.py +%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/zetterling.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/conftest.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_boxmc.py @@ -77,6 +78,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_opp.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_step.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_union.py +%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_zetterling.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_quick_compress.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_scale.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_shape.py @@ -315,7 +317,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_cuda.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_cuda.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_host.h -%%NO_NOMPI%%%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_lib_config.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_lib_config.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_local_fft_config.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/mkl_single_interface.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/gsd.h @@ -461,6 +463,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/PairPotentialOPP.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/PairPotentialStep.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/PairPotentialUnion.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/PairPotentialZetterling.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeConvexPolygon.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeConvexPolyhedron.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeEllipsoid.h @@ -517,9 +520,11 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ComputeThermoHMATypes.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ComputeThermoTypes.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ConstantForceCompute.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ConstantForceComputeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ConstantForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/CosineSqAngleForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/CosineSqAngleForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/CosineSqAngleForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/CustomForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorBondFENE.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorBondHarmonic.h @@ -539,6 +544,8 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairExpandedMie.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairForceShiftedLJ.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairFourier.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairFrictionLJBase.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairFrictionLJVariants.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairGB.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairGauss.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairLJ.h @@ -552,25 +559,37 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairTWF.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairTable.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairWangFrenkel.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairYLZ.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairYukawa.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairZBL.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairZetterling.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorSpecialPairCoulomb.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorSpecialPairLJ.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorTersoff.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorWalls.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FIREEnergyMinimizer.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FIREEnergyMinimizerGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FIREEnergyMinimizerGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceComposite.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceCompositeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceCompositeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceDistanceConstraint.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceDistanceConstraintGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceDistanceConstraintGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FrictionPair.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FrictionPairGPU.cuh +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FrictionPairGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicAngleForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicAngleForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicAngleForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicDihedralForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicDihedralForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicDihedralForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicImproperForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicImproperForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicImproperForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HelfrichMeshForceCompute.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HelfrichMeshForceComputeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HelfrichMeshForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/IntegrationMethodTwoStep.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/IntegratorTwoStep.h @@ -581,28 +600,37 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ManifoldSphere.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ManifoldXYPlane.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ManifoldZCylinder.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MeshDynamicBondUpdater.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MeshForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MolecularForceCompute.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MolecularForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MuellerPlatheFlow.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MuellerPlatheFlowEnum.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MuellerPlatheFlowGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MuellerPlatheFlowGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborList.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListBinned.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUBinned.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUStencil.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUStencil.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUTree.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUTree.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListStencil.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListTree.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/OPLSDihedralForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/OPLSDihedralForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/OPLSDihedralForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PPPMForceCompute.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PPPMForceComputeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PPPMForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PairModulator.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PatchEnvelope.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PeriodicImproper.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PeriodicImproperForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PeriodicImproperForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PeriodicImproperForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialBond.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialBondGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialBondGPU.h @@ -623,6 +651,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialTersoffGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableAngleForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableAngleForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableAngleForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableDihedralForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableDihedralForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TriangleAreaConservationMeshForceCompute.h @@ -632,10 +661,14 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepBD.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepBDGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantPressure.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantPressureGPU.cuh +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantPressureGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantVolume.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantVolumeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantVolumeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepLangevin.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepLangevinBase.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepLangevinGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepLangevinGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepNVTAlchemy.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepRATTLEBD.h @@ -648,6 +681,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepRATTLENVEGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepRATTLENVEGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/VolumeConservationMeshForceCompute.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/VolumeConservationMeshForceComputeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/VolumeConservationMeshForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/VolumeConservationMeshParameters.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/WallData.h @@ -728,6 +762,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/md/nlist.py %%PYTHON_SITELIBDIR%%/hoomd/md/pair/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/md/pair/aniso.py +%%PYTHON_SITELIBDIR%%/hoomd/md/pair/friction.py %%PYTHON_SITELIBDIR%%/hoomd/md/pair/pair.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/aniso_forces_and_energies.json @@ -756,6 +791,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_kernel_parameters.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_manifolds.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_meshpotential.py +%%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_meshupdater.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_meta_wall_list.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_methods.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_minimize_fire.py @@ -773,6 +809,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_update_group_dof.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_wall_data.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_wall_potential.py +%%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_ylz.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_zero_momentum.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/true_pair_list.json %%PYTHON_SITELIBDIR%%/hoomd/md/special_pair.py diff --git a/science/py-icet/Makefile b/science/py-icet/Makefile index 2a01864fa3b9..9797bd59dace 100644 --- a/science/py-icet/Makefile +++ b/science/py-icet/Makefile @@ -1,5 +1,5 @@ PORTNAME= icet -DISTVERSION= 3.1 +DISTVERSION= 3.2 CATEGORIES= science # chemistry, physics #MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -16,10 +16,10 @@ BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PYTHON_PKGNAMEPREFIX}pybind11>0:devel/py-pybind11@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}numba>0:devel/py-numba@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numba>=0.55:devel/py-numba@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0.23:math/py-pandas@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.0.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spglib>=1.12.0:science/py-spglib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}trainstation>=1.1:science/py-trainstation@${PY_FLAVOR} @@ -28,13 +28,16 @@ USE_PYTHON= pep517 autoplist pytest USE_GITLAB= yes GL_ACCOUNT= materials-modeling -GL_TAGNAME= 3.1 TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +TEST_WRKSRC= ${WRKSRC}/tests post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/_icet.cpython-311.so -# tests fail to run, see https://gitlab.com/materials-modeling/icet/-/issues/623 +pre-test: # this test causes the whole testsuite to hard-fail in the beginning for some reason + @${RM} -rf ${TEST_WRKSRC}/unittest/test_mchammer/test_site_occupancy_observer.py + +# tests as of 3.2: 33 failed, 794 passed, 5 warnings in 166.64s (0:02:46), see https://gitlab.com/materials-modeling/icet/-/issues/630 .include <bsd.port.mk> diff --git a/science/py-icet/distinfo b/science/py-icet/distinfo index 27b719b500bf..0480aa1107b7 100644 --- a/science/py-icet/distinfo +++ b/science/py-icet/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1758905344 -SHA256 (icet-3.1.tar.bz2) = b942fa3001fd53095cca9e19f4fdcea7c3716a69cf0bb2f4e735c8b997f1de5b -SIZE (icet-3.1.tar.bz2) = 3740838 +TIMESTAMP = 1761704195 +SHA256 (icet-3.2.tar.bz2) = aea80945c2a100f6fa8f14004f0d4f570843ba4450154fe2eb4896251917b70c +SIZE (icet-3.2.tar.bz2) = 3863159 diff --git a/science/py-icet/files/patch-pyproject.toml b/science/py-icet/files/patch-pyproject.toml index f1953b314896..17fb311bb81b 100644 --- a/science/py-icet/files/patch-pyproject.toml +++ b/science/py-icet/files/patch-pyproject.toml @@ -1,4 +1,4 @@ ---- pyproject.toml.orig 2025-09-28 03:59:57 UTC +--- pyproject.toml.orig 2025-10-26 21:34:57 UTC +++ pyproject.toml @@ -1,6 +1,6 @@ requires = [ [build-system] @@ -8,3 +8,12 @@ "wheel", "pybind11>=2.10", ] +@@ -25,8 +25,6 @@ maintainers = [ + maintainers = [ + {name = "The icet developer team"} + ] +-license = "MPL-2.0" +-license-files = ["LICENSE"] + readme = "README.rst" + requires-python = ">=3.9" + keywords = ["chemistry", "physics", "scientific"] diff --git a/science/py-inequality/Makefile b/science/py-inequality/Makefile index cc8f4eea51b7..09cf630db61e 100644 --- a/science/py-inequality/Makefile +++ b/science/py-inequality/Makefile @@ -1,6 +1,5 @@ PORTNAME= inequality -PORTVERSION= 1.1.1 -PORTREVISION= 1 +PORTVERSION= 1.1.2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,12 +14,13 @@ LICENSE= BSD3CLAUSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=61.0:devel/py-setuptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}setuptools-scm>=6.2:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}libpysal>=4.5:science/py-libpysal@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.6:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}numpy>=1.23,1:math/py-numpy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=1.8:science/py-scipy@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}libpysal>=4.12:science/py-libpysal@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.8:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.26,1:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=2.1,1:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.12:science/py-scipy@${PY_FLAVOR} -USES= python +USES= python:3.11+ USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-inequality/distinfo b/science/py-inequality/distinfo index 4c4e22e9fc8a..e62122c7a0a1 100644 --- a/science/py-inequality/distinfo +++ b/science/py-inequality/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1738606495 -SHA256 (inequality-1.1.1.tar.gz) = a093aa58effc26a9152b021a02330be3b184053f5c1c35152c725f022c50395b -SIZE (inequality-1.1.1.tar.gz) = 3700846 +TIMESTAMP = 1752254567 +SHA256 (inequality-1.1.2.tar.gz) = 2010253c26cfe3745d36beb02aeff5503e1b21cb06e1d52aa7f13c37acd9adf1 +SIZE (inequality-1.1.2.tar.gz) = 2675815 diff --git a/science/py-libpysal/Makefile b/science/py-libpysal/Makefile index 43b12ba58113..51a39b19aa7a 100644 --- a/science/py-libpysal/Makefile +++ b/science/py-libpysal/Makefile @@ -1,6 +1,5 @@ PORTNAME= libpysal -PORTVERSION= 4.7.0 -PORTREVISION= 2 +PORTVERSION= 4.13.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,20 +12,34 @@ WWW= https://pysal.org/libpysal/ \ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=61.0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}setuptools-scm>=6.2:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}beautifulsoup>=0:www/py-beautifulsoup@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}Jinja2>=0:devel/py-Jinja2@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}numpy>=1.3,1:math/py-numpy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}packaging>=0:devel/py-packaging@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pandas>=0,1:math/py-pandas@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}platformdirs>=0:devel/py-platformdirs@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}requests>=0:www/py-requests@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=0.11:science/py-scipy@${PY_FLAVOR} - -USES= python +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}beautifulsoup>=4.10:www/py-beautifulsoup@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}geopandas>=0.10.0:graphics/py-geopandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.22,1:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}packaging>=22:devel/py-packaging@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=1.4,1:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}platformdirs>=2.0.2:devel/py-platformdirs@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>=2.27:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.1:science/py-scikit-learn@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.8:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}shapely>=2.0.1:devel/py-shapely@${PY_FLAVOR} + +USES= python:3.10+ 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/py-libpysal/distinfo b/science/py-libpysal/distinfo index ee7253480047..0763c6e35a3e 100644 --- a/science/py-libpysal/distinfo +++ b/science/py-libpysal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1669057943 -SHA256 (libpysal-4.7.0.tar.gz) = a4730688e2c8134930ff4de42d7be58e360c03904b859fa374dfd70dca1f93bf -SIZE (libpysal-4.7.0.tar.gz) = 2398742 +TIMESTAMP = 1744227170 +SHA256 (libpysal-4.13.0.tar.gz) = 71a07f7a2e705632862c15c51af5171a42391c874a7efd6711f06c7e4e9c6f53 +SIZE (libpysal-4.13.0.tar.gz) = 6713348 diff --git a/science/py-libpysal/files/patch-setup.py b/science/py-libpysal/files/patch-setup.py deleted file mode 100644 index c8415013de9b..000000000000 --- a/science/py-libpysal/files/patch-setup.py +++ /dev/null @@ -1,10 +0,0 @@ ---- setup.py.orig 2020-03-29 00:21:04 UTC -+++ setup.py -@@ -74,7 +74,6 @@ def setup_package(): - license="BSD", - py_modules=["libpysal"], - packages=find_packages(), -- setup_requires=["pytest-runner"], - tests_require=["pytest"], - keywords="spatial statistics", - classifiers=[ diff --git a/science/py-mne/Makefile b/science/py-mne/Makefile index 3f15411d9c98..bf89de5d9db3 100644 --- a/science/py-mne/Makefile +++ b/science/py-mne/Makefile @@ -1,5 +1,5 @@ PORTNAME= mne -PORTVERSION= 1.10.1 +PORTVERSION= 1.11.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -10,14 +10,13 @@ WWW= https://mne.tools/stable/ \ https://github.com/mne-tools/mne-python LICENSE= BSD3CLAUSE -LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}hatchling>0:devel/py-hatchling@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}hatch-vcs>0:devel/py-hatch-vcs@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}decorator>0:devel/py-decorator@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>0:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lazy_loader>=0.3:devel/py-lazy_loader@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.7:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.8:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pooch>=1.5:devel/py-pooch@${PY_FLAVOR} \ diff --git a/science/py-mne/distinfo b/science/py-mne/distinfo index f63a12725683..c24c3f5eff30 100644 --- a/science/py-mne/distinfo +++ b/science/py-mne/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1759525649 -SHA256 (mne-1.10.1.tar.gz) = a93e3d772d551e43ec5ddcd3495fffe0f98e3e384045bcd96497636e86a32a0b -SIZE (mne-1.10.1.tar.gz) = 7123187 +TIMESTAMP = 1763923010 +SHA256 (mne-1.11.0.tar.gz) = 0a89b8fc44133b81218a35cdcba74ad0f8ae2e265136249b365b9ce04864c688 +SIZE (mne-1.11.0.tar.gz) = 7152794 diff --git a/science/py-neo/Makefile b/science/py-neo/Makefile index af57025f1e56..87932cd97b3c 100644 --- a/science/py-neo/Makefile +++ b/science/py-neo/Makefile @@ -1,5 +1,5 @@ PORTNAME= neo -PORTVERSION= 0.14.2 +PORTVERSION= 0.14.3 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,12 +12,20 @@ WWW= https://neo.readthedocs.io/en/latest/ \ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}quantities>=0.16.1:science/py-quantities@${PY_FLAVOR} USES= python -USE_PYTHON= distutils autoplist concurrent pytest +USE_PYTHON= pep517 autoplist concurrent pytest + +TEST_ENV= ${MAKE_ENV} \ + PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} \ + DISPLAY=${DISPLAY} \ + XAUTHORITY=${XAUTHORITY} +TEST_WRKSRC= ${WRKSRC}/neo/test NO_ARCH= yes diff --git a/science/py-neo/distinfo b/science/py-neo/distinfo index 11e758623a41..656ae38760b3 100644 --- a/science/py-neo/distinfo +++ b/science/py-neo/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1759525621 -SHA256 (neo-0.14.2.tar.gz) = 76517503e114fffcc38aa3600c04dd8be48b1ee5e2c8162bc0db8fb92476811f -SIZE (neo-0.14.2.tar.gz) = 5067423 +TIMESTAMP = 1761805461 +SHA256 (neo-0.14.3.tar.gz) = 50d473fb9070d1728ec6fd72bdad16262b40f7c99df7ff5e8d927ebc2680b080 +SIZE (neo-0.14.3.tar.gz) = 5076523 diff --git a/science/py-neo/files/patch-pyproject.toml b/science/py-neo/files/patch-pyproject.toml new file mode 100644 index 000000000000..e5bbf1113b30 --- /dev/null +++ b/science/py-neo/files/patch-pyproject.toml @@ -0,0 +1,11 @@ +--- pyproject.toml.orig 2025-10-30 06:25:36 UTC ++++ pyproject.toml +@@ -36,7 +36,7 @@ download = "http://pypi.python.org/pypi/neo" + + + [build-system] +-requires = ["setuptools>=78.0.2"] ++requires = ["setuptools"] + build-backend = "setuptools.build_meta" + + [project.optional-dependencies] diff --git a/science/py-netCDF4/Makefile b/science/py-netCDF4/Makefile index 4058f7c0949e..c67bc700866e 100644 --- a/science/py-netCDF4/Makefile +++ b/science/py-netCDF4/Makefile @@ -5,7 +5,7 @@ MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:tl}-${DISTVERSION} -MAINTAINER= bofh@FreeBSD.org +MAINTAINER= ports@FreeBSD.org COMMENT= Python Interface to the NetCDF Library (versions 3 and 4) WWW= https://unidata.github.io/netcdf4-python/ diff --git a/science/py-nglview/Makefile b/science/py-nglview/Makefile index 02f126f60974..2d3e5fd808ba 100644 --- a/science/py-nglview/Makefile +++ b/science/py-nglview/Makefile @@ -1,5 +1,5 @@ PORTNAME= nglview -DISTVERSION= 3.1.2 +DISTVERSION= 4.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,8 +13,13 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}jupyter-packaging>=0.7.9:devel/py-jupyter-packaging@${PY_FLAVOR} \ ${PY_SETUPTOOLS} \ - ${PYTHON_PKGNAMEPREFIX}versioneer-518>0:devel/py-versioneer-518@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ipywidgets>=8:devel/py-ipywidgets@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}jupyterlab>=3:devel/py-jupyterlab@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}jupyterlab-widgets>0:devel/py-jupyterlab-widgets@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}notebook>=7:www/py-notebook@${PY_FLAVOR} \ + ${PYNUMPY} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ipywidgets>0:devel/py-ipywidgets@${PY_FLAVOR} USES= python diff --git a/science/py-nglview/distinfo b/science/py-nglview/distinfo index f9cc451d6e06..24a14400baef 100644 --- a/science/py-nglview/distinfo +++ b/science/py-nglview/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713599805 -SHA256 (nglview-3.1.2.tar.gz) = 7f672efa2b6ca0db34de968e5b5766b14b1b3dade212d2f8a083c600a11345ce -SIZE (nglview-3.1.2.tar.gz) = 5477602 +TIMESTAMP = 1761806359 +SHA256 (nglview-4.0.tar.gz) = 2c0cff2c5b1e2a0a72e3393087ce44ae0308524c5aa5f95357812d3edbc26e83 +SIZE (nglview-4.0.tar.gz) = 26194155 diff --git a/science/py-nglview/files/patch-pyproject.toml b/science/py-nglview/files/patch-pyproject.toml index 05acfb963d8a..267363cda32d 100644 --- a/science/py-nglview/files/patch-pyproject.toml +++ b/science/py-nglview/files/patch-pyproject.toml @@ -1,7 +1,11 @@ ---- pyproject.toml.orig 2023-08-01 09:06:19 UTC +--- pyproject.toml.orig 2025-10-02 14:50:35 UTC +++ pyproject.toml -@@ -1,3 +1,3 @@ - [build-system] --requires = ["jupyter_packaging~=0.7.9", "setuptools>=40.8.0", "wheel", "versioneer-518"] -+requires = ["jupyter_packaging", "setuptools>=40.8.0", "wheel", "versioneer-518"] +@@ -2,7 +2,7 @@ requires = [ + requires = [ + "jupyter_packaging>=0.7.9; python_version<'3.13'", + "jupyter_packaging>=0.12.2; python_version>='3.13'", +- "setuptools>=75.6.0", ++ "setuptools", + "wheel", + ] build-backend = "setuptools.build_meta" diff --git a/science/py-nibabel/Makefile b/science/py-nibabel/Makefile index 35a7a51932e5..755f4718340e 100644 --- a/science/py-nibabel/Makefile +++ b/science/py-nibabel/Makefile @@ -24,7 +24,7 @@ TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest-cov>0:devel/py-pytest-cov@${PY_FLAVO ${PYTHON_PKGNAMEPREFIX}pytest-xdist>0:devel/py-pytest-xdist@${PY_FLAVOR} TEST_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}pydicom>0:science/py-pydicom@${PY_FLAVOR} -USES= python:3.9+ +USES= python USE_PYTHON= pep517 concurrent autoplist pytest # 2 test fail, 1 error, see https://github.com/nipy/nibabel/issues/1386 NO_ARCH= yes 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-periodictable/Makefile b/science/py-periodictable/Makefile index 420e86cadd21..20aaeeb60dc4 100644 --- a/science/py-periodictable/Makefile +++ b/science/py-periodictable/Makefile @@ -1,22 +1,28 @@ PORTNAME= periodictable -DISTVERSION= 1.7.1 -PORTREVISION= 1 +DISTVERSIONPREFIX= v +DISTVERSION= 2.0.2 CATEGORIES= science python -MASTER_SITES= PYPI +#MASTER_SITES= PYPI # no tarball available PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Extensible periodic table of the elements pre-populated with data -WWW= https://periodictable.readthedocs.io/en/latest/ +WWW= https://periodictable.readthedocs.io/en/latest/ \ + https://github.com/python-periodictable/periodictable LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pyparsing>0:devel/py-pyparsing@${PY_FLAVOR} USES= python -USE_PYTHON= distutils autoplist pytest # 3 tests fail, see https://github.com/pkienzle/periodictable/issues/84 +USE_PYTHON= pep517 autoplist pytest # tests fail to run, see https://github.com/python-periodictable/periodictable/issues/106 + +USE_GITHUB= yes +GH_ACCOUNT= python-periodictable NO_ARCH= yes diff --git a/science/py-periodictable/distinfo b/science/py-periodictable/distinfo index 31b87009f74b..883867657320 100644 --- a/science/py-periodictable/distinfo +++ b/science/py-periodictable/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1720515377 -SHA256 (periodictable-1.7.1.tar.gz) = 43d7db7233d6b33962f83d79ea54f47c3b923d3e83403cbc03f58f353af4b52c -SIZE (periodictable-1.7.1.tar.gz) = 1003709 +TIMESTAMP = 1761805268 +SHA256 (python-periodictable-periodictable-v2.0.2_GH0.tar.gz) = 5a8aed4759e74dabb38fda0ecbe59b6f7fef42b0babf83f25d8dfaee3c6798f8 +SIZE (python-periodictable-periodictable-v2.0.2_GH0.tar.gz) = 934995 diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile index 3ec6ed90d710..79dbf1631966 100644 --- a/science/py-phonopy/Makefile +++ b/science/py-phonopy/Makefile @@ -1,6 +1,6 @@ PORTNAME= phonopy DISTVERSION= 2.42.