diff options
Diffstat (limited to 'science')
38 files changed, 217 insertions, 194 deletions
diff --git a/science/R-cran-udunits2/Makefile b/science/R-cran-udunits2/Makefile index 3825ea143033..c8fb34cb9bba 100644 --- a/science/R-cran-udunits2/Makefile +++ b/science/R-cran-udunits2/Makefile @@ -1,6 +1,5 @@ PORTNAME= udunits2 -PORTVERSION= 0.13.2.1 -PORTREVISION= 1 +PORTVERSION= 0.13.2.2 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} @@ -10,8 +9,8 @@ WWW= https://cran.r-project.org/web/packages/udunits2/ LICENSE= GPLv2 -LIB_DEPENDS= libudunits2.so:science/udunits \ - libexpat.so:textproc/expat2 +LIB_DEPENDS= libexpat.so:textproc/expat2 \ + libudunits2.so:science/udunits USES= cran:auto-plist,compiles diff --git a/science/R-cran-udunits2/distinfo b/science/R-cran-udunits2/distinfo index 4049bcc2344c..095995f9577f 100644 --- a/science/R-cran-udunits2/distinfo +++ b/science/R-cran-udunits2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1647094615 -SHA256 (udunits2_0.13.2.1.tar.gz) = 9f5429c04a24930f7d037d506e5b154b6154df69247dcdaa6261075291d7f902 -SIZE (udunits2_0.13.2.1.tar.gz) = 68485 +TIMESTAMP = 1753248089 +SHA256 (udunits2_0.13.2.2.tar.gz) = 3e6dc4a12c155fa3e77f982084adbd6cb75d7a106d0b1a49ddc50a17fa4d045b +SIZE (udunits2_0.13.2.2.tar.gz) = 68840 diff --git a/science/abinit/Makefile b/science/abinit/Makefile index a310bee72cd0..2347581589fd 100644 --- a/science/abinit/Makefile +++ b/science/abinit/Makefile @@ -1,6 +1,5 @@ PORTNAME= abinit -DISTVERSION= 10.2.7 -PORTREVISION= 1 +DISTVERSION= 10.4.5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/abinit/distinfo b/science/abinit/distinfo index fa923cfa81d0..3cc29d915b5d 100644 --- a/science/abinit/distinfo +++ b/science/abinit/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1739946724 -SHA256 (abinit-abinit-10.2.7_GH0.tar.gz) = 0cd5c5755d151ef6a95b107cdcf0ec496818e34356ae8d26b2b4842bf641aec4 -SIZE (abinit-abinit-10.2.7_GH0.tar.gz) = 141254516 +TIMESTAMP = 1753132807 +SHA256 (abinit-abinit-10.4.5_GH0.tar.gz) = ccb3af00603f574208b6d5bea6f857d7040be5748e7a93a689ffad84eb6a65ce +SIZE (abinit-abinit-10.4.5_GH0.tar.gz) = 153582604 diff --git a/science/afni/Makefile b/science/afni/Makefile index e34ebda6079c..bd4a59145946 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 25.2.03 +DISTVERSION= 25.2.05 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index abca1b2a8470..933eea829f78 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1751801040 -SHA256 (afni-afni-AFNI_25.2.03_GH0.tar.gz) = 5fa4d0c4e28b078e7c038792def0685fe6218084f91fcad93c067eca13b52ebc -SIZE (afni-afni-AFNI_25.2.03_GH0.tar.gz) = 53315485 +TIMESTAMP = 1753208153 +SHA256 (afni-afni-AFNI_25.2.05_GH0.tar.gz) = 7648e71187874d1602afdaa0c776b945c8d236e3a9c6b48439cf0a160d97c4a8 +SIZE (afni-afni-AFNI_25.2.05_GH0.tar.gz) = 53317967 diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile index bca3ebaed373..aa0f3083bca2 100644 --- a/science/gemmi/Makefile +++ b/science/gemmi/Makefile @@ -1,11 +1,12 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.7.1 +DISTVERSION= 0.7.3 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Macromolecular crystallography library and utilities -WWW= https://gemmi.readthedocs.io/en/latest/ +WWW= https://gemmi.readthedocs.io/en/latest/ \ + https://github.com/project-gemmi/gemmi LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt @@ -25,7 +26,7 @@ FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= USE_FORTRAN FORTRAN_BROKEN= project option doesn't do anything, see https://github.com/project-gemmi/gemmi/issues/232 -# tests as of 0.7.1 (run work/.build/cpptest): +# tests as of 0.7.3 (run work/.build/cpptest): # [doctest] test cases: 14 | 14 passed | 0 failed | 0 skipped # [doctest] assertions: 129 | 129 passed | 0 failed | # [doctest] Status: SUCCESS! diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo index 49c83ebc50e8..a7884ddf53a9 100644 --- a/science/gemmi/distinfo +++ b/science/gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742884325 -SHA256 (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393 -SIZE (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 1910265 +TIMESTAMP = 1753139349 +SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3 +SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234 diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist index c28c9d130ae7..965571f541a2 100644 --- a/science/gemmi/pkg-plist +++ b/science/gemmi/pkg-plist @@ -23,6 +23,7 @@ include/gemmi/crd.hpp include/gemmi/ddl.hpp include/gemmi/dencalc.hpp include/gemmi/dirwalk.hpp +include/gemmi/dssp.hpp include/gemmi/ecalc.hpp include/gemmi/eig3.hpp include/gemmi/elem.hpp diff --git a/science/phonopy/Makefile b/science/phonopy/Makefile index 15241ef5732b..87062e5bc90e 100644 --- a/science/phonopy/Makefile +++ b/science/phonopy/Makefile @@ -1,6 +1,6 @@ PORTNAME= phonopy DISTVERSIONPREFIX= v -DISTVERSION= 2.41.2 +DISTVERSION= 2.42.0 CATEGORIES= science python MAINTAINER= yuri@FreeBSD.org diff --git a/science/phonopy/distinfo b/science/phonopy/distinfo index 242c3100549a..7a515ee74037 100644 --- a/science/phonopy/distinfo +++ b/science/phonopy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1752739755 -SHA256 (phonopy-phonopy-v2.41.2_GH0.tar.gz) = e78053c18dc6550bab6533b78704162c8d5bf0207ffcf3d61d636c0a4f9cbb33 -SIZE (phonopy-phonopy-v2.41.2_GH0.tar.gz) = 7717842 +TIMESTAMP = 1753085727 +SHA256 (phonopy-phonopy-v2.42.0_GH0.tar.gz) = db7efd4acb881114a9679a8f6730f127c196090d82077009746325ad2bc53041 +SIZE (phonopy-phonopy-v2.42.0_GH0.tar.gz) = 7718436 diff --git a/science/py-OpenMC/Makefile b/science/py-OpenMC/Makefile index 6a295606f93b..77f10b2454d9 100644 --- a/science/py-OpenMC/Makefile +++ b/science/py-OpenMC/Makefile @@ -1,7 +1,7 @@ PORTNAME= OpenMC DISTVERSIONPREFIX= v DISTVERSION= 0.15.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,7 +15,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ diff --git a/science/py-asdf/Makefile b/science/py-asdf/Makefile index 8efabf947d4c..3986edee3d15 100644 --- a/science/py-asdf/Makefile +++ b/science/py-asdf/Makefile @@ -1,5 +1,5 @@ PORTNAME= asdf -PORTVERSION= 4.2.0 +PORTVERSION= 4.3.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-asdf/distinfo b/science/py-asdf/distinfo index 6de3b3412bd5..f3a2707208d2 100644 --- a/science/py-asdf/distinfo +++ b/science/py-asdf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1748831252 -SHA256 (asdf-4.2.0.tar.gz) = cba00a10cde18deb20100e001fe41022f5c0cda02720dda9f716fb2150a46cf7 -SIZE (asdf-4.2.0.tar.gz) = 892353 +TIMESTAMP = 1753265788 +SHA256 (asdf-4.3.0.tar.gz) = 961d75fb1f1c4868b4533f885655b7ea9a3f0d257c65b49d728da53fe6df087d +SIZE (asdf-4.3.0.tar.gz) = 897816 diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile index 2aac5d8717f0..9e7f9f8d7544 100644 --- a/science/py-gemmi/Makefile +++ b/science/py-gemmi/Makefile @@ -1,12 +1,13 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.7.1 +DISTVERSION= 0.7.3 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Macromolecular crystallography library and utilities -WWW= https://gemmi.readthedocs.io/en/latest/ +WWW= https://gemmi.readthedocs.io/en/latest/ \ + https://github.com/project-gemmi/gemmi LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt @@ -36,4 +37,6 @@ PLIST_SUB= VER=${PORTVERSION} do-test: @cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -v tests/ +# tests as of 0.7.3: test 'test_syntax_error' fails with syntax error, see https://github.com/project-gemmi/gemmi/issues/384 + .include <bsd.port.mk> diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo index 9050772d8cc8..b40d35b8cada 100644 --- a/science/py-gemmi/distinfo +++ b/science/py-gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742885714 -SHA256 (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393 -SIZE (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 1910265 +TIMESTAMP = 1753140186 +SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3 +SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234 diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt index d75096e3228b..62637e7014cd 100644 --- a/science/py-gemmi/files/patch-CMakeLists.txt +++ b/science/py-gemmi/files/patch-CMakeLists.txt @@ -1,4 +1,4 @@ ---- CMakeLists.txt.orig 2025-03-24 16:35:30 UTC +--- CMakeLists.txt.orig 2025-07-05 13:51:16 UTC +++ CMakeLists.txt @@ -6,7 +6,7 @@ string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-de string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-dev)?