diff options
Diffstat (limited to 'science')
139 files changed, 1139 insertions, 715 deletions
diff --git a/science/Makefile b/science/Makefile index 9141575c630d..3462aaf49dd6 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 @@ -351,7 +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 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 2251d579cd4b..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= compilation fails with clang-19, see https://github.com/arbor-sim/arbor/issues/2424 #BROKEN_armv7= compilation fails: unknown type name 'float64x2_t' BUILD_DEPENDS= bash:shells/bash \ libfmt>0:devel/libfmt \ 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/axom/Makefile b/science/axom/Makefile index 58c94b7ba017..25a79bc28304 100644 --- a/science/axom/Makefile +++ b/science/axom/Makefile @@ -1,7 +1,7 @@ PORTNAME= axom DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org 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 6b140beda671..230527ca7a16 100644 --- a/science/csvtk/Makefile +++ b/science/csvtk/Makefile @@ -1,7 +1,6 @@ PORTNAME= csvtk DISTVERSIONPREFIX= v -DISTVERSION= 0.34.0 -PORTREVISION= 4 +DISTVERSION= 0.35.0 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/kalzium/distinfo b/science/kalzium/distinfo index 2ed98aa072cd..599d7e0e8674 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 = 1759875001 +SHA256 (KDE/release-service/25.08.2/kalzium-25.08.2.tar.xz) = 99f1da3eb04aee31b45d928b5dd30a1675dc204194ba643f8973f4ae6fdbcfed +SIZE (KDE/release-service/25.08.2/kalzium-25.08.2.tar.xz) = 22663504 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/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/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/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..e52c446ec9df 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= 7.3.0 DISTVERSIONSUFFIX= -release CATEGORIES= science diff --git a/science/nwchem-data/distinfo b/science/nwchem-data/distinfo index 480ac53a0703..1e12361d7a92 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 = 1762147577 +SHA256 (nwchemgit-nwchem-v7.3.0-release_GH0.tar.gz) = 42148e705956113bf6082d5e5520927a09f51a4309e19b6bde69d65c01a6367d +SIZE (nwchemgit-nwchem-v7.3.0-release_GH0.tar.gz) = 216145612 diff --git a/science/nwchem/Makefile b/science/nwchem/Makefile index 1d58b0dd7435..bcf73b0c428a 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= 7.3.0 +DISTVERSIONSUFFIX= -release.revision-e60d3d90-src.2025-10-24 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..7f2e16ed88e6 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 = 1762156432 +SHA256 (nwchem-7.3.0/nwchem-7.3.0-release.revision-e60d3d90-src.2025-10-24.tar.gz) = e462db097bb6abb155603219adb55bacaa6ba220e5afdba9d0a91a8d9a60418d +SIZE (nwchem-7.3.0/nwchem-7.3.0-release.revision-e60d3d90-src.2025-10-24.tar.gz) = 236380823 +SHA256 (nwchem-7.3.0/dftd3.tgz) = d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59 +SIZE (nwchem-7.3.0/dftd3.tgz) = 555804 +SHA256 (nwchem-7.3.0/libxc-7.0.0.tar.gz) = 8d4e343041c9cd869833822f57744872076ae709a613c118d70605539fb13a77 +SIZE (nwchem-7.3.0/libxc-7.0.0.tar.gz) = 67985837 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 4621c2660c8a..cf8110adbcb9 100644 --- a/science/orthanc-dicomweb/Makefile +++ b/science/orthanc-dicomweb/Makefile @@ -1,47 +1,42 @@ PORTNAME= orthanc-dicomweb -DISTVERSION= 1.8 -PORTREVISION= 15 +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 c5bbe0d89ec5..37620e7c7b54 100644 --- a/science/orthanc-mysql/Makefile +++ b/science/orthanc-mysql/Makefile @@ -1,40 +1,36 @@ PORTNAME= orthanc-mysql -DISTVERSION= 4.3 -PORTREVISION= 12 +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 3479520ad2ed..8b89f3124aee 100644 --- a/science/orthanc-postgresql/Makefile +++ b/science/orthanc-postgresql/Makefile @@ -1,40 +1,38 @@ PORTNAME= orthanc-postgresql -DISTVERSION= 