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -26,7 +26,7 @@ RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}symfc>=1.1.6:science/py-symfc@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyyaml>=5.3:devel/py-pyyaml@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}nose>0:devel/py-nose@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}hiphive>0:science/py-hiphive@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}hiPhive>0:science/py-hiPive@${PY_FLAVOR} USES= python USE_PYTHON= pep517 cython autoplist pytest diff --git a/science/py-pygeodesy/Makefile b/science/py-pygeodesy/Makefile index 38999bdbee9d..3b01d8be019c 100644 --- a/science/py-pygeodesy/Makefile +++ b/science/py-pygeodesy/Makefile @@ -16,7 +16,7 @@ LICENSE= MIT BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} -USES= python:3.9+ zip +USES= python zip USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes 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/py-pysal/Makefile b/science/py-pysal/Makefile new file mode 100644 index 000000000000..8b1a1cf157ea --- /dev/null +++ b/science/py-pysal/Makefile @@ -0,0 +1,62 @@ +PORTNAME= pysal +PORTVERSION= 25.7 +CATEGORIES= science python +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= sunpoet@FreeBSD.org +COMMENT= Meta Package for PySAL - A library of spatial analysis functions +WWW= https://pysal.org/pysal/ \ + https://github.com/pysal/pysal + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=61.0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}setuptools-scm>=6.2:devel/py-setuptools-scm@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}access>=1.1.9:science/py-access@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}beautifulsoup>=4.10:www/py-beautifulsoup@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}esda>=2.7.1:science/py-esda@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}geopandas>=0.10.0:graphics/py-geopandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}giddy>=2.3.6:graphics/py-giddy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}inequality>=1.1.2:science/py-inequality@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}libpysal>=4.13.0:science/py-libpysal@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}mapclassify>=2.10.0:graphics/py-mapclassify@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}mgwr>=2.2.1:graphics/py-mgwr@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}momepy>=0.10.0:graphics/py-momepy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.22,1:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}packaging>=22:devel/py-packaging@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=1.4:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}platformdirs>=2.0.2:devel/py-platformdirs@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pointpats>=2.5.1:graphics/py-pointpats@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>=2.27:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.1:science/py-scikit-learn@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.8,1:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}segregation>=2.5.2:science/py-segregation@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}shapely>=2.0.1:devel/py-shapely@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}spaghetti>=1.7.6:science/py-spaghetti@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}spglm>=1.1.0:math/py-spglm@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}spint>=1.0.7:math/py-spint@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}splot>=1.1.7:math/py-splot@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}spopt>=0.7.0:math/py-spopt@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}spreg>=1.8.3:math/py-spreg@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tobler>=0.12.1:science/py-tobler@${PY_FLAVOR} + +USES= python +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} \ + ${PYTHON_PKGNAMEPREFIX}networkx>=2.7,2:math/py-networkx@${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/py-pysal/distinfo b/science/py-pysal/distinfo new file mode 100644 index 000000000000..8dfb4ce03b7d --- /dev/null +++ b/science/py-pysal/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1755202412 +SHA256 (pysal-25.7.tar.gz) = ca1452a1d57811cbc4708002a38ece6fe58b8597f966b310731e2e4014ddf21b +SIZE (pysal-25.7.tar.gz) = 5454676 diff --git a/science/py-pysal/pkg-descr b/science/py-pysal/pkg-descr new file mode 100644 index 000000000000..be3e218a7ef0 --- /dev/null +++ b/science/py-pysal/pkg-descr @@ -0,0 +1,10 @@ +PySAL, the Python spatial analysis library, is an open source cross-platform +library for geospatial data science with an emphasis on geospatial vector data +written in Python. It supports the development of high level applications for +spatial analysis, such as +- detection of spatial clusters, hot-spots, and outliers +- construction of graphs from spatial data +- spatial regression and statistical modeling on geographically embedded + networks +- spatial econometrics +- exploratory spatio-temporal data analysis diff --git a/science/py-qcelemental/Makefile b/science/py-qcelemental/Makefile index b1a5efde166b..059ced2ffca3 100644 --- a/science/py-qcelemental/Makefile +++ b/science/py-qcelemental/Makefile @@ -1,6 +1,5 @@ PORTNAME= qcelemental -DISTVERSION= 0.28.0 -PORTREVISION= 1 +DISTVERSION= 0.29.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,12 +12,14 @@ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}poetry-core>0:devel/py-poetry-core@${PY_FLAVOR} -RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}pint>=0.10.0:devel/py-pint@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pydantic2>=1.8.2:devel/py-pydantic2@${PY_FLAVOR} -RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}ipykernel>0:devel/py-ipykernel@${PY_FLAVOR} \ +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}importlib-metadata>=4.8:devel/py-importlib-metadata@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}ipykernel>0:devel/py-ipykernel@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nglview>=3.0.3:science/py-nglview@${PY_FLAVOR} \ + ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}packaging>=24.1:devel/py-packaging@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pint>=0.10.0:devel/py-pint@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pydantic2>=1.8.2:devel/py-pydantic2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.9.0:science/py-scipy@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>=4.0.0:devel/py-pytest@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-cov>0:devel/py-pytest-cov@${PY_FLAVOR} \ @@ -35,4 +36,6 @@ NO_ARCH= yes do-test: @cd ${WRKSRC} && ${SETENV} ${TEST_ENV} pytest -rs --pyargs qcelemental +# tests as of 0.29.0: 1 failed, 1191 passed, 2 skipped, 2 xpassed, 1 warning in 12.71s, see https://github.com/MolSSI/QCElemental/issues/380 + .include <bsd.port.mk> diff --git a/science/py-qcelemental/distinfo b/science/py-qcelemental/distinfo index 26f2d8e967da..3ee8f7f4c3eb 100644 --- a/science/py-qcelemental/distinfo +++ b/science/py-qcelemental/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1720845708 -SHA256 (qcelemental-0.28.0.tar.gz) = da96fddb88c1701f812b25369a6a169d35f2d5446c37c62e86048cb0f1b168a2 -SIZE (qcelemental-0.28.0.tar.gz) = 301172 +TIMESTAMP = 1761809140 +SHA256 (qcelemental-0.29.0.tar.gz) = bf634ee652e7d95e906e291989513224233b1d705c26afeac86e451f316b3c04 +SIZE (qcelemental-0.29.0.tar.gz) = 306949 diff --git a/science/py-qiskit/Makefile b/science/py-qiskit/Makefile index 9e1c3667b27d..26690ce9ba2e 100644 --- a/science/py-qiskit/Makefile +++ b/science/py-qiskit/Makefile @@ -1,5 +1,5 @@ PORTNAME= qiskit -DISTVERSION= 2.1.2 +DISTVERSION= 2.2.1 PORTREVISION= 1 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-qiskit/Makefile.crates b/science/py-qiskit/Makefile.crates index 790b3238b85a..cdf76056ece6 100644 --- a/science/py-qiskit/Makefile.crates +++ b/science/py-qiskit/Makefile.crates @@ -1,61 +1,60 @@ -CARGO_CRATES= ahash-0.7.0 \ +CARGO_CRATES= ahash-0.7.8 \ ahash-0.8.12 \ aho-corasick-1.1.3 \ allocator-api2-0.2.21 \ - anstream-0.6.18 \ - anstyle-1.0.10 \ - anstyle-parse-0.2.6 \ - anstyle-query-1.1.2 \ - anstyle-wincon-3.0.7 \ + anstream-0.6.20 \ + anstyle-1.0.11 \ + anstyle-parse-0.2.7 \ + anstyle-query-1.1.4 \ + anstyle-wincon-3.0.10 \ + anyhow-1.0.99 \ approx-0.5.1 \ ariadne-0.3.0 \ - autocfg-1.4.0 \ + autocfg-1.5.0 \ bincode-1.3.3 \ bitfield-struct-0.9.5 \ bitflags-1.3.2 \ - bitflags-2.9.0 \ + bitflags-2.9.4 \ block-buffer-0.10.4 \ boolenum-0.1.0 \ - bytemuck-1.23.0 \ - bytemuck_derive-1.8.1 \ + bytemuck-1.23.2 \ + bytemuck_derive-1.10.1 \ byteorder-1.5.0 \ cbindgen-0.29.0 \ - cfg-if-1.0.0 \ - clap-4.5.31 \ - clap_builder-4.5.31 \ - clap_lex-0.7.4 \ - coe-rs-0.1.2 \ - colorchoice-1.0.3 \ + cfg-if-1.0.3 \ + clap-4.5.47 \ + clap_builder-4.5.47 \ + clap_lex-0.7.5 \ + colorchoice-1.0.4 \ concolor-0.1.1 \ concolor-query-0.3.3 \ countme-3.0.1 \ - cov-mark-2.0.0 \ + cov-mark-2.1.0 \ cpufeatures-0.2.17 \ crossbeam-deque-0.8.6 \ crossbeam-epoch-0.9.18 \ crossbeam-utils-0.8.21 \ - crunchy-0.2.3 \ + crunchy-0.2.4 \ crypto-common-0.1.6 \ - dbgf-0.1.2 \ digest-0.10.7 \ drop_bomb-0.1.5 \ - dyn-stack-0.10.0 \ dyn-stack-0.13.0 \ - either-1.14.0 \ + either-1.15.0 \ enum-as-inner-0.6.1 \ equator-0.2.2 \ equator-0.4.2 \ equator-macro-0.2.1 \ equator-macro-0.4.2 \ equivalent-1.0.2 \ - errno-0.3.10 \ - faer-0.19.4 \ - faer-entity-0.19.2 \ - faer-ext-0.3.0 \ + errno-0.3.14 \ + faer-0.21.9 \ + faer-ext-0.5.0 \ + faer-macros-0.21.0 \ + faer-traits-0.21.5 \ fastrand-2.3.0 \ fixedbitset-0.4.2 \ fixedbitset-0.5.7 \ - foldhash-0.1.4 \ + foldhash-0.1.5 \ gemm-0.18.2 \ gemm-c32-0.18.2 \ gemm-c64-0.18.2 \ @@ -63,18 +62,19 @@ CARGO_CRATES= ahash-0.7.0 \ gemm-f16-0.18.2 \ gemm-f32-0.18.2 \ gemm-f64-0.18.2 \ + generativity-1.1.0 \ generic-array-0.14.7 \ - getrandom-0.2.15 \ - getrandom-0.3.1 \ - half-2.4.1 \ + getrandom-0.2.16 \ + getrandom-0.3.3 \ + half-2.6.0 \ hash32-0.3.1 \ hashbrown-0.12.3 \ hashbrown-0.14.5 \ - hashbrown-0.15.2 \ + hashbrown-0.15.5 \ heapless-0.8.0 \ heck-0.5.0 \ - hermit-abi-0.5.1 \ - indexmap-2.9.0 \ + hermit-abi-0.5.2 \ + indexmap-2.11.3 \ indoc-2.0.6 \ is-terminal-0.4.16 \ is_terminal_polyfill-1.70.1 \ @@ -83,19 +83,17 @@ CARGO_CRATES= ahash-0.7.0 \ itertools-0.14.0 \ itoa-1.0.15 \ lazy_static-1.5.0 \ - libc-0.2.170 \ - libm-0.2.11 \ - linux-raw-sys-0.4.15 \ - log-0.4.26 \ - matrixcompare-0.3.0 \ - matrixcompare-core-0.1.0 \ - matrixmultiply-0.3.9 \ - memchr-2.7.4 \ + libc-0.2.175 \ + libm-0.2.15 \ + linux-raw-sys-0.11.0 \ + log-0.4.28 \ + matrixmultiply-0.3.10 \ + memchr-2.7.5 \ memoffset-0.9.1 \ minimal-lexical-0.2.1 \ nalgebra-0.33.2 \ nalgebra-macros-0.2.2 \ - nano-gemm-0.1.2 \ + nano-gemm-0.1.3 \ nano-gemm-c32-0.1.0 \ nano-gemm-c64-0.1.0 \ nano-gemm-codegen-0.1.0 \ @@ -114,38 +112,39 @@ CARGO_CRATES= ahash-0.7.0 \ num-traits-0.2.19 \ numpy-0.25.0 \ once_cell-1.21.3 \ + once_cell_polyfill-1.70.1 \ oq3_lexer-0.7.0 \ oq3_parser-0.7.0 \ oq3_semantics-0.7.0 \ oq3_source_file-0.7.0 \ oq3_syntax-0.7.0 \ paste-1.0.15 \ - pest-2.8.0 \ - pest_derive-2.8.0 \ - pest_generator-2.8.0 \ - pest_meta-2.8.0 \ + pest-2.8.2 \ + pest_derive-2.8.2 \ + pest_generator-2.8.2 \ + pest_meta-2.8.2 \ petgraph-0.6.5 \ petgraph-0.7.1 \ - portable-atomic-1.11.0 \ + portable-atomic-1.11.1 \ portable-atomic-util-0.2.4 \ ppv-lite86-0.2.21 \ - priority-queue-2.1.2 \ + priority-queue-2.6.0 \ proc-macro-error-1.0.4 \ proc-macro-error-attr-1.0.4 \ - proc-macro2-1.0.94 \ - pulp-0.18.22 \ + proc-macro2-1.0.101 \ pulp-0.21.5 \ pulp-macro-0.1.1 \ py_literal-0.4.0 \ - pyo3-0.25.0 \ - pyo3-build-config-0.25.0 \ - pyo3-ffi-0.25.0 \ - pyo3-macros-0.25.0 \ - pyo3-macros-backend-0.25.0 \ - quote-1.0.39 \ + pyo3-0.25.1 \ + pyo3-build-config-0.25.1 \ + pyo3-ffi-0.25.1 \ + pyo3-macros-0.25.1 \ + pyo3-macros-backend-0.25.1 \ + quote-1.0.40 \ + r-efi-5.3.0 \ ra_ap_limit-0.0.188 \ rand-0.8.5 \ - rand-0.9.0 \ + rand-0.9.2 \ rand_chacha-0.3.1 \ rand_chacha-0.9.0 \ rand_core-0.6.4 \ @@ -154,90 +153,106 @@ CARGO_CRATES= ahash-0.7.0 \ rand_distr-0.5.1 \ rand_pcg-0.3.1 \ rand_pcg-0.9.0 \ - raw-cpuid-11.4.0 \ + raw-cpuid-11.6.0 \ rawpointer-0.2.1 \ - rayon-1.10.0 \ + rayon-1.11.0 \ rayon-cond-0.3.0 \ - rayon-core-1.12.1 \ + rayon-cond-0.4.0 \ + rayon-core-1.13.0 \ reborrow-0.5.5 \ - regex-1.11.1 \ - regex-automata-0.4.9 \ - regex-syntax-0.8.5 \ + regex-1.11.2 \ + regex-automata-0.4.10 \ + regex-syntax-0.8.6 \ rowan-0.15.15 \ rstar-0.12.2 \ rustc-hash-1.1.0 \ rustc-hash-2.1.1 \ rustiq-core-0.0.11 \ - rustix-0.38.44 \ - rustversion-1.0.20 \ + rustix-1.1.2 \ + rustversion-1.0.22 \ rustworkx-core-0.16.0 \ ryu-1.0.20 \ safe_arch-0.7.4 \ same-file-1.0.6 \ seq-macro-0.3.6 \ - serde-1.0.219 \ - serde_derive-1.0.219 \ - serde_json-1.0.140 \ - serde_spanned-0.6.8 \ - sha2-0.10.8 \ - simba-0.9.0 \ - smallvec-1.15.0 \ + serde-1.0.225 \ + serde_core-1.0.225 \ + serde_derive-1.0.225 \ + serde_json-1.0.145 \ + serde_spanned-0.6.9 \ + sha2-0.10.9 \ + simba-0.9.1 \ + smallvec-1.15.1 \ smol_str-0.2.2 \ stable_deref_trait-1.2.0 \ strsim-0.11.1 \ syn-1.0.109 \ - syn-2.0.99 \ + syn-2.0.106 \ sysctl-0.6.0 \ - target-lexicon-0.12.16 \ - target-lexicon-0.13.2 \ - tempfile-3.17.1 \ + target-lexicon-0.13.3 \ + tempfile-3.22.0 \ text-size-1.1.1 \ thiserror-1.0.69 \ - thiserror-2.0.12 \ + thiserror-2.0.16 \ thiserror-impl-1.0.69 \ - thiserror-impl-2.0.12 \ - toml-0.8.20 \ - toml_datetime-0.6.8 \ - toml_edit-0.22.24 \ + thiserror-impl-2.0.16 \ + toml-0.8.23 \ + toml_datetime-0.6.11 \ + toml_edit-0.22.27 \ + toml_write-0.1.2 \ triomphe-0.1.11 \ typenum-1.18.0 \ ucd-trie-0.1.7 \ - unicode-ident-1.0.18 \ + unicode-ident-1.0.19 \ unicode-properties-0.1.3 \ unicode-width-0.1.14 \ unicode-xid-0.2.6 \ unindent-0.2.4 \ utf8parse-0.2.2 \ - uuid-1.17.0 \ + uuid-1.18.1 \ version_check-0.9.5 \ walkdir-2.5.0 \ - wasi-0.11.0+wasi-snapshot-preview1 \ - wasi-0.13.3+wasi-0.2.2 \ - wide-0.7.32 \ - winapi-util-0.1.9 \ + wasi-0.11.1+wasi-snapshot-preview1 \ + wasi-0.14.7+wasi-0.2.4 \ + wasip2-1.0.1+wasi-0.2.4 \ + wide-0.7.33 \ + winapi-util-0.1.11 \ + windows-link-0.1.3 \ + windows-link-0.2.0 \ windows-sys-0.45.0 \ windows-sys-0.59.0 \ + windows-sys-0.60.2 \ + windows-sys-0.61.0 \ windows-targets-0.42.2 \ windows-targets-0.52.6 \ + windows-targets-0.53.3 \ windows_aarch64_gnullvm-0.42.2 \ windows_aarch64_gnullvm-0.52.6 \ + windows_aarch64_gnullvm-0.53.0 \ windows_aarch64_msvc-0.42.2 \ windows_aarch64_msvc-0.52.6 \ + windows_aarch64_msvc-0.53.0 \ windows_i686_gnu-0.42.2 \ windows_i686_gnu-0.52.6 \ + windows_i686_gnu-0.53.0 \ windows_i686_gnullvm-0.52.6 \ + windows_i686_gnullvm-0.53.0 \ windows_i686_msvc-0.42.2 \ windows_i686_msvc-0.52.6 \ + windows_i686_msvc-0.53.0 \ windows_x86_64_gnu-0.42.2 \ windows_x86_64_gnu-0.52.6 \ + windows_x86_64_gnu-0.53.0 \ windows_x86_64_gnullvm-0.42.2 \ windows_x86_64_gnullvm-0.52.6 \ + windows_x86_64_gnullvm-0.53.0 \ windows_x86_64_msvc-0.42.2 \ windows_x86_64_msvc-0.52.6 \ - winnow-0.7.3 \ - wit-bindgen-rt-0.33.0 \ + windows_x86_64_msvc-0.53.0 \ + winnow-0.7.13 \ + wit-bindgen-0.46.0 \ xshell-0.2.7 \ xshell-macros-0.2.7 \ yansi-0.5.1 \ - zerocopy-0.8.25 \ - zerocopy-derive-0.8.25 + zerocopy-0.8.27 \ + zerocopy-derive-0.8.27 diff --git a/science/py-qiskit/distinfo b/science/py-qiskit/distinfo index 40086a88e8e1..000080ba686a 100644 --- a/science/py-qiskit/distinfo +++ b/science/py-qiskit/distinfo @@ -1,68 +1,68 @@ -TIMESTAMP = 1757578345 -SHA256 (rust/crates/ahash-0.7.0.crate) = efa60d2eadd8b12a996add391db32bd1153eac697ba4869660c0016353611426 -SIZE (rust/crates/ahash-0.7.0.crate) = 55813 +TIMESTAMP = 1759971062 +SHA256 (rust/crates/ahash-0.7.8.crate) = 891477e0c6a8957309ee5c45a6368af3ae14bb510732d2684ffa19af310920f9 +SIZE (rust/crates/ahash-0.7.8.crate) = 38550 SHA256 (rust/crates/ahash-0.8.12.crate) = 5a15f179cd60c4584b8a8c596927aadc462e27f2ca70c04e0071964a73ba7a75 SIZE (rust/crates/ahash-0.8.12.crate) = 43413 SHA256 (rust/crates/aho-corasick-1.1.3.crate) = 8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916 SIZE (rust/crates/aho-corasick-1.1.3.crate) = 183311 SHA256 (rust/crates/allocator-api2-0.2.21.crate) = 683d7910e743518b0e34f1186f92494becacb047c7b6bf616c96772180fef923 SIZE (rust/crates/allocator-api2-0.2.21.crate) = 63622 -SHA256 (rust/crates/anstream-0.6.18.crate) = 8acc5369981196006228e28809f761875c0327210a891e941f4c683b3a99529b -SIZE (rust/crates/anstream-0.6.18.crate) = 29681 -SHA256 (rust/crates/anstyle-1.0.10.crate) = 55cc3b69f167a1ef2e161439aa98aed94e6028e5f9a59be9a6ffb47aef1651f9 -SIZE (rust/crates/anstyle-1.0.10.crate) = 15725 -SHA256 (rust/crates/anstyle-parse-0.2.6.crate) = 3b2d16507662817a6a20a9ea92df6652ee4f94f914589377d69f3b21bc5798a9 -SIZE (rust/crates/anstyle-parse-0.2.6.crate) = 22343 -SHA256 (rust/crates/anstyle-query-1.1.2.crate) = 79947af37f4177cfead1110013d678905c37501914fba0efea834c3fe9a8d60c -SIZE (rust/crates/anstyle-query-1.1.2.crate) = 9969 -SHA256 (rust/crates/anstyle-wincon-3.0.7.crate) = ca3534e77181a9cc07539ad51f2141fe32f6c3ffd4df76db8ad92346b003ae4e -SIZE (rust/crates/anstyle-wincon-3.0.7.crate) = 12400 +SHA256 (rust/crates/anstream-0.6.20.crate) = 3ae563653d1938f79b1ab1b5e668c87c76a9930414574a6583a7b7e11a8e6192 +SIZE (rust/crates/anstream-0.6.20.crate) = 28797 +SHA256 (rust/crates/anstyle-1.0.11.crate) = 862ed96ca487e809f1c8e5a8447f6ee2cf102f846893800b20cebdf541fc6bbd +SIZE (rust/crates/anstyle-1.0.11.crate) = 15880 +SHA256 (rust/crates/anstyle-parse-0.2.7.crate) = 4e7644824f0aa2c7b9384579234ef10eb7efb6a0deb83f9630a49594dd9c15c2 +SIZE (rust/crates/anstyle-parse-0.2.7.crate) = 21707 +SHA256 (rust/crates/anstyle-query-1.1.4.crate) = 9e231f6134f61b71076a3eab506c379d4f36122f2af15a9ff04415ea4c3339e2 +SIZE (rust/crates/anstyle-query-1.1.4.crate) = 10192 +SHA256 (rust/crates/anstyle-wincon-3.0.10.crate) = 3e0633414522a32ffaac8ac6cc8f748e090c5717661fddeea04219e2344f5f2a +SIZE (rust/crates/anstyle-wincon-3.0.10.crate) = 12558 +SHA256 (rust/crates/anyhow-1.0.99.crate) = b0674a1ddeecb70197781e945de4b3b8ffb61fa939a5597bcf48503737663100 +SIZE (rust/crates/anyhow-1.0.99.crate) = 53809 SHA256 (rust/crates/approx-0.5.1.crate) = cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6 SIZE (rust/crates/approx-0.5.1.crate) = 15100 SHA256 (rust/crates/ariadne-0.3.0.crate) = 72fe02fc62033df9ba41cba57ee19acf5e742511a140c7dbc3a873e19a19a1bd SIZE (rust/crates/ariadne-0.3.0.crate) = 21829 -SHA256 (rust/crates/autocfg-1.4.0.crate) = ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26 -SIZE (rust/crates/autocfg-1.4.0.crate) = 17712 +SHA256 (rust/crates/autocfg-1.5.0.crate) = c08606f8c3cbf4ce6ec8e28fb0014a2c086708fe954eaa885384a6165172e7e8 +SIZE (rust/crates/autocfg-1.5.0.crate) = 18729 SHA256 (rust/crates/bincode-1.3.3.crate) = b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad SIZE (rust/crates/bincode-1.3.3.crate) = 28958 SHA256 (rust/crates/bitfield-struct-0.9.5.crate) = b2869c63ccf4f8bf0d485070b880e60e097fb7aeea80ee82a0a94a957e372a0b SIZE (rust/crates/bitfield-struct-0.9.5.crate) = 15953 SHA256 (rust/crates/bitflags-1.3.2.crate) = bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a SIZE (rust/crates/bitflags-1.3.2.crate) = 23021 -SHA256 (rust/crates/bitflags-2.9.0.crate) = 5c8214115b7bf84099f1309324e63141d4c5d7cc26862f97a0a857dbefe165bd -SIZE (rust/crates/bitflags-2.9.0.crate) = 47654 +SHA256 (rust/crates/bitflags-2.9.4.crate) = 2261d10cca569e4643e526d8dc2e62e433cc8aba21ab764233731f8d369bf394 +SIZE (rust/crates/bitflags-2.9.4.crate) = 47950 SHA256 (rust/crates/block-buffer-0.10.4.crate) = 3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71 SIZE (rust/crates/block-buffer-0.10.4.crate) = 10538 SHA256 (rust/crates/boolenum-0.1.0.crate) = a6c8abd585d7026df20a9ae12982127ba5e81cc7a09397b957e71659da8c5de8 SIZE (rust/crates/boolenum-0.1.0.crate) = 3444 -SHA256 (rust/crates/bytemuck-1.23.0.crate) = 9134a6ef01ce4b366b50689c94f82c14bc72bc5d0386829828a2e2752ef7958c -SIZE (rust/crates/bytemuck-1.23.0.crate) = 52534 -SHA256 (rust/crates/bytemuck_derive-1.8.1.crate) = 3fa76293b4f7bb636ab88fd78228235b5248b4d05cc589aed610f954af5d7c7a -SIZE (rust/crates/bytemuck_derive-1.8.1.crate) = 23100 +SHA256 (rust/crates/bytemuck-1.23.2.crate) = 3995eaeebcdf32f91f980d360f78732ddc061097ab4e39991ae7a6ace9194677 +SIZE (rust/crates/bytemuck-1.23.2.crate) = 53021 +SHA256 (rust/crates/bytemuck_derive-1.10.1.crate) = 4f154e572231cb6ba2bd1176980827e3d5dc04cc183a75dea38109fbdd672d29 +SIZE (rust/crates/bytemuck_derive-1.10.1.crate) = 25122 SHA256 (rust/crates/byteorder-1.5.0.crate) = 1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b SIZE (rust/crates/byteorder-1.5.0.crate) = 23288 SHA256 (rust/crates/cbindgen-0.29.0.crate) = 975982cdb7ad6a142be15bdf84aea7ec6a9e5d4d797c004d43185b24cfe4e684 SIZE (rust/crates/cbindgen-0.29.0.crate) = 226905 -SHA256 (rust/crates/cfg-if-1.0.0.crate) = baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd -SIZE (rust/crates/cfg-if-1.0.0.crate) = 7934 -SHA256 (rust/crates/clap-4.5.31.crate) = 027bb0d98429ae334a8698531da7077bdf906419543a35a55c2cb1b66437d767 -SIZE (rust/crates/clap-4.5.31.crate) = 56084 -SHA256 (rust/crates/clap_builder-4.5.31.crate) = 5589e0cba072e0f3d23791efac0fd8627b49c829c196a492e88168e6a669d863 -SIZE (rust/crates/clap_builder-4.5.31.crate) = 168303 -SHA256 (rust/crates/clap_lex-0.7.4.crate) = f46ad14479a25103f283c0f10005961cf086d8dc42205bb44c46ac563475dca6 -SIZE (rust/crates/clap_lex-0.7.4.crate) = 12858 -SHA256 (rust/crates/coe-rs-0.1.2.crate) = 7e8f1e641542c07631228b1e0dc04b69ae3c1d58ef65d5691a439711d805c698 -SIZE (rust/crates/coe-rs-0.1.2.crate) = 2819 -SHA256 (rust/crates/colorchoice-1.0.3.crate) = 5b63caa9aa9397e2d9480a9b13673856c78d8ac123288526c37d7839f2a86990 -SIZE (rust/crates/colorchoice-1.0.3.crate) = 7923 +SHA256 (rust/crates/cfg-if-1.0.3.crate) = 2fd1289c04a9ea8cb22300a459a72a385d7c73d3259e2ed7dcb2af674838cfa9 +SIZE (rust/crates/cfg-if-1.0.3.crate) = 8719 +SHA256 (rust/crates/clap-4.5.47.crate) = 7eac00902d9d136acd712710d71823fb8ac8004ca445a89e73a41d45aa712931 +SIZE (rust/crates/clap-4.5.47.crate) = 58354 +SHA256 (rust/crates/clap_builder-4.5.47.crate) = 2ad9bbf750e73b5884fb8a211a9424a1906c1e156724260fdae972f31d70e1d6 +SIZE (rust/crates/clap_builder-4.5.47.crate) = 170016 +SHA256 (rust/crates/clap_lex-0.7.5.crate) = b94f61472cee1439c0b966b47e3aca9ae07e45d070759512cd390ea2bebc6675 +SIZE (rust/crates/clap_lex-0.7.5.crate) = 13469 +SHA256 (rust/crates/colorchoice-1.0.4.crate) = b05b61dc5112cbb17e4b6cd61790d9845d13888356391624cbe7e41efeac1e75 +SIZE (rust/crates/colorchoice-1.0.4.crate) = 8196 SHA256 (rust/crates/concolor-0.1.1.crate) = 0b946244a988c390a94667ae0e3958411fa40cc46ea496a929b263d883f5f9c3 SIZE (rust/crates/concolor-0.1.1.crate) = 10093 SHA256 (rust/crates/concolor-query-0.3.3.crate) = 88d11d52c3d7ca2e6d0040212be9e4dbbcd78b6447f535b6b561f449427944cf SIZE (rust/crates/concolor-query-0.3.3.crate) = 8337 SHA256 (rust/crates/countme-3.0.1.crate) = 7704b5fdd17b18ae31c4c1da5a2e0305a2bf17b5249300a9ee9ed7b72114c636 SIZE (rust/crates/countme-3.0.1.crate) = 10784 -SHA256 (rust/crates/cov-mark-2.0.0.crate) = 0570650661aa447e7335f1d5e4f499d8e58796e617bedc9267d971e51c8b49d4 -SIZE (rust/crates/cov-mark-2.0.0.crate) = 7890 +SHA256 (rust/crates/cov-mark-2.1.0.crate) = 3f1d92727879fb4f24cec33a35e3bff74035541326cbc12ad44ba8886d1927b0 +SIZE (rust/crates/cov-mark-2.1.0.crate) = 8715 SHA256 (rust/crates/cpufeatures-0.2.17.crate) = 59ed5838eebb26a2bb2e58f6d5b5316989ae9d08bab10e0e6d103e656d1b0280 SIZE (rust/crates/cpufeatures-0.2.17.crate) = 13466 SHA256 (rust/crates/crossbeam-deque-0.8.6.crate) = 9dd111b7b7f7d55b72c0a6ae361660ee5853c9af73f70c3c2ef6858b950e2e51 @@ -71,22 +71,18 @@ SHA256 (rust/crates/crossbeam-epoch-0.9.18.crate) = 5b82ac4a3c2ca9c3460964f020e1 SIZE (rust/crates/crossbeam-epoch-0.9.18.crate) = 46875 SHA256 (rust/crates/crossbeam-utils-0.8.21.crate) = d0a5c400df2834b80a4c3327b3aad3a4c4cd4de0629063962b03235697506a28 SIZE (rust/crates/crossbeam-utils-0.8.21.crate) = 42691 -SHA256 (rust/crates/crunchy-0.2.3.crate) = 43da5946c66ffcc7745f48db692ffbb10a83bfe0afd96235c5c2a4fb23994929 -SIZE (rust/crates/crunchy-0.2.3.crate) = 3775 +SHA256 (rust/crates/crunchy-0.2.4.crate) = 460fbee9c2c2f33933d720630a6a0bac33ba7053db5344fac858d4b8952d77d5 +SIZE (rust/crates/crunchy-0.2.4.crate) = 3887 SHA256 (rust/crates/crypto-common-0.1.6.crate) = 1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3 SIZE (rust/crates/crypto-common-0.1.6.crate) = 8760 -SHA256 (rust/crates/dbgf-0.1.2.crate) = e6ca96b45ca70b8045e0462f191bd209fcb3c3bfe8dbfb1257ada54c4dd59169 -SIZE (rust/crates/dbgf-0.1.2.crate) = 1310 SHA256 (rust/crates/digest-0.10.7.crate) = 9ed9a281f7bc9b7576e61468ba615a66a5c8cfdff42420a70aa82701a3b1e292 SIZE (rust/crates/digest-0.10.7.crate) = 19557 SHA256 (rust/crates/drop_bomb-0.1.5.crate) = 9bda8e21c04aca2ae33ffc2fd8c23134f3cac46db123ba97bd9d3f3b8a4a85e1 SIZE (rust/crates/drop_bomb-0.1.5.crate) = 6859 -SHA256 (rust/crates/dyn-stack-0.10.0.crate) = 56e53799688f5632f364f8fb387488dd05db9fe45db7011be066fc20e7027f8b -SIZE (rust/crates/dyn-stack-0.10.0.crate) = 10753 SHA256 (rust/crates/dyn-stack-0.13.0.crate) = 490bd48eb68fffcfed519b4edbfd82c69cbe741d175b84f0e0cbe8c57cbe0bdd SIZE (rust/crates/dyn-stack-0.13.0.crate) = 21828 -SHA256 (rust/crates/either-1.14.0.crate) = b7914353092ddf589ad78f25c5c1c21b7f80b0ff8621e7c814c3485b5306da9d -SIZE (rust/crates/either-1.14.0.crate) = 19890 +SHA256 (rust/crates/either-1.15.0.crate) = 48c757948c5ede0e46177b7add2e67155f70e33c07fea8284df6576da70b3719 +SIZE (rust/crates/either-1.15.0.crate) = 20114 SHA256 (rust/crates/enum-as-inner-0.6.1.crate) = a1e6a265c649f3f5979b601d26f1d05ada116434c87741c9493cb56218f76cbc SIZE (rust/crates/enum-as-inner-0.6.1.crate) = 12190 SHA256 (rust/crates/equator-0.2.2.crate) = c35da53b5a021d2484a7cc49b2ac7f2d840f8236a286f84202369bd338d761ea @@ -99,22 +95,24 @@ SHA256 (rust/crates/equator-macro-0.4.2.crate) = 44f23cf4b44bfce11a86ace86f8a73f SIZE (rust/crates/equator-macro-0.4.2.crate) = 6407 SHA256 (rust/crates/equivalent-1.0.2.crate) = 877a4ace8713b0bcf2a4e7eec82529c029f1d0619886d18145fea96c3ffe5c0f SIZE (rust/crates/equivalent-1.0.2.crate) = 7419 -SHA256 (rust/crates/errno-0.3.10.crate) = 33d852cb9b869c2a9b3df2f71a3074817f01e1844f839a144f5fcef059a4eb5d -SIZE (rust/crates/errno-0.3.10.crate) = 11824 -SHA256 (rust/crates/faer-0.19.4.crate) = 64bc4855cb2792ae3520e8af22051a47a6d6dc8300ebc0ddf51ad73f65bd0dc9 -SIZE (rust/crates/faer-0.19.4.crate) = 879450 -SHA256 (rust/crates/faer-entity-0.19.2.crate) = c9c752ab2bff6f0b9597c6a1adc0112f7fd41fb343bc5a009a6274ae9d32fd03 -SIZE (rust/crates/faer-entity-0.19.2.crate) = 13481 -SHA256 (rust/crates/faer-ext-0.3.0.crate) = fa0b66079aff3caae4e41177b37487914cbcb377651e86a838d6a2088fb4b666 -SIZE (rust/crates/faer-ext-0.3.0.crate) = 7002 +SHA256 (rust/crates/errno-0.3.14.crate) = 39cab71617ae0d63f51a36d69f866391735b51691dbda63cf6f96d042b63efeb +SIZE (rust/crates/errno-0.3.14.crate) = 12002 +SHA256 (rust/crates/faer-0.21.9.crate) = ebe9ac2a073e05ca749eeea503fae16a91440b20d2e92b6fc6f6c6919b9964eb +SIZE (rust/crates/faer-0.21.9.crate) = 576636 +SHA256 (rust/crates/faer-ext-0.5.0.crate) = 9756e068191bf4f6b6a36dd131687f1f802cd2e3fce8b1ec4dbd5a5f5dfbafe1 +SIZE (rust/crates/faer-ext-0.5.0.crate) = 19830 +SHA256 (rust/crates/faer-macros-0.21.0.crate) = 9d0a255d1442b5825c61812a7eafda9034ec53d969c98555251085e148428e6a +SIZE (rust/crates/faer-macros-0.21.0.crate) = 3857 +SHA256 (rust/crates/faer-traits-0.21.5.crate) = 1430e111b20872c7eaa82c7ada071bff1c3e3ac09cc6f4df676065fd2d41eb62 +SIZE (rust/crates/faer-traits-0.21.5.crate) = 13192 SHA256 (rust/crates/fastrand-2.3.0.crate) = 37909eebbb50d72f9059c3b6d82c0463f2ff062c9e95845c43a6c9c0355411be SIZE (rust/crates/fastrand-2.3.0.crate) = 15076 SHA256 (rust/crates/fixedbitset-0.4.2.crate) = 0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80 SIZE (rust/crates/fixedbitset-0.4.2.crate) = 15954 SHA256 (rust/crates/fixedbitset-0.5.7.crate) = 1d674e81391d1e1ab681a28d99df07927c6d4aa5b027d7da16ba32d1d21ecd99 SIZE (rust/crates/fixedbitset-0.5.7.crate) = 26537 -SHA256 (rust/crates/foldhash-0.1.4.crate) = a0d2fde1f7b3d48b8395d5f2de76c18a528bd6a9cdde438df747bfcba3e05d6f -SIZE (rust/crates/foldhash-0.1.4.crate) = 13764 +SHA256 (rust/crates/foldhash-0.1.5.crate) = d9c4f5dac5e15c24eb999c26181a6ca40b39fe946cbe4c263c7209467bc83af2 +SIZE (rust/crates/foldhash-0.1.5.crate) = 21901 SHA256 (rust/crates/gemm-0.18.2.crate) = ab96b703d31950f1aeddded248bc95543c9efc7ac9c4a21fda8703a83ee35451 SIZE (rust/crates/gemm-0.18.2.crate) = 20056 SHA256 (rust/crates/gemm-c32-0.18.2.crate) = f6db9fd9f40421d00eea9dd0770045a5603b8d684654816637732463f4073847 @@ -129,30 +127,32 @@ SHA256 (rust/crates/gemm-f32-0.18.2.crate) = bc8d3d4385393304f407392f754cd2dc4b3 SIZE (rust/crates/gemm-f32-0.18.2.crate) = 7320 SHA256 (rust/crates/gemm-f64-0.18.2.crate) = 35b2a4f76ce4b8b16eadc11ccf2e083252d8237c1b589558a49b0183545015bd SIZE (rust/crates/gemm-f64-0.18.2.crate) = 7199 +SHA256 (rust/crates/generativity-1.1.0.crate) = 5881e4c3c2433fe4905bb19cfd2b5d49d4248274862b68c27c33d9ba4e13f9ec +SIZE (rust/crates/generativity-1.1.0.crate) = 12947 SHA256 (rust/crates/generic-array-0.14.7.crate) = 85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a SIZE (rust/crates/generic-array-0.14.7.crate) = 15950 -SHA256 (rust/crates/getrandom-0.2.15.crate) = c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7 -SIZE (rust/crates/getrandom-0.2.15.crate) = 37163 -SHA256 (rust/crates/getrandom-0.3.1.crate) = 43a49c392881ce6d5c3b8cb70f98717b7c07aabbdff06687b9030dbfbe2725f8 -SIZE (rust/crates/getrandom-0.3.1.crate) = 42449 -SHA256 (rust/crates/half-2.4.1.crate) = 6dd08c532ae367adf81c312a4580bc67f1d0fe8bc9c460520283f4c0ff277888 -SIZE (rust/crates/half-2.4.1.crate) = 50892 +SHA256 (rust/crates/getrandom-0.2.16.crate) = 335ff9f135e4384c8150d6f27c6daed433577f86b4750418338c01a1a2528592 +SIZE (rust/crates/getrandom-0.2.16.crate) = 40163 +SHA256 (rust/crates/getrandom-0.3.3.crate) = 26145e563e54f2cadc477553f1ec5ee650b00862f0a58bcd12cbdc5f0ea2d2f4 +SIZE (rust/crates/getrandom-0.3.3.crate) = 49493 +SHA256 (rust/crates/half-2.6.0.crate) = 459196ed295495a68f7d7fe1d84f6c4b7ff0e21fe3017b2f283c6fac3ad803c9 +SIZE (rust/crates/half-2.6.0.crate) = 59507 SHA256 (rust/crates/hash32-0.3.1.crate) = 47d60b12902ba28e2730cd37e95b8c9223af2808df9e902d4df49588d1470606 SIZE (rust/crates/hash32-0.3.1.crate) = 10273 SHA256 (rust/crates/hashbrown-0.12.3.crate) = 8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888 SIZE (rust/crates/hashbrown-0.12.3.crate) = 102968 SHA256 (rust/crates/hashbrown-0.14.5.crate) = e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1 SIZE (rust/crates/hashbrown-0.14.5.crate) = 141498 -SHA256 (rust/crates/hashbrown-0.15.2.crate) = bf151400ff0baff5465007dd2f3e717f3fe502074ca563069ce3a6629d07b289 -SIZE (rust/crates/hashbrown-0.15.2.crate) = 138478 +SHA256 (rust/crates/hashbrown-0.15.5.crate) = 9229cfe53dfd69f0609a49f65461bd93001ea1ef889cd5529dd176593f5338a1 +SIZE (rust/crates/hashbrown-0.15.5.crate) = 140908 SHA256 (rust/crates/heapless-0.8.0.crate) = 0bfb9eb618601c89945a70e254898da93b13be0388091d42117462b265bb3fad SIZE (rust/crates/heapless-0.8.0.crate) = 77802 SHA256 (rust/crates/heck-0.5.0.crate) = 2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea SIZE (rust/crates/heck-0.5.0.crate) = 11517 -SHA256 (rust/crates/hermit-abi-0.5.1.crate) = f154ce46856750ed433c8649605bf7ed2de3bc35fd9d2a9f30cddd873c80cb08 -SIZE (rust/crates/hermit-abi-0.5.1.crate) = 17549 -SHA256 (rust/crates/indexmap-2.9.0.crate) = cea70ddb795996207ad57735b50c5982d8844f38ba9ee5f1aedcfb708a2aa11e -SIZE (rust/crates/indexmap-2.9.0.crate) = 91214 +SHA256 (rust/crates/hermit-abi-0.5.2.crate) = fc0fef456e4baa96da950455cd02c081ca953b141298e41db3fc7e36b1da849c +SIZE (rust/crates/hermit-abi-0.5.2.crate) = 17435 +SHA256 (rust/crates/indexmap-2.11.3.crate) = 92119844f513ffa41556430369ab02c295a3578af21cf945caa3e9e0c2481ac3 +SIZE (rust/crates/indexmap-2.11.3.crate) = 100271 SHA256 (rust/crates/indoc-2.0.6.crate) = f4c7245a08504955605670dbf141fceab975f15ca21570696aebe9d2e71576bd SIZE (rust/crates/indoc-2.0.6.crate) = 17164 SHA256 (rust/crates/is-terminal-0.4.16.crate) = e04d7f318608d35d4b61ddd75cbdaee86b023ebe2bd5a66ee0915f0bf93095a9 @@ -169,22 +169,18 @@ SHA256 (rust/crates/itoa-1.0.15.crate) = 4a5f13b858c8d314ee3e8f639011f7ccefe71f9 SIZE (rust/crates/itoa-1.0.15.crate) = 11231 SHA256 (rust/crates/lazy_static-1.5.0.crate) = bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe SIZE (rust/crates/lazy_static-1.5.0.crate) = 14025 -SHA256 (rust/crates/libc-0.2.170.crate) = 875b3680cb2f8f71bdcf9a30f38d48282f5d3c95cbf9b3fa57269bb5d5c06828 -SIZE (rust/crates/libc-0.2.170.crate) = 760076 -SHA256 (rust/crates/libm-0.2.11.crate) = 8355be11b20d696c8f18f6cc018c4e372165b1fa8126cef092399c9951984ffa -SIZE (rust/crates/libm-0.2.11.crate) = 111477 -SHA256 (rust/crates/linux-raw-sys-0.4.15.crate) = d26c52dbd32dccf2d10cac7725f8eae5296885fb5703b261f7d0a0739ec807ab -SIZE (rust/crates/linux-raw-sys-0.4.15.crate) = 2150898 -SHA256 (rust/crates/log-0.4.26.crate) = 30bde2b3dc3671ae49d8e2e9f044c7c005836e7a023ee57cffa25ab82764bb9e -SIZE (rust/crates/log-0.4.26.crate) = 47022 -SHA256 (rust/crates/matrixcompare-0.3.0.crate) = 37832ba820e47c93d66b4360198dccb004b43c74abc3ac1ce1fed54e65a80445 -SIZE (rust/crates/matrixcompare-0.3.0.crate) = 27568 -SHA256 (rust/crates/matrixcompare-core-0.1.0.crate) = b0bdabb30db18805d5290b3da7ceaccbddba795620b86c02145d688e04900a73 -SIZE (rust/crates/matrixcompare-core-0.1.0.crate) = 1221 -SHA256 (rust/crates/matrixmultiply-0.3.9.crate) = 9380b911e3e96d10c1f415da0876389aaf1b56759054eeb0de7df940c456ba1a -SIZE (rust/crates/matrixmultiply-0.3.9.crate) = 57819 -SHA256 (rust/crates/memchr-2.7.4.crate) = 78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3 -SIZE (rust/crates/memchr-2.7.4.crate) = 96670 +SHA256 (rust/crates/libc-0.2.175.crate) = 6a82ae493e598baaea5209805c49bbf2ea7de956d50d7da0da1164f9c6d28543 +SIZE (rust/crates/libc-0.2.175.crate) = 788728 +SHA256 (rust/crates/libm-0.2.15.crate) = f9fbbcab51052fe104eb5e5d351cf728d30a5be1fe14d9be8a3b097481fb97de +SIZE (rust/crates/libm-0.2.15.crate) = 156108 +SHA256 (rust/crates/linux-raw-sys-0.11.0.crate) = df1d3c3b53da64cf5760482273a98e575c651a67eec7f77df96b5b642de8f039 +SIZE (rust/crates/linux-raw-sys-0.11.0.crate) = 2659624 +SHA256 (rust/crates/log-0.4.28.crate) = 34080505efa8e45a4b816c349525ebe327ceaa8559756f0356cba97ef3bf7432 +SIZE (rust/crates/log-0.4.28.crate) = 51131 +SHA256 (rust/crates/matrixmultiply-0.3.10.crate) = a06de3016e9fae57a36fd14dba131fccf49f74b40b7fbdb472f96e361ec71a08 +SIZE (rust/crates/matrixmultiply-0.3.10.crate) = 58170 +SHA256 (rust/crates/memchr-2.7.5.crate) = 32a282da65faaf38286cf3be983213fcf1d2e2a58700e808f83f4ea9a4804bc0 +SIZE (rust/crates/memchr-2.7.5.crate) = 97603 SHA256 (rust/crates/memoffset-0.9.1.crate) = 488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a SIZE (rust/crates/memoffset-0.9.1.crate) = 9032 SHA256 (rust/crates/minimal-lexical-0.2.1.crate) = 68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a @@ -193,8 +189,8 @@ SHA256 (rust/crates/nalgebra-0.33.2.crate) = 26aecdf64b707efd1310e3544d709c5c0ac SIZE (rust/crates/nalgebra-0.33.2.crate) = 385768 SHA256 (rust/crates/nalgebra-macros-0.2.2.crate) = 254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc SIZE (rust/crates/nalgebra-macros-0.2.2.crate) = 7545 -SHA256 (rust/crates/nano-gemm-0.1.2.crate) = f563548d38f390ef9893e4883ec38c1fb312f569e98d76bededdd91a3b41a043 -SIZE (rust/crates/nano-gemm-0.1.2.crate) = 8360 +SHA256 (rust/crates/nano-gemm-0.1.3.crate) = bb5ba2bea1c00e53de11f6ab5bd0761ba87dc0045d63b0c87ee471d2d3061376 +SIZE (rust/crates/nano-gemm-0.1.3.crate) = 22920 SHA256 (rust/crates/nano-gemm-c32-0.1.0.crate) = a40449e57a5713464c3a1208c4c3301c8d29ee1344711822cf022bc91373a91b SIZE (rust/crates/nano-gemm-c32-0.1.0.crate) = 1736 SHA256 (rust/crates/nano-gemm-c64-0.1.0.crate) = 743a6e6211358fba85d1009616751e4107da86f4c95b24e684ce85f25c25b3bf @@ -231,6 +227,8 @@ SHA256 (rust/crates/numpy-0.25.0.crate) = 29f1dee9aa8d3f6f8e8b9af3803006101bb365 SIZE (rust/crates/numpy-0.25.0.crate) = 81623 SHA256 (rust/crates/once_cell-1.21.3.crate) = 42f5e15c9953c5e4ccceeb2e7382a716482c34515315f7b03532b8b4e8393d2d SIZE (rust/crates/once_cell-1.21.3.crate) = 34534 +SHA256 (rust/crates/once_cell_polyfill-1.70.1.crate) = a4895175b425cb1f87721b59f0f286c2092bd4af812243672510e1ac53e2e0ad +SIZE (rust/crates/once_cell_polyfill-1.70.1.crate) = 7510 SHA256 (rust/crates/oq3_lexer-0.7.0.crate) = a27bbc91e3e9d6193a44aac8f5d62c1507c41669af71a4e7e0ef66fd6470e960 SIZE (rust/crates/oq3_lexer-0.7.0.crate) = 16877 SHA256 (rust/crates/oq3_parser-0.7.0.crate) = 9a72022fcb414e8a0912920a1cf46417b6aa95f19d4b38778df7450f8a3c17fa @@ -243,58 +241,58 @@ SHA256 (rust/crates/oq3_syntax-0.7.0.crate) = 42c754ce1d9da28d6c0334c212d64b5212 SIZE (rust/crates/oq3_syntax-0.7.0.crate) = 63066 SHA256 (rust/crates/paste-1.0.15.crate) = 57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a SIZE (rust/crates/paste-1.0.15.crate) = 18374 -SHA256 (rust/crates/pest-2.8.0.crate) = 198db74531d58c70a361c42201efde7e2591e976d518caf7662a47dc5720e7b6 -SIZE (rust/crates/pest-2.8.0.crate) = 128955 -SHA256 (rust/crates/pest_derive-2.8.0.crate) = d725d9cfd79e87dccc9341a2ef39d1b6f6353d68c4b33c177febbe1a402c97c5 -SIZE (rust/crates/pest_derive-2.8.0.crate) = 42196 -SHA256 (rust/crates/pest_generator-2.8.0.crate) = db7d01726be8ab66ab32f9df467ae8b1148906685bbe75c82d1e65d7f5b3f841 -SIZE (rust/crates/pest_generator-2.8.0.crate) = 18617 -SHA256 (rust/crates/pest_meta-2.8.0.crate) = 7f9f832470494906d1fca5329f8ab5791cc60beb230c74815dff541cbd2b5ca0 -SIZE (rust/crates/pest_meta-2.8.0.crate) = 42931 +SHA256 (rust/crates/pest-2.8.2.crate) = 21e0a3a33733faeaf8651dfee72dd0f388f0c8e5ad496a3478fa5a922f49cfa8 +SIZE (rust/crates/pest-2.8.2.crate) = 130430 +SHA256 (rust/crates/pest_derive-2.8.2.crate) = bc58706f770acb1dbd0973e6530a3cff4746fb721207feb3a8a6064cd0b6c663 +SIZE (rust/crates/pest_derive-2.8.2.crate) = 42335 +SHA256 (rust/crates/pest_generator-2.8.2.crate) = 6d4f36811dfe07f7b8573462465d5cb8965fffc2e71ae377a33aecf14c2c9a2f +SIZE (rust/crates/pest_generator-2.8.2.crate) = 18669 +SHA256 (rust/crates/pest_meta-2.8.2.crate) = 42919b05089acbd0a5dcd5405fb304d17d1053847b81163d09c4ad18ce8e8420 +SIZE (rust/crates/pest_meta-2.8.2.crate) = 42952 SHA256 (rust/crates/petgraph-0.6.5.crate) = b4c5cc86750666a3ed20bdaf5ca2a0344f9c67674cae0515bec2da16fbaa47db SIZE (rust/crates/petgraph-0.6.5.crate) = 710970 SHA256 (rust/crates/petgraph-0.7.1.crate) = 3672b37090dbd86368a4145bc067582552b29c27377cad4e0a306c97f9bd7772 SIZE (rust/crates/petgraph-0.7.1.crate) = 736025 -SHA256 (rust/crates/portable-atomic-1.11.0.crate) = 350e9b48cbc6b0e028b0473b114454c6316e57336ee184ceab6e53f72c178b3e -SIZE (rust/crates/portable-atomic-1.11.0.crate) = 181258 +SHA256 (rust/crates/portable-atomic-1.11.1.crate) = f84267b20a16ea918e43c6a88433c2d54fa145c92a811b5b047ccbe153674483 +SIZE (rust/crates/portable-atomic-1.11.1.crate) = 185506 SHA256 (rust/crates/portable-atomic-util-0.2.4.crate) = d8a2f0d8d040d7848a709caf78912debcc3f33ee4b3cac47d73d1e1069e83507 SIZE (rust/crates/portable-atomic-util-0.2.4.crate) = 47043 SHA256 (rust/crates/ppv-lite86-0.2.21.crate) = 85eae3c4ed2f50dcfe72643da4befc30deadb458a9b590d720cde2f2b1e97da9 SIZE (rust/crates/ppv-lite86-0.2.21.crate) = 22522 -SHA256 (rust/crates/priority-queue-2.1.2.crate) = 090ded312ed32a928fb49cb91ab4db6523ae3767225e61fbf6ceaaec3664ed26 -SIZE (rust/crates/priority-queue-2.1.2.crate) = 36557 +SHA256 (rust/crates/priority-queue-2.6.0.crate) = 3e7f4ffd8645efad783fc2844ac842367aa2e912d484950192564d57dc039a3a +SIZE (rust/crates/priority-queue-2.6.0.crate) = 50215 SHA256 (rust/crates/proc-macro-error-1.0.4.crate) = da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c SIZE (rust/crates/proc-macro-error-1.0.4.crate) = 25293 SHA256 (rust/crates/proc-macro-error-attr-1.0.4.crate) = a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869 SIZE (rust/crates/proc-macro-error-attr-1.0.4.crate) = 7971 -SHA256 (rust/crates/proc-macro2-1.0.94.crate) = a31971752e70b8b2686d7e46ec17fb38dad4051d94024c88df49b667caea9c84 -SIZE (rust/crates/proc-macro2-1.0.94.crate) = 52391 -SHA256 (rust/crates/pulp-0.18.22.crate) = a0a01a0dc67cf4558d279f0c25b0962bd08fc6dec0137699eae304103e882fe6 -SIZE (rust/crates/pulp-0.18.22.crate) = 117838 +SHA256 (rust/crates/proc-macro2-1.0.101.crate) = 89ae43fd86e4158d6db51ad8e2b80f313af9cc74f5c0e03ccb87de09998732de +SIZE (rust/crates/proc-macro2-1.0.101.crate) = 53886 SHA256 (rust/crates/pulp-0.21.5.crate) = 96b86df24f0a7ddd5e4b95c94fc9ed8a98f1ca94d3b01bdce2824097e7835907 SIZE (rust/crates/pulp-0.21.5.crate) = 136353 SHA256 (rust/crates/pulp-macro-0.1.1.crate) = d315b3197b780e4873bc0e11251cb56a33f65a6032a3d39b8d1405c255513766 SIZE (rust/crates/pulp-macro-0.1.1.crate) = 3268 SHA256 (rust/crates/py_literal-0.4.0.crate) = 102df7a3d46db9d3891f178dcc826dc270a6746277a9ae6436f8d29fd490a8e1 SIZE (rust/crates/py_literal-0.4.0.crate) = 16747 -SHA256 (rust/crates/pyo3-0.25.0.crate) = f239d656363bcee73afef85277f1b281e8ac6212a1d42aa90e55b90ed43c47a4 -SIZE (rust/crates/pyo3-0.25.0.crate) = 1120850 -SHA256 (rust/crates/pyo3-build-config-0.25.0.crate) = 755ea671a1c34044fa165247aaf6f419ca39caa6003aee791a0df2713d8f1b6d -SIZE (rust/crates/pyo3-build-config-0.25.0.crate) = 34122 -SHA256 (rust/crates/pyo3-ffi-0.25.0.crate) = fc95a2e67091e44791d4ea300ff744be5293f394f1bafd9f78c080814d35956e -SIZE (rust/crates/pyo3-ffi-0.25.0.crate) = 77991 -SHA256 (rust/crates/pyo3-macros-0.25.0.crate) = a179641d1b93920829a62f15e87c0ed791b6c8db2271ba0fd7c2686090510214 -SIZE (rust/crates/pyo3-macros-0.25.0.crate) = 8876 -SHA256 (rust/crates/pyo3-macros-backend-0.25.0.crate) = 9dff85ebcaab8c441b0e3f7ae40a6963ecea8a9f5e74f647e33fcf5ec9a1e89e -SIZE (rust/crates/pyo3-macros-backend-0.25.0.crate) = 75089 -SHA256 (rust/crates/quote-1.0.39.crate) = c1f1914ce909e1658d9907913b4b91947430c7d9be598b15a1912935b8c04801 -SIZE (rust/crates/quote-1.0.39.crate) = 31206 +SHA256 (rust/crates/pyo3-0.25.1.crate) = 8970a78afe0628a3e3430376fc5fd76b6b45c4d43360ffd6cdd40bdde72b682a +SIZE (rust/crates/pyo3-0.25.1.crate) = 1121993 +SHA256 (rust/crates/pyo3-build-config-0.25.1.crate) = 458eb0c55e7ece017adeba38f2248ff3ac615e53660d7c71a238d7d2a01c7598 +SIZE (rust/crates/pyo3-build-config-0.25.1.crate) = 34126 +SHA256 (rust/crates/pyo3-ffi-0.25.1.crate) = 7114fe5457c61b276ab77c5055f206295b812608083644a5c5b2640c3102565c +SIZE (rust/crates/pyo3-ffi-0.25.1.crate) = 78058 +SHA256 (rust/crates/pyo3-macros-0.25.1.crate) = a8725c0a622b374d6cb051d11a0983786448f7785336139c3c94f5aa6bef7e50 +SIZE (rust/crates/pyo3-macros-0.25.1.crate) = 8886 +SHA256 (rust/crates/pyo3-macros-backend-0.25.1.crate) = 4109984c22491085343c05b0dbc54ddc405c3cf7b4374fc533f5c3313a572ccc +SIZE (rust/crates/pyo3-macros-backend-0.25.1.crate) = 76006 +SHA256 (rust/crates/quote-1.0.40.crate) = 1885c039570dc00dcb4ff087a89e185fd56bae234ddc7f056a945bf36467248d +SIZE (rust/crates/quote-1.0.40.crate) = 31063 +SHA256 (rust/crates/r-efi-5.3.0.crate) = 69cdb34c158ceb288df11e18b4bd39de994f6657d83847bdffdbd7f346754b0f +SIZE (rust/crates/r-efi-5.3.0.crate) = 64532 SHA256 (rust/crates/ra_ap_limit-0.0.188.crate) = 92d33758724f997689f84146e5401e28d875a061804f861f113696f44f5232aa SIZE (rust/crates/ra_ap_limit-0.0.188.crate) = 1283 SHA256 (rust/crates/rand-0.8.5.crate) = 34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404 SIZE (rust/crates/rand-0.8.5.crate) = 87113 -SHA256 (rust/crates/rand-0.9.0.crate) = 3779b94aeb87e8bd4e834cee3650289ee9e0d5677f976ecdb6d219e5f4f6cd94 -SIZE (rust/crates/rand-0.9.0.crate) = 97798 +SHA256 (rust/crates/rand-0.9.2.crate) = 6db2770f06117d490610c7488547d543617b21bfa07796d7a12f6f1bd53850d1 +SIZE (rust/crates/rand-0.9.2.crate) = 99930 SHA256 (rust/crates/rand_chacha-0.3.1.crate) = e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88 SIZE (rust/crates/rand_chacha-0.3.1.crate) = 15251 SHA256 (rust/crates/rand_chacha-0.9.0.crate) = d3022b5f1df60f26e1ffddd6c66e8aa15de382ae63b3a0c1bfc0e4d3e3f325cb @@ -311,24 +309,26 @@ SHA256 (rust/crates/rand_pcg-0.3.1.crate) = 59cad018caf63deb318e5a4586d99a24424a SIZE (rust/crates/rand_pcg-0.3.1.crate) = 11983 SHA256 (rust/crates/rand_pcg-0.9.0.crate) = b48ac3f7ffaab7fac4d2376632268aa5f89abdb55f7ebf8f4d11fffccb2320f7 SIZE (rust/crates/rand_pcg-0.9.0.crate) = 15179 -SHA256 (rust/crates/raw-cpuid-11.4.0.crate) = 529468c1335c1c03919960dfefdb1b3648858c20d7ec2d0663e728e4a717efbc -SIZE (rust/crates/raw-cpuid-11.4.0.crate) = 110368 +SHA256 (rust/crates/raw-cpuid-11.6.0.crate) = 498cd0dc59d73224351ee52a95fee0f1a617a2eae0e7d9d720cc622c73a54186 +SIZE (rust/crates/raw-cpuid-11.6.0.crate) = 117569 SHA256 (rust/crates/rawpointer-0.2.1.crate) = 60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3 SIZE (rust/crates/rawpointer-0.2.1.crate) = 7490 -SHA256 (rust/crates/rayon-1.10.0.crate) = b418a60154510ca1a002a752ca9714984e21e4241e804d32555251faf8b78ffa -SIZE (rust/crates/rayon-1.10.0.crate) = 180155 +SHA256 (rust/crates/rayon-1.11.0.crate) = 368f01d005bf8fd9b1206fb6fa653e6c4a81ceb1466406b81792d87c5677a58f +SIZE (rust/crates/rayon-1.11.0.crate) = 182470 SHA256 (rust/crates/rayon-cond-0.3.0.crate) = 059f538b55efd2309c9794130bc149c6a553db90e9d99c2030785c82f0bd7df9 SIZE (rust/crates/rayon-cond-0.3.0.crate) = 9913 -SHA256 (rust/crates/rayon-core-1.12.1.crate) = 1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2 -SIZE (rust/crates/rayon-core-1.12.1.crate) = 70701 +SHA256 (rust/crates/rayon-cond-0.4.0.crate) = 2964d0cf57a3e7a06e8183d14a8b527195c706b7983549cd5462d5aa3747438f +SIZE (rust/crates/rayon-cond-0.4.0.crate) = 10659 +SHA256 (rust/crates/rayon-core-1.13.0.crate) = 22e18b0f0062d30d4230b2e85ff77fdfe4326feb054b9783a3460d8435c8ab91 +SIZE (rust/crates/rayon-core-1.13.0.crate) = 73151 SHA256 (rust/crates/reborrow-0.5.5.crate) = 03251193000f4bd3b042892be858ee50e8b3719f2b08e5833ac4353724632430 SIZE (rust/crates/reborrow-0.5.5.crate) = 3789 -SHA256 (rust/crates/regex-1.11.1.crate) = b544ef1b4eac5dc2db33ea63606ae9ffcfac26c1416a2806ae0bf5f56b201191 -SIZE (rust/crates/regex-1.11.1.crate) = 254170 -SHA256 (rust/crates/regex-automata-0.4.9.crate) = 809e8dc61f6de73b46c85f4c96486310fe304c434cfa43669d7b40f711150908 -SIZE (rust/crates/regex-automata-0.4.9.crate) = 618525 -SHA256 (rust/crates/regex-syntax-0.8.5.crate) = 2b15c43186be67a4fd63bee50d0303afffcef381492ebe2c5d87f324e1b8815c -SIZE (rust/crates/regex-syntax-0.8.5.crate) = 357541 +SHA256 (rust/crates/regex-1.11.2.crate) = 23d7fd106d8c02486a8d64e778353d1cffe08ce79ac2e82f540c86d0facf6912 +SIZE (rust/crates/regex-1.11.2.crate) = 166265 +SHA256 (rust/crates/regex-automata-0.4.10.crate) = 6b9458fa0bfeeac22b5ca447c63aaf45f28439a709ccd244698632f9aa6394d6 +SIZE (rust/crates/regex-automata-0.4.10.crate) = 622754 +SHA256 (rust/crates/regex-syntax-0.8.6.crate) = caf4aa5b0f434c91fe5c7f1ecb6a5ece2130b02ad2a590589dda5146df959001 +SIZE (rust/crates/regex-syntax-0.8.6.crate) = 358808 SHA256 (rust/crates/rowan-0.15.15.crate) = 32a58fa8a7ccff2aec4f39cc45bf5f985cec7125ab271cf681c279fd00192b49 SIZE (rust/crates/rowan-0.15.15.crate) = 39971 SHA256 (rust/crates/rstar-0.12.2.crate) = 421400d13ccfd26dfa5858199c30a5d76f9c54e0dba7575273025b43c5175dbb @@ -339,10 +339,10 @@ SHA256 (rust/crates/rustc-hash-2.1.1.crate) = 357703d41365b4b27c590e3ed91eabb1b6 SIZE (rust/crates/rustc-hash-2.1.1.crate) = 14154 SHA256 (rust/crates/rustiq-core-0.0.11.crate) = 51bfa802a80a4fa591941e4caaf2d6d7793ae3ffd307022afe0739453fae07a6 SIZE (rust/crates/rustiq-core-0.0.11.crate) = 41963 -SHA256 (rust/crates/rustix-0.38.44.crate) = fdb5bc1ae2baa591800df16c9ca78619bf65c0488b41b96ccec5d11220d8c154 -SIZE (rust/crates/rustix-0.38.44.crate) = 379347 -SHA256 (rust/crates/rustversion-1.0.20.crate) = eded382c5f5f786b989652c49544c4877d9f015cc22e145a5ea8ea66c2921cd2 -SIZE (rust/crates/rustversion-1.0.20.crate) = 20666 +SHA256 (rust/crates/rustix-1.1.2.crate) = cd15f8a2c5551a84d56efdc1cd049089e409ac19a3072d5037a17fd70719ff3e +SIZE (rust/crates/rustix-1.1.2.crate) = 422717 +SHA256 (rust/crates/rustversion-1.0.22.crate) = b39cdef0fa800fc44525c84ccb54a029961a8215f9619753635a9c0d2538d46d +SIZE (rust/crates/rustversion-1.0.22.crate) = 21096 SHA256 (rust/crates/rustworkx-core-0.16.0.crate) = f8a4717d3df536ce531369b8c9a0c7f9624a51cf9c3948038ed3cb18e9a16c92 SIZE (rust/crates/rustworkx-core-0.16.0.crate) = 134307 SHA256 (rust/crates/ryu-1.0.20.crate) = 28d3b2b1366ec20994f1fd18c3c594f05c5dd4bc44d8bb0c1c632c8d6829481f @@ -353,20 +353,22 @@ SHA256 (rust/crates/same-file-1.0.6.crate) = 93fc1dc3aaa9bfed95e02e6eadabb4baf7e SIZE (rust/crates/same-file-1.0.6.crate) = 10183 SHA256 (rust/crates/seq-macro-0.3.6.crate) = 1bc711410fbe7399f390ca1c3b60ad0f53f80e95c5eb935e52268a0e2cd49acc SIZE (rust/crates/seq-macro-0.3.6.crate) = 16031 -SHA256 (rust/crates/serde-1.0.219.crate) = 5f0e2c6ed6606019b4e29e69dbaba95b11854410e5347d525002456dbbb786b6 -SIZE (rust/crates/serde-1.0.219.crate) = 78983 -SHA256 (rust/crates/serde_derive-1.0.219.crate) = 5b0276cf7f2c73365f7157c8123c21cd9a50fbbd844757af28ca1f5925fc2a00 -SIZE (rust/crates/serde_derive-1.0.219.crate) = 57798 -SHA256 (rust/crates/serde_json-1.0.140.crate) = 20068b6e96dc6c9bd23e01df8827e6c7e1f2fddd43c21810382803c136b99373 -SIZE (rust/crates/serde_json-1.0.140.crate) = 154852 -SHA256 (rust/crates/serde_spanned-0.6.8.crate) = 87607cb1398ed59d48732e575a4c28a7a8ebf2454b964fe3f224f2afc07909e1 -SIZE (rust/crates/serde_spanned-0.6.8.crate) = 9330 -SHA256 (rust/crates/sha2-0.10.8.crate) = 793db75ad2bcafc3ffa7c68b215fee268f537982cd901d132f89c6343f3a3dc8 -SIZE (rust/crates/sha2-0.10.8.crate) = 26357 -SHA256 (rust/crates/simba-0.9.0.crate) = b3a386a501cd104797982c15ae17aafe8b9261315b5d07e3ec803f2ea26be0fa -SIZE (rust/crates/simba-0.9.0.crate) = 52680 -SHA256 (rust/crates/smallvec-1.15.0.crate) = 8917285742e9f3e1683f0a9c4e6b57960b7314d0b08d30d1ecd426713ee2eee9 -SIZE (rust/crates/smallvec-1.15.0.crate) = 38113 +SHA256 (rust/crates/serde-1.0.225.crate) = fd6c24dee235d0da097043389623fb913daddf92c76e9f5a1db88607a0bcbd1d +SIZE (rust/crates/serde-1.0.225.crate) = 28467 +SHA256 (rust/crates/serde_core-1.0.225.crate) = 659356f9a0cb1e529b24c01e43ad2bdf520ec4ceaf83047b83ddcc2251f96383 +SIZE (rust/crates/serde_core-1.0.225.crate) = 63004 +SHA256 (rust/crates/serde_derive-1.0.225.crate) = 0ea936adf78b1f766949a4977b91d2f5595825bd6ec079aa9543ad2685fc4516 +SIZE (rust/crates/serde_derive-1.0.225.crate) = 58560 +SHA256 (rust/crates/serde_json-1.0.145.crate) = 402a6f66d8c709116cf22f558eab210f5a50187f702eb4d7e5ef38d9a7f1c79c +SIZE (rust/crates/serde_json-1.0.145.crate) = 155748 +SHA256 (rust/crates/serde_spanned-0.6.9.crate) = bf41e0cfaf7226dca15e8197172c295a782857fcb97fad1808a166870dee75a3 +SIZE (rust/crates/serde_spanned-0.6.9.crate) = 10210 +SHA256 (rust/crates/sha2-0.10.9.crate) = a7507d819769d01a365ab707794a4084392c824f54a7a6a7862f8c3d0892b283 +SIZE (rust/crates/sha2-0.10.9.crate) = 29271 +SHA256 (rust/crates/simba-0.9.1.crate) = c99284beb21666094ba2b75bbceda012e610f5479dfcc2d6e2426f53197ffd95 +SIZE (rust/crates/simba-0.9.1.crate) = 57448 +SHA256 (rust/crates/smallvec-1.15.1.crate) = 67b1b7a3b5fe4f1376887184045fcf45c69e92af734b7aaddc05fb777b6fbd03 +SIZE (rust/crates/smallvec-1.15.1.crate) = 38116 SHA256 (rust/crates/smol_str-0.2.2.crate) = dd538fb6910ac1099850255cf94a94df6551fbdd602454387d0adb2d1ca6dead SIZE (rust/crates/smol_str-0.2.2.crate) = 15840 SHA256 (rust/crates/stable_deref_trait-1.2.0.crate) = a8f112729512f8e442d81f95a8a7ddf2b7c6b8a1a6f509a95864142b30cab2d3 @@ -375,40 +377,40 @@ SHA256 (rust/crates/strsim-0.11.1.crate) = 7da8b5736845d9f2fcb837ea5d9e2628564b3 SIZE (rust/crates/strsim-0.11.1.crate) = 14266 SHA256 (rust/crates/syn-1.0.109.crate) = 72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237 SIZE (rust/crates/syn-1.0.109.crate) = 237611 -SHA256 (rust/crates/syn-2.0.99.crate) = e02e925281e18ffd9d640e234264753c43edc62d64b2d4cf898f1bc5e75f3fc2 -SIZE (rust/crates/syn-2.0.99.crate) = 297762 +SHA256 (rust/crates/syn-2.0.106.crate) = ede7c438028d4436d71104916910f5bb611972c5cfd7f89b8300a8186e6fada6 +SIZE (rust/crates/syn-2.0.106.crate) = 301514 SHA256 (rust/crates/sysctl-0.6.0.crate) = 01198a2debb237c62b6826ec7081082d951f46dbb64b0e8c7649a452230d1dfc SIZE (rust/crates/sysctl-0.6.0.crate) = 18829 -SHA256 (rust/crates/target-lexicon-0.12.16.crate) = 61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1 -SIZE (rust/crates/target-lexicon-0.12.16.crate) = 26488 -SHA256 (rust/crates/target-lexicon-0.13.2.crate) = e502f78cdbb8ba4718f566c418c52bc729126ffd16baee5baa718cf25dd5a69a -SIZE (rust/crates/target-lexicon-0.13.2.crate) = 27923 -SHA256 (rust/crates/tempfile-3.17.1.crate) = 22e5a0acb1f3f55f65cc4a866c361b2fb2a0ff6366785ae6fbb5f85df07ba230 -SIZE (rust/crates/tempfile-3.17.1.crate) = 39240 +SHA256 (rust/crates/target-lexicon-0.13.3.crate) = df7f62577c25e07834649fc3b39fafdc597c0a3527dc1c60129201ccfcbaa50c +SIZE (rust/crates/target-lexicon-0.13.3.crate) = 28498 +SHA256 (rust/crates/tempfile-3.22.0.crate) = 84fa4d11fadde498443cca10fd3ac23c951f0dc59e080e9f4b93d4df4e4eea53 +SIZE (rust/crates/tempfile-3.22.0.crate) = 43044 SHA256 (rust/crates/text-size-1.1.1.crate) = f18aa187839b2bdb1ad2fa35ead8c4c2976b64e4363c386d45ac0f7ee85c9233 SIZE (rust/crates/text-size-1.1.1.crate) = 12553 SHA256 (rust/crates/thiserror-1.0.69.crate) = b6aaf5339b578ea85b50e080feb250a3e8ae8cfcdff9a461c9ec2904bc923f52 SIZE (rust/crates/thiserror-1.0.69.crate) = 22198 -SHA256 (rust/crates/thiserror-2.0.12.crate) = 567b8a2dae586314f7be2a752ec7474332959c6460e02bde30d702a66d488708 -SIZE (rust/crates/thiserror-2.0.12.crate) = 28693 +SHA256 (rust/crates/thiserror-2.0.16.crate) = 3467d614147380f2e4e374161426ff399c91084acd2363eaf549172b3d5e60c0 +SIZE (rust/crates/thiserror-2.0.16.crate) = 29095 SHA256 (rust/crates/thiserror-impl-1.0.69.crate) = 4fee6c4efc90059e10f81e6d42c60a18f76588c3d74cb83a0b242a2b6c7504c1 SIZE (rust/crates/thiserror-impl-1.0.69.crate) = 18365 -SHA256 (rust/crates/thiserror-impl-2.0.12.crate) = 7f7cf42b4507d8ea322120659672cf1b9dbb93f8f2d4ecfd6e51350ff5b17a1d -SIZE (rust/crates/thiserror-impl-2.0.12.crate) = 21141 -SHA256 (rust/crates/toml-0.8.20.crate) = cd87a5cdd6ffab733b2f74bc4fd7ee5fff6634124999ac278c35fc78c6120148 -SIZE (rust/crates/toml-0.8.20.crate) = 51095 -SHA256 (rust/crates/toml_datetime-0.6.8.crate) = 0dd7358ecb8fc2f8d014bf86f6f638ce72ba252a2c3a2572f2a795f1d23efb41 -SIZE (rust/crates/toml_datetime-0.6.8.crate) = 12028 -SHA256 (rust/crates/toml_edit-0.22.24.crate) = 17b4795ff5edd201c7cd6dca065ae59972ce77d1b80fa0a84d94950ece7d1474 -SIZE (rust/crates/toml_edit-0.22.24.crate) = 106399 +SHA256 (rust/crates/thiserror-impl-2.0.16.crate) = 6c5e1be1c48b9172ee610da68fd9cd2770e7a4056cb3fc98710ee6906f0c7960 +SIZE (rust/crates/thiserror-impl-2.0.16.crate) = 21214 +SHA256 (rust/crates/toml-0.8.23.crate) = dc1beb996b9d83529a9e75c17a1686767d148d70663143c7854d8b4a09ced362 +SIZE (rust/crates/toml-0.8.23.crate) = 36050 +SHA256 (rust/crates/toml_datetime-0.6.11.crate) = 22cddaf88f4fbc13c51aebbf5f8eceb5c7c5a9da2ac40a13519eb5b0a0e8f11c +SIZE (rust/crates/toml_datetime-0.6.11.crate) = 16125 +SHA256 (rust/crates/toml_edit-0.22.27.crate) = 41fe8c660ae4257887cf66394862d21dbca4a6ddd26f04a3560410406a2f819a +SIZE (rust/crates/toml_edit-0.22.27.crate) = 78602 +SHA256 (rust/crates/toml_write-0.1.2.crate) = 5d99f8c9a7727884afe522e9bd5edbfc91a3312b36a77b5fb8926e4c31a41801 +SIZE (rust/crates/toml_write-0.1.2.crate) = 15660 SHA256 (rust/crates/triomphe-0.1.11.crate) = 859eb650cfee7434994602c3a68b25d77ad9e68c8a6cd491616ef86661382eb3 SIZE (rust/crates/triomphe-0.1.11.crate) = 28299 SHA256 (rust/crates/typenum-1.18.0.crate) = 1dccffe3ce07af9386bfd29e80c0ab1a8205a2fc34e4bcd40364df902cfa8f3f SIZE (rust/crates/typenum-1.18.0.crate) = 74871 SHA256 (rust/crates/ucd-trie-0.1.7.crate) = 2896d95c02a80c6d6a5d6e953d479f5ddf2dfdb6a244441010e373ac0fb88971 SIZE (rust/crates/ucd-trie-0.1.7.crate) = 46795 -SHA256 (rust/crates/unicode-ident-1.0.18.crate) = 5a5f39404a5da50712a4c1eecf25e90dd62b613502b7e925fd4e4d19b5c96512 -SIZE (rust/crates/unicode-ident-1.0.18.crate) = 47743 +SHA256 (rust/crates/unicode-ident-1.0.19.crate) = f63a545481291138910575129486daeaf8ac54aee4387fe7906919f7830c7d9d +SIZE (rust/crates/unicode-ident-1.0.19.crate) = 47480 SHA256 (rust/crates/unicode-properties-0.1.3.crate) = e70f2a8b45122e719eb623c01822704c4e0907e7e426a05927e1a1cfff5b75d0 SIZE (rust/crates/unicode-properties-0.1.3.crate) = 42252 SHA256 (rust/crates/unicode-width-0.1.14.crate) = 7dd6e30e90baa6f72411720665d41d89b9a3d039dc45b8faea1ddd07f617f6af @@ -419,71 +421,99 @@ SHA256 (rust/crates/unindent-0.2.4.crate) = 7264e107f553ccae879d21fbea1d6724ac78 SIZE (rust/crates/unindent-0.2.4.crate) = 7422 SHA256 (rust/crates/utf8parse-0.2.2.crate) = 06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821 SIZE (rust/crates/utf8parse-0.2.2.crate) = 13499 -SHA256 (rust/crates/uuid-1.17.0.crate) = 3cf4199d1e5d15ddd86a694e4d0dffa9c323ce759fea589f00fef9d81cc1931d -SIZE (rust/crates/uuid-1.17.0.crate) = 59014 +SHA256 (rust/crates/uuid-1.18.1.crate) = 2f87b8aa10b915a06587d0dec516c282ff295b475d94abf425d62b57710070a2 +SIZE (rust/crates/uuid-1.18.1.crate) = 60468 SHA256 (rust/crates/version_check-0.9.5.crate) = 0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a SIZE (rust/crates/version_check-0.9.5.crate) = 15554 SHA256 (rust/crates/walkdir-2.5.0.crate) = 29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b SIZE (rust/crates/walkdir-2.5.0.crate) = 23951 -SHA256 (rust/crates/wasi-0.11.0+wasi-snapshot-preview1.crate) = 9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423 -SIZE (rust/crates/wasi-0.11.0+wasi-snapshot-preview1.crate) = 28131 -SHA256 (rust/crates/wasi-0.13.3+wasi-0.2.2.crate) = 26816d2e1a4a36a2940b96c5296ce403917633dff8f3440e9b236ed6f6bacad2 -SIZE (rust/crates/wasi-0.13.3+wasi-0.2.2.crate) = 136754 -SHA256 (rust/crates/wide-0.7.32.crate) = 41b5576b9a81633f3e8df296ce0063042a73507636cbe956c61133dd7034ab22 -SIZE (rust/crates/wide-0.7.32.crate) = 95848 -SHA256 (rust/crates/winapi-util-0.1.9.crate) = cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb -SIZE (rust/crates/winapi-util-0.1.9.crate) = 12464 +SHA256 (rust/crates/wasi-0.11.1+wasi-snapshot-preview1.crate) = ccf3ec651a847eb01de73ccad15eb7d99f80485de043efb2f370cd654f4ea44b +SIZE (rust/crates/wasi-0.11.1+wasi-snapshot-preview1.crate) = 28477 +SHA256 (rust/crates/wasi-0.14.7+wasi-0.2.4.crate) = 883478de20367e224c0090af9cf5f9fa85bed63a95c1abf3afc5c083ebc06e8c +SIZE (rust/crates/wasi-0.14.7+wasi-0.2.4.crate) = 18219 +SHA256 (rust/crates/wasip2-1.0.1+wasi-0.2.4.crate) = 0562428422c63773dad2c345a1882263bbf4d65cf3f42e90921f787ef5ad58e7 +SIZE (rust/crates/wasip2-1.0.1+wasi-0.2.4.crate) = 132087 +SHA256 (rust/crates/wide-0.7.33.crate) = 0ce5da8ecb62bcd8ec8b7ea19f69a51275e91299be594ea5cc6ef7819e16cd03 +SIZE (rust/crates/wide-0.7.33.crate) = 99792 +SHA256 (rust/crates/winapi-util-0.1.11.crate) = c2a7b1c03c876122aa43f3020e6c3c3ee5c05081c9a00739faf7503aeba10d22 +SIZE (rust/crates/winapi-util-0.1.11.crate) = 13368 +SHA256 (rust/crates/windows-link-0.1.3.crate) = 5e6ad25900d524eaabdbbb96d20b4311e1e7ae1699af4fb28c17ae66c80d798a +SIZE (rust/crates/windows-link-0.1.3.crate) = 6154 +SHA256 (rust/crates/windows-link-0.2.0.crate) = 45e46c0661abb7180e7b9c281db115305d49ca1709ab8242adf09666d2173c65 +SIZE (rust/crates/windows-link-0.2.0.crate) = 6170 SHA256 (rust/crates/windows-sys-0.45.0.crate) = 75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0 SIZE (rust/crates/windows-sys-0.45.0.crate) = 2568659 SHA256 (rust/crates/windows-sys-0.59.0.crate) = 1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b SIZE (rust/crates/windows-sys-0.59.0.crate) = 2387323 +SHA256 (rust/crates/windows-sys-0.60.2.crate) = f2f500e4d28234f72040990ec9d39e3a6b950f9f22d3dba18416c35882612bcb +SIZE (rust/crates/windows-sys-0.60.2.crate) = 2518479 +SHA256 (rust/crates/windows-sys-0.61.0.crate) = e201184e40b2ede64bc2ea34968b28e33622acdbbf37104f0e4a33f7abe657aa +SIZE (rust/crates/windows-sys-0.61.0.crate) = 2517134 SHA256 (rust/crates/windows-targets-0.42.2.crate) = 8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071 SIZE (rust/crates/windows-targets-0.42.2.crate) = 5492 SHA256 (rust/crates/windows-targets-0.52.6.crate) = 9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973 SIZE (rust/crates/windows-targets-0.52.6.crate) = 6403 +SHA256 (rust/crates/windows-targets-0.53.3.crate) = d5fe6031c4041849d7c496a8ded650796e7b6ecc19df1a431c1a363342e5dc91 +SIZE (rust/crates/windows-targets-0.53.3.crate) = 7099 SHA256 (rust/crates/windows_aarch64_gnullvm-0.42.2.crate) = 597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8 SIZE (rust/crates/windows_aarch64_gnullvm-0.42.2.crate) = 364071 SHA256 (rust/crates/windows_aarch64_gnullvm-0.52.6.crate) = 32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3 SIZE (rust/crates/windows_aarch64_gnullvm-0.52.6.crate) = 435718 +SHA256 (rust/crates/windows_aarch64_gnullvm-0.53.0.crate) = 86b8d5f90ddd19cb4a147a5fa63ca848db3df085e25fee3cc10b39b6eebae764 +SIZE (rust/crates/windows_aarch64_gnullvm-0.53.0.crate) = 782443 SHA256 (rust/crates/windows_aarch64_msvc-0.42.2.crate) = e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43 SIZE (rust/crates/windows_aarch64_msvc-0.42.2.crate) = 666981 SHA256 (rust/crates/windows_aarch64_msvc-0.52.6.crate) = 09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469 SIZE (rust/crates/windows_aarch64_msvc-0.52.6.crate) = 832615 +SHA256 (rust/crates/windows_aarch64_msvc-0.53.0.crate) = c7651a1f62a11b8cbd5e0d42526e55f2c99886c77e007179efff86c2b137e66c +SIZE (rust/crates/windows_aarch64_msvc-0.53.0.crate) = 834446 SHA256 (rust/crates/windows_i686_gnu-0.42.2.crate) = c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f SIZE (rust/crates/windows_i686_gnu-0.42.2.crate) = 736236 SHA256 (rust/crates/windows_i686_gnu-0.52.6.crate) = 8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b SIZE (rust/crates/windows_i686_gnu-0.52.6.crate) = 880402 +SHA256 (rust/crates/windows_i686_gnu-0.53.0.crate) = c1dc67659d35f387f5f6c479dc4e28f1d4bb90ddd1a5d3da2e5d97b42d6272c3 +SIZE (rust/crates/windows_i686_gnu-0.53.0.crate) = 936973 SHA256 (rust/crates/windows_i686_gnullvm-0.52.6.crate) = 0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66 SIZE (rust/crates/windows_i686_gnullvm-0.52.6.crate) = 475940 +SHA256 (rust/crates/windows_i686_gnullvm-0.53.0.crate) = 9ce6ccbdedbf6d6354471319e781c0dfef054c81fbc7cf83f338a4296c0cae11 +SIZE (rust/crates/windows_i686_gnullvm-0.53.0.crate) = 854056 SHA256 (rust/crates/windows_i686_msvc-0.42.2.crate) = 44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060 SIZE (rust/crates/windows_i686_msvc-0.42.2.crate) = 724951 SHA256 (rust/crates/windows_i686_msvc-0.52.6.crate) = 240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66 SIZE (rust/crates/windows_i686_msvc-0.52.6.crate) = 901163 +SHA256 (rust/crates/windows_i686_msvc-0.53.0.crate) = 581fee95406bb13382d2f65cd4a908ca7b1e4c2f1917f143ba16efe98a589b5d +SIZE (rust/crates/windows_i686_msvc-0.53.0.crate) = 903450 SHA256 (rust/crates/windows_x86_64_gnu-0.42.2.crate) = 8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36 SIZE (rust/crates/windows_x86_64_gnu-0.42.2.crate) = 699373 SHA256 (rust/crates/windows_x86_64_gnu-0.52.6.crate) = 147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78 SIZE (rust/crates/windows_x86_64_gnu-0.52.6.crate) = 836363 +SHA256 (rust/crates/windows_x86_64_gnu-0.53.0.crate) = 2e55b5ac9ea33f2fc1716d1742db15574fd6fc8dadc51caab1c16a3d3b4190ba +SIZE (rust/crates/windows_x86_64_gnu-0.53.0.crate) = 902585 SHA256 (rust/crates/windows_x86_64_gnullvm-0.42.2.crate) = 26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3 SIZE (rust/crates/windows_x86_64_gnullvm-0.42.2.crate) = 364068 SHA256 (rust/crates/windows_x86_64_gnullvm-0.52.6.crate) = 24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d SIZE (rust/crates/windows_x86_64_gnullvm-0.52.6.crate) = 435707 +SHA256 (rust/crates/windows_x86_64_gnullvm-0.53.0.crate) = 0a6e035dd0599267ce1ee132e51c27dd29437f63325753051e71dd9e42406c57 +SIZE (rust/crates/windows_x86_64_gnullvm-0.53.0.crate) = 782434 SHA256 (rust/crates/windows_x86_64_msvc-0.42.2.crate) = 9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0 SIZE (rust/crates/windows_x86_64_msvc-0.42.2.crate) = 666936 SHA256 (rust/crates/windows_x86_64_msvc-0.52.6.crate) = 589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec SIZE (rust/crates/windows_x86_64_msvc-0.52.6.crate) = 832564 -SHA256 (rust/crates/winnow-0.7.3.crate) = 0e7f4ea97f6f78012141bcdb6a216b2609f0979ada50b20ca5b52dde2eac2bb1 -SIZE (rust/crates/winnow-0.7.3.crate) = 171602 -SHA256 (rust/crates/wit-bindgen-rt-0.33.0.crate) = 3268f3d866458b787f390cf61f4bbb563b922d091359f9608842999eaee3943c -SIZE (rust/crates/wit-bindgen-rt-0.33.0.crate) = 3357 +SHA256 (rust/crates/windows_x86_64_msvc-0.53.0.crate) = 271414315aff87387382ec3d271b52d7ae78726f5d44ac98b4f4030c91880486 +SIZE (rust/crates/windows_x86_64_msvc-0.53.0.crate) = 834400 +SHA256 (rust/crates/winnow-0.7.13.crate) = 21a0236b59786fed61e2a80582dd500fe61f18b5dca67a4a067d0bc9039339cf +SIZE (rust/crates/winnow-0.7.13.crate) = 174454 +SHA256 (rust/crates/wit-bindgen-0.46.0.crate) = f17a85883d4e6d00e8a97c586de764dabcc06133f7f1d55dce5cdc070ad7fe59 +SIZE (rust/crates/wit-bindgen-0.46.0.crate) = 60508 SHA256 (rust/crates/xshell-0.2.7.crate) = 9e7290c623014758632efe00737145b6867b66292c42167f2ec381eb566a373d SIZE (rust/crates/xshell-0.2.7.crate) = 24653 SHA256 (rust/crates/xshell-macros-0.2.7.crate) = 32ac00cd3f8ec9c1d33fb3e7958a82df6989c42d747bd326c822b1d625283547 SIZE (rust/crates/xshell-macros-0.2.7.crate) = 2890 SHA256 (rust/crates/yansi-0.5.1.crate) = 09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec SIZE (rust/crates/yansi-0.5.1.crate) = 16525 -SHA256 (rust/crates/zerocopy-0.8.25.crate) = a1702d9583232ddb9174e01bb7c15a2ab8fb1bc6f227aa1233858c351a3ba0cb -SIZE (rust/crates/zerocopy-0.8.25.crate) = 252714 -SHA256 (rust/crates/zerocopy-derive-0.8.25.crate) = 28a6e20d751156648aa063f3800b706ee209a32c0b4d9f24be3d980b01be55ef -SIZE (rust/crates/zerocopy-derive-0.8.25.crate) = 87671 -SHA256 (Qiskit-qiskit-2.1.2_GH0.tar.gz) = 23559ca58042d263152b233843af24f6753d591500de5a84df14a68a54f4a7db -SIZE (Qiskit-qiskit-2.1.2_GH0.tar.gz) = 7100760 +SHA256 (rust/crates/zerocopy-0.8.27.crate) = 0894878a5fa3edfd6da3f88c4805f4c8558e2b996227a3d864f47fe11e38282c +SIZE (rust/crates/zerocopy-0.8.27.crate) = 252663 +SHA256 (rust/crates/zerocopy-derive-0.8.27.crate) = 88d2b8d9c68ad2b9e4340d7832716a4d21a22a1154777ad56ea55c51a9cf3831 +SIZE (rust/crates/zerocopy-derive-0.8.27.crate) = 89827 +SHA256 (Qiskit-qiskit-2.2.1_GH0.tar.gz) = c2cd53ca4d979760dd2e14757aad0d0c5b8870259eb406aebbde10505ddbffff +SIZE (Qiskit-qiskit-2.2.1_GH0.tar.gz) = 7318815 diff --git a/science/py-scikit-learn/Makefile b/science/py-scikit-learn/Makefile index 48e776557e4e..3fb44ba9428f 100644 --- a/science/py-scikit-learn/Makefile +++ b/science/py-scikit-learn/Makefile @@ -1,9 +1,9 @@ PORTNAME= scikit-learn -DISTVERSION= 1.4.0 -PORTREVISION= 1 +DISTVERSION= 1.7.2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= scikit_learn-${DISTVERSION} MAINTAINER= wen@FreeBSD.org COMMENT= Machine learning algorithms for python @@ -12,19 +12,20 @@ WWW= https://scikit-learn.