\"" "\\1" @@ -27,7 +27,7 @@ -target_include_directories(gemmi_headers INTERFACE - "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>" - "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>") --target_compile_features(gemmi_headers INTERFACE cxx_std_17) +-target_compile_features(gemmi_headers INTERFACE cxx_std_14) -set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers) - -add_library(gemmi_cpp @@ -37,7 +37,7 @@ - src/monlib.cpp src/mtz.cpp src/mtz2cif.cpp - src/pdb.cpp src/polyheur.cpp src/read_cif.cpp - src/resinfo.cpp src/riding_h.cpp -- src/select.cpp src/sprintf.cpp src/symmetry.cpp +- src/select.cpp src/sprintf.cpp src/dssp.cpp src/symmetry.cpp - src/to_json.cpp src/to_mmcif.cpp src/to_pdb.cpp src/topo.cpp - src/xds_ascii.cpp) -add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp) @@ -98,8 +98,8 @@ target_include_directories(gemmi-${target} PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") endfunction() -@@ -336,7 +274,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) - prog/xds2mtz.cpp +@@ -337,7 +275,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) + prog/wcn.cpp prog/xds2mtz.cpp $<TARGET_OBJECTS:options>) add_executable(gemmi::prog ALIAS gemmi_prog) -target_link_libraries(gemmi_prog PRIVATE gemmi_cpp) @@ -107,7 +107,7 @@ target_include_directories(gemmi_prog PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1) set_target_properties(gemmi_prog PROPERTIES OUTPUT_NAME gemmi EXPORT_NAME prog) -@@ -376,7 +314,7 @@ target_compile_definitions(cpptest PRIVATE USE_STD_SNP +@@ -377,17 +315,17 @@ target_compile_definitions(cpptest PRIVATE USE_STD_SNP add_executable(cpptest EXCLUDE_FROM_ALL tests/main.cpp tests/cif.cpp tests/windowsh.cpp) target_compile_definitions(cpptest PRIVATE USE_STD_SNPRINTF=1) @@ -115,11 +115,9 @@ +target_link_libraries(cpptest PRIVATE gemmi) target_include_directories(cpptest PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") - add_executable(hello EXCLUDE_FROM_ALL examples/hello.cpp) -@@ -384,11 +322,11 @@ add_executable(doc_example EXCLUDE_FROM_ALL add_executable(doc_example EXCLUDE_FROM_ALL docs/code/sym.cpp docs/code/elem.cpp docs/code/resinfo.cpp - docs/code/cell.cpp docs/code/mutate.cpp src/resinfo.cpp) + docs/code/cell.cpp docs/code/mutate.cpp) -target_link_libraries(doc_example PRIVATE gemmi_cpp) +target_link_libraries(doc_example PRIVATE gemmi) add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp) @@ -130,7 +128,7 @@ # always compile these tests with assertions enabled if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") -@@ -396,14 +334,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu +@@ -395,14 +333,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu endif() add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp) @@ -148,16 +146,16 @@ enable_testing() -@@ -440,7 +378,7 @@ if (benchmark_FOUND) +@@ -439,7 +377,7 @@ if (benchmark_FOUND) foreach(b stoi elem mod niggli pdb resinfo round sym writecif) add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp) - if (b MATCHES "elem|resinfo|pdb|writecif") + if (b MATCHES "elem|resinfo|pdb|sym|writecif") - target_link_libraries(${b}-bm PRIVATE gemmi_cpp) + target_link_libraries(${b}-bm PRIVATE gemmi) endif() target_link_libraries(${b}-bm PRIVATE gemmi_headers benchmark::benchmark) set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY -@@ -481,11 +419,11 @@ if (USE_PYTHON) +@@ -480,11 +418,11 @@ if (USE_PYTHON) python/unitcell.cpp python/write.cpp) if (STANDALONE_PYTHON_MODULE) @@ -172,7 +170,7 @@ endif() set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi_ext) if (CMAKE_CONFIGURATION_TYPES) -@@ -568,19 +506,19 @@ endif() +@@ -567,19 +505,19 @@ endif() install(TARGETS gemmi_prog EXPORT GemmiTargets) endif() diff --git a/science/py-gemmi/pkg-plist b/science/py-gemmi/pkg-plist index 7cf8db927729..9201705db9d6 100644 --- a/science/py-gemmi/pkg-plist +++ b/science/py-gemmi/pkg-plist @@ -7,7 +7,6 @@ %%PYTHON_SITELIBDIR%%/gemmi/examples/cif_i_sigi.py %%PYTHON_SITELIBDIR%%/gemmi/examples/col_order.py %%PYTHON_SITELIBDIR%%/gemmi/examples/from_json.py -%%PYTHON_SITELIBDIR%%/gemmi/examples/hello.py %%PYTHON_SITELIBDIR%%/gemmi/examples/long_geom.py %%PYTHON_SITELIBDIR%%/gemmi/examples/map2mtz.py %%PYTHON_SITELIBDIR%%/gemmi/examples/maskcheck.py @@ -22,6 +21,7 @@ %%PYTHON_SITELIBDIR%%/gemmi/examples/qq-plot.py %%PYTHON_SITELIBDIR%%/gemmi/examples/rama_gather.py %%PYTHON_SITELIBDIR%%/gemmi/examples/rama_plot.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/read_cif.py %%PYTHON_SITELIBDIR%%/gemmi/examples/refln-stats.py %%PYTHON_SITELIBDIR%%/gemmi/examples/simple_search.py %%PYTHON_SITELIBDIR%%/gemmi/examples/sub_ccd.py diff --git a/science/py-obspy/Makefile b/science/py-obspy/Makefile index 682927b7f136..b0a3b8b4c973 100644 --- a/science/py-obspy/Makefile +++ b/science/py-obspy/Makefile @@ -1,5 +1,6 @@ PORTNAME= obspy PORTVERSION= 1.4.2 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,7 +15,7 @@ BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}future>=0.12.4:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.3.0:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>=2.2:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>=2.2:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}decorator>=0:devel/py-decorator@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlalchemy10>=0:databases/py-sqlalchemy10@${PY_FLAVOR} diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile index 43101eaa6ecd..b298e416ecf5 100644 --- a/science/py-phonopy/Makefile +++ b/science/py-phonopy/Makefile @@ -1,5 +1,5 @@ PORTNAME= phonopy -DISTVERSION= 2.41.2 +DISTVERSION= 2.42.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-phonopy/distinfo b/science/py-phonopy/distinfo index 740077509ed3..fa7a9f63de51 100644 --- a/science/py-phonopy/distinfo +++ b/science/py-phonopy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1752739793 -SHA256 (phonopy-2.41.2.tar.gz) = 850f1c298c1013c641ecbc94cd181cef3261b213655859d4bd88038ee442b232 -SIZE (phonopy-2.41.2.tar.gz) = 4713884 +TIMESTAMP = 1753085744 +SHA256 (phonopy-2.42.0.tar.gz) = f157afabc461d6b86c3ff09b139534890ca365ac4fd468cad1a0d0e9233776ce +SIZE (phonopy-2.42.0.tar.gz) = 4715307 diff --git a/science/py-pycsw/Makefile b/science/py-pycsw/Makefile index be76bccd65c7..0e08e20fb106 100644 --- a/science/py-pycsw/Makefile +++ b/science/py-pycsw/Makefile @@ -1,5 +1,6 @@ PORTNAME= pycsw PORTVERSION= 2.6.2 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,7 +16,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geolinks>=0:science/py-geolinks@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyproj>=0:graphics/py-pyproj@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}shapely>=0:devel/py-shapely@${PY_FLAVOR} \ diff --git a/science/py-pygeometa/Makefile b/science/py-pygeometa/Makefile index dd1b60da1fc8..df12a82e2163 100644 --- a/science/py-pygeometa/Makefile +++ b/science/py-pygeometa/Makefile @@ -1,6 +1,6 @@ PORTNAME= pygeometa PORTVERSION= 0.15.3 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -18,7 +18,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLA RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=0:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}jsonschema>=0:devel/py-jsonschema@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyyaml>=0:devel/py-pyyaml@${PY_FLAVOR} diff --git a/science/py-pyteomics/Makefile b/science/py-pyteomics/Makefile index cbcc08f885f8..6ef21f18727d 100644 --- a/science/py-pyteomics/Makefile +++ b/science/py-pyteomics/Makefile @@ -1,5 +1,6 @@ PORTNAME= pyteomics PORTVERSION= 4.7.5 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -30,9 +31,9 @@ XML_DESC= XML support