4.0 -PORTREVISION= 12 +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 f05e3a9795cb..c88b6e69e403 100644 --- a/science/orthanc-webviewer/Makefile +++ b/science/orthanc-webviewer/Makefile @@ -1,43 +1,39 @@ PORTNAME= orthanc-webviewer -DISTVERSION= 2.9 -PORTREVISION= 2 +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 e2760ebdd218..69612bbb386b 100644 --- a/science/orthanc/Makefile +++ b/science/orthanc/Makefile @@ -1,35 +1,29 @@ PORTNAME= orthanc -DISTVERSION= 1.12.6 -PORTREVISION= 4 +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/polytope/Makefile b/science/polytope/Makefile index 2afc875ea600..983c12d09a54 100644 --- a/science/polytope/Makefile +++ b/science/polytope/Makefile @@ -1,10 +1,11 @@ PORTNAME= polytope -DISTVERSION= 0.7.3 +DISTVERSION= 0.7.3-18 +DISTVERSIONSUFFIX= -gcf83206 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 0.7.3-18: 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..f53895c10660 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 = 1761847798 +SHA256 (LLNL-polytope-0.7.3-18-gcf83206_GH0.tar.gz) = 4800b6f16d33b9c909d7cd39f8507d75584abd93ffab86ad38170e8c41572839 +SIZE (LLNL-polytope-0.7.3-18-gcf83206_GH0.tar.gz) = 6854889 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/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-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-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-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-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-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-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-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-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-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} ${TEST_ENV} ./runselftest.py +# tests as of 4.2: All tests 76/76 PASSED + .include <bsd.port.mk> diff --git a/science/py-veusz/distinfo b/science/py-veusz/distinfo index 2ba43a228774..1a271d94ceaf 100644 --- a/science/py-veusz/distinfo +++ b/science/py-veusz/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1677561281 -SHA256 (veusz-veusz-veusz-3.6.2_GH0.tar.gz) = e3be63af13b5982177fa039617a224fefa420c06446988a838d12a36f2747a96 -SIZE (veusz-veusz-veusz-3.6.2_GH0.tar.gz) = 2457035 +TIMESTAMP = 1761675812 +SHA256 (veusz-veusz-veusz-4.2_GH0.tar.gz) = 617588c9cab19fcd3246bffcc5fd4de5dfe9c0688ea970a250865fe8ce85131e +SIZE (veusz-veusz-veusz-4.2_GH0.tar.gz) = 2996410 diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index 6f80768ea090..9b740c002de8 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,12 +1,19 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ -DISTVERSION= 2025_03_1 -PORTREVISION= 3 +DISTVERSION= 2025_09_1 CATEGORIES= science -MASTER_SITES= LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font -DISTFILES= ComicNeue-Regular.ttf:font +MASTER_SITES= https://github.com/schrodinger/maeparser/archive/:maeparser \ + https://github.com/schrodinger/coordgenlibs/archive/:coordgen \ + https://codeload.github.com/Glysade/chemdraw/tar.gz/refs/tags/:chemdraw \ + https://github.com/Tencent/rapidjson/archive/:rapidjson \ + LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font +DISTFILES= v${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 @@ -16,20 +23,14 @@ WWW= https://www.rdkit.org/ \ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt -BROKEN_FreeBSD_15_aarch64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 -BROKEN_FreeBSD_15_amd64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 -BROKEN_FreeBSD_15_i386= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 -BROKEN_FreeBSD_16_amd64= clang-17 crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 +BROKEN_FreeBSD_16_amd64= clang crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652 BUILD_DEPENDS= catch>0:devel/catch \ - flex:textproc/flex \ - rapidjson>=0:devel/rapidjson + flex:textproc/flex LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ - libcoordgen.so:science/coordgenlibs \ - libfreetype.so:print/freetype2 \ - libmaeparser.so:science/maeparser + libfreetype.so:print/freetype2 -USES= bison:build cmake:testing compiler:c++11-lang eigen:3 gnome python +USES= bison:build cmake:testing compiler:c++11-lang eigen:3 gnome pkgconfig python USE_GNOME= cairo USE_LDCONFIG= yes @@ -38,6 +39,11 @@ GH_TUPLE= rareylab:RingDecomposerLib:v1.1.3_rdkit:RingDecomposerLib/External/Rin GH_TUPLE+= ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-align3d \ aantron:better-enums:520d8ee:better_enums/better_enums +MAEPARSER_VERSION= 1.3.3 +COORDGEN_VERSION= 3.0.2 +CHEMDRAW_VERSION= 1.0.10 +RAPIDJSON_VERSION= 1.1.0 + CMAKE_ON= RDK_BUILD_CAIRO_SUPPORT CMAKE_OFF= RDK_INSTALL_INTREE RDK_USE_FLEXBISON \ RDK_INSTALL_STATIC_LIBS RDK_SWIG_STATIC RDK_PGSQL_STATIC \ @@ -90,14 +96,35 @@ PLIST_SUB+= LITTLE_ENDIAN="" .endif post-extract: - @${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' \ + ${WRKSRC}/External/rapidjson/rapidjson-1.1.0/include/rapidjson/document.h + post-install-PGSQL-on: @${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 .include <bsd.port.mk> diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo index fe4d068e756e..e84d47fcbb7e 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 = 1761887207 +SHA256 (rdkit-2025.09.1/v1.3.3.tar.gz) = 78e7571a779ea4952e752ecef57c62fb26463947e29ef7f4b31b11988d88ca07 +SIZE (rdkit-2025.09.1/v1.3.3.tar.gz) = 39896 +SHA256 (rdkit-2025.09.1/v3.0.2.tar.gz) = f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3 +SIZE (rdkit-2025.09.1/v3.0.2.tar.gz) = 166817 +SHA256 (rdkit-2025.09.1/v1.0.10) = 300680457c92a61ba49b678405906054ab64d3635c49309e37ea2a96c513fa8d +SIZE (rdkit-2025.09.1/v1.0.10) = 1043718 +SHA256 (rdkit-2025.09.1/v1.1.0.tar.gz) = bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e +SIZE (rdkit-2025.09.1/v1.1.0.tar.gz) = 1019402 +SHA256 (rdkit-2025.09.1/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 +SIZE (rdkit-2025.09.1/ComicNeue-Regular.ttf) = 21915 +SHA256 (rdkit-2025.09.1/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz) = 7fb3510b69af358009e2d0763c1d9665ac34f4c2cd3314cf5210ee3d5a33d501 +SIZE (rdkit-2025.09.1/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz) = 82885226 +SHA256 (rdkit-2025.09.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 +SIZE (rdkit-2025.09.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 +SHA256 (rdkit-2025.09.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0 +SIZE (rdkit-2025.09.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376 +SHA256 (rdkit-2025.09.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5 +SIZE (rdkit-2025.09.1/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..c4c3acd8b3c9 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 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/spheral/Makefile b/science/spheral/Makefile index c6c14ef6c84b..da4a51d13363 100644 --- a/science/spheral/Makefile +++ b/science/spheral/Makefile @@ -1,7 +1,7 @@ PORTNAME= spheral DISTVERSIONPREFIX= v -DISTVERSION= 2024.06.1 -PORTREVISION= 6 +DISTVERSION= 2025.06.1 +PORTREVISION= 1 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..2c5c6332d628 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 = 1759875004 +SHA256 (KDE/release-service/25.08.2/step-25.08.2.tar.xz) = c00d24fff1645eb2496a615e8e4736544ee35fd38cc1b84b735e5a251ac82c33 +SIZE (KDE/release-service/25.08.2/step-25.08.2.tar.xz) = 1016200 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..f968a9897145 100644 --- a/science/tblite/Makefile +++ b/science/tblite/Makefile @@ -1,15 +1,15 @@ 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 .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture 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 |