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}joblib>0:devel/py-joblib@${PY_FLAVOR} \ +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}joblib>=1.3.0:devel/py-joblib@${PY_FLAVOR} \ ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=1.3.2:science/py-scipy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}threadpoolctl>=0:devel/py-threadpoolctl@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}scipy>=1.10.0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}threadpoolctl>=3.2.0:devel/py-threadpoolctl@${PY_FLAVOR} RUN_DEPENDS:= ${BUILD_DEPENDS} +BUILD_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}meson-python>=0.17.1:devel/meson-python@${PY_FLAVOR} -USES= fortran python localbase -USE_PYTHON= distutils autoplist cython +USES= fortran python localbase shebangfix +USE_PYTHON= autoplist cython3 pep517 pytest -POST_PLIST= fix-plist +TEST_ARGS= sklearn +TEST_WRKSRC= ${STAGEDIR}${PYTHON_SITELIBDIR} -fix-plist: # https://github.com/scikit-learn/scikit-learn/issues/12681 - @${REINPLACE_CMD} -e "s|lib/python.*/sklearn/datasets/tests/data/openml$$||" ${TMPPLIST} +SHEBANG_FILES= sklearn/_build_utils/version.py post-install: # strip binaries @${STRIP_CMD} \ diff --git a/science/py-scikit-learn/distinfo b/science/py-scikit-learn/distinfo index d36e630a9747..2f21dc52ebc2 100644 --- a/science/py-scikit-learn/distinfo +++ b/science/py-scikit-learn/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1705575324 -SHA256 (scikit-learn-1.4.0.tar.gz) = d4373c984eba20e393216edd51a3e3eede56cbe93d4247516d205643c3b93121 -SIZE (scikit-learn-1.4.0.tar.gz) = 7706781 +TIMESTAMP = 1761685556 +SHA256 (scikit_learn-1.7.2.tar.gz) = 20e9e49ecd130598f1ca38a1d85090e1a600147b9c02fa6f15d69cb53d968fda +SIZE (scikit_learn-1.7.2.tar.gz) = 7193136 diff --git a/science/py-scikit-learn/files/patch-pyproject.toml b/science/py-scikit-learn/files/patch-pyproject.toml new file mode 100644 index 000000000000..7f238de2e52b --- /dev/null +++ b/science/py-scikit-learn/files/patch-pyproject.toml @@ -0,0 +1,11 @@ +--- pyproject.toml.orig 2025-10-28 21:25:52 UTC ++++ pyproject.toml +@@ -99,7 +99,7 @@ build-backend = "mesonpy" + requires = [ + "meson-python>=0.16.0,<0.19.0", + "Cython>=3.0.10,<3.2.0", +- "numpy>=2,<2.4.0", ++ "numpy", + "scipy>=1.8.0,<1.17.0", + ] + diff --git a/science/py-scikit-sparse/Makefile b/science/py-scikit-sparse/Makefile index e80c63af51fe..07833b0bb0eb 100644 --- a/science/py-scikit-sparse/Makefile +++ b/science/py-scikit-sparse/Makefile @@ -1,7 +1,7 @@ PORTNAME= scikit-sparse DISTVERSIONPREFIX= v DISTVERSION= 0.4.16 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python #MASTER_SITES= PYPI # missing files under tests/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-scikit-sparse/distinfo b/science/py-scikit-sparse/distinfo index ee3f17141528..2278af1b41e1 100644 --- a/science/py-scikit-sparse/distinfo +++ b/science/py-scikit-sparse/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1745401659 -SHA256 (scikit-sparse-scikit-sparse-v0.4.16_GH0.tar.gz) = 88183df0aca206d22cecec479a96b656785ab8a8681e0429a36cc7d6f464425f -SIZE (scikit-sparse-scikit-sparse-v0.4.16_GH0.tar.gz) = 414739 +TIMESTAMP = 1761722287 +SHA256 (scikit-sparse-scikit-sparse-v0.4.16_GH0.tar.gz) = be75af5e8a9ff4bb947c2de02936d26b7727b1f92aa74fbd6cdb57414946e82f +SIZE (scikit-sparse-scikit-sparse-v0.4.16_GH0.tar.gz) = 414706 diff --git a/science/py-scipy/Makefile b/science/py-scipy/Makefile index 4c6e83b43d50..46f54d016a56 100644 --- a/science/py-scipy/Makefile +++ b/science/py-scipy/Makefile @@ -37,7 +37,7 @@ TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}gmpy2>0:math/py-gmpy2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-xdist>0:devel/py-pytest-xdist@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-umfpack>0:math/py-scikit-umfpack@${PY_FLAVOR} -USES= compiler:c++14-lang cpe fortran python:3.9-3.11 shebangfix +USES= compiler:c++14-lang cpe fortran python:3.10-3.11 shebangfix USE_PYTHON= autoplist concurrent cython distutils FFLAGS+= -std=legacy diff --git a/science/py-segregation/Makefile b/science/py-segregation/Makefile index 88bd0223be01..45c0e6a206cf 100644 --- a/science/py-segregation/Makefile +++ b/science/py-segregation/Makefile @@ -1,6 +1,5 @@ PORTNAME= segregation -PORTVERSION= 2.5 -PORTREVISION= 2 +PORTVERSION= 2.5.2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-segregation/distinfo b/science/py-segregation/distinfo index 15fdc5337c67..562ab0b0feab 100644 --- a/science/py-segregation/distinfo +++ b/science/py-segregation/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1722711247 -SHA256 (segregation-2.5.tar.gz) = 0329668682fe3e7c114ebe586619d7702af05d978b124efda0a5fce08b4afe8d -SIZE (segregation-2.5.tar.gz) = 15929712 +TIMESTAMP = 1748831254 +SHA256 (segregation-2.5.2.tar.gz) = e2a2e580818032f7924b871ee43257cfc684572305df3a9f27ff6e1d647643c6 +SIZE (segregation-2.5.2.tar.gz) = 15930587 diff --git a/science/py-spaghetti/Makefile b/science/py-spaghetti/Makefile index ad697e57e285..308535880617 100644 --- a/science/py-spaghetti/Makefile +++ b/science/py-spaghetti/Makefile @@ -1,5 +1,5 @@ PORTNAME= spaghetti -PORTVERSION= 1.7.4 +PORTVERSION= 1.7.6 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,12 +15,14 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=61.0:devel/py-setuptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}setuptools-scm>=6.2:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}esda>=0:science/py-esda@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}libpysal>=0:science/py-libpysal@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pandas>=1.0,1:math/py-pandas@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}rtree>=0:devel/py-rtree@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=1.0:science/py-scipy@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}esda>=2.1:science/py-esda@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}geopandas>=0.12:graphics/py-geopandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}libpysal>=4.6:science/py-libpysal@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.22,1:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=1.4,1:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}rtree>=1.0:devel/py-rtree@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.8:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}shapely>=2.0.1:devel/py-shapely@${PY_FLAVOR} USES= python USE_PYTHON= autoplist concurrent pep517 diff --git a/science/py-spaghetti/distinfo b/science/py-spaghetti/distinfo index cc03fdb89878..d7979b32775c 100644 --- a/science/py-spaghetti/distinfo +++ b/science/py-spaghetti/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1688166308 -SHA256 (spaghetti-1.7.4.tar.gz) = 9898ea86744b6ced9923f8bc213964045615f31ce14f304d20db0aecca40728d -SIZE (spaghetti-1.7.4.tar.gz) = 22151842 +TIMESTAMP = 1721710289 +SHA256 (spaghetti-1.7.6.tar.gz) = c9beddbb3bf285e88745d36aee886c78ac6e6a416f0f9b1a441265c8c08f923d +SIZE (spaghetti-1.7.6.tar.gz) = 22156350 diff --git a/science/py-vedo/Makefile b/science/py-vedo/Makefile index ca0e5d9e8df8..d5ab3ddf354d 100644 --- a/science/py-vedo/Makefile +++ b/science/py-vedo/Makefile @@ -1,13 +1,13 @@ PORTNAME= vedo -DISTVERSION= 2024.5.3 -PORTREVISION= 1 +DISTVERSION= 2025.5.4 CATEGORIES= science graphics python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python module for scientific analysis and visualization of 3D objects -WWW= https://vedo.embl.es/ +WWW= https://vedo.embl.es/ \ + https://github.com/marcomusy/vedo LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/science/py-vedo/distinfo b/science/py-vedo/distinfo index d37849216547..2b5cfd067279 100644 --- a/science/py-vedo/distinfo +++ b/science/py-vedo/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1738040119 -SHA256 (vedo-2024.5.3.tar.gz) = 4828016ecd11387aa7339a2fc117d65751fbacaddd6c9a59f32fb11d62db90a5 -SIZE (vedo-2024.5.3.tar.gz) = 2704730 +TIMESTAMP = 1761675508 +SHA256 (vedo-2025.5.4.tar.gz) = feb585782b99f44f8d2890e689418d593bdeefc2f8c58a80aa2d9ec3a39253a4 +SIZE (vedo-2025.5.4.tar.gz) = 2714801 diff --git a/science/py-veusz/Makefile b/science/py-veusz/Makefile index 0e37c1d52248..6ee685c3877c 100644 --- a/science/py-veusz/Makefile +++ b/science/py-veusz/Makefile @@ -1,13 +1,13 @@ PORTNAME= veusz DISTVERSIONPREFIX= ${PORTNAME}- -DISTVERSION= 3.6.2 -PORTREVISION= 5 +DISTVERSION= 4.2 CATEGORIES= science PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Scientific plotting package -WWW= https://veusz.github.io/ +WWW= https://veusz.github.io/ \ + https://github.com/veusz/veusz LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING @@ -16,11 +16,11 @@ BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}tomli>0:textproc/py-tomli@${PY_FLAVOR} RUN_DEPENDS= ${PYNUMPY} -USES= compiler:c++11-lang python pyqt:5 qt:5 shebangfix +USES= compiler:c++11-lang python pyqt:6 qt:6 shebangfix USE_GITHUB= yes -USE_PYQT= pyqt5 sip:build +USE_PYQT= pyqt6 sip:build USE_PYTHON= distutils concurrent autoplist pytest -USE_QT= core gui xml widgets qmake:build +USE_QT= base tools:build SHEBANG_FILES= tests/runselftest.py examples/embedexample.py @@ -33,4 +33,6 @@ post-install: do-test: @cd ${WRKSRC}/tests && ${SETENV} ${TEST_ENV} ./runselftest.py +# tests as of 4.2: All tests 76/76 PASSED + .include <bsd.port.mk> diff --git a/science/py-veusz/distinfo b/science/py-veusz/distinfo index 2ba43a228774..1a271d94ceaf 100644 --- a/science/py-veusz/distinfo +++ b/science/py-veusz/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1677561281 -SHA256 (veusz-veusz-veusz-3.6.2_GH0.tar.gz) = e3be63af13b5982177fa039617a224fefa420c06446988a838d12a36f2747a96 -SIZE (veusz-veusz-veusz-3.6.2_GH0.tar.gz) = 2457035 +TIMESTAMP = 1761675812 +SHA256 (veusz-veusz-veusz-4.2_GH0.tar.gz) = 617588c9cab19fcd3246bffcc5fd4de5dfe9c0688ea970a250865fe8ce85131e +SIZE (veusz-veusz-veusz-4.2_GH0.tar.gz) = 2996410 diff --git a/science/qiskit-aer/Makefile b/science/qiskit-aer/Makefile index 9a818aa16f08..569eeaf1f786 100644 --- a/science/qiskit-aer/Makefile +++ b/science/qiskit-aer/Makefile @@ -1,6 +1,6 @@ PORTNAME= qiskit-aer DISTVERSION= 0.16.0.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science # quantum-computing MAINTAINER= yuri@FreeBSD.org diff --git a/science/qmcpack/Makefile b/science/qmcpack/Makefile index e53ffec135e8..7bec4719c90a 100644 --- a/science/qmcpack/Makefile +++ b/science/qmcpack/Makefile @@ -1,7 +1,6 @@ PORTNAME= qmcpack DISTVERSIONPREFIX= v -DISTVERSION= 4.0.0 -PORTREVISION= 3 +DISTVERSION= 4.1.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -17,7 +16,7 @@ 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/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/quantum-espresso/Makefile b/science/quantum-espresso/Makefile index 9557826c3c85..90d7bb73b6ca 100644 --- a/science/quantum-espresso/Makefile +++ b/science/quantum-espresso/Makefile @@ -1,7 +1,6 @@ PORTNAME= quantum-espresso DISTVERSIONPREFIX= qe- -DISTVERSION= 7.4 -PORTREVISION= 1 +DISTVERSION= 7.5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -13,24 +12,26 @@ WWW= https://www.quantum-espresso.org \ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/License -BROKEN_aarch64= compilation fails: cannot find an intrinsic module named 'ieee_arithmetic', see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=278942 -BROKEN_armv6= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory -BROKEN_armv7= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory +ONLY_FOR_ARCHS= amd64 i386 +ONLY_FOR_ARCHS_REASON= requires the intrinsic module 'ieee_arithmetic' which is not available on other architectures +#BROKEN_aarch64= compilation fails: cannot find an intrinsic module named 'ieee_arithmetic', see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=278942 +#BROKEN_armv6= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory +#BROKEN_armv7= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory -BUILD_DEPENDS= fox-xml>0:textproc/fox-xml \ +#BUILD_DEPENDS= fox-xml>0:textproc/fox-xml \ bash:shells/bash LIB_DEPENDS= libblas.so:math/blas \ libfftw3.so:math/fftw3 \ liblapack.so:math/lapack \ libopenblas.so:math/openblas -USES= cmake fortran python shebangfix +USES= cmake fortran localbase:ldflags python shebangfix GNU_CONFIGURE= yes USE_GITHUB= yes GH_ACCOUNT= QEF GH_PROJECT= q-e -GH_TUPLE= anharmonic:d3q:de47183:anharmonic_d3q/external/d3q \ +GH_TUPLE= anharmonic:d3q:6e5f978:anharmonic_d3q/external/d3q \ pietrodelugas:fox:3453648e6837658b747b895bb7bef4b1ed2eac40:pietrodelugas_fox/external/fox \ Reference-LAPACK:lapack:12d825396fcef1e0a1b27be9f119f9e554621e55:Reference_LAPACK_lapack/external/lapack \ libmbd:libmbd:89a3cc1:libmbd_libmbd/external/mbd \ @@ -57,7 +58,7 @@ OPTIONS_DEFAULT= OPENMPI MPICH_USES= mpi:mpich -OPENMPI_USES= mpi:openmpi +OPENMPI_USES= mpi:mpich # SEGV with openmpi4 .include <bsd.port.pre.mk> @@ -80,13 +81,18 @@ post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.x do-test: - @cd ${WRKSRC}/test-suite && ${GMAKE} run-tests + @cd ${WRKSRC}/test-suite && \ + ${GMAKE} ESPRESSO_BUILD=${BUILD_WRKSRC} ESPRESSO_PSEUDO=${WRKSRC}/pseudo run-tests run-examples: build .for c in PP PW PWCOND PHonon - @cd ${WRKSRC}/$c/examples && PREFIX=${STAGEDIR}${PREFIX} ./run_all_examples + @cd ${WRKSRC}/$c/examples && PREFIX=${STAGEDIR}${PREFIX} PSEUDO_DIR=/usr/local/share/quantum-espresso ./run_all_examples .endfor -# all tests fail, possibly due to wrong pseudo-potentials, see https://gitlab.com/QEF/q-e/-/issues/745 +# tests as of QE 7.5: 243 out of 247 tests passed (5 skipped, 4 unknown) + +# many pseudopotentials that can be used with QE are listed in https://pseudopotentials.quantum-espresso.org/ +# QE became so popular that many other parties develop and distribute pseudopotentials compatible with QE +# ESPRESSO_PSEUDO is an env variable that can be set to point to a directory with pseudopotentials .include <bsd.port.post.mk> diff --git a/science/quantum-espresso/distinfo b/science/quantum-espresso/distinfo index 835b6e262ce3..bbe9a16b0148 100644 --- a/science/quantum-espresso/distinfo +++ b/science/quantum-espresso/distinfo @@ -1,8 +1,8 @@ -TIMESTAMP = 1737938704 -SHA256 (QEF-q-e-qe-7.4_GH0.tar.gz) = b15dcfe25f4fbf15ccd34c1194021e90996393478226e601d876f7dea481d104 -SIZE (QEF-q-e-qe-7.4_GH0.tar.gz) = 71424988 -SHA256 (anharmonic-d3q-de47183_GH0.tar.gz) = 36477748aa9a445d465974e7ba8e3e2e09c9fac7b2114c24cc768fa72510e807 -SIZE (anharmonic-d3q-de47183_GH0.tar.gz) = 24080083 +TIMESTAMP = 1762823217 +SHA256 (QEF-q-e-qe-7.5_GH0.tar.gz) = 7e1f7a9a21b63192f5135218bee20a5321b66582e4756536681b76e9c59b3cc8 +SIZE (QEF-q-e-qe-7.5_GH0.tar.gz) = 72479566 +SHA256 (anharmonic-d3q-6e5f978_GH0.tar.gz) = f49158ed25709e82fcd793f9f56a1534b1130833937ec9e2236b7670b8d6eda6 +SIZE (anharmonic-d3q-6e5f978_GH0.tar.gz) = 24095924 SHA256 (pietrodelugas-fox-3453648e6837658b747b895bb7bef4b1ed2eac40_GH0.tar.gz) = 107b1d58eb6a0a730c98520a8f99a6459b2a0e06b06f4b037abf358b29d50df1 SIZE (pietrodelugas-fox-3453648e6837658b747b895bb7bef4b1ed2eac40_GH0.tar.gz) = 988789 SHA256 (Reference-LAPACK-lapack-12d825396fcef1e0a1b27be9f119f9e554621e55_GH0.tar.gz) = 2ae8b6eb09e9c1d3b5d66bb778a5a5119af13575bb7fd8016f5cabb319253257 diff --git a/science/quantum-espresso/files/patch-CMakeLists.txt b/science/quantum-espresso/files/patch-CMakeLists.txt index d315d0c9420b..40e483c19d13 100644 --- a/science/quantum-espresso/files/patch-CMakeLists.txt +++ b/science/quantum-espresso/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2024-03-16 03:53:23 UTC +--- CMakeLists.txt.orig 2025-08-19 09:57:12 UTC +++ CMakeLists.txt -@@ -395,14 +395,14 @@ endif(QE_ENABLE_MPI) +@@ -415,14 +415,14 @@ endif(QE_ENABLE_MPI) ########################################################### # Git ########################################################### diff --git a/science/quantum-espresso/files/patch-environment__variables b/science/quantum-espresso/files/patch-environment__variables index afa3ad0d0e6d..e241b507051a 100644 --- a/science/quantum-espresso/files/patch-environment__variables +++ b/science/quantum-espresso/files/patch-environment__variables @@ -1,4 +1,4 @@ ---- environment_variables.orig 2024-02-29 10:18:05 UTC +--- environment_variables.orig 2025-08-19 09:57:12 UTC +++ environment_variables @@ -66,12 +66,16 @@ # For this reason, a plain "diff" of your results against the reference @@ -12,7 +12,7 @@ # $PREFIX is the root of the Quantum ESPRESSO source tree. BIN_DIR=$PREFIX/bin -PSEUDO_DIR=$PREFIX/pseudo -+PSEUDO_DIR=$PREFIX/share/quantum-espresso/pseudo ++PSEUDO_DIR=$PREFIX/share/quantum-espresso +ESPRESSO_PSEUDO=/tmp # Beware: everything in $TMP_DIR will be destroyed ! -TMP_DIR=$PREFIX/tempdir diff --git a/science/quantum-espresso/pkg-plist b/science/quantum-espresso/pkg-plist index 00abbc0f54cb..8842a50352e7 100644 --- a/science/quantum-espresso/pkg-plist +++ b/science/quantum-espresso/pkg-plist @@ -53,11 +53,13 @@ bin/merge_wann.x bin/molecularnexafs.x bin/molecularpdos.x bin/neb.x +bin/nscf2supercond.x bin/open_grid.x bin/path_interpolation.x bin/pawplot.x bin/ph.x bin/phcg.x +bin/pioud.x bin/plan_avg.x bin/plotband.x bin/plotproj.x @@ -126,8 +128,8 @@ include/qe/qe_atomic/kli.mod include/qe/qe_atomic/ld1_parameters.mod include/qe/qe_atomic/ld1inc.mod include/qe/qe_atomic/paw_type.mod +include/qe/qe_couple/libqecouple.h include/qe/qe_cpv/betax.mod -include/qe/qe_cpv/cell_nose.mod include/qe/qe_cpv/cg_module.mod include/qe/qe_cpv/cg_sub.mod include/qe/qe_cpv/core.mod @@ -136,6 +138,7 @@ include/qe/qe_cpv/cp_electronic_mass.mod include/qe/qe_cpv/cp_interfaces.mod include/qe/qe_cpv/cp_main_variables.mod include/qe/qe_cpv/cp_restart_new.mod +include/qe/qe_cpv/cp_wavefunctions.mod include/qe/qe_cpv/dener.mod include/qe/qe_cpv/efcalc.mod include/qe/qe_cpv/efield_module.mod @@ -147,7 +150,6 @@ include/qe/qe_cpv/ensemble_dft.mod include/qe/qe_cpv/environ_cp_module.mod include/qe/qe_cpv/exx_module.mod include/qe/qe_cpv/input.mod -include/qe/qe_cpv/ions_nose.mod include/qe/qe_cpv/ions_positions.mod include/qe/qe_cpv/kohn_sham_states.mod include/qe/qe_cpv/ldau_cp.mod @@ -196,6 +198,8 @@ include/qe/qe_epw/cumulant.mod include/qe/qe_epw/dvqpsi.mod include/qe/qe_epw/ep_coarse.mod include/qe/qe_epw/ep_constants.mod +include/qe/qe_epw/exphonon.mod +include/qe/qe_epw/expolaron.mod include/qe/qe_epw/global_var.mod include/qe/qe_epw/ifconstants.mod include/qe/qe_epw/indabs.mod @@ -212,6 +216,7 @@ include/qe/qe_epw/kfold.mod include/qe/qe_epw/longrange.mod include/qe/qe_epw/low_lvl.mod include/qe/qe_epw/parallelism.mod +include/qe/qe_epw/phph.mod include/qe/qe_epw/polaron.mod include/qe/qe_epw/printing.mod include/qe/qe_epw/pw2wan.mod @@ -227,7 +232,13 @@ include/qe/qe_epw/supercond_common.mod include/qe/qe_epw/supercond_coul.mod include/qe/qe_epw/supercond_driver.mod include/qe/qe_epw/supercond_iso.mod +include/qe/qe_epw/supercond_vertex.mod include/qe/qe_epw/symmetry.mod +include/qe/qe_epw/tdbe_common.mod +include/qe/qe_epw/tdbe_driver.mod +include/qe/qe_epw/tdbe_eph_common.mod +include/qe/qe_epw/tdbe_mod.mod +include/qe/qe_epw/tdbe_phph_common.mod include/qe/qe_epw/transport.mod include/qe/qe_epw/transport_legacy.mod include/qe/qe_epw/transport_mag.mod @@ -342,6 +353,7 @@ include/qe/qe_modules/bfgs_module.mod include/qe/qe_modules/bspline.mod include/qe/qe_modules/bz_form.mod include/qe/qe_modules/cell_base.mod +include/qe/qe_modules/cell_nose.mod include/qe/qe_modules/check_stop.mod include/qe/qe_modules/command_line_options.mod include/qe/qe_modules/constants.mod @@ -373,6 +385,7 @@ include/qe/qe_modules/io_files.mod include/qe/qe_modules/io_global.mod include/qe/qe_modules/io_rism_xml.mod include/qe/qe_modules/ions_base.mod +include/qe/qe_modules/ions_nose.mod include/qe/qe_modules/kinds.mod include/qe/qe_modules/lauefft.mod include/qe/qe_modules/libmbd_interface.mod @@ -470,6 +483,7 @@ include/qe/qe_phonon_ph/cryst_ph.mod include/qe/qe_phonon_ph/d2nsq_bare_module.mod include/qe/qe_phonon_ph/dfile_autoname.mod include/qe/qe_phonon_ph/dfile_star.mod +include/qe/qe_phonon_ph/dfpt_kernels.mod include/qe/qe_phonon_ph/dielectric.mod include/qe/qe_phonon_ph/diffs.mod include/qe/qe_phonon_ph/disp.mod @@ -502,7 +516,6 @@ include/qe/qe_phonon_ph/ramanm.mod include/qe/qe_phonon_ph/recover_mod.mod include/qe/qe_phonon_ph/rigid.mod include/qe/qe_phonon_ph/save_ph.mod -include/qe/qe_phonon_ph/sym_def_module.mod include/qe/qe_phonon_ph/symmetry.mod include/qe/qe_phonon_ph/term_one_1_module.mod include/qe/qe_phonon_ph/term_one_module.mod @@ -511,6 +524,16 @@ include/qe/qe_phonon_ph/term_three_module.mod include/qe/qe_phonon_ph/units_ph.mod include/qe/qe_phonon_ph/write_hub.mod include/qe/qe_phonon_ph/yambo.mod +include/qe/qe_pioud/fcp_opt_routines.mod +include/qe/qe_pioud/fcp_variables.mod +include/qe/qe_pioud/pimd_variables.mod +include/qe/qe_pioud/random_pioud.mod +include/qe/qe_pioud/ring_formats.mod +include/qe/qe_pioud/ring_input_parameters_module.mod +include/qe/qe_pioud/ring_io_units_module.mod +include/qe/qe_pioud/ring_variables.mod +include/qe/qe_pioud/trpmd_base.mod +include/qe/qe_pioud/trpmd_io_routines.mod include/qe/qe_pp/adduscore.mod include/qe/qe_pp/atproj.mod include/qe/qe_pp/chdens_module.mod @@ -543,7 +566,6 @@ include/qe/qe_pw/cellmd.mod include/qe/qe_pw/coul_cut_2d.mod include/qe/qe_pw/d3hess_mod.mod include/qe/qe_pw/dfunct.mod -include/qe/qe_pw/dfunct_gpum.mod include/qe/qe_pw/dynamics_module.mod include/qe/qe_pw/ener.mod include/qe/qe_pw/environ_pw_module.mod @@ -565,7 +587,6 @@ include/qe/qe_pw/fcp_relaxation.mod include/qe/qe_pw/fixed_occ.mod include/qe/qe_pw/force_mod.mod include/qe/qe_pw/g_psi_mod.mod -include/qe/qe_pw/g_psi_mod_gpum.mod include/qe/qe_pw/gcscf_module.mod include/qe/qe_pw/io_rho_xml.mod include/qe/qe_pw/klist.mod @@ -615,7 +636,6 @@ include/qe/qe_pwcond_exe/scattnl_cond.mod include/qe/qe_tddfpt/charg_resp.mod include/qe/qe_tddfpt/environ_td_module.mod include/qe/qe_tddfpt/linear_solvers.mod -include/qe/qe_tddfpt/lr_dav_debug.mod include/qe/qe_tddfpt/lr_dav_routines.mod include/qe/qe_tddfpt/lr_dav_variables.mod include/qe/qe_tddfpt/lr_exx_kernel.mod @@ -759,7 +779,6 @@ lib/libqe_kssolver_davidson.a lib/libqe_kssolver_davidsonrci.a lib/libqe_kssolver_dense.a lib/libqe_kssolver_paro.a -lib/libqe_kssolver_ppcg.a lib/libqe_kssolver_rmmdiis.a lib/libqe_lax.a lib/libqe_libbeef.a @@ -771,6 +790,7 @@ lib/libqe_phonon_fd.a lib/libqe_phonon_gamma.a lib/libqe_phonon_ph.a lib/libqe_phonon_phaux.a +lib/libqe_pioud.a lib/libqe_pp.a lib/libqe_pw.a lib/libqe_tddfpt.a @@ -1065,6 +1085,5 @@ share/GUI/QE-modes/qe-modes/qe-funcs.el share/GUI/QE-modes/qe-modes/qe-mode.el share/GUI/QE-modes/qe-modes/qe-modes.el share/GUI/README -@dir include/qe/qe_couple @dir include/qe/qe_device_lapack @dir include/qe/qe_qeheat_exe diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index dd2255f3a900..f02115771af1 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,12 +1,19 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ -DISTVERSION= 2025_03_1 -PORTREVISION= 2 +DISTVERSION= 2025_09_2 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 +MASTER_SITES= https://github.com/schrodinger/maeparser/archive/:maeparser \ + https://github.com/schrodinger/coordgenlibs/archive/:coordgen \ + https://codeload.github.com/Glysade/chemdraw/tar.gz/refs/tags/:chemdraw \ + https://github.com/Tencent/rapidjson/archive/:rapidjson \ + LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font +DISTFILES= v${MAEPARSER_VERSION}.tar.gz:maeparser \ + v${COORDGEN_VERSION}.tar.gz:coordgen \ + v${CHEMDRAW_VERSION}:chemdraw \ + v${RAPIDJSON_VERSION}.tar.gz:rapidjson \ + ComicNeue-Regular.ttf:font DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} -EXTRACT_ONLY= ${DISTFILES:C/:.*//:N*.ttf} +EXTRACT_ONLY= ${DISTFILES:C/:.*//:Nv*:N*.ttf} MAINTAINER= yuri@FreeBSD.org COMMENT= Collection of cheminformatics and machine-learning software @@ -16,19 +23,14 @@ WWW= https://www.rdkit.org/ \ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt -BROKEN_FreeBSD_15_aarch64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 -BROKEN_FreeBSD_15_amd64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 -BROKEN_FreeBSD_15_i386= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 +BROKEN_FreeBSD_16_amd64= clang crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 BUILD_DEPENDS= catch>0:devel/catch \ - flex:textproc/flex \ - rapidjson>=0:devel/rapidjson -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ - libcoordgen.so:science/coordgenlibs \ - libfreetype.so:print/freetype2 \ - libmaeparser.so:science/maeparser - -USES= bison:build cmake:testing compiler:c++11-lang eigen:3 gnome python + flex:textproc/flex +LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ + libfreetype.so:print/freetype2 + +USES= bison:build cmake:testing compiler:c++11-lang eigen:3 gnome pkgconfig python USE_GNOME= cairo USE_LDCONFIG= yes @@ -37,6 +39,11 @@ GH_TUPLE= rareylab:RingDecomposerLib:v1.1.3_rdkit:RingDecomposerLib/External/Rin GH_TUPLE+= ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-align3d \ aantron:better-enums:520d8ee:better_enums/better_enums +MAEPARSER_VERSION= 1.3.3 +COORDGEN_VERSION= 3.0.2 +CHEMDRAW_VERSION= 1.0.11 +RAPIDJSON_VERSION= 1.1.0 + CMAKE_ON= RDK_BUILD_CAIRO_SUPPORT CMAKE_OFF= RDK_INSTALL_INTREE RDK_USE_FLEXBISON \ RDK_INSTALL_STATIC_LIBS RDK_SWIG_STATIC RDK_PGSQL_STATIC \ @@ -89,14 +96,39 @@ PLIST_SUB+= LITTLE_ENDIAN="" .endif post-extract: - @${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0 - @cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include + #@${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0 + #@cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include @cd ${WRKSRC}/Data/Fonts && ${CP} ${DISTDIR}/${DIST_SUBDIR}/ComicNeue-Regular.ttf . @${CP} ${WRKSRC}/better_enums/enum.h ${WRKSRC}/Code/RDGeneral +post-patch: + # replace the URLs for fetched libs with the local file path to the distfiles, so that it can be used without internet access + @${REINPLACE_CMD} \ + -e 's|https://github.com/schrodinger/maeparser/archive/|file://${DISTDIR}/${DIST_SUBDIR}/|g' \ + ${WRKSRC}/External/CoordGen/CMakeLists.txt + @${REINPLACE_CMD} \ + -e 's|https://github.com/schrodinger/coordgenlibs/archive/|file://${DISTDIR}/${DIST_SUBDIR}/|g' \ + ${WRKSRC}/External/CoordGen/CMakeLists.txt + @${REINPLACE_CMD} \ + -e 's|https://codeload.github.com/Glysade/chemdraw/tar.gz/refs/tags/|file://${DISTDIR}/${DIST_SUBDIR}/|g' \ + ${WRKSRC}/External/ChemDraw/CMakeLists.txt + @${REINPLACE_CMD} \ + -e 's|https://github.com/Tencent/rapidjson/archive/|file://${DISTDIR}/${DIST_SUBDIR}/|g' \ + ${WRKSRC}/Code/GraphMol/MolInterchange/CMakeLists.txt + +pre-build: + @${REINPLACE_CMD} \ + -e 's|const SizeType length;|SizeType length;|g' \ + ${WRKSRC}/External/rapidjson/rapidjson-1.1.0/include/rapidjson/document.h + +post-install: + @${RM} -f ${STAGEDIR}${PREFIX}/lib/libexpat.a + post-install-PGSQL-on: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/postgresql/rdkit.so # many tests fail, see https://github.com/rdkit/rdkit/issues/7779 +# tests as of 2025_09_1: 65% tests passed, 24 tests failed out of 68 +# tests as of 2025_09_2: 63% tests passed, 26 tests failed out of 70 .include <bsd.port.mk> diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo index fe4d068e756e..2dd40d607202 100644 --- a/science/rdkit/distinfo +++ b/science/rdkit/distinfo @@ -1,11 +1,19 @@ -TIMESTAMP = 1744735395 -SHA256 (rdkit-2025.03.1/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 -SIZE (rdkit-2025.03.1/ComicNeue-Regular.ttf) = 21915 -SHA256 (rdkit-2025.03.1/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz) = 947e5aa004047fbec4bf4ba93b84a50ca7f68e248a0654080d8ca0cdb06e3534 -SIZE (rdkit-2025.03.1/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz) = 82192067 -SHA256 (rdkit-2025.03.