DF_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pandas>=0.17,1:math/py-pandas@${PY_FLAVOR} GRAPHICS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR} TDA_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} -UNIMOD_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ +UNIMOD_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlalchemy14>=0:databases/py-sqlalchemy14@${PY_FLAVOR} -XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ +XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} .include <bsd.port.mk> diff --git a/science/py-qiskit/Makefile b/science/py-qiskit/Makefile index e28c1d3cd27c..c55d7b2e49e3 100644 --- a/science/py-qiskit/Makefile +++ b/science/py-qiskit/Makefile @@ -1,6 +1,5 @@ PORTNAME= qiskit -DISTVERSION= 2.0.0 -PORTREVISION= 2 +DISTVERSION= 2.1.1 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-qiskit/Makefile.crates b/science/py-qiskit/Makefile.crates index ff8fa8febab4..790b3238b85a 100644 --- a/science/py-qiskit/Makefile.crates +++ b/science/py-qiskit/Makefile.crates @@ -1,5 +1,5 @@ -CARGO_CRATES= ahash-0.7.8 \ - ahash-0.8.11 \ +CARGO_CRATES= ahash-0.7.0 \ + ahash-0.8.12 \ aho-corasick-1.1.3 \ allocator-api2-0.2.21 \ anstream-0.6.18 \ @@ -10,15 +10,16 @@ CARGO_CRATES= ahash-0.7.8 \ approx-0.5.1 \ ariadne-0.3.0 \ autocfg-1.4.0 \ + bincode-1.3.3 \ bitfield-struct-0.9.5 \ bitflags-1.3.2 \ bitflags-2.9.0 \ block-buffer-0.10.4 \ boolenum-0.1.0 \ - bytemuck-1.22.0 \ + bytemuck-1.23.0 \ bytemuck_derive-1.8.1 \ byteorder-1.5.0 \ - cbindgen-0.28.0 \ + cbindgen-0.29.0 \ cfg-if-1.0.0 \ clap-4.5.31 \ clap_builder-4.5.31 \ @@ -66,19 +67,20 @@ CARGO_CRATES= ahash-0.7.8 \ getrandom-0.2.15 \ getrandom-0.3.1 \ half-2.4.1 \ + hash32-0.3.1 \ hashbrown-0.12.3 \ hashbrown-0.14.5 \ hashbrown-0.15.2 \ - heck-0.4.1 \ + heapless-0.8.0 \ heck-0.5.0 \ - hermit-abi-0.4.0 \ - indexmap-2.7.1 \ + hermit-abi-0.5.1 \ + indexmap-2.9.0 \ indoc-2.0.6 \ - is-terminal-0.4.15 \ + is-terminal-0.4.16 \ is_terminal_polyfill-1.70.1 \ itertools-0.10.5 \ itertools-0.11.0 \ - itertools-0.13.0 \ + itertools-0.14.0 \ itoa-1.0.15 \ lazy_static-1.5.0 \ libc-0.2.170 \ @@ -90,6 +92,7 @@ CARGO_CRATES= ahash-0.7.8 \ matrixmultiply-0.3.9 \ memchr-2.7.4 \ memoffset-0.9.1 \ + minimal-lexical-0.2.1 \ nalgebra-0.33.2 \ nalgebra-macros-0.2.2 \ nano-gemm-0.1.2 \ @@ -101,43 +104,44 @@ CARGO_CRATES= ahash-0.7.8 \ nano-gemm-f64-0.1.0 \ ndarray-0.16.1 \ ndarray-einsum-0.8.0 \ - npyz-0.8.3 \ + nom-7.1.3 \ + nom-unicode-0.3.0 \ + npyz-0.8.4 \ num-bigint-0.4.6 \ num-complex-0.4.6 \ num-integer-0.1.46 \ num-rational-0.4.2 \ num-traits-0.2.19 \ - numpy-0.23.0 \ - once_cell-1.20.3 \ + numpy-0.25.0 \ + once_cell-1.21.3 \ oq3_lexer-0.7.0 \ oq3_parser-0.7.0 \ oq3_semantics-0.7.0 \ oq3_source_file-0.7.0 \ oq3_syntax-0.7.0 \ paste-1.0.15 \ - pest-2.7.15 \ - pest_derive-2.7.15 \ - pest_generator-2.7.15 \ - pest_meta-2.7.15 \ + pest-2.8.0 \ + pest_derive-2.8.0 \ + pest_generator-2.8.0 \ + pest_meta-2.8.0 \ petgraph-0.6.5 \ petgraph-0.7.1 \ portable-atomic-1.11.0 \ portable-atomic-util-0.2.4 \ - ppv-lite86-0.2.20 \ + ppv-lite86-0.2.21 \ priority-queue-2.1.2 \ proc-macro-error-1.0.4 \ proc-macro-error-attr-1.0.4 \ proc-macro2-1.0.94 \ pulp-0.18.22 \ - pulp-0.21.4 \ + pulp-0.21.5 \ pulp-macro-0.1.1 \ py_literal-0.4.0 \ - pyo3-0.23.5 \ - pyo3-build-config-0.23.5 \ - pyo3-build-config-0.24.0 \ - pyo3-ffi-0.23.5 \ - pyo3-macros-0.23.5 \ - pyo3-macros-backend-0.23.5 \ + pyo3-0.25.0 \ + pyo3-build-config-0.25.0 \ + pyo3-ffi-0.25.0 \ + pyo3-macros-0.25.0 \ + pyo3-macros-backend-0.25.0 \ quote-1.0.39 \ ra_ap_limit-0.0.188 \ rand-0.8.5 \ @@ -160,9 +164,10 @@ CARGO_CRATES= ahash-0.7.8 \ regex-automata-0.4.9 \ regex-syntax-0.8.5 \ rowan-0.15.15 \ + rstar-0.12.2 \ rustc-hash-1.1.0 \ rustc-hash-2.1.1 \ - rustiq-core-0.0.10 \ + rustiq-core-0.0.11 \ rustix-0.38.44 \ rustversion-1.0.20 \ rustworkx-core-0.16.0 \ @@ -170,14 +175,15 @@ CARGO_CRATES= ahash-0.7.8 \ safe_arch-0.7.4 \ same-file-1.0.6 \ seq-macro-0.3.6 \ - serde-1.0.218 \ - serde_derive-1.0.218 \ + serde-1.0.219 \ + serde_derive-1.0.219 \ serde_json-1.0.140 \ serde_spanned-0.6.8 \ sha2-0.10.8 \ simba-0.9.0 \ - smallvec-1.14.0 \ + smallvec-1.15.0 \ smol_str-0.2.2 \ + stable_deref_trait-1.2.0 \ strsim-0.11.1 \ syn-1.0.109 \ syn-2.0.99 \ @@ -202,6 +208,7 @@ CARGO_CRATES= ahash-0.7.8 \ unicode-xid-0.2.6 \ unindent-0.2.4 \ utf8parse-0.2.2 \ + uuid-1.17.0 \ version_check-0.9.5 \ walkdir-2.5.0 \ wasi-0.11.0+wasi-snapshot-preview1 \ @@ -232,7 +239,5 @@ CARGO_CRATES= ahash-0.7.8 \ xshell-0.2.7 \ xshell-macros-0.2.7 \ yansi-0.5.1 \ - zerocopy-0.7.35 \ - zerocopy-0.8.21 \ - zerocopy-derive-0.7.35 \ - zerocopy-derive-0.8.21 + zerocopy-0.8.25 \ + zerocopy-derive-0.8.25 diff --git a/science/py-qiskit/distinfo b/science/py-qiskit/distinfo index 5614a20c079c..f1f98a1c4ce5 100644 --- a/science/py-qiskit/distinfo +++ b/science/py-qiskit/distinfo @@ -1,8 +1,8 @@ -TIMESTAMP = 1745542321 -SHA256 (rust/crates/ahash-0.7.8.crate) = 891477e0c6a8957309ee5c45a6368af3ae14bb510732d2684ffa19af310920f9 -SIZE (rust/crates/ahash-0.7.8.crate) = 38550 -SHA256 (rust/crates/ahash-0.8.11.crate) = e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011 -SIZE (rust/crates/ahash-0.8.11.crate) = 43607 +TIMESTAMP = 1753430083 +SHA256 (rust/crates/ahash-0.7.0.crate) = efa60d2eadd8b12a996add391db32bd1153eac697ba4869660c0016353611426 +SIZE (rust/crates/ahash-0.7.0.crate) = 55813 +SHA256 (rust/crates/ahash-0.8.12.crate) = 5a15f179cd60c4584b8a8c596927aadc462e27f2ca70c04e0071964a73ba7a75 +SIZE (rust/crates/ahash-0.8.12.crate) = 43413 SHA256 (rust/crates/aho-corasick-1.1.3.crate) = 8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916 SIZE (rust/crates/aho-corasick-1.1.3.crate) = 183311 SHA256 (rust/crates/allocator-api2-0.2.21.crate) = 683d7910e743518b0e34f1186f92494becacb047c7b6bf616c96772180fef923 @@ -23,6 +23,8 @@ SHA256 (rust/crates/ariadne-0.3.0.crate) = 72fe02fc62033df9ba41cba57ee19acf5e742 SIZE (rust/crates/ariadne-0.3.0.crate) = 21829 SHA256 (rust/crates/autocfg-1.4.0.crate) = ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26 SIZE (rust/crates/autocfg-1.4.0.crate) = 17712 +SHA256 (rust/crates/bincode-1.3.3.crate) = b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad +SIZE (rust/crates/bincode-1.3.3.crate) = 28958 SHA256 (rust/crates/bitfield-struct-0.9.5.crate) = b2869c63ccf4f8bf0d485070b880e60e097fb7aeea80ee82a0a94a957e372a0b SIZE (rust/crates/bitfield-struct-0.9.5.crate) = 15953 SHA256 (rust/crates/bitflags-1.3.2.crate) = bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a @@ -33,14 +35,14 @@ SHA256 (rust/crates/block-buffer-0.10.4.crate) = 3078c7629b62d3f0439517fa394996a SIZE (rust/crates/block-buffer-0.10.4.crate) = 10538 SHA256 (rust/crates/boolenum-0.1.0.crate) = a6c8abd585d7026df20a9ae12982127ba5e81cc7a09397b957e71659da8c5de8 SIZE (rust/crates/boolenum-0.1.0.crate) = 3444 -SHA256 (rust/crates/bytemuck-1.22.0.crate) = b6b1fc10dbac614ebc03540c9dbd60e83887fda27794998c6528f1782047d540 -SIZE (rust/crates/bytemuck-1.22.0.crate) = 52451 +SHA256 (rust/crates/bytemuck-1.23.0.crate) = 9134a6ef01ce4b366b50689c94f82c14bc72bc5d0386829828a2e2752ef7958c +SIZE (rust/crates/bytemuck-1.23.0.crate) = 52534 SHA256 (rust/crates/bytemuck_derive-1.8.1.crate) = 3fa76293b4f7bb636ab88fd78228235b5248b4d05cc589aed610f954af5d7c7a SIZE (rust/crates/bytemuck_derive-1.8.1.crate) = 23100 SHA256 (rust/crates/byteorder-1.5.0.crate) = 1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b SIZE (rust/crates/byteorder-1.5.0.crate) = 23288 -SHA256 (rust/crates/cbindgen-0.28.0.crate) = eadd868a2ce9ca38de7eeafdcec9c7065ef89b42b32f0839278d55f35c54d1ff -SIZE (rust/crates/cbindgen-0.28.0.crate) = 223401 +SHA256 (rust/crates/cbindgen-0.29.0.crate) = 975982cdb7ad6a142be15bdf84aea7ec6a9e5d4d797c004d43185b24cfe4e684 +SIZE (rust/crates/cbindgen-0.29.0.crate) = 226905 SHA256 (rust/crates/cfg-if-1.0.0.crate) = baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd SIZE (rust/crates/cfg-if-1.0.0.crate) = 7934 SHA256 (rust/crates/clap-4.5.31.crate) = 027bb0d98429ae334a8698531da7077bdf906419543a35a55c2cb1b66437d767 @@ -135,32 +137,34 @@ SHA256 (rust/crates/getrandom-0.3.1.crate) = 