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 -SIZE (rdkit-2025.03.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 -SHA256 (rdkit-2025.03.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0 -SIZE (rdkit-2025.03.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376 -SHA256 (rdkit-2025.03.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5 -SIZE (rdkit-2025.03.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 136592 +TIMESTAMP = 1762809861 +SHA256 (rdkit-2025.09.2/v1.3.3.tar.gz) = 78e7571a779ea4952e752ecef57c62fb26463947e29ef7f4b31b11988d88ca07 +SIZE (rdkit-2025.09.2/v1.3.3.tar.gz) = 39896 +SHA256 (rdkit-2025.09.2/v3.0.2.tar.gz) = f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3 +SIZE (rdkit-2025.09.2/v3.0.2.tar.gz) = 166817 +SHA256 (rdkit-2025.09.2/v1.0.11) = 405869fc8b3f73395047bc7c54e1da62ef66c08d48bd71af66e47ec9cbe86814 +SIZE (rdkit-2025.09.2/v1.0.11) = 1043261 +SHA256 (rdkit-2025.09.2/v1.1.0.tar.gz) = bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e +SIZE (rdkit-2025.09.2/v1.1.0.tar.gz) = 1019402 +SHA256 (rdkit-2025.09.2/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 +SIZE (rdkit-2025.09.2/ComicNeue-Regular.ttf) = 21915 +SHA256 (rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz) = db3254e88ef17cac7bb8480e6da9d1e69dfe180c21774b11637d8a17b5a98fb9 +SIZE (rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz) = 82911180 +SHA256 (rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 +SIZE (rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 +SHA256 (rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0 +SIZE (rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376 +SHA256 (rdkit-2025.09.2/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5 +SIZE (rdkit-2025.09.2/aantron-better-enums-520d8ee_GH0.tar.gz) = 136592 diff --git a/science/rdkit/files/patch-CMakeLists.txt b/science/rdkit/files/patch-CMakeLists.txt index 2145ea31191e..4d7146e3b2c3 100644 --- a/science/rdkit/files/patch-CMakeLists.txt +++ b/science/rdkit/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2025-03-31 18:11:10 UTC +--- CMakeLists.txt.orig 2025-09-30 06:13:45 UTC +++ CMakeLists.txt -@@ -78,12 +78,12 @@ if(NOT MSVC) +@@ -81,12 +81,12 @@ if(NOT MSVC) if(NOT MSVC) if(RDK_OPTIMIZE_POPCNT) @@ -17,26 +17,23 @@ endif() endif() endif() -@@ -166,18 +166,6 @@ endif() +@@ -179,15 +179,7 @@ endif() FetchContent_MakeAvailable(Catch2) endif() --#include better-enums --find_package(better_enums 0 QUIET) --if(NOT better_enums) -- Include(FetchContent) -- -- FetchContent_Declare( -- better_enums -- GIT_REPOSITORY https://github.com/aantron/better-enums.git -- GIT_TAG c35576bed0295689540b39873126129adfa0b4c8 # 0.11.3 -- ) --endif() +-# make sure we have better_enums +-Include(FetchContent) + +-FetchContent_Declare( +- better_enums +- GIT_REPOSITORY https://github.com/aantron/better-enums.git +- GIT_TAG c35576bed0295689540b39873126129adfa0b4c8 # 0.11.3 +-) - if(RDK_INSTALL_INTREE) set(RDKit_BinDir "${CMAKE_SOURCE_DIR}/bin") set(RDKit_LibDir "${CMAKE_SOURCE_DIR}/lib") -@@ -530,12 +518,14 @@ if(NOT RDK_INSTALL_INTREE) +@@ -535,12 +527,14 @@ if(NOT RDK_INSTALL_INTREE) COMPONENT data PATTERN ".svn" EXCLUDE ) diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist index db5a4c43384e..3cd23f7e900b 100644 --- a/science/rdkit/pkg-plist +++ b/science/rdkit/pkg-plist @@ -133,6 +133,8 @@ include/rdkit/GraphMol/Descriptors/USRDescriptor.h include/rdkit/GraphMol/Descriptors/WHIM.h include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h include/rdkit/GraphMol/DistGeomHelpers/Embedder.h +include/rdkit/GraphMol/EnumerateStereoisomers/EnumerateStereoisomers.h +include/rdkit/GraphMol/EnumerateStereoisomers/Flippers.h include/rdkit/GraphMol/FMCS/FMCS.h include/rdkit/GraphMol/FMCS/Graph.h include/rdkit/GraphMol/FileParsers/CDXMLParser.h @@ -291,6 +293,8 @@ include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h include/rdkit/GraphMol/Trajectory/Snapshot.h include/rdkit/GraphMol/Trajectory/Trajectory.h include/rdkit/GraphMol/atomic_data.h +include/rdkit/GraphMol/chemdraw.h +include/rdkit/GraphMol/chemdrawreaction.h include/rdkit/GraphMol/details.h include/rdkit/GraphMol/new_canon.h include/rdkit/Numerics/Alignment/AlignPoints.h @@ -381,6 +385,9 @@ lib/libRDKitCIPLabeler.so.1.%%SHLIB_VER%% lib/libRDKitCatalogs.so lib/libRDKitCatalogs.so.1 lib/libRDKitCatalogs.so.1.%%SHLIB_VER%% +lib/libRDKitChemDraw.so +lib/libRDKitChemDraw.so.1 +lib/libRDKitChemDraw.so.1.%%SHLIB_VER%% lib/libRDKitChemReactions.so lib/libRDKitChemReactions.so.1 lib/libRDKitChemReactions.so.1.%%SHLIB_VER%% @@ -411,6 +418,9 @@ lib/libRDKitDistGeometry.so.1.%%SHLIB_VER%% lib/libRDKitEigenSolvers.so lib/libRDKitEigenSolvers.so.1 lib/libRDKitEigenSolvers.so.1.%%SHLIB_VER%% +lib/libRDKitEnumerateStereoisomers.so +lib/libRDKitEnumerateStereoisomers.so.1 +lib/libRDKitEnumerateStereoisomers.so.1.%%SHLIB_VER%% lib/libRDKitFMCS.so lib/libRDKitFMCS.so.1 lib/libRDKitFMCS.so.1.%%SHLIB_VER%% @@ -498,6 +508,12 @@ lib/libRDKitPubChemShape.so.1.%%SHLIB_VER%% %%PYTHON%%lib/libRDKitRDBoost.so %%PYTHON%%lib/libRDKitRDBoost.so.1 %%PYTHON%%lib/libRDKitRDBoost.so.1.%%SHLIB_VER%% +lib/libRDKitRDChemDrawLib.so +lib/libRDKitRDChemDrawLib.so.1 +lib/libRDKitRDChemDrawLib.so.1.%%SHLIB_VER%% +lib/libRDKitRDChemDrawReactionLib.so +lib/libRDKitRDChemDrawReactionLib.so.1 +lib/libRDKitRDChemDrawReactionLib.so.1.%%SHLIB_VER%% lib/libRDKitRDGeneral.so lib/libRDKitRDGeneral.so.1 lib/libRDKitRDGeneral.so.1.%%SHLIB_VER%% @@ -552,12 +568,18 @@ lib/libRDKitTautomerQuery.so.1.%%SHLIB_VER%% lib/libRDKitTrajectory.so lib/libRDKitTrajectory.so.1 lib/libRDKitTrajectory.so.1.%%SHLIB_VER%% +lib/libRDKitcoordgen.so +lib/libRDKitcoordgen.so.1 +lib/libRDKitcoordgen.so.1.%%SHLIB_VER%% lib/libRDKitga.so lib/libRDKitga.so.1 lib/libRDKitga.so.1.%%SHLIB_VER%% %%LITTLE_ENDIAN%%lib/libRDKithc.so %%LITTLE_ENDIAN%%lib/libRDKithc.so.1 %%LITTLE_ENDIAN%%lib/libRDKithc.so.1.%%SHLIB_VER%% +lib/libRDKitmaeparser.so +lib/libRDKitmaeparser.so.1 +lib/libRDKitmaeparser.so.1.%%SHLIB_VER%% %%PGSQL%%lib/postgresql/rdkit.so %%PYTHON%%lib/libRDKitpubchem_align3d.so %%PYTHON%%lib/libRDKitpubchem_align3d.so.1 @@ -688,12 +710,14 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdAbbreviations.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdCIPLabeler.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdChemDraw.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdChemReactions.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdChemicalFeatures.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdCoordGen.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDepictor.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDeprotect.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDistGeom.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdEnumerateStereoisomers.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFMCS.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFingerprintGenerator.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdForceFieldHelpers.so @@ -1176,6 +1200,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%PYTHON%%%%DATADIR%%/Scripts/create_deb_packages.sh %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/__init__.py %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/__main__.py +%%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/patch/rdkit/Chem/inchi.pyi.diff %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/worker.py %%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__init__.py %%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__main__.py 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/seacas/Makefile b/science/seacas/Makefile index 21b0c9a3d190..814973f35c55 100644 --- a/science/seacas/Makefile +++ b/science/seacas/Makefile @@ -1,7 +1,6 @@ PORTNAME= seacas DISTVERSIONPREFIX= v -DISTVERSION= 2025-03-13 -PORTREVISION= 1 +DISTVERSION= 2025-10-14 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/seacas/distinfo b/science/seacas/distinfo index 7b8b4b23ae14..c3ed5edbd1ea 100644 --- a/science/seacas/distinfo +++ b/science/seacas/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742021767 -SHA256 (sandialabs-seacas-v2025-03-13_GH0.tar.gz) = 406aff5b8908d6a3bf6687d825905990101caa9cf8c1213a508938eed2134d6d -SIZE (sandialabs-seacas-v2025-03-13_GH0.tar.gz) = 34945929 +TIMESTAMP = 1760797736 +SHA256 (sandialabs-seacas-v2025-10-14_GH0.tar.gz) = f9351a8f1a555a015020f249b1e5c26a282fbb6e274f9b71eb38720d61267dda +SIZE (sandialabs-seacas-v2025-10-14_GH0.tar.gz) = 37692693 diff --git a/science/seacas/pkg-plist b/science/seacas/pkg-plist index fa7fd816d59e..0d4898d8b6a9 100644 --- a/science/seacas/pkg-plist +++ b/science/seacas/pkg-plist @@ -28,6 +28,7 @@ bin/genshell bin/getopt.seacas bin/gjoin bin/grepos +bin/grope bin/io_info bin/io_modify bin/io_shell @@ -45,7 +46,6 @@ bin/slice bin/sphgen bin/txtexo bin/zellij -grope include/CatalystCGNSMeshBase.h include/CatalystExodusMeshBase.h include/CatalystManagerBase.h @@ -233,7 +233,6 @@ include/Iovs_exodus_DatabaseIO.h include/Iovs_exodus_IOFactory.h include/SEACASIoss_config.h include/SeacasConfig.cmake -include/Seacas_version_date.h include/Zoltan_config.h include/apr_symrec.h include/apr_tokenize.h @@ -468,12 +467,11 @@ lib/libblotlib.a lib/libchaco.so lib/libchaco.so.2 lib/libchaco.so.2.0 -lib/libexoIIv2c.a +lib/libexoIIv2for.a lib/libexoIIv2for32.a lib/libexoIIv2for32.so lib/libexoIIv2for32.so.2 lib/libexoIIv2for32.so.2.0 -lib/libexodus.a lib/libexodus.so lib/libexodus.so.2 lib/libexodus.so.2.0 @@ -516,4 +514,3 @@ lib/tests/exomerge_unit_test.e lib/tests/exomerge_unit_test.py lib/tests/test-assembly.exo lib/tests/test_exodus3.py -libexoIIv2for.a diff --git a/science/serac/Makefile b/science/serac/Makefile index 79535619d3e5..9ced914a7e86 100644 --- a/science/serac/Makefile +++ b/science/serac/Makefile @@ -1,6 +1,6 @@ PORTNAME= serac PORTVERSION= g20220823 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/silo/Makefile b/science/silo/Makefile index 9759d1b7565c..dac1c6649952 100644 --- a/science/silo/Makefile +++ b/science/silo/Makefile @@ -1,7 +1,5 @@ PORTNAME= silo -DISTVERSION= 4.11-68 -PORTREVISION= 1 -DISTVERSIONSUFFIX= -g819658e +DISTVERSION= 4.12.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -19,6 +17,7 @@ USE_GITHUB= yes GH_ACCOUNT= LLNL GH_PROJECT= Silo +CMAKE_ON= SILO_ENABLE_INSTALL_LITE_HEADERS CMAKE_TESTING_ON= SILO_ENABLE_TESTS # 3 tests fail, see https://github.com/LLNL/Silo/issues/289 CMAKE_TESTING_TARGET= check diff --git a/science/silo/distinfo b/science/silo/distinfo index a3cf26715bd2..2fe4efe79810 100644 --- a/science/silo/distinfo +++ b/science/silo/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1670041617 -SHA256 (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 3a7a75e196c9e39922998054378efa02b2d24dc57ab126ab15a631e2645bd0ce -SIZE (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 14028123 +TIMESTAMP = 1763923185 +SHA256 (LLNL-Silo-4.12.0_GH0.tar.gz) = 5251816e43b08c19c925480b2daf85cc9b75e494b91df37df0eacc092279cfd0 +SIZE (LLNL-Silo-4.12.0_GH0.tar.gz) = 99198889 diff --git a/science/silo/files/patch-CMakeLists.txt b/science/silo/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..1d76b4832b67 --- /dev/null +++ b/science/silo/files/patch-CMakeLists.txt @@ -0,0 +1,13 @@ +- workaround for https://github.com/LLNL/Silo/issues/501 + +--- CMakeLists.txt.orig 2025-11-23 19:03:43 UTC ++++ CMakeLists.txt +@@ -700,7 +700,7 @@ install(FILES ${silo_public_headers} DESTINATION ${CMA + WORLD_READ) + + # Symlink old style silo_f77.inc +-if(SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER) ++if(FALSE AND SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER) + install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink silo.inc silo_f77.inc + WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})") + endif() diff --git a/science/silo/files/patch-git-commit-be29ddf b/science/silo/files/patch-git-commit-be29ddf deleted file mode 100644 index fba494b0b956..000000000000 --- a/science/silo/files/patch-git-commit-be29ddf +++ /dev/null @@ -1,44 +0,0 @@ -commit be29ddf0352bc8e5a7eecc8772a3acb64dfde18c -Author: miller86 <miller86@llnl.gov> -Date: Fri Dec 2 19:00:20 2022 -0800 - - fix obj-case-macro - -diff --git src/hdf5_drv/silo_hdf5.c src/hdf5_drv/silo_hdf5.c -index 17af250..c45d689 100644 ---- src/hdf5_drv/silo_hdf5.c -+++ src/hdf5_drv/silo_hdf5.c -@@ -1809,7 +1809,7 @@ db_hdf5_cwg(DBfile *_dbfile) - *dscount = m.MEMCNT; \ - *dsnames = (char **) calloc(*dscount, sizeof(char**)); \ - for (i = 0; i < *dscount; i++) \ -- (*dsnames)[i] = strdup(m.MEMNAME[i]); \ -+ (*dsnames)[i] = strdup(m.MEMNAME); \ - break; \ - } - -@@ -1857,15 +1857,15 @@ db_hdf5_get_obj_dsnames(DBfile *_dbfile, char const *name, int *dscount, char ** - - switch(_objtype) - { -- DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value) -- /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord) wont work for rect case */ -- DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord) -- DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord) -- DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value) -- DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord) -- DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data) -- DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord) -- DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals) -+ DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value[i]) -+ /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord[i]) wont work for rect case */ -+ DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord[i]) -+ DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord[i]) -+ DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value[i]) -+ DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord[i]) -+ DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data[i]) -+ DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord[i]) -+ DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals[i]) - DB_OBJ_CASE(DB_CURVE, DBcurve_mt, npts?1:1, yvarname) - } - H5Tclose(o); diff --git a/science/silo/files/patch-src_silo_silo.c b/science/silo/files/patch-src_silo_silo.c deleted file mode 100644 index d20855c5ca9b..000000000000 --- a/science/silo/files/patch-src_silo_silo.c +++ /dev/null @@ -1,39 +0,0 @@ ---- src/silo/silo.c.orig 2022-12-03 02:30:10 UTC -+++ src/silo/silo.c -@@ -238,12 +238,8 @@ typedef struct db_silo_stat_t { - #ifndef SIZEOF_OFF64_T - #error missing definition for SIZEOF_OFF64_T in silo_private.h - #else --#if SIZEOF_OFF64_T > 4 -- struct stat64 s; --#else - struct stat s; - #endif --#endif - #ifdef _WIN32 - DWORD fileindexlo; - DWORD fileindexhi; -@@ -2121,11 +2117,7 @@ db_silo_stat_one_file(const char *name, db_silo_stat_t - errno = 0; - memset(&(statbuf->s), 0, sizeof(statbuf->s)); - --#if SIZEOF_OFF64_T > 4 -- retval = stat64(name, &(statbuf->s)); --#else - retval = stat(name, &(statbuf->s)); --#endif /* #if SIZEOF_OFF64_T > 4 */ - - #ifdef _WIN32 - if (retval == 0) -@@ -4136,11 +4128,7 @@ DBOpenReal(const char *name, int type, int mode) - /********************************/ - /* System level error occured. */ - /********************************/ --#if SIZEOF_OFF64_T > 4 -- printf("stat64() failed with error: "); --#else - printf("stat() failed with error: "); --#endif - switch (errno) - { - case EACCES: printf("EACCES\n"); break; diff --git a/science/silo/files/patch-src_silo_silo__json.c b/science/silo/files/patch-src_silo_silo__json.c index 576f7eea757f..331a87c8890e 100644 --- a/science/silo/files/patch-src_silo_silo__json.c +++ b/science/silo/files/patch-src_silo_silo__json.c @@ -1,6 +1,6 @@ ---- src/silo/silo_json.c.orig 2022-12-03 02:30:10 UTC +--- src/silo/silo_json.c.orig 2025-11-21 05:30:59 UTC +++ src/silo/silo_json.c -@@ -441,11 +441,7 @@ json_object_from_binary_file(char const *filename) +@@ -446,11 +446,7 @@ json_object_from_binary_file(char const *filename) #ifndef SIZEOF_OFF64_T #error missing definition for SIZEOF_OFF64_T in silo_private.h #else diff --git a/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake b/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake deleted file mode 100644 index c25272a9a103..000000000000 --- a/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake +++ /dev/null @@ -1,13 +0,0 @@ -- workaround for https://github.com/LLNL/Silo/issues/288 - ---- tests/CMake/SiloMakeCheckRunner.cmake.orig 2022-12-03 06:53:38 UTC -+++ tests/CMake/SiloMakeCheckRunner.cmake -@@ -72,7 +72,7 @@ function(silo_add_make_check_runner) - message(WARNING "silo_add_make_check_runner: NAME argument is required.") - return() - endif() -- set(test_cmd ${samcr_NAME}) -+ set(test_cmd "./${samcr_NAME}") - if("ARGS" IN_LIST samcr_KEYWORDS_MISSING_VALUES) - message(WARNING "silo_add_make_check_runner: ARGS argument provided without a value.") - return() diff --git a/science/silo/pkg-plist b/science/silo/pkg-plist index c55c7a873580..fc056e66313d 100644 --- a/science/silo/pkg-plist +++ b/science/silo/pkg-plist @@ -3,18 +3,19 @@ %%SILOCK%%bin/silock %%BROWSER%%bin/silodiff %%BROWSER%%bin/silofile -cmake/SiloConfig.cmake -cmake/SiloConfigVersion.cmake -cmake/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake -cmake/SiloTargets.cmake include/lite_pdb.h include/lite_score.h -include/pdform.h include/pmpio.h include/silo.h -include/silo.inc +%%FORTRAN%%include/silo.inc %%FORTRAN%%include/silo_FC.h include/silo_exports.h include/silo_f9x.inc %%PYTHON%%lib/Silo.so +lib/cmake/Silo/SiloConfig.cmake +lib/cmake/Silo/SiloConfigVersion.cmake +lib/cmake/Silo/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/Silo/SiloTargets.cmake lib/libsilo%%SUFX_HDF5%%.so +lib/libsilo%%SUFX_HDF5%%.so.4.12.0 +lib/libsilo%%SUFX_HDF5%%.so.412 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..ff71b782cb40 100644 --- a/science/sirius/Makefile +++ b/science/sirius/Makefile @@ -1,6 +1,6 @@ PORTNAME= sirius DISTVERSIONPREFIX= v -DISTVERSION= 7.7.0 +DISTVERSION= 7.9.0 CATEGORIES= science PKGNAMESUFFIX= -quantum-chemistry # other software also has the name "sirius" @@ -11,8 +11,6 @@ WWW= https://github.com/electronic-structure/SIRIUS/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_FreeBSD_15= clang crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=276196 - LIB_DEPENDS= libcosta.so:math/costa \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ diff --git a/science/sirius/distinfo b/science/sirius/distinfo index d5ebd5f7c131..0ccf421fe2c8 100644 --- a/science/sirius/distinfo +++ b/science/sirius/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1744882296 -SHA256 (electronic-structure-SIRIUS-v7.7.0_GH0.tar.gz) = be0bdc76db9eb8afdcb950f0ccaf7535b8e85d72a4232dc92246f54fa68d9d7b -SIZE (electronic-structure-SIRIUS-v7.7.0_GH0.tar.gz) = 31681398 +TIMESTAMP = 1762415259 +SHA256 (electronic-structure-SIRIUS-v7.9.0_GH0.tar.gz) = c36e9a00637b9626f83c0db740751440bfe06ef4c8d7cadb9822dd3cf03c1046 +SIZE (electronic-structure-SIRIUS-v7.9.0_GH0.tar.gz) = 33082823 diff --git a/science/sirius/pkg-plist b/science/sirius/pkg-plist index 2b186e8fac07..a45b47ea765b 100644 --- a/science/sirius/pkg-plist +++ b/science/sirius/pkg-plist @@ -36,6 +36,7 @@ include/sirius/src/core/cmd_args.hpp include/sirius/src/core/constants.hpp include/sirius/src/core/debug.hpp include/sirius/src/core/env/env.hpp +include/sirius/src/core/expected.hpp include/sirius/src/core/fft/fft.hpp include/sirius/src/core/fft/fft3d_grid.hpp include/sirius/src/core/fft/gvec.hpp @@ -43,6 +44,7 @@ include/sirius/src/core/hdf5_tree.hpp include/sirius/src/core/json.hpp include/sirius/src/core/la/blacs_grid.hpp include/sirius/src/core/la/blas_lapack.h +include/sirius/src/core/la/dlaf.hpp include/sirius/src/core/la/dmatrix.hpp include/sirius/src/core/la/eigenproblem.hpp include/sirius/src/core/la/eigensolver.hpp @@ -139,6 +141,8 @@ include/sirius/src/nlcglib/overlap.hpp include/sirius/src/nlcglib/preconditioner/diag_mm.hpp include/sirius/src/nlcglib/preconditioner/ultrasoft_precond_k.hpp include/sirius/src/nlcglib/ultrasoft_precond.hpp +include/sirius/src/potential/dftd3_correction.hpp +include/sirius/src/potential/dftd4_correction.hpp include/sirius/src/potential/potential.hpp include/sirius/src/potential/xc_functional.hpp include/sirius/src/potential/xc_functional_base.hpp @@ -180,6 +184,8 @@ lib/cmake/sirius/siriusTargets.cmake lib/cmake/sirius_cxx/cudalibs_target.cmake lib/cmake/sirius_cxx/hdf5_target.cmake lib/cmake/sirius_cxx/modules/FindCRAY_LIBSCI.cmake +lib/cmake/sirius_cxx/modules/FindDFTD3.cmake +lib/cmake/sirius_cxx/modules/FindDFTD4.cmake lib/cmake/sirius_cxx/modules/FindElpa.cmake lib/cmake/sirius_cxx/modules/FindLibSPG.cmake lib/cmake/sirius_cxx/modules/FindLibVDWXC.cmake diff --git a/science/spheral/Makefile b/science/spheral/Makefile index 7365b12d8edd..d35d06393bf2 100644 --- a/science/spheral/Makefile +++ b/science/spheral/Makefile @@ -1,7 +1,7 @@ PORTNAME= spheral DISTVERSIONPREFIX= v -DISTVERSION= 2024.06.1 -PORTREVISION= 5 +DISTVERSION= 2025.06.1 +PORTREVISION= 4 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org @@ -9,18 +9,26 @@ COMMENT= Environment for hydrodynamical & gravitational numerical simulations WWW= https://github.com/LLNL/spheral LICENSE= BSD3CLAUSE -LICENSE_FILE= ${WRKSRC}/License.txt +LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${LOCALBASE}/include/polyclipper2d.hh:math/polyclipper -LIB_DEPENDS= libaxom_core.so:science/axom \ +LIB_DEPENDS= libadiak.so:misc/adiak \ + libaxom_core.so:science/axom \ libboost_filesystem.so:devel/boost-libs \ + libcamp.so:devel/camp \ + libchai.so:devel/chai \ libconduit.so:science/conduit \ + libfmt.so:devel/libfmt \ libhdf5.so:science/hdf5 \ libmfem.so:math/mfem \ libosdCPU.so:graphics/opensubdiv \ libpolytope.so:science/polytope \ libqhull_r.so:math/qhull \ - libsiloh5.so:science/silo + libRAJA.so:misc/raja \ + libsiloh5.so:science/silo \ + libsz.so:science/libaec \ + libsundials_core.so:math/sundials \ + libumpire.so:devel/umpire USES= cmake:testing compiler:c++14-lang eigen:3 fortran localbase:ldflags lua mpi:mpich python USE_LDCONFIG= yes @@ -53,7 +61,9 @@ CMAKE_OFF= ENABLE_TESTS ENABLE_DOCS \ ENABLE_ANEOS \ ENABLE_CUDA CMAKE_ON= ENABLE_CXXONLY # disable Python support which is still for Python-2.7, see https://github.com/LLNL/spheral/issues/183 -CMAKE_ON+= ENABLE_OPENMP +CMAKE_ON+= ENABLE_OPENMP \ + USE_EXTERNAL_CHAI \ + ENABLE_SUNDIALS CMAKE_TESTING_ON= ENABLE_TESTS # tests fail to build, see https://github.com/LLNL/spheral/issues/230 CXXFLAGS+= -I${LOCALBASE}/include/eigen3 diff --git a/science/spheral/distinfo b/science/spheral/distinfo index 9ce4e897f727..ec724d252052 100644 --- a/science/spheral/distinfo +++ b/science/spheral/distinfo @@ -1,6 +1,6 @@ -TIMESTAMP = 1720767460 -SHA256 (LLNL-spheral-v2024.06.1_GH0.tar.gz) = 18892ad49195157623b95c93d55b55bfea2602003726c00d789419f7bdfe0fc1 -SIZE (LLNL-spheral-v2024.06.1_GH0.tar.gz) = 6727017 +TIMESTAMP = 1761812772 +SHA256 (LLNL-spheral-v2025.06.1_GH0.tar.gz) = d4048308b5f79cf5a4e0ac7a00a16d7da9f75501283b20432f2a09c7253454ed +SIZE (LLNL-spheral-v2025.06.1_GH0.tar.gz) = 6691841 SHA256 (LLNL-PolyClipper-e1fe47c_GH0.tar.gz) = 52b358f32f523e6030ed090411c90f0811db12046b6cb6fa8e4cafe4f8b3567e SIZE (LLNL-PolyClipper-e1fe47c_GH0.tar.gz) = 274184 SHA256 (LLNL-PYB11Generator-7160812_GH0.tar.gz) = 9f257b9a5b2503aaacdba48d785bd349c95849a282e1e181ccee2c0f319135cb diff --git a/science/spheral/files/patch-cmake_InstallTPLs.cmake b/science/spheral/files/patch-cmake_InstallTPLs.cmake new file mode 100644 index 000000000000..526dbd25c3d4 --- /dev/null +++ b/science/spheral/files/patch-cmake_InstallTPLs.cmake @@ -0,0 +1,85 @@ +--- cmake/InstallTPLs.cmake.orig 2025-07-23 20:11:18 UTC ++++ cmake/InstallTPLs.cmake +@@ -84,7 +84,9 @@ set(SPHERAL_FP_DIRS ) + set(SPHERAL_FP_DIRS ) + + # Use find_package to get axom (which brings in fmt) and patch fmt +-find_package(axom REQUIRED NO_DEFAULT_PATH PATHS ${axom_DIR}/lib/cmake) ++message("YURI CMAKE_PREFIX_PATH: ${CMAKE_PREFIX_PATH}") ++set(CMAKE_PREFIX_PATH "/usr/local/lib/cmake") # not sure why this is needed here ++find_package(axom REQUIRED) + list(APPEND SPHERAL_BLT_DEPENDS axom ) + list(APPEND SPHERAL_FP_TPLS axom) + list(APPEND SPHERAL_FP_DIRS ${axom_DIR}/lib/cmake) +@@ -102,7 +104,7 @@ message("--------------------------------------------- + + message("-----------------------------------------------------------------------------") + # Use find_package to get adiak +-find_package(adiak REQUIRED NO_DEFAULT_PATH PATHS ${adiak_DIR}/lib/cmake/adiak) ++find_package(adiak REQUIRED) + if(adiak_FOUND) + list(APPEND SPHERAL_BLT_DEPENDS adiak::adiak) + list(APPEND SPHERAL_FP_TPLS adiak) +@@ -112,7 +114,7 @@ message("--------------------------------------------- + + message("-----------------------------------------------------------------------------") + # Use find_package to get polytope +-find_package(polytope NO_DEFAULT_PATH PATHS ${polytope_DIR}/lib/cmake) ++find_package(polytope REQUIRED) + if(POLYTOPE_FOUND) + list(APPEND SPHERAL_BLT_DEPENDS polytope) + list(APPEND SPHERAL_FP_TPLS polytope) +@@ -141,7 +143,7 @@ if (ENABLE_TIMER) + # Only save if it does not exists already + set(CONFIG_CALIPER_DIR "${caliper_DIR}" CACHE PATH "Configuration Caliper directory") + endif() +- find_package(caliper REQUIRED NO_DEFAULT_PATH PATHS ${caliper_DIR}/share/cmake/caliper) ++ find_package(caliper REQUIRED PATHS ${caliper_DIR}/share/cmake/caliper) + if(caliper_FOUND) + list(APPEND SPHERAL_BLT_DEPENDS caliper) + list(APPEND SPHERAL_FP_TPLS caliper) +@@ -151,14 +153,14 @@ message("--------------------------------------------- + endif() + + message("-----------------------------------------------------------------------------") +-find_package(RAJA REQUIRED NO_DEFAULT_PATH PATHS ${raja_DIR}) ++find_package(RAJA REQUIRED) + if (RAJA_FOUND) + message("Found RAJA External Package.") + blt_convert_to_system_includes(TARGET RAJA) + endif() + + message("-----------------------------------------------------------------------------") +-find_package(umpire REQUIRED NO_DEFAULT_PATH PATHS ${umpire_DIR}) ++find_package(umpire REQUIRED) + if (umpire_FOUND) + message("Found umpire External Package.") + blt_convert_to_system_includes(TARGET umpire) +@@ -166,8 +168,8 @@ message("--------------------------------------------- + + message("-----------------------------------------------------------------------------") + # Chai +-if(chai_DIR AND USE_EXTERNAL_CHAI) +- find_package(chai REQUIRED NO_DEFAULT_PATH PATHS ${chai_DIR}) ++if(USE_EXTERNAL_CHAI) ++ find_package(chai REQUIRED) + if (chai_FOUND) + message("Found chai External Package.") + endif() +@@ -190,12 +192,11 @@ if (ENABLE_SUNDIALS) + # Use find_package to get Sundials + if (ENABLE_SUNDIALS) + set(SUNDIALS_DIR "${sundials_DIR}") +- find_package(SUNDIALS REQUIRED NO_DEFAULT_PATH +- COMPONENTS kinsol nvecparallel nvecmpiplusx nvecserial +- PATHS ${sundials_DIR}/lib64/cmake/sundials ${sundials_DIR}/lib/cmake/sundials) ++ find_package(SUNDIALS REQUIRED ++ COMPONENTS kinsol nvecparallel nvecmpiplusx nvecserial ) + if(SUNDIALS_FOUND) +- list(APPEND SPHERAL_BLT_DEPENDS SUNDIALS::kinsol_static SUNDIALS::nvecparallel_static SUNDIALS::nvecmpiplusx_static SUNDIALS::nvecserial_static) +- list(APPEND SPHERAL_FP_TPLS SUNDIALS::kinsol_static SUNDIALS::nvecparallel_static SUNDIALS::nvecmpiplusx_static SUNDIALS::nvecserial_static) ++ list(APPEND SPHERAL_BLT_DEPENDS SUNDIALS::kinsol SUNDIALS::nvecparallel SUNDIALS::nvecmpiplusx SUNDIALS::nvecserial) ++ list(APPEND SPHERAL_FP_TPLS SUNDIALS::kinsol SUNDIALS::nvecparallel SUNDIALS::nvecmpiplusx SUNDIALS::nvecserial) + list(APPEND SPHERAL_FP_DIRS ${sundials_DIR}) + message("Found SUNDIALS External Package") + endif() diff --git a/science/spheral/files/patch-cmake_SetupSpheral.cmake b/science/spheral/files/patch-cmake_SetupSpheral.cmake index 6f422eff5c33..86ef0b406a80 100644 --- a/science/spheral/files/patch-cmake_SetupSpheral.cmake +++ b/science/spheral/files/patch-cmake_SetupSpheral.cmake @@ -1,8 +1,8 @@ - eliminate the need to use git ---- cmake/SetupSpheral.cmake.orig 2024-07-11 14:54:59 UTC +--- cmake/SetupSpheral.cmake.orig 2025-07-23 20:11:18 UTC +++ cmake/SetupSpheral.cmake -@@ -21,8 +21,8 @@ include(Compilers) +@@ -27,8 +27,8 @@ include(Compilers) #------------------------------------------------------------------------------- # Need to define Python paths here as BLT finds it's own Python package. @@ -13,12 +13,3 @@ set(ENABLE_MPI ON CACHE BOOL "") set(ENABLE_OPENMP ON CACHE BOOL "") -@@ -167,7 +167,7 @@ if (ENABLE_TESTS) - set(test_files1 "") - if (EXISTS "${CMAKE_SOURCE_DIR}/.git") - execute_process( -- COMMAND git ls-files tests -+ COMMAND find tests -type f - WORKING_DIRECTORY ${SPHERAL_ROOT_DIR} - OUTPUT_VARIABLE test_files1) - else() diff --git a/science/spheral/files/patch-cmake_tpl_boost.cmake b/science/spheral/files/patch-cmake_tpl_boost.cmake new file mode 100644 index 000000000000..521cfe62b4b8 --- /dev/null +++ b/science/spheral/files/patch-cmake_tpl_boost.cmake @@ -0,0 +1,7 @@ +--- cmake/tpl/boost.cmake.orig 2025-10-30 22:36:06 UTC ++++ cmake/tpl/boost.cmake +@@ -1,3 +1,3 @@ if (NOT BOOST_HEADER_ONLY) + if (NOT BOOST_HEADER_ONLY) +- set(${lib_name}_libs libboost_filesystem.so libboost_system.so) ++ set(${lib_name}_libs libboost_filesystem.so) + endif() diff --git a/science/spheral/pkg-plist b/science/spheral/pkg-plist index 48df7b1d08f8..a6108abb6a13 100644 --- a/science/spheral/pkg-plist +++ b/science/spheral/pkg-plist @@ -1,28 +1,20 @@ include/ArtificialConduction/ArtificialConduction.hh include/ArtificialConduction/ArtificialConductionPolicy.hh include/ArtificialViscosity/ArtificialViscosity.hh -include/ArtificialViscosity/ArtificialViscosityInline.hh -include/ArtificialViscosity/ArtificialViscosityList.hh -include/ArtificialViscosity/CheapVonNeumanViscosity.hh +include/ArtificialViscosity/ArtificialViscosityHandle.hh +include/ArtificialViscosity/ArtificialViscosityHandleInline.hh include/ArtificialViscosity/CullenDehnenViscosity.hh include/ArtificialViscosity/FiniteVolumeViscosity.hh -include/ArtificialViscosity/GradPressureViscosity.hh include/ArtificialViscosity/IncrementCullenMultipliers.hh include/ArtificialViscosity/LimitedMonaghanGingoldViscosity.hh include/ArtificialViscosity/LimitedMonaghanGingoldViscosityRZ.hh -include/ArtificialViscosity/MASHVonNeumanViscosity.hh -include/ArtificialViscosity/MonaghanGingoldKurapatenkoViscosity.hh -include/ArtificialViscosity/MonaghanGingoldSumViscosity.hh include/ArtificialViscosity/MonaghanGingoldViscosity.hh include/ArtificialViscosity/MonaghanGingoldViscosityGSRZ.hh include/ArtificialViscosity/MonaghanGingoldViscosityRZ.hh include/ArtificialViscosity/MorrisMonaghanReducingViscosity.hh -include/ArtificialViscosity/NohViscosity.hh -include/ArtificialViscosity/RadialViscosity.hh include/ArtificialViscosity/TensorCRKSPHViscosity.hh include/ArtificialViscosity/TensorMonaghanGingoldViscosity.hh include/ArtificialViscosity/TensorSVPHViscosity.hh -include/ArtificialViscosity/VonNeumanViscosity.hh include/Boundary/AxisBoundaryRZ.hh include/Boundary/Boundary.hh include/Boundary/BoundaryInline.hh @@ -56,13 +48,12 @@ include/Boundary/SphericalOriginBoundary.hh include/Boundary/ThreeOneDimensionBoundary.hh include/Boundary/findNodesTouchingThroughPlanes.hh include/Boundary/mapPositionThroughPlanes.hh -include/CRKSPH/CRKSPHHydroBase.hh -include/CRKSPH/CRKSPHHydroBaseInline.hh -include/CRKSPH/CRKSPHHydroBaseRZ.hh +include/CRKSPH/CRKSPH.hh +include/CRKSPH/CRKSPHBase.hh +include/CRKSPH/CRKSPHRZ.hh include/CRKSPH/CRKSPHVariant.hh -include/CRKSPH/SolidCRKSPHHydroBase.hh -include/CRKSPH/SolidCRKSPHHydroBaseInline.hh -include/CRKSPH/SolidCRKSPHHydroBaseRZ.hh +include/CRKSPH/SolidCRKSPH.hh +include/CRKSPH/SolidCRKSPHRZ.hh include/CRKSPH/centerOfMass.hh include/CRKSPH/computeCRKSPHEvaluation.hh include/CRKSPH/computeCRKSPHIntegral.hh @@ -95,7 +86,6 @@ include/DEM/setUniqueNodeIDsInline.hh include/Damage/DamageGradientNodeCoupling.hh include/Damage/DamageGradientPolicy.hh include/Damage/DamageModel.hh -include/Damage/DamageModelInline.hh include/Damage/EffectiveTensorDamagePolicy.hh include/Damage/GradyKippScalarDamage.hh include/Damage/IvanoviSALEDamageModel.hh @@ -143,11 +133,11 @@ include/DataBase/ReplaceBoundedState.hh include/DataBase/ReplaceBoundedStateInline.hh include/DataBase/ReplaceState.hh include/DataBase/ReplaceStateInline.hh +include/DataBase/ReplaceWithRatioPolicy.hh include/DataBase/State.hh include/DataBase/StateBase.hh include/DataBase/StateBaseInline.hh include/DataBase/StateDerivatives.hh -include/DataBase/StateDerivativesInline.hh include/DataBase/StateInline.hh include/DataBase/UpdatePolicyBase.hh include/DataBase/UpdatePolicyBaseInline.hh @@ -178,8 +168,11 @@ include/Distributed/NestedGridUtilities.hh include/Distributed/ParmetisRedistributeNodes.hh include/Distributed/ParmetisRedistributeNodesInline.hh include/Distributed/PeanoHilbertOrderRedistributeNodes.hh +include/Distributed/Process.hh include/Distributed/RedistributeNodes.hh include/Distributed/RedistributeNodesInline.hh +include/Distributed/RegisterMPIDataTypes.hh +include/Distributed/RegisterMPIDataTypesInline.hh include/Distributed/SortAndDivideRedistributeNodes.hh include/Distributed/SortAndDivideRedistributeNodes1d.hh include/Distributed/SortAndDivideRedistributeNodes2d.hh @@ -189,6 +182,7 @@ include/Distributed/SpaceFillingCurveRedistributeNodes.hh include/Distributed/TreeDistributedBoundary.hh include/Distributed/TreeDistributedBoundaryInline.hh include/Distributed/VoronoiRedistributeNodes.hh +include/Distributed/allReduce.hh include/Distributed/waitAllWithDeadlockDetection.hh include/ExternalForce/ConstantAcceleration.hh include/ExternalForce/ConstantAccelerationInline.hh @@ -201,8 +195,8 @@ include/ExternalForce/PointPotentialInline.hh include/FSISPH/FSIFieldNames.hh include/FSISPH/SlideSurface.hh include/FSISPH/SlideSurfaceInline.hh -include/FSISPH/SolidFSISPHHydroBase.hh -include/FSISPH/SolidFSISPHHydroBaseInline.hh +include/FSISPH/SolidFSISPH.hh +include/FSISPH/SolidFSISPHInline.hh include/FSISPH/computeFSISPHSumMassDensity.hh include/FSISPH/computeHWeightedFSISPHSumMassDensity.hh include/FSISPH/computeInterfacePressureCorrectedSumMassDensity.hh @@ -256,19 +250,22 @@ include/GSPH/BarthJespersenLimiter.hh include/GSPH/CompatibleMFVSpecificThermalEnergyPolicy.hh include/GSPH/DavisWaveSpeed.hh include/GSPH/EinfeldtWaveSpeed.hh +include/GSPH/GSPH.hh include/GSPH/GSPHFieldNames.hh -include/GSPH/GSPHHydroBase.hh +include/GSPH/GSPHInline.hh include/GSPH/GenericRiemannHydro.hh +include/GSPH/GenericRiemannHydroInline.hh include/GSPH/HLLC.hh include/GSPH/LimiterBase.hh -include/GSPH/MFMHydroBase.hh -include/GSPH/MFVHydroBase.hh +include/GSPH/MFM.hh +include/GSPH/MFMInline.hh +include/GSPH/MFV.hh include/GSPH/MFVIncrementSpecificThermalEnergyPolicy.hh include/GSPH/MFVIncrementVelocityPolicy.hh +include/GSPH/MFVInline.hh include/GSPH/MassFluxPolicy.hh include/GSPH/MinModLimiter.hh include/GSPH/OspreLimiter.hh -include/GSPH/ReplaceWithRatioPolicy.hh include/GSPH/RiemannSolverBase.hh include/GSPH/SecondOrderArtificialViscosity.hh include/GSPH/SuperbeeLimiter.hh @@ -276,7 +273,6 @@ include/GSPH/VanAlbaLimiter.hh include/GSPH/VanLeerLimiter.hh include/GSPH/WaveSpeedBase.hh include/GSPH/computeMFMDensity.hh -include/GSPH/computeSPHVolume.hh include/GSPH/computeSumVolume.hh include/GSPH/initializeGradients.hh include/Geometry/Box1d.hh @@ -364,28 +360,25 @@ include/Hydro/CompatibleDifferenceSpecificThermalEnergyPolicy.hh include/Hydro/EntropyPolicy.hh include/Hydro/GammaPolicy.hh include/Hydro/HydroFieldNames.hh -include/Hydro/HydroInline.hh include/Hydro/NonSymmetricSpecificThermalEnergyPolicy.hh include/Hydro/PressurePolicy.hh include/Hydro/RZNonSymmetricSpecificThermalEnergyPolicy.hh -include/Hydro/SecondMomentHourglassControl.hh -include/Hydro/SecondMomentHourglassControlInline.hh include/Hydro/SoundSpeedPolicy.hh include/Hydro/SpecificFromTotalThermalEnergyPolicy.hh include/Hydro/SpecificThermalEnergyPolicy.hh include/Hydro/SumVoronoiMassDensityPolicy.hh -include/Hydro/ThirdMomentHourglassControl.hh -include/Hydro/ThirdMomentHourglassControlInline.hh include/Hydro/VolumePolicy.hh -include/Hydro/VoronoiHourglassControl.hh -include/Hydro/VoronoiHourglassControlInline.hh include/Hydro/VoronoiMassDensityPolicy.hh +include/Hydro/computeSPHVolume.hh include/Hydro/entropyWeightingFunction.hh +include/Integrator/BackwardEuler.hh include/Integrator/CheapSynchronousRK2.hh +include/Integrator/CrankNicolson.hh +include/Integrator/ForwardEuler.hh +include/Integrator/ImplicitIntegrationVectorOperator.hh +include/Integrator/ImplicitIntegrator.hh include/Integrator/Integrator.hh -include/Integrator/IntegratorInline.hh include/Integrator/PredictorCorrector.hh -include/Integrator/SynchronousRK1.hh include/Integrator/SynchronousRK2.hh include/Integrator/SynchronousRK4.hh include/Integrator/Verlet.hh @@ -488,7 +481,11 @@ include/Neighbor/Neighbor.hh include/Neighbor/NeighborInline.hh include/Neighbor/NestedGridNeighbor.hh include/Neighbor/NestedGridNeighborInline.hh +include/Neighbor/NodePairIdxType.hh include/Neighbor/NodePairList.hh +include/Neighbor/PairwiseField.hh +include/Neighbor/PairwiseFieldElementAccessor.hh +include/Neighbor/PairwiseFieldInline.hh include/Neighbor/TreeNeighbor.hh include/NodeGenerators/centroidalRelaxNodesImpl.hh include/NodeGenerators/chooseRandomNonoverlappingCenter.hh @@ -497,10 +494,8 @@ include/NodeGenerators/fillFacetedVolume.hh include/NodeGenerators/generateCylDistributionFromRZ.hh include/NodeGenerators/readSiloPolyMesh.hh include/NodeGenerators/relaxNodeDistribution.hh -include/NodeList/ASPHSmoothingScale.hh include/NodeList/DEMNodeList.hh include/NodeList/DEMNodeListInline.hh -include/NodeList/FixedSmoothingScale.hh include/NodeList/FluidNodeList.hh include/NodeList/FluidNodeListInline.hh include/NodeList/FluidNodeTraits.hh @@ -508,19 +503,13 @@ include/NodeList/NodeList.hh include/NodeList/NodeListInline.hh include/NodeList/NodeListRegistrar.hh include/NodeList/NodeListRegistrarInline.hh -include/NodeList/SPHSmoothingScale.hh -include/NodeList/SmoothingScaleBase.hh -include/NodeList/SmoothingScaleBaseInline.hh include/NodeList/SolidNodeList.hh include/NodeList/SolidNodeListInline.hh include/NodeList/generateVoidNodes.hh include/NodeList/nthNodalMoment.hh -include/NodeList/secondMomentUtilities.hh include/Physics/GenericBodyForce.hh include/Physics/GenericHydro.hh -include/Physics/GenericHydroInline.hh include/Physics/Physics.hh -include/Physics/PhysicsInline.hh include/Porosity/PalphaPorosity.hh include/Porosity/PorosityModel.hh include/Porosity/PorosityModelInline.hh @@ -544,20 +533,17 @@ include/RK/computeHullVolumes.hh include/RK/computeOccupancyVolume.hh include/RK/computeRKSumVolume.hh include/RK/computeRKVolumes.hh -include/RK/computeVoronoiVolume.hh include/RK/gradientRK.hh include/RK/hessianRK.hh include/RK/interpolateRK.hh -include/SPH/PSPHHydroBase.hh -include/SPH/PSPHHydroBaseInline.hh -include/SPH/SPHHydroBase.hh -include/SPH/SPHHydroBaseInline.hh -include/SPH/SPHHydroBaseRZ.hh -include/SPH/SolidSPHHydroBase.hh -include/SPH/SolidSPHHydroBaseInline.hh -include/SPH/SolidSPHHydroBaseRZ.hh -include/SPH/SolidSphericalSPHHydroBase.hh -include/SPH/SphericalSPHHydroBase.hh +include/SPH/PSPH.hh +include/SPH/SPH.hh +include/SPH/SPHBase.hh +include/SPH/SPHRZ.hh +include/SPH/SolidSPH.hh +include/SPH/SolidSPHRZ.hh +include/SPH/SolidSphericalSPH.hh +include/SPH/SphericalSPH.hh include/SPH/computeHydrostaticEquilibriumPressure.hh include/SPH/computePSPHCorrections.hh include/SPH/computeSPHOmegaGradhCorrection.hh @@ -566,7 +552,6 @@ include/SPH/computeSumVoronoiCellMassDensity.hh include/SPH/correctSPHSumMassDensity.hh include/SVPH/CellPressurePolicy.hh include/SVPH/CompatibleFaceSpecificThermalEnergyPolicy.hh -include/SVPH/MeshIdealHPolicy.hh include/SVPH/SVPHCorrectionsPolicy.hh include/SVPH/SVPHFacetedHydroBase.hh include/SVPH/SVPHFacetedHydroBaseInline.hh @@ -580,6 +565,16 @@ include/SVPH/computeSVPHCorrectionsOnFaces.hh include/SVPH/computeSumVoronoiCellMassDensityFromFaces.hh include/SVPH/gradientFieldListSVPH.hh include/SVPH/sampleFieldListSVPH.hh +include/SmoothingScale/ASPHClassicSmoothingScale.hh +include/SmoothingScale/ASPHRadialFunctor.hh +include/SmoothingScale/ASPHSmoothingScale.hh +include/SmoothingScale/ASPHSmoothingScaleUserFilter.hh +include/SmoothingScale/FixedSmoothingScale.hh +include/SmoothingScale/IncrementASPHHtensor.hh +include/SmoothingScale/SPHSmoothingScale.hh +include/SmoothingScale/SmoothingScaleBase.hh +include/SmoothingScale/SmoothingScaleBaseInline.hh +include/SmoothingScale/polySecondMoment.hh include/SolidMaterial/ANEOS.hh include/SolidMaterial/CollinsStrength.hh include/SolidMaterial/ConstantStrength.hh @@ -605,6 +600,8 @@ include/SolidMaterial/StrengthModel.hh include/SolidMaterial/TillotsonEquationOfState.hh include/SolidMaterial/TillotsonEquationOfStateInline.hh include/SolidMaterial/iSALEROCKStrength.hh +include/Solvers/KINSOL.hh +include/Solvers/SolverFunction.hh include/Strength/BulkModulusPolicy.hh include/Strength/DeviatoricStressPolicy.hh include/Strength/MeltEnergyPolicy.hh @@ -613,6 +610,7 @@ include/Strength/ShearModulusPolicy.hh include/Strength/SolidFieldNames.hh include/Strength/YieldStrengthPolicy.hh include/Strength/effectiveKernelVolume.hh +include/Utilities/AnyVisitor.hh include/Utilities/Bessel.hh include/Utilities/BiCubicInterpolator.hh include/Utilities/BiCubicInterpolatorInline.hh @@ -633,29 +631,29 @@ include/Utilities/FieldDataTypeTraits.hh include/Utilities/Functors.hh include/Utilities/GeometricUtilities.hh include/Utilities/KeyTraits.hh +include/Utilities/LinearInterpolator.hh +include/Utilities/LinearInterpolatorInline.hh include/Utilities/NodeCoupling.hh include/Utilities/NodeListHashMap.hh include/Utilities/OpenMP_wrapper.hh include/Utilities/PairComparisons.hh include/Utilities/PeanoHilbertTransform.hh -include/Utilities/Process.hh include/Utilities/QuadraticInterpolator.hh include/Utilities/QuadraticInterpolatorInline.hh include/Utilities/RedistributionNotification.hh include/Utilities/RedistributionNotificationHandle.hh include/Utilities/RedistributionRegistrar.hh include/Utilities/RedistributionRegistrarInline.hh -include/Utilities/RegisterMPIDataTypes.hh -include/Utilities/RegisterMPIDataTypesInline.hh include/Utilities/SafeIndexMap.hh include/Utilities/SpheralFunctions.hh +include/Utilities/SpheralMessage.hh +include/Utilities/StrideIterator.hh include/Utilities/SurfaceNodeCoupling.hh include/Utilities/Timer.hh include/Utilities/Tree.hh include/Utilities/TreeInline.hh include/Utilities/XYInterpolator.hh include/Utilities/XYInterpolatorInline.hh -include/Utilities/allReduce.hh include/Utilities/bisectRoot.hh include/Utilities/bisectSearch.hh include/Utilities/boundPointWithinBox.hh @@ -679,7 +677,6 @@ include/Utilities/lineSegmentIntersections.hh include/Utilities/log2.hh include/Utilities/medianPosition.hh include/Utilities/mortonOrderIndices.hh -include/Utilities/mpiUtilities.hh include/Utilities/newtonRaphson.hh include/Utilities/nodeBoundingBoxes.hh include/Utilities/nodeBoundingBoxesInline.hh @@ -694,12 +691,12 @@ include/Utilities/pointInPolygon.hh include/Utilities/pointInPolyhedron.hh include/Utilities/pointOnPolygon.hh include/Utilities/pointOnPolyhedron.hh +include/Utilities/range.hh include/Utilities/refinePolyhedron.hh include/Utilities/registerWithRedistribution.hh include/Utilities/removeElements.hh include/Utilities/rotationMatrix.hh include/Utilities/safeInv.hh -include/Utilities/scan.hh include/Utilities/segmentIntersectEdges.hh include/Utilities/setGlobalFlags.hh include/Utilities/simpsonsIntegration.hh @@ -709,6 +706,9 @@ include/Utilities/testBoxIntersection.hh include/Utilities/timingUtilities.hh include/Utilities/uniform_random.hh include/Utilities/uniform_random_Inline.hh +include/VoronoiCells/SubPointPressureHourglassControl.hh +include/VoronoiCells/VoronoiCells.hh +include/VoronoiCells/computeVoronoiVolume.hh lib/cmake/spheral_cxx-config.cmake lib/cmake/spheral_cxx-targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/spheral_cxx-targets.cmake diff --git a/science/step/distinfo b/science/step/distinfo index 5db7278905a9..21ad428a5628 100644 --- a/science/step/distinfo +++ b/science/step/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1757410252 -SHA256 (KDE/release-service/25.08.1/step-25.08.1.tar.xz) = d5ae8c25718f6a647556210f2d4055de1ccd342d3b948f14f9e2ee27ab48b154 -SIZE (KDE/release-service/25.08.1/step-25.08.1.tar.xz) = 1007604 +TIMESTAMP = 1762264758 +SHA256 (KDE/release-service/25.08.3/step-25.08.3.tar.xz) = b1ddce4f52a0b75188616c062be4fa7ad5d3d7725c211ec011719a9ad27e86f9 +SIZE (KDE/release-service/25.08.3/step-25.08.3.tar.xz) = 1016244 diff --git a/science/step/pkg-plist b/science/step/pkg-plist index 4186212eb37b..2fe4b8582cad 100644 --- a/science/step/pkg-plist +++ b/science/step/pkg-plist @@ -33,6 +33,8 @@ share/icons/hicolor/48x48/apps/step.png share/icons/hicolor/64x64/apps/step.png share/knsrcfiles/step.knsrc share/locale/ar/LC_MESSAGES/step.mo +share/locale/ar/LC_MESSAGES/step_example_files.mo +share/locale/ar/LC_MESSAGES/step_objinfo_files.mo share/locale/ar/LC_MESSAGES/step_qt.qm share/locale/be/LC_MESSAGES/step.mo share/locale/be/LC_MESSAGES/step_qt.qm @@ -214,6 +216,23 @@ share/locale/zh_TW/LC_MESSAGES/step_objinfo_files.mo share/locale/zh_TW/LC_MESSAGES/step_qt.qm share/metainfo/org.kde.step.appdata.xml share/mime/packages/org.kde.step.xml +%%DATADIR%%/examples/ar/brownian.step +%%DATADIR%%/examples/ar/doublependulum.step +%%DATADIR%%/examples/ar/eightpendula.step +%%DATADIR%%/examples/ar/first.step +%%DATADIR%%/examples/ar/fourpendula.step +%%DATADIR%%/examples/ar/gas.step +%%DATADIR%%/examples/ar/graph.step +%%DATADIR%%/examples/ar/liquid.step +%%DATADIR%%/examples/ar/lissajous.step +%%DATADIR%%/examples/ar/motor.step +%%DATADIR%%/examples/ar/motor1.step +%%DATADIR%%/examples/ar/note.step +%%DATADIR%%/examples/ar/resonance.step +%%DATADIR%%/examples/ar/softbody.step +%%DATADIR%%/examples/ar/solar.step +%%DATADIR%%/examples/ar/springs.step +%%DATADIR%%/examples/ar/wave.step %%DATADIR%%/examples/bg/brownian.step %%DATADIR%%/examples/bg/doublependulum.step %%DATADIR%%/examples/bg/eightpendula.step @@ -818,6 +837,25 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/objinfo/gasljforce.html %%DATADIR%%/objinfo/gasparticle.html %%DATADIR%%/objinfo/gravitationforce.html +%%DATADIR%%/objinfo/l10n/ar/anchor.html +%%DATADIR%%/objinfo/l10n/ar/box.html +%%DATADIR%%/objinfo/l10n/ar/chargedparticle.html +%%DATADIR%%/objinfo/l10n/ar/coulombforce.html +%%DATADIR%%/objinfo/l10n/ar/disk.html +%%DATADIR%%/objinfo/l10n/ar/gas.html +%%DATADIR%%/objinfo/l10n/ar/gasljforce.html +%%DATADIR%%/objinfo/l10n/ar/gasparticle.html +%%DATADIR%%/objinfo/l10n/ar/gravitationforce.html +%%DATADIR%%/objinfo/l10n/ar/linearmotor.html +%%DATADIR%%/objinfo/l10n/ar/meter.html +%%DATADIR%%/objinfo/l10n/ar/note.html +%%DATADIR%%/objinfo/l10n/ar/particle.html +%%DATADIR%%/objinfo/l10n/ar/pin.html +%%DATADIR%%/objinfo/l10n/ar/polygon.html +%%DATADIR%%/objinfo/l10n/ar/softbody.html +%%DATADIR%%/objinfo/l10n/ar/spring.html +%%DATADIR%%/objinfo/l10n/ar/weightforce.html +%%DATADIR%%/objinfo/l10n/ar/world.html %%DATADIR%%/objinfo/l10n/bg/anchor.html %%DATADIR%%/objinfo/l10n/bg/box.html %%DATADIR%%/objinfo/l10n/bg/chargedparticle.html @@ -1493,6 +1531,11 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/objinfo/spring.html %%DATADIR%%/objinfo/weightforce.html %%DATADIR%%/objinfo/world.html +%%DATADIR%%/tutorials/ar/tutorial1.step +%%DATADIR%%/tutorials/ar/tutorial2.step +%%DATADIR%%/tutorials/ar/tutorial3.step +%%DATADIR%%/tutorials/ar/tutorial4.step +%%DATADIR%%/tutorials/ar/tutorial5.step %%DATADIR%%/tutorials/bg/tutorial1.step %%DATADIR%%/tutorials/bg/tutorial2.step %%DATADIR%%/tutorials/bg/tutorial3.step diff --git a/science/tblite/Makefile b/science/tblite/Makefile index 1764e8c96a3f..c1314fe73bb0 100644 --- a/science/tblite/Makefile +++ b/science/tblite/Makefile @@ -1,16 +1,17 @@ PORTNAME= tblite DISTVERSIONPREFIX= v -DISTVERSION= 0.4.0 -PORTREVISION= 1 +DISTVERSION= 0.5.0 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Light-weight tight-binding framework -WWW= https://github.com/tblite/tblite +WWW= https://tblite.readthedocs.io/ \ + https://github.com/tblite/tblite/ -LICENSE= GPLv3 -LICENSE_FILE= ${WRKSRC}/COPYING +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 diff --git a/science/tblite/distinfo b/science/tblite/distinfo index 5be96927f362..380451730bd2 100644 --- a/science/tblite/distinfo +++ b/science/tblite/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1731994102 -SHA256 (tblite-tblite-v0.4.0_GH0.tar.gz) = c4a67dfbe04827095fd7598183e076fa3017a5a475c4f90fd28e78992dc19ea7 -SIZE (tblite-tblite-v0.4.0_GH0.tar.gz) = 624375 +TIMESTAMP = 1762018807 +SHA256 (tblite-tblite-v0.5.0_GH0.tar.gz) = 65ede0d66ad38f7748cb1c93367db3bd9b67f6439d8e45539bcf55182489c287 +SIZE (tblite-tblite-v0.5.0_GH0.tar.gz) = 825498 diff --git a/science/tblite/pkg-plist b/science/tblite/pkg-plist index 87b99403b73c..83194bcdbc64 100644 --- a/science/tblite/pkg-plist +++ b/science/tblite/pkg-plist @@ -8,6 +8,7 @@ include/tblite/error.h include/tblite/macros.h include/tblite/param.h include/tblite/result.h +include/tblite/solvation.h include/tblite/structure.h include/tblite/table.h include/tblite/tblite_adjlist.mod @@ -18,6 +19,7 @@ include/tblite/tblite_api_double_dictionary.mod include/tblite/tblite_api_error.mod include/tblite/tblite_api_param.mod include/tblite/tblite_api_result.mod +include/tblite/tblite_api_solvation.mod include/tblite/tblite_api_structure.mod include/tblite/tblite_api_table.mod include/tblite/tblite_api_utils.mod @@ -74,6 +76,15 @@ include/tblite/tblite_integral_multipole.mod include/tblite/tblite_integral_overlap.mod include/tblite/tblite_integral_trafo.mod include/tblite/tblite_integral_type.mod +include/tblite/tblite_io_numpy.mod +include/tblite/tblite_io_numpy_constants.mod +include/tblite/tblite_io_numpy_crc32.mod +include/tblite/tblite_io_numpy_load.mod +include/tblite/tblite_io_numpy_loadz.mod +include/tblite/tblite_io_numpy_save.mod +include/tblite/tblite_io_numpy_savez.mod +include/tblite/tblite_io_numpy_utils.mod +include/tblite/tblite_io_numpy_zip.mod include/tblite/tblite_io_tag.mod include/tblite/tblite_lapack.mod include/tblite/tblite_lapack_getrf.mod @@ -108,15 +119,18 @@ include/tblite/tblite_param_post_processing.mod include/tblite/tblite_param_repulsion.mod include/tblite/tblite_param_serde.mod include/tblite/tblite_param_thirdorder.mod +include/tblite/tblite_param_xtbml_features.mod include/tblite/tblite_post_processing_bond_orders.mod include/tblite/tblite_post_processing_list.mod include/tblite/tblite_post_processing_molecular_moments.mod include/tblite/tblite_post_processing_type.mod +include/tblite/tblite_post_processing_xtbml_features.mod include/tblite/tblite_repulsion.mod include/tblite/tblite_repulsion_effective.mod include/tblite/tblite_repulsion_type.mod include/tblite/tblite_results.mod include/tblite/tblite_scf.mod +include/tblite/tblite_scf_diag.mod include/tblite/tblite_scf_info.mod include/tblite/tblite_scf_iterator.mod include/tblite/tblite_scf_mixer.mod @@ -128,10 +142,15 @@ include/tblite/tblite_solvation.mod include/tblite/tblite_solvation_alpb.mod include/tblite/tblite_solvation_born.mod include/tblite/tblite_solvation_cds.mod +include/tblite/tblite_solvation_cm5.mod include/tblite/tblite_solvation_cpcm.mod include/tblite/tblite_solvation_cpcm_dd.mod include/tblite/tblite_solvation_data.mod +include/tblite/tblite_solvation_data_alpb.mod +include/tblite/tblite_solvation_data_cds.mod +include/tblite/tblite_solvation_data_shift.mod include/tblite/tblite_solvation_input.mod +include/tblite/tblite_solvation_shift.mod include/tblite/tblite_solvation_surface.mod include/tblite/tblite_solvation_type.mod include/tblite/tblite_spin.mod @@ -142,6 +161,7 @@ include/tblite/tblite_wavefunction.mod include/tblite/tblite_wavefunction_fermi.mod include/tblite/tblite_wavefunction_guess.mod include/tblite/tblite_wavefunction_mulliken.mod +include/tblite/tblite_wavefunction_restart.mod include/tblite/tblite_wavefunction_spin.mod include/tblite/tblite_wavefunction_type.mod include/tblite/tblite_wignerseitz.mod @@ -154,6 +174,13 @@ include/tblite/tblite_xtb_h0.mod include/tblite/tblite_xtb_ipea1.mod include/tblite/tblite_xtb_singlepoint.mod include/tblite/tblite_xtb_spec.mod +include/tblite/tblite_xtbml_atomic_frontier.mod +include/tblite/tblite_xtbml_convolution.mod +include/tblite/tblite_xtbml_density_based.mod +include/tblite/tblite_xtbml_energy_features.mod +include/tblite/tblite_xtbml_feature_type.mod +include/tblite/tblite_xtbml_geometry_based.mod +include/tblite/tblite_xtbml_orbital_energy.mod include/tblite/version.h lib/cmake/tblite/Finddftd4.cmake lib/cmake/tblite/Findmctc-lib.cmake @@ -168,5 +195,5 @@ lib/cmake/tblite/tblite-targets.cmake lib/cmake/tblite/tblite-utils.cmake lib/libtblite.so lib/libtblite.so.0 -lib/libtblite.so.0.4.0 +lib/libtblite.so.0.5.0 libdata/pkgconfig/tblite.pc 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/tinker/Makefile b/science/tinker/Makefile index 5723eb9b39db..f66cb43850b0 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,12 +1,12 @@ PORTNAME= tinker -DISTVERSION= 25.5 -PORTREVISION= 1 +DISTVERSIONPREFIX= v +DISTVERSION= 25.5.4 CATEGORIES= science -MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ MAINTAINER= yuri@FreeBSD.org COMMENT= General purpose molecular modelling package -WWW= https://dasher.wustl.edu/tinker/ +WWW= https://dasher.wustl.edu/tinker/ \ + https://github.com/TinkerTools/tinker LICENSE= TINKER LICENSE_NAME= TINKER license agreement @@ -16,8 +16,9 @@ LICENSE_PERMS= auto-accept # internal academic purposes only, no commercial use LIB_DEPENDS= libfftw3.so:math/fftw3 USES= fortran gmake +USE_GITHUB= yes +GH_ACCOUNT= TinkerTools -WRKSRC= ${WRKDIR}/${PORTNAME} BUILD_WRKSRC= ${WRKSRC}/source INSTALL_WRKSRC= ${WRKSRC}/source diff --git a/science/tinker/distinfo b/science/tinker/distinfo index b452890259c0..c80318510948 100644 --- a/science/tinker/distinfo +++ b/science/tinker/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1759481421 -SHA256 (tinker-25.5.tar.gz) = 10e24742d262a09a4b191eb73ef994cc8987e1e5e18ac7759420b36f07a02036 -SIZE (tinker-25.5.tar.gz) = 81137927 +TIMESTAMP = 1763921430 +SHA256 (TinkerTools-tinker-v25.5.4_GH0.tar.gz) = 410d02d3fe7b42b124cc38cef8cf3c077037a099465c799259f60bdae4e367b2 +SIZE (TinkerTools-tinker-v25.5.4_GH0.tar.gz) = 34197683 diff --git a/science/tinker/files/patch-make_Makefile b/science/tinker/files/patch-make_Makefile index 7e1f679a86a0..b92cb6e976c7 100644 --- a/science/tinker/files/patch-make_Makefile +++ b/science/tinker/files/patch-make_Makefile @@ -1,6 +1,6 @@ ---- make/Makefile.orig 2025-09-30 16:25:57 UTC +--- make/Makefile.orig 2025-11-21 04:02:18 UTC +++ make/Makefile -@@ -813,138 +813,138 @@ rename_bin: +@@ -818,72 +818,72 @@ rename_bin: cat *.f *.c > tinker.txt rename_bin: @@ -20,6 +20,7 @@ - mv gda.x $(BINDIR)/gda - mv intedit.x $(BINDIR)/intedit - mv intxyz.x $(BINDIR)/intxyz +- mv mdavg.x $(BINDIR)/mdavg - mv minimize.x $(BINDIR)/minimize - mv minirot.x $(BINDIR)/minirot - mv minrigid.x $(BINDIR)/minrigid @@ -85,6 +86,7 @@ + ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda + ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit + ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz ++ ${BSD_INSTALL_PROGRAM} mdavg.x $(BINDIR)/mdavg + ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize + ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot + ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid @@ -136,136 +138,4 @@ + ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb rename_exe: -- mv alchemy.x $(BINDIR)/alchemy.exe -- mv analyze.x $(BINDIR)/analyze.exe -- mv anneal.x $(BINDIR)/anneal.exe -- mv arcedit.x $(BINDIR)/arcedit.exe -- mv bar.x $(BINDIR)/bar.exe -- mv correlate.x $(BINDIR)/correlate.exe -- mv critical.x $(BINDIR)/critical.exe -- mv crystal.x $(BINDIR)/crystal.exe -- mv diffuse.x $(BINDIR)/diffuse.exe -- mv distgeom.x $(BINDIR)/distgeom.exe -- mv document.x $(BINDIR)/document.exe -- mv dynamic.x $(BINDIR)/dynamic.exe -- mv freefix.x $(BINDIR)/freefix.exe -- mv gda.x $(BINDIR)/gda.exe -- mv intedit.x $(BINDIR)/intedit.exe -- mv intxyz.x $(BINDIR)/intxyz.exe -- mv minimize.x $(BINDIR)/minimize.exe -- mv minirot.x $(BINDIR)/minirot.exe -- mv minrigid.x $(BINDIR)/minrigid.exe -- mv mol2xyz.x $(BINDIR)/mol2xyz.exe -- mv molxyz.x $(BINDIR)/molxyz.exe -- mv monte.x $(BINDIR)/monte.exe -- mv newton.x $(BINDIR)/newton.exe -- mv newtrot.x $(BINDIR)/newtrot.exe -- mv nucleic.x $(BINDIR)/nucleic.exe -- mv optimize.x $(BINDIR)/optimize.exe -- mv optirot.x $(BINDIR)/optirot.exe -- mv optrigid.x $(BINDIR)/optrigid.exe -- mv path.x $(BINDIR)/path.exe -- mv pdbxyz.x $(BINDIR)/pdbxyz.exe -- mv polarize.x $(BINDIR)/polarize.exe -- mv poledit.x $(BINDIR)/poledit.exe -- mv potential.x $(BINDIR)/potential.exe -- mv prmedit.x $(BINDIR)/prmedit.exe -- mv protein.x $(BINDIR)/protein.exe -- mv pss.x $(BINDIR)/pss.exe -- mv pssrigid.x $(BINDIR)/pssrigid.exe -- mv pssrot.x $(BINDIR)/pssrot.exe -- mv radial.x $(BINDIR)/radial.exe -- mv saddle.x $(BINDIR)/saddle.exe -- mv scan.x $(BINDIR)/scan.exe -- mv sniffer.x $(BINDIR)/sniffer.exe -- mv spacefill.x $(BINDIR)/spacefill.exe -- mv spectrum.x $(BINDIR)/spectrum.exe -- mv superpose.x $(BINDIR)/superpose.exe -- mv testgrad.x $(BINDIR)/testgrad.exe -- mv testhess.x $(BINDIR)/testhess.exe -- mv testpair.x $(BINDIR)/testpair.exe -- mv testpol.x $(BINDIR)/testpol.exe -- mv testrot.x $(BINDIR)/testrot.exe -- mv testsurf.x $(BINDIR)/testsurf.exe -- mv testvir.x $(BINDIR)/testvir.exe -- mv timer.x $(BINDIR)/timer.exe -- mv timerot.x $(BINDIR)/timerot.exe -- mv torsfit.x $(BINDIR)/torsfit.exe -- mv valence.x $(BINDIR)/valence.exe -- mv vibbig.x $(BINDIR)/vibbig.exe -- mv vibrate.x $(BINDIR)/vibrate.exe -- mv vibrot.x $(BINDIR)/vibrot.exe -- mv xtalfit.x $(BINDIR)/xtalfit.exe -- mv xtalmin.x $(BINDIR)/xtalmin.exe -- mv xyzedit.x $(BINDIR)/xyzedit.exe -- mv xyzint.x $(BINDIR)/xyzint.exe -- mv xyzmol2.x $(BINDIR)/xyzmol2.exe -- mv xyzpdb.x $(BINDIR)/xyzpdb.exe -+ ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy.exe -+ ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze.exe -+ ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal.exe -+ ${BSD_INSTALL_PROGRAM} arcedit.x $(BINDIR)/arcedit.exe -+ ${BSD_INSTALL_PROGRAM} bar.x $(BINDIR)/bar.exe -+ ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate.exe -+ ${BSD_INSTALL_PROGRAM} critical.x $(BINDIR)/critical.exe -+ ${BSD_INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal.exe -+ ${BSD_INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse.exe -+ ${BSD_INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom.exe -+ ${BSD_INSTALL_PROGRAM} document.x $(BINDIR)/document.exe -+ ${BSD_INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic.exe -+ ${BSD_INSTALL_PROGRAM} freefix.x $(BINDIR)/freefix.exe -+ ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda.exe -+ ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit.exe -+ ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz.exe -+ ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize.exe -+ ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot.exe -+ ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid.exe -+ ${BSD_INSTALL_PROGRAM} mol2xyz.x $(BINDIR)/mol2xyz.exe -+ ${BSD_INSTALL_PROGRAM} molxyz.x $(BINDIR)/molxyz.exe -+ ${BSD_INSTALL_PROGRAM} monte.x $(BINDIR)/monte.exe -+ ${BSD_INSTALL_PROGRAM} newton.x $(BINDIR)/newton.exe -+ ${BSD_INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot.exe -+ ${BSD_INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic.exe -+ ${BSD_INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize.exe -+ ${BSD_INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot.exe -+ ${BSD_INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid.exe -+ ${BSD_INSTALL_PROGRAM} path.x $(BINDIR)/path.exe -+ ${BSD_INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz.exe -+ ${BSD_INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize.exe -+ ${BSD_INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit.exe -+ ${BSD_INSTALL_PROGRAM} potential.x $(BINDIR)/potential.exe -+ ${BSD_INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit.exe -+ ${BSD_INSTALL_PROGRAM} protein.x $(BINDIR)/protein.exe -+ ${BSD_INSTALL_PROGRAM} pss.x $(BINDIR)/pss.exe -+ ${BSD_INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid.exe -+ ${BSD_INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot.exe -+ ${BSD_INSTALL_PROGRAM} radial.x $(BINDIR)/radial.exe -+ ${BSD_INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle.exe -+ ${BSD_INSTALL_PROGRAM} scan.x $(BINDIR)/scan.exe -+ ${BSD_INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer.exe -+ ${BSD_INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill.exe -+ ${BSD_INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum.exe -+ ${BSD_INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose.exe -+ ${BSD_INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad.exe -+ ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess.exe -+ ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair.exe -+ ${BSD_INSTALL_PROGRAM} testpol.x $(BINDIR)/testpol.exe -+ ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot.exe -+ ${BSD_INSTALL_PROGRAM} testsurf.x $(BINDIR)/testsurf.exe -+ ${BSD_INSTALL_PROGRAM} testvir.x $(BINDIR)/testvir.exe -+ ${BSD_INSTALL_PROGRAM} timer.x $(BINDIR)/timer.exe -+ ${BSD_INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot.exe -+ ${BSD_INSTALL_PROGRAM} torsfit.x $(BINDIR)/torsfit.exe -+ ${BSD_INSTALL_PROGRAM} valence.x $(BINDIR)/valence.exe -+ ${BSD_INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig.exe -+ ${BSD_INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate.exe -+ ${BSD_INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot.exe -+ ${BSD_INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit.exe -+ ${BSD_INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin.exe -+ ${BSD_INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit.exe -+ ${BSD_INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint.exe -+ ${BSD_INSTALL_PROGRAM} xyzmol2.x $(BINDIR)/xyzmol2.exe -+ ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb.exe - - remove_links: - rm -f $(LINKDIR)/alchemy + mv alchemy.x $(BINDIR)/alchemy.exe diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist index 723615e476ff..cf05ef8ea37c 100644 --- a/science/tinker/pkg-plist +++ b/science/tinker/pkg-plist @@ -14,6 +14,7 @@ bin/freefix bin/gda bin/intedit bin/intxyz +bin/mdavg bin/minimize bin/minirot bin/minrigid @@ -85,7 +86,7 @@ bin/xyzpdb %%DATADIR%%/params/charmm19.prm %%DATADIR%%/params/charmm22.prm %%DATADIR%%/params/charmm27.prm -%%DATADIR%%/params/charmm36.prm +%%DATADIR%%/params/charmm36m.prm %%DATADIR%%/params/dang.prm %%DATADIR%%/params/hippo19.prm %%DATADIR%%/params/hoch.prm @@ -96,9 +97,7 @@ bin/xyzpdb %%DATADIR%%/params/mmff94.prm %%DATADIR%%/params/mmff94s.prm %%DATADIR%%/params/oplsaa08.prm -%%DATADIR%%/params/oplsaa24.prm %%DATADIR%%/params/oplsaal.prm -%%DATADIR%%/params/oplsaam.prm %%DATADIR%%/params/oplsua.prm %%DATADIR%%/params/smoothaa.prm %%DATADIR%%/params/smoothua.prm diff --git a/science/trilinos/Makefile b/science/trilinos/Makefile index d2c8f9e9253c..bf02f46f6ed9 100644 --- a/science/trilinos/Makefile +++ b/science/trilinos/Makefile @@ -1,17 +1,15 @@ PORTNAME= trilinos -DISTVERSIONPREFIX= trilinos-release- -DISTVERSION= 16-1-0 -PORTREVISION= 1 +DISTVERSION= 16.2.0 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Solver for multi-physics engineering and scientific problems -WWW= https://trilinos.github.io/ +WWW= https://trilinos.github.io/ \ + https://github.com/trilinos/trilinos LICENSE= BSD3CLAUSE LGPL20 # Trilinos is licensed on a per-package basis. Most packages are under a BSD license, some are published under the (L)GPL. LICENSE_COMB= multi -BROKEN_FreeBSD_15= compilation fails with clang-19, see https://github.com/trilinos/Trilinos/issues/13570 BROKEN_armv6= kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found 4-byte BROKEN_armv7= kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found 4-byte BROKEN_i386= kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found 4-byte @@ -95,4 +93,6 @@ post-install: # remove MPI headers that it installs @${RM} ${STAGEDIR}${PREFIX}/include/mpi*.h +# Tests fail to compile, see https://github.com/trilinos/Trilinos/issues/14748 + .include <bsd.port.mk> diff --git a/science/trilinos/distinfo b/science/trilinos/distinfo index d9e1b7f1a849..09f91c91366b 100644 --- a/science/trilinos/distinfo +++ b/science/trilinos/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1743061355 -SHA256 (trilinos-Trilinos-trilinos-release-16-1-0_GH0.tar.gz) = e9651c88f581049457036cfc01b527a9d3903c257338eeeab942befd7452f23a -SIZE (trilinos-Trilinos-trilinos-release-16-1-0_GH0.tar.gz) = 197260161 +TIMESTAMP = 1764144792 +SHA256 (trilinos-Trilinos-16.2.0_GH0.tar.gz) = a5dd61e7752b6c0c53e89495aa68e099a5f68b6b775fff49e324c3b177174488 +SIZE (trilinos-Trilinos-16.2.0_GH0.tar.gz) = 198602159 diff --git a/science/trilinos/files/patch-packages_zoltan_src_driver_dr__random__io.c b/science/trilinos/files/patch-packages_zoltan_src_driver_dr__random__io.c new file mode 100644 index 000000000000..42037d4236a8 --- /dev/null +++ b/science/trilinos/files/patch-packages_zoltan_src_driver_dr__random__io.c @@ -0,0 +1,13 @@ +--- packages/zoltan/src/driver/dr_random_io.c.orig 2025-11-26 08:50:26 UTC ++++ packages/zoltan/src/driver/dr_random_io.c +@@ -42,10 +42,6 @@ extern "C" { + #define MAX_STR_LENGTH 80 + #endif + +-#ifdef M_PIl +-#error "HAVE M_PI1" +-#endif +- + /****************************************************************************/ + /****************************************************************************/ + /****************************************************************************/ diff --git a/science/trilinos/pkg-plist b/science/trilinos/pkg-plist index 4c08fb328b63..32e53c10a615 100644 --- a/science/trilinos/pkg-plist +++ b/science/trilinos/pkg-plist @@ -62,7 +62,6 @@ include/Amesos2_SolverCore_decl.hpp include/Amesos2_SolverCore_def.hpp include/Amesos2_SolverTraits.hpp include/Amesos2_Solver_MP_Vector.hpp -include/Amesos2_Solver_UQ_PCE.hpp include/Amesos2_Solver_decl.hpp include/Amesos2_Status.hpp include/Amesos2_Tacho.hpp @@ -180,6 +179,7 @@ include/Anasazi_LOCA_Sort.H include/Anasazi_config.h include/Anasaziepetra_DLLExportMacro.h include/Anasaziepetra_ModeLaplace_DLLExportMacro.h +include/Anasazitpetra_ModeLaplace_DLLExportMacro.h include/AssemblyUtils.hpp include/Aztec2Petra.h include/AztecOO.h @@ -312,7 +312,6 @@ include/Belos_SolverManager_MP_Vector.hpp include/Belos_StatusTest_GenResNorm_MP_Vector.hpp include/Belos_StatusTest_ImpResNorm_MP_Vector.hpp include/Belos_TpetraAdapter_MP_Vector.hpp -include/Belos_TpetraAdapter_UQ_PCE.hpp include/Belos_Tpetra_Cg.hpp include/Belos_Tpetra_CgPipeline.hpp include/Belos_Tpetra_CgSingleReduce.hpp @@ -504,6 +503,8 @@ include/Galeri_FileGrid.h include/Galeri_FiniteElements.h include/Galeri_GalerkinVariational.h include/Galeri_Hanowa.h +include/Galeri_HelmholtzFEM2DProblem.hpp +include/Galeri_HelmholtzFEM3DProblem.hpp include/Galeri_HexCubeGrid.h include/Galeri_HexQuadrature.h include/Galeri_Hilbert.h @@ -525,6 +526,7 @@ include/Galeri_Ones.h include/Galeri_Parter.h include/Galeri_Pei.h include/Galeri_Problem.hpp +include/Galeri_Problem_Helmholtz.hpp include/Galeri_QuadQuadrature.h include/Galeri_QuadRectangleGrid.h include/Galeri_Random.h @@ -547,6 +549,7 @@ include/Galeri_Utils.h include/Galeri_Vander.h include/Galeri_VbrMatrices.h include/Galeri_VectorTraits.hpp +include/Galeri_VelocityModel.hpp include/Galeri_Version.h include/Galeri_Workspace.h include/Galeri_XpetraCartesian.hpp @@ -566,6 +569,7 @@ include/Ifpack2_AdditiveSchwarz_def.hpp include/Ifpack2_BandedContainer.hpp include/Ifpack2_BandedContainer_decl.hpp include/Ifpack2_BandedContainer_def.hpp +include/Ifpack2_BlockComputeResidualAndSolve.hpp include/Ifpack2_BlockComputeResidualVector.hpp include/Ifpack2_BlockHelper.hpp include/Ifpack2_BlockHelper_Timers.hpp @@ -674,7 +678,6 @@ include/Ifpack2_Diagonal_def.hpp include/Ifpack2_DropFilter.hpp include/Ifpack2_DropFilter_decl.hpp include/Ifpack2_DropFilter_def.hpp -include/Ifpack2_ETIHelperMacros.h include/Ifpack2_Experimental_RBILUK.hpp include/Ifpack2_Experimental_RBILUK_decl.hpp include/Ifpack2_Experimental_RBILUK_def.hpp @@ -1099,6 +1102,12 @@ include/KokkosBatched_GMRES.hpp include/KokkosBatched_GMRES_Serial_Impl.hpp include/KokkosBatched_GMRES_TeamVector_Impl.hpp include/KokkosBatched_GMRES_Team_Impl.hpp +include/KokkosBatched_Gbtrf.hpp +include/KokkosBatched_Gbtrf_Serial_Impl.hpp +include/KokkosBatched_Gbtrf_Serial_Internal.hpp +include/KokkosBatched_Gbtrs.hpp +include/KokkosBatched_Gbtrs_Serial_Impl.hpp +include/KokkosBatched_Gbtrs_Serial_Internal.hpp include/KokkosBatched_Gemm_Decl.hpp include/KokkosBatched_Gemm_Serial_Impl.hpp include/KokkosBatched_Gemm_Serial_Internal.hpp @@ -1111,8 +1120,17 @@ include/KokkosBatched_Gemv_TeamVector_Impl.hpp include/KokkosBatched_Gemv_TeamVector_Internal.hpp include/KokkosBatched_Gemv_Team_Impl.hpp include/KokkosBatched_Gemv_Team_Internal.hpp +include/KokkosBatched_Ger.hpp +include/KokkosBatched_Ger_Serial_Impl.hpp +include/KokkosBatched_Ger_Serial_Internal.hpp include/KokkosBatched_Gesv.hpp include/KokkosBatched_Gesv_Impl.hpp +include/KokkosBatched_Getrf.hpp +include/KokkosBatched_Getrf_Serial_Impl.hpp +include/KokkosBatched_Getrf_Serial_Internal.hpp +include/KokkosBatched_Getrs.hpp +include/KokkosBatched_Getrs_Serial_Impl.hpp +include/KokkosBatched_Getrs_Serial_Internal.hpp include/KokkosBatched_Givens_Serial_Internal.hpp include/KokkosBatched_HadamardProduct.hpp include/KokkosBatched_HadamardProduct_Impl.hpp @@ -1147,7 +1165,6 @@ include/KokkosBatched_InnerLU_Serial_Impl.hpp include/KokkosBatched_InnerTrsm_Decl.hpp include/KokkosBatched_InnerTrsm_Serial_Impl.hpp include/KokkosBatched_InverseLU_Decl.hpp -include/KokkosBatched_InverseLU_Serial_Impl.hpp include/KokkosBatched_JacobiPrec.hpp include/KokkosBatched_Kernel_Handle.hpp include/KokkosBatched_Krylov_Handle.hpp @@ -1157,6 +1174,9 @@ include/KokkosBatched_LU_Serial_Impl.hpp include/KokkosBatched_LU_Serial_Internal.hpp include/KokkosBatched_LU_Team_Impl.hpp include/KokkosBatched_LU_Team_Internal.hpp +include/KokkosBatched_Lacgv.hpp +include/KokkosBatched_Lacgv_Serial_Impl.hpp +include/KokkosBatched_Lacgv_Serial_Internal.hpp include/KokkosBatched_Laswp.hpp include/KokkosBatched_Laswp_Serial_Impl.hpp include/KokkosBatched_Laswp_Serial_Internal.hpp @@ -1205,6 +1225,9 @@ include/KokkosBatched_Spmv.hpp include/KokkosBatched_Spmv_Serial_Impl.hpp include/KokkosBatched_Spmv_TeamVector_Impl.hpp include/KokkosBatched_Spmv_Team_Impl.hpp +include/KokkosBatched_Syr.hpp +include/KokkosBatched_Syr_Serial_Impl.hpp +include/KokkosBatched_Syr_Serial_Internal.hpp include/KokkosBatched_Tbsv.hpp include/KokkosBatched_Tbsv_Serial_Impl.hpp include/KokkosBatched_Tbsv_Serial_Internal.hpp @@ -1435,7 +1458,6 @@ include/KokkosCompat_config.h include/KokkosExp_View_Fad.hpp include/KokkosExp_View_Fad_Contiguous.hpp include/KokkosExp_View_MP_Vector_Contiguous.hpp -include/KokkosExp_View_UQ_PCE_Contiguous.hpp include/KokkosGraph_BFS_impl.hpp include/KokkosGraph_CoarsenConstruct.hpp include/KokkosGraph_CoarsenHeuristics.hpp @@ -1450,6 +1472,8 @@ include/KokkosGraph_ExplicitCoarsening.hpp include/KokkosGraph_ExplicitCoarsening_impl.hpp include/KokkosGraph_GraphColorHandle.hpp include/KokkosGraph_MIS2.hpp +include/KokkosGraph_RCB.hpp +include/KokkosGraph_RCB_impl.hpp include/KokkosGraph_RCM.hpp include/KokkosGraph_Triangle.hpp include/KokkosGraph_color_d1_spec.hpp @@ -1474,6 +1498,7 @@ include/KokkosKernels_PrintConfiguration.hpp include/KokkosKernels_PrintUtils.hpp include/KokkosKernels_SafeCompare.hpp include/KokkosKernels_SimpleUtils.hpp +include/KokkosKernels_Singleton.hpp include/KokkosKernels_Sorting.hpp include/KokkosKernels_TplsVersion.hpp include/KokkosKernels_Uniform_Initialized_MemoryPool.hpp @@ -1525,6 +1550,8 @@ include/KokkosSparse_MatrixPrec.hpp include/KokkosSparse_OrdinalTraits.hpp include/KokkosSparse_Preconditioner.hpp include/KokkosSparse_SortCrs.hpp +include/KokkosSparse_StaticCcsGraph.hpp +include/KokkosSparse_StaticCrsGraph.hpp include/KokkosSparse_Utils.hpp include/KokkosSparse_Utils_cusparse.hpp include/KokkosSparse_Utils_mkl.hpp @@ -1673,31 +1700,22 @@ include/KokkosSparse_twostage_gauss_seidel_impl.hpp include/Kokkos_AnalyzeStokhosShape.hpp include/Kokkos_ArithTraits.hpp include/Kokkos_ArithTraits_MP_Vector.hpp -include/Kokkos_ArithTraits_UQ_PCE.hpp include/Kokkos_Atomic_MP_Vector.hpp -include/Kokkos_Atomic_UQ_PCE.hpp include/Kokkos_Blas1_MP_Vector.hpp -include/Kokkos_Blas1_UQ_PCE.hpp include/Kokkos_CrsMatrix_MP_Vector.hpp include/Kokkos_CrsMatrix_MP_Vector_Cuda.hpp -include/Kokkos_CrsMatrix_UQ_PCE.hpp -include/Kokkos_CrsMatrix_UQ_PCE_Cuda.hpp include/Kokkos_DynRankView_Fad.hpp include/Kokkos_DynRankView_Fad_Contiguous.hpp include/Kokkos_InnerProductSpaceTraits.hpp include/Kokkos_InnerProductSpaceTraits_MP_Vector.hpp -include/Kokkos_InnerProductSpaceTraits_UQ_PCE.hpp include/Kokkos_LayoutContiguous.hpp include/Kokkos_LayoutNatural.hpp include/Kokkos_MV_MP_Vector.hpp -include/Kokkos_MV_UQ_PCE.hpp include/Kokkos_MpiTypeTraits.hpp include/Kokkos_Parallel_MP_Vector.hpp include/Kokkos_Random_MP_Vector.hpp -include/Kokkos_Random_UQ_PCE.hpp include/Kokkos_TeuchosCommAdapters.hpp include/Kokkos_TeuchosCommAdapters_MP_Vector.hpp -include/Kokkos_TeuchosCommAdapters_UQ_PCE.hpp include/Kokkos_ViewFactory.hpp include/Kokkos_View_Fad.hpp include/Kokkos_View_Fad_Fwd.hpp @@ -1705,9 +1723,6 @@ include/Kokkos_View_MP_Vector.hpp include/Kokkos_View_MP_Vector_Fwd.hpp include/Kokkos_View_MP_Vector_Interlaced.hpp include/Kokkos_View_MP_Vector_Utils.hpp -include/Kokkos_View_UQ_PCE.hpp -include/Kokkos_View_UQ_PCE_Fwd.hpp -include/Kokkos_View_UQ_PCE_Utils.hpp include/Kokkos_View_Utils.hpp include/Kokkos_View_Utils_Def.hpp include/LOCA.H @@ -1882,7 +1897,7 @@ include/LOCA_TurningPoint_MooreSpence_PhippsBordering.H include/LOCA_TurningPoint_MooreSpence_SalingerBordering.H include/LOCA_TurningPoint_MooreSpence_SolverFactory.H include/LOCA_TurningPoint_MooreSpence_SolverStrategy.H -include/ML_Linker.hpp +include/Legendre.hpp include/MatrixMarket_Tpetra.hpp include/MatrixMarket_TpetraNew.hpp include/MiniTensor.h @@ -1926,6 +1941,7 @@ include/MiniTensor_version.h include/ModalProblem.h include/ModeLaplace.h include/ModeLaplace1DQ1.h +include/ModeLaplace1DQ1.hpp include/ModeLaplace1DQ2.h include/ModeLaplace2DQ1.h include/ModeLaplace2DQ2.h @@ -2093,6 +2109,7 @@ include/MueLu_CoupledRBMFactory_def.hpp include/MueLu_CoupledRBMFactory_fwd.hpp include/MueLu_CreateTpetraPreconditioner.hpp include/MueLu_CreateXpetraPreconditioner.hpp +include/MueLu_CrsMatrixUtils.hpp include/MueLu_CutDrop.hpp include/MueLu_DemoFactory.hpp include/MueLu_DemoFactory_decl.hpp @@ -2214,6 +2231,7 @@ include/MueLu_Ifpack2Smoother_def.hpp include/MueLu_Ifpack2Smoother_fwd.hpp include/MueLu_IfpackSmoother.hpp include/MueLu_IfpackSmoother_fwd.hpp +include/MueLu_ImportUtils.hpp include/MueLu_IndefBlockedDiagonalSmoother.hpp include/MueLu_IndefBlockedDiagonalSmoother_decl.hpp include/MueLu_IndefBlockedDiagonalSmoother_def.hpp @@ -2254,7 +2272,9 @@ include/MueLu_IsorropiaInterface.hpp include/MueLu_IsorropiaInterface_decl.hpp include/MueLu_IsorropiaInterface_def.hpp include/MueLu_IsorropiaInterface_fwd.hpp +include/MueLu_IteratorOps.hpp include/MueLu_KeepType.hpp +include/MueLu_KokkosTuningInterface.hpp include/MueLu_LWGraph.hpp include/MueLu_LWGraphBase.hpp include/MueLu_LWGraphBase_fwd.hpp @@ -2339,7 +2359,6 @@ include/MueLu_MultiVectorTransferFactory.hpp include/MueLu_MultiVectorTransferFactory_decl.hpp include/MueLu_MultiVectorTransferFactory_def.hpp include/MueLu_MultiVectorTransferFactory_fwd.hpp -include/MueLu_MutuallyExclusiveTime.hpp include/MueLu_NoFactory.hpp include/MueLu_NodePartitionInterface.hpp include/MueLu_NodePartitionInterface_decl.hpp @@ -2488,6 +2507,10 @@ include/MueLu_RepartitionInterface.hpp include/MueLu_RepartitionInterface_decl.hpp include/MueLu_RepartitionInterface_def.hpp include/MueLu_RepartitionInterface_fwd.hpp +include/MueLu_RepartitionUtilities.hpp +include/MueLu_RepartitionUtilities_decl.hpp +include/MueLu_RepartitionUtilities_def.hpp +include/MueLu_RepartitionUtilities_fwd.hpp include/MueLu_ReplicatePFactory.hpp include/MueLu_ReplicatePFactory_decl.hpp include/MueLu_ReplicatePFactory_def.hpp @@ -2508,6 +2531,13 @@ include/MueLu_SaPFactory_kokkos.hpp include/MueLu_SaPFactory_kokkos_decl.hpp include/MueLu_SaPFactory_kokkos_def.hpp include/MueLu_SaPFactory_kokkos_fwd.hpp +include/MueLu_ScalarDroppingBase.hpp +include/MueLu_ScalarDroppingClassical.hpp +include/MueLu_ScalarDroppingClassical_decl.hpp +include/MueLu_ScalarDroppingClassical_def.hpp +include/MueLu_ScalarDroppingDistanceLaplacian.hpp +include/MueLu_ScalarDroppingDistanceLaplacian_decl.hpp +include/MueLu_ScalarDroppingDistanceLaplacian_def.hpp include/MueLu_ScaledNullspaceFactory.hpp include/MueLu_ScaledNullspaceFactory_decl.hpp include/MueLu_ScaledNullspaceFactory_def.hpp @@ -2530,7 +2560,11 @@ include/MueLu_SemiCoarsenPFactory_kokkos_def.hpp include/MueLu_SemiCoarsenPFactory_kokkos_fwd.hpp include/MueLu_ShiftedLaplacian.hpp include/MueLu_ShiftedLaplacianOperator.hpp +include/MueLu_ShiftedLaplacianOperator_decl.hpp +include/MueLu_ShiftedLaplacianOperator_def.hpp include/MueLu_ShiftedLaplacianOperator_fwd.hpp +include/MueLu_ShiftedLaplacian_decl.hpp +include/MueLu_ShiftedLaplacian_def.hpp include/MueLu_ShiftedLaplacian_fwd.hpp include/MueLu_SimpleSmoother.hpp include/MueLu_SimpleSmoother_decl.hpp @@ -2676,6 +2710,13 @@ include/MueLu_VariableDofLaplacianFactory.hpp include/MueLu_VariableDofLaplacianFactory_decl.hpp include/MueLu_VariableDofLaplacianFactory_def.hpp include/MueLu_VariableDofLaplacianFactory_fwd.hpp +include/MueLu_VectorDroppingBase.hpp +include/MueLu_VectorDroppingClassical.hpp +include/MueLu_VectorDroppingClassical_decl.hpp +include/MueLu_VectorDroppingClassical_def.hpp +include/MueLu_VectorDroppingDistanceLaplacian.hpp +include/MueLu_VectorDroppingDistanceLaplacian_decl.hpp +include/MueLu_VectorDroppingDistanceLaplacian_def.hpp include/MueLu_VerboseObject.hpp include/MueLu_VerbosityLevel.hpp include/MueLu_Version.hpp @@ -2821,8 +2862,13 @@ include/NOX_Thyra_MatrixFreeJacobianOperator_impl.hpp include/NOX_Thyra_MultiVector.H include/NOX_Thyra_Vector.H include/NOX_TpetraTypedefs.hpp +include/NOX_Tpetra_MultiVector.hpp +include/NOX_Tpetra_MultiVector_def.hpp +include/NOX_Tpetra_Vector.hpp +include/NOX_Tpetra_Vector_def.hpp include/NOX_Utils.H include/OED_SplitComm.hpp +include/ObjectLifetimeSpy.hpp include/PamgenStrLoopLimits.h include/Pamgen_config.h include/PanzerCore_config.hpp @@ -2883,12 +2929,12 @@ include/Phalanx_KokkosViewOfViews.hpp include/Phalanx_KokkosView_AllocationSize.hpp include/Phalanx_KokkosView_CreateView.hpp include/Phalanx_KokkosView_HiddenDimensionForSFINAE.hpp -include/Phalanx_Kokkos_PrintViewValues.hpp include/Phalanx_Kokkos_Tools_CheckStreams.hpp include/Phalanx_MDField.hpp include/Phalanx_MDField_UnmanagedAllocator.hpp include/Phalanx_MemoryManager.hpp include/Phalanx_Print.hpp +include/Phalanx_PrintValues.hpp include/Phalanx_Scratch_Utilities.hpp include/Phalanx_TemplateIterator.hpp include/Phalanx_TemplateManager.hpp @@ -2901,8 +2947,6 @@ include/Piro_CustomLBFGSSecant.hpp include/Piro_Helpers.hpp include/Piro_InvertMassMatrixDecorator.hpp include/Piro_InvertMassMatrixDecorator_Def.hpp -include/Piro_LOCAAdaptiveSolver.hpp -include/Piro_LOCAAdaptiveSolver_Def.hpp include/Piro_LOCASolver.hpp include/Piro_LOCASolver_Def.hpp include/Piro_MatrixFreeDecorator.hpp @@ -2943,8 +2987,6 @@ include/Piro_TransientSolver_Def.hpp include/Piro_TrapezoidRuleSolver.hpp include/Piro_TrapezoidRuleSolver_Def.hpp include/Piro_ValidPiroParameters.hpp -include/Piro_VelocityVerletSolver.hpp -include/Piro_VelocityVerletSolver_Def.hpp include/Piro_Version.hpp include/Piro_config.hpp include/ProblemLOCAPrototype.H @@ -3134,6 +3176,7 @@ include/ROL_GenMoreauYosidaCVaR.hpp include/ROL_GenericFunction.hpp include/ROL_GenericUnaryFunction.hpp include/ROL_GetTestProblems.hpp +include/ROL_GlobalMPISession.hpp include/ROL_GoldenSection.hpp include/ROL_GoldenSectionScalarMinimization.hpp include/ROL_GradientStep.hpp @@ -3800,6 +3843,10 @@ include/Sacado_Fad_GeneralFad.hpp include/Sacado_Fad_GeneralFadExpr.hpp include/Sacado_Fad_GeneralFadTestingHelpers.hpp include/Sacado_Fad_GeneralFad_MP_Vector.hpp +include/Sacado_Fad_Kokkos_Specialization.hpp +include/Sacado_Fad_Kokkos_TeuchosComm.hpp +include/Sacado_Fad_Kokkos_ThreadLocalScalar.hpp +include/Sacado_Fad_Kokkos_View_Support.hpp include/Sacado_Fad_LAPACK.hpp include/Sacado_Fad_LAPACKImp.hpp include/Sacado_Fad_MP_Vector.hpp @@ -3881,10 +3928,6 @@ include/Sacado_TemplateIterator.hpp include/Sacado_TemplateManager.hpp include/Sacado_TemplateManagerImp.hpp include/Sacado_Traits.hpp -include/Sacado_UQ_PCE.hpp -include/Sacado_UQ_PCE_Imp.hpp -include/Sacado_UQ_PCE_ScalarTraitsImp.hpp -include/Sacado_UQ_PCE_Traits.hpp include/Sacado_Version.hpp include/Sacado_cmath.hpp include/Sacado_config.h @@ -3941,6 +3984,7 @@ include/Shards_config.h include/ShyLU_NodeFastILU_config.h include/SideGeometry.hpp include/Simd.hpp +include/SimdAVX512Specializations.hpp include/SimdBool.hpp include/SimdBoolF.hpp include/SimdDouble.hpp @@ -3951,6 +3995,7 @@ include/SimdFloat.hpp include/SimdFloatLoadStore.hpp include/SimdFloatMath.hpp include/SimdFloatOperators.hpp +include/SimdLoadStoreImpl.hpp include/SortingTools.h include/StkMath.hpp include/StkPlane.hpp @@ -3963,7 +4008,6 @@ include/Stokhos_AdaptivityUtils.hpp include/Stokhos_AlgebraicOrthogPolyExpansion.hpp include/Stokhos_AlgebraicOrthogPolyExpansionImp.hpp include/Stokhos_Amesos2_MP_Vector.hpp -include/Stokhos_Amesos2_UQ_PCE.hpp include/Stokhos_AnisoSparseGridQuadrature.hpp include/Stokhos_AnisoSparseGridQuadratureImp.hpp include/Stokhos_ApproxGaussSeidelPreconditioner.hpp @@ -4032,7 +4076,6 @@ include/Stokhos_GrowthRules.hpp include/Stokhos_HermiteBasis.hpp include/Stokhos_HermiteBasisImp.hpp include/Stokhos_Ifpack2_MP_Vector.hpp -include/Stokhos_Ifpack2_UQ_PCE.hpp include/Stokhos_IfpackPreconditionerFactory.hpp include/Stokhos_InterlacedOperator.hpp include/Stokhos_InversePreconditioner.hpp @@ -4085,7 +4128,6 @@ include/Stokhos_MonomialProjGramSchmidtPCEBasis2.hpp include/Stokhos_MonomialProjGramSchmidtPCEBasis2Imp.hpp include/Stokhos_MonomialProjGramSchmidtPCEBasisImp.hpp include/Stokhos_MueLu_MP_Vector.hpp -include/Stokhos_MueLu_UQ_PCE.hpp include/Stokhos_Multiply.hpp include/Stokhos_OneDOrthogPolyBasis.hpp include/Stokhos_Operator.hpp @@ -4151,7 +4193,6 @@ include/Stokhos_Sacado.hpp include/Stokhos_Sacado_Kokkos.hpp include/Stokhos_Sacado_Kokkos_MP_Vector.hpp include/Stokhos_Sacado_Kokkos_MathFunctions.hpp -include/Stokhos_Sacado_Kokkos_UQ_PCE.hpp include/Stokhos_Sacado_MathFunctions.hpp include/Stokhos_SchurPreconditioner.hpp include/Stokhos_SchurPreconditionerImp.hpp @@ -4197,13 +4238,9 @@ include/Stokhos_TotalOrderBasisImp.hpp include/Stokhos_Tpetra_CG.hpp include/Stokhos_Tpetra_ETI_Helpers_MP_Vector.hpp include/Stokhos_Tpetra_ETI_Helpers_MP_Vector_ENSEMBLE_SIZE_DEVICE.hpp -include/Stokhos_Tpetra_ETI_Helpers_UQ_PCE.hpp -include/Stokhos_Tpetra_ETI_Helpers_UQ_PCE_DEVICE.hpp include/Stokhos_Tpetra_MP_Vector.hpp -include/Stokhos_Tpetra_UQ_PCE.hpp include/Stokhos_Tpetra_Utilities.hpp include/Stokhos_Tpetra_Utilities_MP_Vector.hpp -include/Stokhos_Tpetra_Utilities_UQ_PCE.hpp include/Stokhos_Update.hpp include/Stokhos_UserDefinedQuadrature.hpp include/Stokhos_UserDefinedQuadratureImp.hpp @@ -4213,7 +4250,6 @@ include/Stokhos_VectorOrthogPolyTraitsEpetra.hpp include/Stokhos_Version.hpp include/Stokhos_ViewStorage.hpp include/Stokhos_Xpetra_MP_Vector.hpp -include/Stokhos_Xpetra_UQ_PCE.hpp include/Stokhos_config.h include/Stokhos_gaussq.h include/Stokhos_mpl_for_each.hpp @@ -4299,6 +4335,7 @@ include/Tacho_MatrixMarket.hpp include/Tacho_ModifyDiagonals.hpp include/Tacho_ModifyDiagonals_Internal.hpp include/Tacho_ModifyDiagonals_OnDevice.hpp +include/Tacho_NonPivLDL_OnDevice.hpp include/Tacho_NumericTools_Base.hpp include/Tacho_NumericTools_Factory.hpp include/Tacho_NumericTools_LevelSet.hpp @@ -4328,6 +4365,10 @@ include/Tacho_TeamFunctor_SolveLowerLU.hpp include/Tacho_TeamFunctor_SolveUpperChol.hpp include/Tacho_TeamFunctor_SolveUpperLDL.hpp include/Tacho_TeamFunctor_SolveUpperLU.hpp +include/Tacho_Trmv.hpp +include/Tacho_Trmv_External.hpp +include/Tacho_Trmv_Internal.hpp +include/Tacho_Trmv_OnDevice.hpp include/Tacho_Trsm.hpp include/Tacho_Trsm_External.hpp include/Tacho_Trsm_Internal.hpp @@ -4340,6 +4381,7 @@ include/Tacho_Trsv_OnDevice.hpp include/Tacho_Trsv_Serial.hpp include/Tacho_Util.hpp include/Tacho_config.h +include/Teko_AdaptivePreconditionerFactory.hpp include/Teko_AddPreconditionerFactory.hpp include/Teko_BlockDiagonalInverseOp.hpp include/Teko_BlockImplicitLinearOp.hpp @@ -4688,148 +4730,6 @@ include/Tempus_WrapperModelEvaluatorSecondOrder.hpp include/Tempus_WrapperModelEvaluatorSecondOrder_decl.hpp include/Tempus_WrapperModelEvaluatorSecondOrder_impl.hpp include/Tempus_config.hpp -include/Test_Batched_BatchedGemm.hpp -include/Test_Batched_BatchedGemm_Complex.hpp -include/Test_Batched_BatchedGemm_Real.hpp -include/Test_Batched_Dense.hpp -include/Test_Batched_DenseUtils.hpp -include/Test_Batched_Dense_GEMM.hpp -include/Test_Batched_SerialAxpy.hpp -include/Test_Batched_SerialAxpy_Complex.hpp -include/Test_Batched_SerialAxpy_Real.hpp -include/Test_Batched_SerialEigendecomposition.hpp -include/Test_Batched_SerialEigendecomposition_Real.hpp -include/Test_Batched_SerialGMRES.hpp -include/Test_Batched_SerialGMRES_Real.hpp -include/Test_Batched_SerialGemm.hpp -include/Test_Batched_SerialGemm_Complex.hpp -include/Test_Batched_SerialGemm_Real.hpp -include/Test_Batched_SerialGesv.hpp -include/Test_Batched_SerialGesv_Real.hpp -include/Test_Batched_SerialIamax.hpp -include/Test_Batched_SerialInverseLU.hpp -include/Test_Batched_SerialInverseLU_Complex.hpp -include/Test_Batched_SerialInverseLU_Real.hpp -include/Test_Batched_SerialLU.hpp -include/Test_Batched_SerialLU_Complex.hpp -include/Test_Batched_SerialLU_Real.hpp -include/Test_Batched_SerialLaswp.hpp -include/Test_Batched_SerialPbtrf.hpp -include/Test_Batched_SerialPbtrf_Complex.hpp -include/Test_Batched_SerialPbtrf_Real.hpp -include/Test_Batched_SerialPbtrs.hpp -include/Test_Batched_SerialPbtrs_Complex.hpp -include/Test_Batched_SerialPbtrs_Real.hpp -include/Test_Batched_SerialPttrf.hpp -include/Test_Batched_SerialPttrf_Complex.hpp -include/Test_Batched_SerialPttrf_Real.hpp -include/Test_Batched_SerialPttrs.hpp -include/Test_Batched_SerialPttrs_Complex.hpp -include/Test_Batched_SerialPttrs_Real.hpp -include/Test_Batched_SerialSVD.hpp -include/Test_Batched_SerialSolveLU.hpp -include/Test_Batched_SerialSolveLU_Complex.hpp -include/Test_Batched_SerialSolveLU_Real.hpp -include/Test_Batched_SerialSpmv.hpp -include/Test_Batched_SerialSpmv_Real.hpp -include/Test_Batched_SerialTbsv.hpp -include/Test_Batched_SerialTbsv_Complex.hpp -include/Test_Batched_SerialTbsv_Real.hpp -include/Test_Batched_SerialTrmm.hpp -include/Test_Batched_SerialTrmm_Complex.hpp -include/Test_Batched_SerialTrmm_Real.hpp -include/Test_Batched_SerialTrsm.hpp -include/Test_Batched_SerialTrsm_Complex.hpp -include/Test_Batched_SerialTrsm_Real.hpp -include/Test_Batched_SerialTrsv.hpp -include/Test_Batched_SerialTrsv_Complex.hpp -include/Test_Batched_SerialTrsv_Real.hpp -include/Test_Batched_SerialTrtri.hpp -include/Test_Batched_SerialTrtri_Complex.hpp -include/Test_Batched_SerialTrtri_Real.hpp -include/Test_Batched_Sparse.hpp -include/Test_Batched_SparseUtils.hpp -include/Test_Batched_TeamAxpy.hpp -include/Test_Batched_TeamAxpy_Complex.hpp -include/Test_Batched_TeamAxpy_Real.hpp -include/Test_Batched_TeamCG.hpp -include/Test_Batched_TeamCG_Real.hpp -include/Test_Batched_TeamGMRES.hpp -include/Test_Batched_TeamGMRES_Real.hpp -include/Test_Batched_TeamGemm.hpp -include/Test_Batched_TeamGemm_Complex.hpp -include/Test_Batched_TeamGemm_Real.hpp -include/Test_Batched_TeamGesv.hpp -include/Test_Batched_TeamGesv_Real.hpp -include/Test_Batched_TeamInverseLU.hpp -include/Test_Batched_TeamInverseLU_Complex.hpp -include/Test_Batched_TeamInverseLU_Real.hpp -include/Test_Batched_TeamLU.hpp -include/Test_Batched_TeamLU_Complex.hpp -include/Test_Batched_TeamLU_Real.hpp -include/Test_Batched_TeamSolveLU.hpp -include/Test_Batched_TeamSolveLU_Complex.hpp -include/Test_Batched_TeamSolveLU_Real.hpp -include/Test_Batched_TeamSpmv.hpp -include/Test_Batched_TeamSpmv_Real.hpp -include/Test_Batched_TeamTrsm.hpp -include/Test_Batched_TeamTrsm_Complex.hpp -include/Test_Batched_TeamTrsm_Real.hpp -include/Test_Batched_TeamTrsv.hpp -include/Test_Batched_TeamTrsv_Complex.hpp -include/Test_Batched_TeamTrsv_Real.hpp -include/Test_Batched_TeamVectorAxpy.hpp -include/Test_Batched_TeamVectorAxpy_Complex.hpp -include/Test_Batched_TeamVectorAxpy_Real.hpp -include/Test_Batched_TeamVectorCG.hpp -include/Test_Batched_TeamVectorCG_Real.hpp -include/Test_Batched_TeamVectorEigendecomposition.hpp -include/Test_Batched_TeamVectorEigendecomposition_Real.hpp -include/Test_Batched_TeamVectorGMRES.hpp -include/Test_Batched_TeamVectorGMRES_Real.hpp -include/Test_Batched_TeamVectorGemm.hpp -include/Test_Batched_TeamVectorGemm_Complex.hpp -include/Test_Batched_TeamVectorGemm_Real.hpp -include/Test_Batched_TeamVectorGesv.hpp -include/Test_Batched_TeamVectorGesv_Real.hpp -include/Test_Batched_TeamVectorQR.hpp -include/Test_Batched_TeamVectorQR_Real.hpp -include/Test_Batched_TeamVectorQR_WithColumnPivoting.hpp -include/Test_Batched_TeamVectorQR_WithColumnPivoting_Real.hpp -include/Test_Batched_TeamVectorSolveUTV.hpp -include/Test_Batched_TeamVectorSolveUTV2.hpp -include/Test_Batched_TeamVectorSolveUTV2_Real.hpp -include/Test_Batched_TeamVectorSolveUTV_Real.hpp -include/Test_Batched_TeamVectorSpmv.hpp -include/Test_Batched_TeamVectorSpmv_Real.hpp -include/Test_Batched_TeamVectorUTV.hpp -include/Test_Batched_TeamVectorUTV_Real.hpp -include/Test_Batched_VectorArithmatic.hpp -include/Test_Batched_VectorLogical.hpp -include/Test_Batched_VectorMath.hpp -include/Test_Batched_VectorMisc.hpp -include/Test_Batched_VectorRelation.hpp -include/Test_Batched_VectorView.hpp -include/Test_Common.hpp -include/Test_Common_AlignPtrTo.hpp -include/Test_Common_ArithTraits.hpp -include/Test_Common_Error.hpp -include/Test_Common_IOUtils.hpp -include/Test_Common_Iota.hpp -include/Test_Common_LowerBound.hpp -include/Test_Common_PrintConfiguration.hpp -include/Test_Common_Sorting.hpp -include/Test_Common_UpperBound.hpp -include/Test_Common_Version.hpp -include/Test_Common_float128.hpp -include/Test_Common_set_bit_count.hpp -include/Test_ODE.hpp -include/Test_ODE_BDF.hpp -include/Test_ODE_Newton.hpp -include/Test_ODE_RK.hpp -include/Test_ODE_RK_chem.hpp -include/Test_ODE_RK_counts.hpp -include/Test_ODE_TestProblems.hpp include/TeuchosCore_ConfigDefs.hpp include/TeuchosCore_config.h include/TeuchosKokkosComm_config.h @@ -4847,9 +4747,9 @@ include/Teuchos_ArrayViewDecl.hpp include/Teuchos_Assert.hpp include/Teuchos_BLAS.hpp include/Teuchos_BLAS_MP_Vector.hpp -include/Teuchos_BLAS_UQ_PCE.hpp include/Teuchos_BLAS_types.hpp include/Teuchos_BLAS_wrappers.hpp +include/Teuchos_Behavior.hpp include/Teuchos_BigUInt.hpp include/Teuchos_BigUIntDecl.hpp include/Teuchos_CTimeMonitor.h @@ -4883,6 +4783,7 @@ include/Teuchos_Details_MpiTypeTraits.hpp include/Teuchos_DummyObjectGetter.hpp include/Teuchos_ENull.hpp include/Teuchos_EReductionType.hpp +include/Teuchos_EnvVariables.hpp include/Teuchos_Exceptions.hpp include/Teuchos_ExpandScalarTypeMacros.hpp include/Teuchos_ExpatHandlerAdapter.hpp @@ -4911,7 +4812,6 @@ include/Teuchos_InvalidConditionException.hpp include/Teuchos_InvalidDependencyException.hpp include/Teuchos_LAPACK.hpp include/Teuchos_LAPACK_MP_Vector.hpp -include/Teuchos_LAPACK_UQ_PCE.hpp include/Teuchos_LAPACK_wrappers.hpp include/Teuchos_LabeledObject.hpp include/Teuchos_Language.hpp @@ -4981,7 +4881,6 @@ include/Teuchos_SerialDenseSolver.hpp include/Teuchos_SerialDenseVector.hpp include/Teuchos_SerialQRDenseSolver.hpp include/Teuchos_SerialQRDenseSolver_MP_Vector.hpp -include/Teuchos_SerialQRDenseSolver_UQ_PCE.hpp include/Teuchos_SerialSpdDenseSolver.hpp include/Teuchos_SerialSymDenseMatrix.hpp include/Teuchos_SerialTriDiMatrix.hpp @@ -5011,6 +4910,7 @@ include/Teuchos_StringIndexedOrderedValueObjectContainer.hpp include/Teuchos_StringInputSource.hpp include/Teuchos_StringInputStream.hpp include/Teuchos_StringToIntMap.hpp +include/Teuchos_SystemInformation.hpp include/Teuchos_TableColumn.hpp include/Teuchos_TableDecl.hpp include/Teuchos_TableEntry.hpp @@ -5420,6 +5320,7 @@ include/Thyra_apply_op_helper_def.hpp include/Thyra_describeLinearOp.hpp include/Thyra_describeLinearOp_decl.hpp include/Thyra_describeLinearOp_def.hpp +include/TpetraCheckingTools.hpp include/TpetraCore_ETIHelperMacros.h include/TpetraCore_config.h include/TpetraExt_MMHelpers.hpp @@ -5439,6 +5340,7 @@ include/TpetraExt_MatrixMatrix_fwd.hpp include/TpetraExt_TripleMatrixMultiply.hpp include/TpetraExt_TripleMatrixMultiply_decl.hpp include/TpetraExt_TripleMatrixMultiply_def.hpp +include/TpetraSortingTools.hpp include/TpetraTSQR_config.h include/Tpetra_Access.hpp include/Tpetra_ApplyOp.hpp @@ -5475,11 +5377,12 @@ include/Tpetra_CrsGraph_fwd.hpp include/Tpetra_CrsMatrix.hpp include/Tpetra_CrsMatrixMultiplyOp.hpp include/Tpetra_CrsMatrixMultiplyOp_fwd.hpp -include/Tpetra_CrsMatrix_UQ_PCE.hpp -include/Tpetra_CrsMatrix_UQ_PCE_def.hpp include/Tpetra_CrsMatrix_decl.hpp include/Tpetra_CrsMatrix_def.hpp include/Tpetra_CrsMatrix_fwd.hpp +include/Tpetra_CrsSingletonFilter_LinearProblem.hpp +include/Tpetra_CrsSingletonFilter_LinearProblem_decl.hpp +include/Tpetra_CrsSingletonFilter_LinearProblem_def.hpp include/Tpetra_Details_Behavior.hpp include/Tpetra_Details_Blas.hpp include/Tpetra_Details_CooMatrix.hpp @@ -5509,6 +5412,8 @@ include/Tpetra_Details_PackTraits.hpp include/Tpetra_Details_PackTriples.hpp include/Tpetra_Details_Profiling.hpp include/Tpetra_Details_Random.hpp +include/Tpetra_Details_Random_decl.hpp +include/Tpetra_Details_Random_def.hpp include/Tpetra_Details_ReadTriples.hpp include/Tpetra_Details_ScalarViewTraits.hpp include/Tpetra_Details_StaticView.hpp @@ -5533,7 +5438,6 @@ include/Tpetra_Details_extractBlockDiagonal.hpp include/Tpetra_Details_extractMpiCommFromTeuchos.hpp include/Tpetra_Details_fill.hpp include/Tpetra_Details_fill_MP_Vector.hpp -include/Tpetra_Details_fill_UQ_PCE.hpp include/Tpetra_Details_gathervPrint.hpp include/Tpetra_Details_get1DConstView.hpp include/Tpetra_Details_getDiagCopyWithoutOffsets.hpp @@ -5617,6 +5521,7 @@ include/Tpetra_FEMultiVector.hpp include/Tpetra_FEMultiVector_decl.hpp include/Tpetra_FEMultiVector_def.hpp include/Tpetra_FEMultiVector_fwd.hpp +include/Tpetra_Filter.hpp include/Tpetra_HashTable.hpp include/Tpetra_HashTable_decl.hpp include/Tpetra_HashTable_def.hpp @@ -5635,10 +5540,8 @@ include/Tpetra_KokkosCompat_ClassicNodeAPI_Wrapper.hpp include/Tpetra_KokkosCompat_DefaultNode.hpp include/Tpetra_KokkosRefactor_Details_MultiVectorDistObjectKernels.hpp include/Tpetra_KokkosRefactor_Details_MultiVectorDistObjectKernels_MP_Vector.hpp -include/Tpetra_KokkosRefactor_Details_MultiVectorDistObjectKernels_UQ_PCE.hpp include/Tpetra_KokkosRefactor_Details_MultiVectorLocalDeepCopy.hpp include/Tpetra_KokkosRefactor_Details_MultiVectorLocalDeepCopy_MP_Vector.hpp -include/Tpetra_KokkosRefactor_Details_MultiVectorLocalDeepCopy_UQ_PCE.hpp include/Tpetra_LinearProblem.hpp include/Tpetra_LinearProblem_decl.hpp include/Tpetra_LinearProblem_def.hpp @@ -5665,6 +5568,15 @@ include/Tpetra_Operator.hpp include/Tpetra_Operator_fwd.hpp include/Tpetra_Packable.hpp include/Tpetra_Packable_fwd.hpp +include/Tpetra_Reindex_CrsMatrix.hpp +include/Tpetra_Reindex_CrsMatrix_decl.hpp +include/Tpetra_Reindex_CrsMatrix_def.hpp +include/Tpetra_Reindex_LinearProblem.hpp +include/Tpetra_Reindex_LinearProblem_decl.hpp +include/Tpetra_Reindex_LinearProblem_def.hpp +include/Tpetra_Reindex_MultiVector.hpp +include/Tpetra_Reindex_MultiVector_decl.hpp +include/Tpetra_Reindex_MultiVector_def.hpp include/Tpetra_RowGraph.hpp include/Tpetra_RowGraph_decl.hpp include/Tpetra_RowGraph_def.hpp @@ -5677,13 +5589,20 @@ include/Tpetra_RowMatrixTransposer_fwd.hpp include/Tpetra_RowMatrix_decl.hpp include/Tpetra_RowMatrix_def.hpp include/Tpetra_RowMatrix_fwd.hpp +include/Tpetra_SolverMap_CrsMatrix.hpp +include/Tpetra_SolverMap_CrsMatrix_decl.hpp +include/Tpetra_SolverMap_CrsMatrix_def.hpp +include/Tpetra_SolverMap_LinearProblem.hpp +include/Tpetra_SolverMap_LinearProblem_decl.hpp +include/Tpetra_SolverMap_LinearProblem_def.hpp include/Tpetra_SrcDistObject.hpp include/Tpetra_TieBreak.hpp include/Tpetra_TieBreak_fwd.hpp +include/Tpetra_Transform.hpp include/Tpetra_TsqrAdaptor.hpp include/Tpetra_TsqrAdaptor_MP_Vector.hpp -include/Tpetra_TsqrAdaptor_UQ_PCE.hpp include/Tpetra_Util.hpp +include/Tpetra_Util_iohb.h include/Tpetra_Vector.hpp include/Tpetra_Vector_decl.hpp include/Tpetra_Vector_def.hpp @@ -5703,6 +5622,8 @@ include/Tpetra_replaceDiagonalCrsMatrix_decl.hpp include/Tpetra_replaceDiagonalCrsMatrix_def.hpp include/Traits.hpp include/TrilinosConfig.cmake +include/TrilinosCouplings_Rebalance_LinearProblem_decl.hpp +include/TrilinosCouplings_Rebalance_LinearProblem_def.hpp include/TrilinosCouplings_Version.h include/TrilinosCouplings_config.h include/TrilinosSS_config.h @@ -5784,7 +5705,6 @@ include/Tsqr_generateStack.hpp include/Tsqr_nodeTestProblem.hpp include/Tsqr_printGlobalMatrix.hpp include/Tsqr_verifyTimerConcept.hpp -include/Xpetra_Access.hpp include/Xpetra_BlockReorderManager.hpp include/Xpetra_BlockedCrsMatrix.hpp include/Xpetra_BlockedCrsMatrix_decl.hpp @@ -5810,7 +5730,6 @@ include/Xpetra_CrsGraph_fwd.hpp include/Xpetra_CrsMatrix.hpp include/Xpetra_CrsMatrixFactory.hpp include/Xpetra_CrsMatrixFactory_fwd.hpp -include/Xpetra_CrsMatrixUtils.hpp include/Xpetra_CrsMatrixUtils_fwd.hpp include/Xpetra_CrsMatrixWrap.hpp include/Xpetra_CrsMatrixWrap_decl.hpp @@ -5860,9 +5779,7 @@ include/Xpetra_IO_def.hpp include/Xpetra_Import.hpp include/Xpetra_ImportFactory.hpp include/Xpetra_ImportFactory_fwd.hpp -include/Xpetra_ImportUtils.hpp include/Xpetra_Import_fwd.hpp -include/Xpetra_IteratorOps.hpp include/Xpetra_Map.hpp include/Xpetra_MapExtractor.hpp include/Xpetra_MapExtractorFactory.hpp @@ -6315,6 +6232,7 @@ include/kokkos/Cuda/Kokkos_Cuda_GraphNode_Impl.hpp include/kokkos/Cuda/Kokkos_Cuda_Graph_Impl.hpp include/kokkos/Cuda/Kokkos_Cuda_Half_Conversion.hpp include/kokkos/Cuda/Kokkos_Cuda_Half_Impl_Type.hpp +include/kokkos/Cuda/Kokkos_Cuda_Half_MathematicalFunctions.hpp include/kokkos/Cuda/Kokkos_Cuda_Instance.hpp include/kokkos/Cuda/Kokkos_Cuda_KernelLaunch.hpp include/kokkos/Cuda/Kokkos_Cuda_MDRangePolicy.hpp @@ -6341,6 +6259,7 @@ include/kokkos/HIP/Kokkos_HIP_Graph_Impl.hpp include/kokkos/HIP/Kokkos_HIP_Half_Conversion.hpp include/kokkos/HIP/Kokkos_HIP_Half_Impl_Type.hpp include/kokkos/HIP/Kokkos_HIP_Instance.hpp +include/kokkos/HIP/Kokkos_HIP_IsXnack.hpp include/kokkos/HIP/Kokkos_HIP_KernelLaunch.hpp include/kokkos/HIP/Kokkos_HIP_MDRangePolicy.hpp include/kokkos/HIP/Kokkos_HIP_ParallelFor_MDRange.hpp @@ -6427,6 +6346,7 @@ include/kokkos/Kokkos_SIMD_AVX512.hpp include/kokkos/Kokkos_SIMD_Common.hpp include/kokkos/Kokkos_SIMD_Common_Math.hpp include/kokkos/Kokkos_SIMD_NEON.hpp +include/kokkos/Kokkos_SIMD_SVE.hpp include/kokkos/Kokkos_SIMD_Scalar.hpp include/kokkos/Kokkos_ScatterView.hpp include/kokkos/Kokkos_ScratchSpace.hpp @@ -6503,6 +6423,7 @@ include/kokkos/SYCL/Kokkos_SYCL_GraphNode_Impl.hpp include/kokkos/SYCL/Kokkos_SYCL_Graph_Impl.hpp include/kokkos/SYCL/Kokkos_SYCL_Half_Conversion.hpp include/kokkos/SYCL/Kokkos_SYCL_Half_Impl_Type.hpp +include/kokkos/SYCL/Kokkos_SYCL_Half_MathematicalFunctions.hpp include/kokkos/SYCL/Kokkos_SYCL_Instance.hpp include/kokkos/SYCL/Kokkos_SYCL_MDRangePolicy.hpp include/kokkos/SYCL/Kokkos_SYCL_ParallelFor_MDRange.hpp @@ -6544,8 +6465,10 @@ include/kokkos/Threads/Kokkos_Threads_UniqueToken.hpp include/kokkos/Threads/Kokkos_Threads_WorkGraphPolicy.hpp include/kokkos/View/Hooks/Kokkos_ViewHooks.hpp include/kokkos/View/Kokkos_BasicView.hpp +include/kokkos/View/Kokkos_ViewAccessPreconditionsCheck.hpp include/kokkos/View/Kokkos_ViewAlloc.hpp include/kokkos/View/Kokkos_ViewAtomic.hpp +include/kokkos/View/Kokkos_ViewCommonType.hpp include/kokkos/View/Kokkos_ViewCtor.hpp include/kokkos/View/Kokkos_ViewDataAnalysis.hpp include/kokkos/View/Kokkos_ViewLegacy.hpp @@ -6665,7 +6588,6 @@ include/kokkos/fwd/Kokkos_Fwd_THREADS.hpp include/kokkos/impl/KokkosExp_Host_IterateTile.hpp include/kokkos/impl/KokkosExp_IterateTileGPU.hpp include/kokkos/impl/Kokkos_AnalyzePolicy.hpp -include/kokkos/impl/Kokkos_BitOps.hpp include/kokkos/impl/Kokkos_Bitset_impl.hpp include/kokkos/impl/Kokkos_CPUDiscovery.hpp include/kokkos/impl/Kokkos_ChaseLev.hpp @@ -6690,6 +6612,7 @@ include/kokkos/impl/Kokkos_GraphImpl_Utilities.hpp include/kokkos/impl/Kokkos_GraphImpl_fwd.hpp include/kokkos/impl/Kokkos_GraphNodeCustomization.hpp include/kokkos/impl/Kokkos_GraphNodeImpl.hpp +include/kokkos/impl/Kokkos_GraphNodeThenImpl.hpp include/kokkos/impl/Kokkos_Half_FloatingPointWrapper.hpp include/kokkos/impl/Kokkos_Half_MathematicalFunctions.hpp include/kokkos/impl/Kokkos_Half_NumericTraits.hpp @@ -6702,6 +6625,7 @@ include/kokkos/impl/Kokkos_InitializationSettings.hpp include/kokkos/impl/Kokkos_LIFO.hpp include/kokkos/impl/Kokkos_LinkedListNode.hpp include/kokkos/impl/Kokkos_MultipleTaskQueue.hpp +include/kokkos/impl/Kokkos_Neon_SVE_bridge.hpp include/kokkos/impl/Kokkos_NvidiaGpuArchitectures.hpp include/kokkos/impl/Kokkos_OptionalRef.hpp include/kokkos/impl/Kokkos_ParseCommandLineArgumentsAndEnvironmentVariables.hpp @@ -6927,6 +6851,7 @@ include/stk_ngp_test/NgpTestDeviceMacros.hpp include/stk_ngp_test/Reporter.hpp include/stk_ngp_test/ngp_test.hpp include/stk_simd/Simd.hpp +include/stk_simd/SimdAVX512Specializations.hpp include/stk_simd/SimdBool.hpp include/stk_simd/SimdBoolF.hpp include/stk_simd/SimdDouble.hpp @@ -6937,6 +6862,7 @@ include/stk_simd/SimdFloat.hpp include/stk_simd/SimdFloatLoadStore.hpp include/stk_simd/SimdFloatMath.hpp include/stk_simd/SimdFloatOperators.hpp +include/stk_simd/SimdLoadStoreImpl.hpp include/stk_simd/Traits.hpp include/stk_simd/kokkos_simd/avx.hpp include/stk_simd/kokkos_simd/avx512.hpp @@ -6967,11 +6893,14 @@ include/stk_topology/topology_utils.hpp include/stk_topology/types.hpp include/stk_unit_test_utils/AssemblyUtils.hpp include/stk_unit_test_utils/CommandLineArgs.hpp +include/stk_unit_test_utils/Legendre.hpp +include/stk_unit_test_utils/ObjectLifetimeSpy.hpp include/stk_unit_test_utils/StkReportRedirector.hpp include/stk_unit_test_utils/algorithmTimer.hpp include/stk_unit_test_utils/getOption.h include/stk_unit_test_utils/stringAndNumberComparisons.hpp -include/stk_util/STK_Trilinos_config.h +include/stk_unit_test_utils/timer.hpp +include/stk_util/STK_cmake_config.h include/stk_util/Version.hpp include/stk_util/command_line/CommandLineParser.hpp include/stk_util/command_line/CommandLineParserParallel.hpp @@ -6979,13 +6908,10 @@ include/stk_util/command_line/CommandLineParserUtils.hpp include/stk_util/diag/FArrayPrint.hpp include/stk_util/diag/Option.hpp include/stk_util/diag/ParallelTimerImpl.hpp -include/stk_util/diag/ParserVarUtil.hpp include/stk_util/diag/Platform.hpp include/stk_util/diag/PrintTable.hpp include/stk_util/diag/PrintTimer.hpp -include/stk_util/diag/Resource2.h include/stk_util/diag/SlibDiagWriter.hpp -include/stk_util/diag/String.hpp include/stk_util/diag/StringUtil.hpp include/stk_util/diag/Timer.hpp include/stk_util/diag/TimerImpl.hpp @@ -7037,6 +6963,7 @@ include/stk_util/util/AlignedAllocator.hpp include/stk_util/util/AllocatorMemoryUsage.hpp include/stk_util/util/AnyData.hpp include/stk_util/util/Array.hpp +include/stk_util/util/Blas.hpp include/stk_util/util/BlasLapack.hpp include/stk_util/util/Bootstrap.hpp include/stk_util/util/CSet.hpp @@ -7051,6 +6978,7 @@ include/stk_util/util/Fortran.hpp include/stk_util/util/GetEnv.hpp include/stk_util/util/GraphCycleDetector.hpp include/stk_util/util/IndentStreambuf.hpp +include/stk_util/util/Lapack.hpp include/stk_util/util/MCSR.hpp include/stk_util/util/MallocUsed.h include/stk_util/util/Marshal.hpp @@ -7059,7 +6987,6 @@ include/stk_util/util/NamedPair.hpp include/stk_util/util/Null_Streambuf.hpp include/stk_util/util/PairIter.hpp include/stk_util/util/ParameterList.hpp -include/stk_util/util/Pool.hpp include/stk_util/util/RadixSort.hpp include/stk_util/util/RemoveIntersection.hpp include/stk_util/util/ReportHandler.hpp @@ -7092,6 +7019,7 @@ include/stk_util/util/string_utils.hpp include/stk_util/util/tokenize.hpp include/stk_util/util/vectorization.hpp include/stringAndNumberComparisons.hpp +include/timer.hpp include/topology_enum.h include/trilinos_UFconfig.h include/trilinos_amd.h @@ -7358,6 +7286,7 @@ lib/cmake/tribits/ci_support/get-tribits-packages-from-files-list.py lib/cmake/tribits/ci_support/get-tribits-packages-from-last-tests-failed.py lib/cmake/tribits/ci_support/get-tribits-packages.py lib/cmake/tribits/ci_support/is_checkin_tested_commit.py +lib/cmake/tribits/common_tpls/FindTPLADIOS2.cmake lib/cmake/tribits/common_tpls/FindTPLBLAS.cmake lib/cmake/tribits/common_tpls/FindTPLBinUtils.cmake lib/cmake/tribits/common_tpls/FindTPLBoost.cmake @@ -8041,316 +7970,304 @@ lib/external_packages/UMFPACK/UMFPACKConfig.cmake lib/external_packages/UMFPACK/UMFPACKConfigVersion.cmake lib/libModeLaplace.so lib/libModeLaplace.so.16 -lib/libModeLaplace.so.16.1.0 +lib/libModeLaplace.so.16.2.0 +lib/libTpetraModeLaplace.so +lib/libTpetraModeLaplace.so.16 +lib/libTpetraModeLaplace.so.16.2.0 lib/libamesos.so lib/libamesos.so.16 -lib/libamesos.so.16.1.0 +lib/libamesos.so.16.2.0 lib/libamesos2.so lib/libamesos2.so.16 -lib/libamesos2.so.16.1.0 +lib/libamesos2.so.16.2.0 lib/libanasazi.so lib/libanasazi.so.16 -lib/libanasazi.so.16.1.0 +lib/libanasazi.so.16.2.0 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-lib/libstokhos_amesos2.so.16.1.0 +lib/libstokhos_amesos2.so.16.2.0 lib/libstokhos_ifpack2.so lib/libstokhos_ifpack2.so.16 -lib/libstokhos_ifpack2.so.16.1.0 +lib/libstokhos_ifpack2.so.16.2.0 lib/libstokhos_ifpack2_mp_16_serial.so lib/libstokhos_ifpack2_mp_16_serial.so.16 -lib/libstokhos_ifpack2_mp_16_serial.so.16.1.0 -lib/libstokhos_ifpack2_pce_serial.so -lib/libstokhos_ifpack2_pce_serial.so.16 -lib/libstokhos_ifpack2_pce_serial.so.16.1.0 +lib/libstokhos_ifpack2_mp_16_serial.so.16.2.0 lib/libstokhos_muelu.so lib/libstokhos_muelu.so.16 -lib/libstokhos_muelu.so.16.1.0 +lib/libstokhos_muelu.so.16.2.0 lib/libstokhos_muelu_mp_16_serial.so lib/libstokhos_muelu_mp_16_serial.so.16 -lib/libstokhos_muelu_mp_16_serial.so.16.1.0 -lib/libstokhos_muelu_pce_serial.so -lib/libstokhos_muelu_pce_serial.so.16 -lib/libstokhos_muelu_pce_serial.so.16.1.0 +lib/libstokhos_muelu_mp_16_serial.so.16.2.0 lib/libstokhos_sacado.so lib/libstokhos_sacado.so.16 -lib/libstokhos_sacado.so.16.1.0 +lib/libstokhos_sacado.so.16.2.0 lib/libstokhos_tpetra.so lib/libstokhos_tpetra.so.16 -lib/libstokhos_tpetra.so.16.1.0 +lib/libstokhos_tpetra.so.16.2.0 lib/libstokhos_tpetra_mp_16_serial.so lib/libstokhos_tpetra_mp_16_serial.so.16 -lib/libstokhos_tpetra_mp_16_serial.so.16.1.0 -lib/libstokhos_tpetra_pce_serial.so -lib/libstokhos_tpetra_pce_serial.so.16 -lib/libstokhos_tpetra_pce_serial.so.16.1.0 +lib/libstokhos_tpetra_mp_16_serial.so.16.2.0 lib/libstokhos_tpetra_sd_mp_16_serial.so lib/libstokhos_tpetra_sd_mp_16_serial.so.16 -lib/libstokhos_tpetra_sd_mp_16_serial.so.16.1.0 -lib/libstokhos_tpetra_sd_pce_serial.so -lib/libstokhos_tpetra_sd_pce_serial.so.16 -lib/libstokhos_tpetra_sd_pce_serial.so.16.1.0 +lib/libstokhos_tpetra_sd_mp_16_serial.so.16.2.0 lib/libstokhos_tpetraext_mp_16_serial.so lib/libstokhos_tpetraext_mp_16_serial.so.16 -lib/libstokhos_tpetraext_mp_16_serial.so.16.1.0 -lib/libstokhos_tpetraext_pce_serial.so -lib/libstokhos_tpetraext_pce_serial.so.16 -lib/libstokhos_tpetraext_pce_serial.so.16.1.0 +lib/libstokhos_tpetraext_mp_16_serial.so.16.2.0 lib/libstokhos_xpetra.so lib/libstokhos_xpetra.so.16 -lib/libstokhos_xpetra.so.16.1.0 +lib/libstokhos_xpetra.so.16.2.0 lib/libstokhos_xpetra_mp_16_serial.so lib/libstokhos_xpetra_mp_16_serial.so.16 -lib/libstokhos_xpetra_mp_16_serial.so.16.1.0 -lib/libstokhos_xpetra_pce_serial.so -lib/libstokhos_xpetra_pce_serial.so.16 -lib/libstokhos_xpetra_pce_serial.so.16.1.0 +lib/libstokhos_xpetra_mp_16_serial.so.16.2.0 lib/libstratimikos.so lib/libstratimikos.so.16 -lib/libstratimikos.so.16.1.0 +lib/libstratimikos.so.16.2.0 lib/libstratimikosamesos2.so lib/libstratimikosamesos2.so.16 -lib/libstratimikosamesos2.so.16.1.0 +lib/libstratimikosamesos2.so.16.2.0 lib/libstratimikosbelos.so lib/libstratimikosbelos.so.16 -lib/libstratimikosbelos.so.16.1.0 +lib/libstratimikosbelos.so.16.2.0 lib/libtacho.so lib/libtacho.so.16 -lib/libtacho.so.16.1.0 +lib/libtacho.so.16.2.0 lib/libteko.so lib/libteko.so.16 -lib/libteko.so.16.1.0 +lib/libteko.so.16.2.0 lib/libtempus.so lib/libtempus.so.16 -lib/libtempus.so.16.1.0 +lib/libtempus.so.16.2.0 lib/libteuchoscomm.so lib/libteuchoscomm.so.16 -lib/libteuchoscomm.so.16.1.0 +lib/libteuchoscomm.so.16.2.0 lib/libteuchoscore.so lib/libteuchoscore.so.16 -lib/libteuchoscore.so.16.1.0 +lib/libteuchoscore.so.16.2.0 lib/libteuchoskokkoscomm.so lib/libteuchoskokkoscomm.so.16 -lib/libteuchoskokkoscomm.so.16.1.0 +lib/libteuchoskokkoscomm.so.16.2.0 lib/libteuchoskokkoscompat.so lib/libteuchoskokkoscompat.so.16 -lib/libteuchoskokkoscompat.so.16.1.0 +lib/libteuchoskokkoscompat.so.16.2.0 lib/libteuchosnumerics.so lib/libteuchosnumerics.so.16 -lib/libteuchosnumerics.so.16.1.0 +lib/libteuchosnumerics.so.16.2.0 lib/libteuchosparameterlist.so lib/libteuchosparameterlist.so.16 -lib/libteuchosparameterlist.so.16.1.0 +lib/libteuchosparameterlist.so.16.2.0 lib/libteuchosparser.so lib/libteuchosparser.so.16 -lib/libteuchosparser.so.16.1.0 +lib/libteuchosparser.so.16.2.0 lib/libteuchosremainder.so lib/libteuchosremainder.so.16 -lib/libteuchosremainder.so.16.1.0 +lib/libteuchosremainder.so.16.2.0 lib/libthyracore.so lib/libthyracore.so.16 -lib/libthyracore.so.16.1.0 +lib/libthyracore.so.16.2.0 lib/libthyratpetra.so lib/libthyratpetra.so.16 -lib/libthyratpetra.so.16.1.0 +lib/libthyratpetra.so.16.2.0 lib/libtpetra.so lib/libtpetra.so.16 -lib/libtpetra.so.16.1.0 +lib/libtpetra.so.16.2.0 lib/libtpetraclassic.so lib/libtpetraclassic.so.16 -lib/libtpetraclassic.so.16.1.0 +lib/libtpetraclassic.so.16.2.0 lib/libtpetraext.so lib/libtpetraext.so.16 -lib/libtpetraext.so.16.1.0 +lib/libtpetraext.so.16.2.0 lib/libtpetrainout.so lib/libtpetrainout.so.16 -lib/libtpetrainout.so.16.1.0 +lib/libtpetrainout.so.16.2.0 lib/libtrilinoscouplings.so lib/libtrilinoscouplings.so.16 -lib/libtrilinoscouplings.so.16.1.0 +lib/libtrilinoscouplings.so.16.2.0 lib/libtrilinosss.so lib/libtrilinosss.so.16 -lib/libtrilinosss.so.16.1.0 +lib/libtrilinosss.so.16.2.0 lib/libtriutils.so lib/libtriutils.so.16 -lib/libtriutils.so.16.1.0 +lib/libtriutils.so.16.2.0 lib/libxpetra.so lib/libxpetra.so.16 -lib/libxpetra.so.16.1.0 +lib/libxpetra.so.16.2.0 lib/libzadelus.so lib/libzadelus.so.16 -lib/libzadelus.so.16.1.0 +lib/libzadelus.so.16.2.0 lib/libzoltan.so lib/libzoltan.so.16 -lib/libzoltan.so.16.1.0 +lib/libzoltan.so.16.2.0 lib/libzoltan2.so lib/libzoltan2.so.16 -lib/libzoltan2.so.16.1.0 +lib/libzoltan2.so.16.2.0 lib/libzoltan2sphynx.so lib/libzoltan2sphynx.so.16 -lib/libzoltan2sphynx.so.16.1.0 +lib/libzoltan2sphynx.so.16.2.0 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/vipster/Makefile b/science/vipster/Makefile index 18acb86d904d..b169d9fafff8 100644 --- a/science/vipster/Makefile +++ b/science/vipster/Makefile @@ -1,8 +1,8 @@ PORTNAME= vipster DISTVERSIONPREFIX= v DISTVERSION= 1.19.1b-109 -PORTREVISION= 1 DISTVERSIONSUFFIX= -gfb4a6ed +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org 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 diff --git a/science/wwplot/Makefile b/science/wwplot/Makefile index ab33bcd5f63e..616d7305b5ff 100644 --- a/science/wwplot/Makefile +++ b/science/wwplot/Makefile @@ -1,7 +1,6 @@ PORTNAME= wwplot DISTVERSIONPREFIX= v -DISTVERSION= 1.0.0 -PORTREVISION= 1 +DISTVERSION= 1.0.1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/wwplot/distinfo b/science/wwplot/distinfo index d13afa21537a..e99d77ecb996 100644 --- a/science/wwplot/distinfo +++ b/science/wwplot/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713505502 -SHA256 (wwmm-wwplot-v1.0.0_GH0.tar.gz) = e2c04731dcd2c4c9ba37510504aef777adba0744ff7b3b8ddcf963dcc9bb6de8 -SIZE (wwmm-wwplot-v1.0.0_GH0.tar.gz) = 438404 +TIMESTAMP = 1762894379 +SHA256 (wwmm-wwplot-v1.0.1_GH0.tar.gz) = 913d264798bd5b807bcb5e385d0a1a91b78e26a476bcd089164045ca4f2cba2e +SIZE (wwmm-wwplot-v1.0.1_GH0.tar.gz) = 439519 diff --git a/science/xdrawchem/Makefile b/science/xdrawchem/Makefile index 0d25d06e5bdd..1107c82018c2 100644 --- a/science/xdrawchem/Makefile +++ b/science/xdrawchem/Makefile @@ -1,25 +1,25 @@ PORTNAME= xdrawchem -DISTVERSION= 1.11.0-2 -PORTREVISION= 2 +DISTVERSION= 1.11.1-2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Two-dimensional molecule drawing program -WWW= https://www.woodsidelabs.com/chemistry/xdrawchem.php +WWW= https://sourceforge.net/projects/xdrawchem/ \ + https://github.com/bryanherger/xdrawchem LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libopenbabel.so:science/openbabel -USES= compiler:c++11-lang gl qmake qt:5 +USES= compiler:c++11-lang gl pkgconfig qmake qt:5 USE_QT= core gui network printsupport svg widgets xml buildtools:build USE_GL= gl USE_GITLAB= yes GL_SITE= https://salsa.debian.org GL_ACCOUNT= georgesk -GL_TAGNAME= a3f74c34eb09fa72ee16848ec6901049ca5309d5 +GL_TAGNAME= 48f2e4817be451550a2cd80263344642a8611b15 pre-configure: ${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|' \ diff --git a/science/xdrawchem/distinfo b/science/xdrawchem/distinfo index c7880162be1b..c421a4325d93 100644 --- a/science/xdrawchem/distinfo +++ b/science/xdrawchem/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1617891979 -SHA256 (georgesk-xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5_GL0.tar.gz) = f1b843ebeca09e8f242e927740a6668c2ceaaf4ff47816bd7a7510f33723ebab -SIZE (georgesk-xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5_GL0.tar.gz) = 720241 +TIMESTAMP = 1762920603 +SHA256 (georgesk-xdrawchem-48f2e4817be451550a2cd80263344642a8611b15_GL0.tar.gz) = ffb94399cebdcdcb9d2011476d4094ec34ee95fe684d8a000b80da4c686f97be +SIZE (georgesk-xdrawchem-48f2e4817be451550a2cd80263344642a8611b15_GL0.tar.gz) = 719899 diff --git a/science/xdrawchem/files/patch-xdrawchem.pro b/science/xdrawchem/files/patch-xdrawchem.pro index f5121eaf6e9b..829d8ac9920c 100644 --- a/science/xdrawchem/files/patch-xdrawchem.pro +++ b/science/xdrawchem/files/patch-xdrawchem.pro @@ -1,38 +1,7 @@ ---- xdrawchem.pro.orig 2021-01-06 18:45:48 UTC +--- xdrawchem.pro.orig 2024-11-15 16:56:22 UTC +++ xdrawchem.pro -@@ -2,17 +2,17 @@ TEMPLATE = app - TARGET = xdrawchem +@@ -3,7 +3,7 @@ isEmpty(PREFIX) { - # edit to match your OB install --exists(/usr/include/openbabel3/openbabel/mol.h) { --INCLUDEPATH += /usr/include/openbabel3 -+exists(%%LOCALBASE%%/include/openbabel3/openbabel/mol.h) { -+INCLUDEPATH += %%LOCALBASE%%/include/openbabel3 - LIBS += -lopenbabel - } --exists(/usr/local/include/openbabel-3.0/openbabel/mol.h) { --INCLUDEPATH += /usr/local/include/openbabel-3.0 -+exists(%%LOCALBASE%%/include/openbabel3/openbabel/mol.h) { -+INCLUDEPATH += %%LOCALBASE%%/include/openbabel3 - LIBS += -lopenbabel - } --exists(/Developer/openbabel-3.0/include/openbabel/mol.h) { --INCLUDEPATH += /Developer/openbabel-3.0/include --LIBS += -L/Developer/openbabel-3.0/lib/Debug -lopenbabel -+exists(%%LOCALBASE%%/openbabel3/include/openbabel/mol.h) { -+INCLUDEPATH += /Developer/openbabel3/include -+LIBS += -L/Developer/openbabel3/lib/Debug -lopenbabel - } - # exit if openbabel wasn't found - contains( LIBS, -lopenbabel ) { -@@ -20,12 +20,12 @@ contains( LIBS, -lopenbabel ) { - error(OpenBabel was not found. Edit xdrawchem.pro and add valid include and lib values) - # if you get this error, comment the above with #, uncomment the variables below, and set - # the paths to match your OpenBabel install --#INCLUDEPATH += /usr/local/include/openbabel-3.0 -+#INCLUDEPATH += %%LOCALBASE%%/include/openbabel-3.0 - #LIBS += -lopenbabel - } # set PREFIX if not set (it is set when building RPM) isEmpty(PREFIX) { -PREFIX = /usr/local diff --git a/science/xtb/Makefile b/science/xtb/Makefile index e3e2acdca569..ed052e598396 100644 --- a/science/xtb/Makefile +++ b/science/xtb/Makefile @@ -4,7 +4,7 @@ DISTVERSION= 6.5.1 PORTREVISION= 4 CATEGORIES= science -MAINTAINER= ports@FreeBSD.org +MAINTAINER= yuri@FreeBSD.org COMMENT= Semiempirical Extended Tight-Binding Program Package WWW= https://github.com/grimme-lab/xtb diff --git a/science/zx/Makefile b/science/zx/Makefile deleted file mode 100644 index 0061dee5a10e..000000000000 --- a/science/zx/Makefile +++ /dev/null @@ -1,31 +0,0 @@ -PORTNAME= zx -PORTVERSION= g20221101 -CATEGORIES= science # quantum-computing - -MAINTAINER= yuri@FreeBSD.org -COMMENT= MQT ZX: A library for working with ZX-diagrams -WWW= https://www.cda.cit.tum.de/research/quantum/ - -LICENSE= MIT -LICENSE_FILE= ${WRKSRC}/LICENSE - -LIB_DEPENDS= libgmp.so:math/gmp - -USES= cmake:testing compiler:c++17-lang python:test - -USE_GITHUB= yes -GH_ACCOUNT= cda-tum -GH_TAGNAME= b01ba5e -GH_TUPLE= boostorg:config:2543ff1:boostorg_config/extern/boost/config \ - boostorg:multiprecision:be4b8e8:boostorg_multiprecision/extern/boost/multiprecision \ - google:googletest:3026483:googletest/extern/googletest - -CMAKE_ON= BUILD_SHARED_LIBS -CMAKE_OFF= BUILD_ZX_TESTS -CMAKE_TESTING_ON= BUILD_ZX_TESTS - -do-install: # workaround for https://github.com/cda-tum/dd_package/issues/115 - cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include - ${INSTALL_LIB} ${BUILD_WRKSRC}/src/libzx.so ${STAGEDIR}${PREFIX}/lib - -.include <bsd.port.mk> diff --git a/science/zx/distinfo b/science/zx/distinfo deleted file mode 100644 index 21d52858dc74..000000000000 --- a/science/zx/distinfo +++ /dev/null @@ -1,9 +0,0 @@ -TIMESTAMP = 1667348044 -SHA256 (cda-tum-zx-g20221101-b01ba5e_GH0.tar.gz) = 4f106f5bb3f8651e91e25fd15c353f7d08c77bb34b5bb61c138a11cca3a7a50f -SIZE (cda-tum-zx-g20221101-b01ba5e_GH0.tar.gz) = 26179 -SHA256 (boostorg-config-2543ff1_GH0.tar.gz) = aed1996926016faee81de7219a74f9fd41c9c3a4bb292f8936b54245b57ad3c2 -SIZE (boostorg-config-2543ff1_GH0.tar.gz) = 379371 -SHA256 (boostorg-multiprecision-be4b8e8_GH0.tar.gz) = 78b681530deb9c911f485f70d438099b9a7f7e63f61dba572ed68f32306e35c2 -SIZE (boostorg-multiprecision-be4b8e8_GH0.tar.gz) = 4144005 -SHA256 (google-googletest-3026483_GH0.tar.gz) = 1790cf41d6b9b023e1751888155b4fe1a20cd5b9842c3aa67633aac4b2610ba2 -SIZE (google-googletest-3026483_GH0.tar.gz) = 859168 diff --git a/science/zx/pkg-descr b/science/zx/pkg-descr deleted file mode 100644 index 51d87020ae3a..000000000000 --- a/science/zx/pkg-descr +++ /dev/null @@ -1,3 +0,0 @@ -zx is a library for working with ZX-diagrams developed by the Chair for Design -Automation at the Technical University of Munich as part of the Munich Quantum -Toolkit (MQT). diff --git a/science/zx/pkg-plist b/science/zx/pkg-plist deleted file mode 100644 index e8e6b0491112..000000000000 --- a/science/zx/pkg-plist +++ /dev/null @@ -1,8 +0,0 @@ -include/Definitions.hpp -include/Expression.hpp -include/Rational.hpp -include/Rules.hpp -include/Simplify.hpp -include/Utils.hpp -include/ZXDiagram.hpp -lib/libzx.so |