43a49c392881ce6d5c3b8cb70f98717b7c0 SIZE (rust/crates/getrandom-0.3.1.crate) = 42449 SHA256 (rust/crates/half-2.4.1.crate) = 6dd08c532ae367adf81c312a4580bc67f1d0fe8bc9c460520283f4c0ff277888 SIZE (rust/crates/half-2.4.1.crate) = 50892 +SHA256 (rust/crates/hash32-0.3.1.crate) = 47d60b12902ba28e2730cd37e95b8c9223af2808df9e902d4df49588d1470606 +SIZE (rust/crates/hash32-0.3.1.crate) = 10273 SHA256 (rust/crates/hashbrown-0.12.3.crate) = 8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888 SIZE (rust/crates/hashbrown-0.12.3.crate) = 102968 SHA256 (rust/crates/hashbrown-0.14.5.crate) = e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1 SIZE (rust/crates/hashbrown-0.14.5.crate) = 141498 SHA256 (rust/crates/hashbrown-0.15.2.crate) = bf151400ff0baff5465007dd2f3e717f3fe502074ca563069ce3a6629d07b289 SIZE (rust/crates/hashbrown-0.15.2.crate) = 138478 -SHA256 (rust/crates/heck-0.4.1.crate) = 95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8 -SIZE (rust/crates/heck-0.4.1.crate) = 11567 +SHA256 (rust/crates/heapless-0.8.0.crate) = 0bfb9eb618601c89945a70e254898da93b13be0388091d42117462b265bb3fad +SIZE (rust/crates/heapless-0.8.0.crate) = 77802 SHA256 (rust/crates/heck-0.5.0.crate) = 2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea SIZE (rust/crates/heck-0.5.0.crate) = 11517 -SHA256 (rust/crates/hermit-abi-0.4.0.crate) = fbf6a919d6cf397374f7dfeeea91d974c7c0a7221d0d0f4f20d859d329e53fcc -SIZE (rust/crates/hermit-abi-0.4.0.crate) = 16310 -SHA256 (rust/crates/indexmap-2.7.1.crate) = 8c9c992b02b5b4c94ea26e32fe5bccb7aa7d9f390ab5c1221ff895bc7ea8b652 -SIZE (rust/crates/indexmap-2.7.1.crate) = 88644 +SHA256 (rust/crates/hermit-abi-0.5.1.crate) = f154ce46856750ed433c8649605bf7ed2de3bc35fd9d2a9f30cddd873c80cb08 +SIZE (rust/crates/hermit-abi-0.5.1.crate) = 17549 +SHA256 (rust/crates/indexmap-2.9.0.crate) = cea70ddb795996207ad57735b50c5982d8844f38ba9ee5f1aedcfb708a2aa11e +SIZE (rust/crates/indexmap-2.9.0.crate) = 91214 SHA256 (rust/crates/indoc-2.0.6.crate) = f4c7245a08504955605670dbf141fceab975f15ca21570696aebe9d2e71576bd SIZE (rust/crates/indoc-2.0.6.crate) = 17164 -SHA256 (rust/crates/is-terminal-0.4.15.crate) = e19b23d53f35ce9f56aebc7d1bb4e6ac1e9c0db7ac85c8d1760c04379edced37 -SIZE (rust/crates/is-terminal-0.4.15.crate) = 7770 +SHA256 (rust/crates/is-terminal-0.4.16.crate) = e04d7f318608d35d4b61ddd75cbdaee86b023ebe2bd5a66ee0915f0bf93095a9 +SIZE (rust/crates/is-terminal-0.4.16.crate) = 7811 SHA256 (rust/crates/is_terminal_polyfill-1.70.1.crate) = 7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf SIZE (rust/crates/is_terminal_polyfill-1.70.1.crate) = 7492 SHA256 (rust/crates/itertools-0.10.5.crate) = b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473 SIZE (rust/crates/itertools-0.10.5.crate) = 115354 SHA256 (rust/crates/itertools-0.11.0.crate) = b1c173a5686ce8bfa551b3563d0c2170bf24ca44da99c7ca4bfdab5418c3fe57 SIZE (rust/crates/itertools-0.11.0.crate) = 125074 -SHA256 (rust/crates/itertools-0.13.0.crate) = 413ee7dfc52ee1a4949ceeb7dbc8a33f2d6c088194d9f922fb8318faf1f01186 -SIZE (rust/crates/itertools-0.13.0.crate) = 146261 +SHA256 (rust/crates/itertools-0.14.0.crate) = 2b192c782037fadd9cfa75548310488aabdbf3d2da73885b31bd0abd03351285 +SIZE (rust/crates/itertools-0.14.0.crate) = 152715 SHA256 (rust/crates/itoa-1.0.15.crate) = 4a5f13b858c8d314ee3e8f639011f7ccefe71f97f96e50151fb991f267928e2c SIZE (rust/crates/itoa-1.0.15.crate) = 11231 SHA256 (rust/crates/lazy_static-1.5.0.crate) = bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe @@ -183,6 +187,8 @@ SHA256 (rust/crates/memchr-2.7.4.crate) = 78ca9ab1a0babb1e7d5695e3530886289c18cf SIZE (rust/crates/memchr-2.7.4.crate) = 96670 SHA256 (rust/crates/memoffset-0.9.1.crate) = 488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a SIZE (rust/crates/memoffset-0.9.1.crate) = 9032 +SHA256 (rust/crates/minimal-lexical-0.2.1.crate) = 68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a +SIZE (rust/crates/minimal-lexical-0.2.1.crate) = 94841 SHA256 (rust/crates/nalgebra-0.33.2.crate) = 26aecdf64b707efd1310e3544d709c5c0ac61c13756046aaaba41be5c4f66a3b SIZE (rust/crates/nalgebra-0.33.2.crate) = 385768 SHA256 (rust/crates/nalgebra-macros-0.2.2.crate) = 254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc @@ -205,8 +211,12 @@ SHA256 (rust/crates/ndarray-0.16.1.crate) = 882ed72dce9365842bf196bdeedf5055305f SIZE (rust/crates/ndarray-0.16.1.crate) = 291026 SHA256 (rust/crates/ndarray-einsum-0.8.0.crate) = f4b2d52dfff9b24d072b6080eab1587cbd54ae24da7b8370072c3a84db221e05 SIZE (rust/crates/ndarray-einsum-0.8.0.crate) = 34449 -SHA256 (rust/crates/npyz-0.8.3.crate) = 13f27ea175875c472b3df61ece89a6d6ef4e0627f43704e400c782f174681ebd -SIZE (rust/crates/npyz-0.8.3.crate) = 75073 +SHA256 (rust/crates/nom-7.1.3.crate) = d273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a +SIZE (rust/crates/nom-7.1.3.crate) = 117570 +SHA256 (rust/crates/nom-unicode-0.3.0.crate) = a5c03a4d71ab9740c752c165329e9df13a808093b146dfbef6170ac260771ffe +SIZE (rust/crates/nom-unicode-0.3.0.crate) = 9378 +SHA256 (rust/crates/npyz-0.8.4.crate) = 9f0e759e014e630f90af745101b614f761306ddc541681e546649068e25ec1b9 +SIZE (rust/crates/npyz-0.8.4.crate) = 77220 SHA256 (rust/crates/num-bigint-0.4.6.crate) = a5e44f723f1133c9deac646763579fdb3ac745e418f2a7af9cd0c431da1f20b9 SIZE (rust/crates/num-bigint-0.4.6.crate) = 102801 SHA256 (rust/crates/num-complex-0.4.6.crate) = 73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495 @@ -217,10 +227,10 @@ SHA256 (rust/crates/num-rational-0.4.2.crate) = f83d14da390562dca69fc84082e73e54 SIZE (rust/crates/num-rational-0.4.2.crate) = 28159 SHA256 (rust/crates/num-traits-0.2.19.crate) = 071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841 SIZE (rust/crates/num-traits-0.2.19.crate) = 51631 -SHA256 (rust/crates/numpy-0.23.0.crate) = b94caae805f998a07d33af06e6a3891e38556051b8045c615470a71590e13e78 -SIZE (rust/crates/numpy-0.23.0.crate) = 79034 -SHA256 (rust/crates/once_cell-1.20.3.crate) = 945462a4b81e43c4e3ba96bd7b49d834c6f61198356aa858733bc4acf3cbe62e -SIZE (rust/crates/once_cell-1.20.3.crate) = 33456 +SHA256 (rust/crates/numpy-0.25.0.crate) = 29f1dee9aa8d3f6f8e8b9af3803006101bb3653866ef056d530d53ae68587191 +SIZE (rust/crates/numpy-0.25.0.crate) = 81623 +SHA256 (rust/crates/once_cell-1.21.3.crate) = 42f5e15c9953c5e4ccceeb2e7382a716482c34515315f7b03532b8b4e8393d2d +SIZE (rust/crates/once_cell-1.21.3.crate) = 34534 SHA256 (rust/crates/oq3_lexer-0.7.0.crate) = a27bbc91e3e9d6193a44aac8f5d62c1507c41669af71a4e7e0ef66fd6470e960 SIZE (rust/crates/oq3_lexer-0.7.0.crate) = 16877 SHA256 (rust/crates/oq3_parser-0.7.0.crate) = 9a72022fcb414e8a0912920a1cf46417b6aa95f19d4b38778df7450f8a3c17fa @@ -233,14 +243,14 @@ SHA256 (rust/crates/oq3_syntax-0.7.0.crate) = 42c754ce1d9da28d6c0334c212d64b5212 SIZE (rust/crates/oq3_syntax-0.7.0.crate) = 63066 SHA256 (rust/crates/paste-1.0.15.crate) = 57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a SIZE (rust/crates/paste-1.0.15.crate) = 18374 -SHA256 (rust/crates/pest-2.7.15.crate) = 8b7cafe60d6cf8e62e1b9b2ea516a089c008945bb5a275416789e7db0bc199dc -SIZE (rust/crates/pest-2.7.15.crate) = 127895 -SHA256 (rust/crates/pest_derive-2.7.15.crate) = 816518421cfc6887a0d62bf441b6ffb4536fcc926395a69e1a85852d4363f57e -SIZE (rust/crates/pest_derive-2.7.15.crate) = 40745 -SHA256 (rust/crates/pest_generator-2.7.15.crate) = 7d1396fd3a870fc7838768d171b4616d5c91f6cc25e377b673d714567d99377b -SIZE (rust/crates/pest_generator-2.7.15.crate) = 18417 -SHA256 (rust/crates/pest_meta-2.7.15.crate) = e1e58089ea25d717bfd31fb534e4f3afcc2cc569c70de3e239778991ea3b7dea -SIZE (rust/crates/pest_meta-2.7.15.crate) = 42121 +SHA256 (rust/crates/pest-2.8.0.crate) = 198db74531d58c70a361c42201efde7e2591e976d518caf7662a47dc5720e7b6 +SIZE (rust/crates/pest-2.8.0.crate) = 128955 +SHA256 (rust/crates/pest_derive-2.8.0.crate) = d725d9cfd79e87dccc9341a2ef39d1b6f6353d68c4b33c177febbe1a402c97c5 +SIZE (rust/crates/pest_derive-2.8.0.crate) = 42196 +SHA256 (rust/crates/pest_generator-2.8.0.crate) = db7d01726be8ab66ab32f9df467ae8b1148906685bbe75c82d1e65d7f5b3f841 +SIZE (rust/crates/pest_generator-2.8.0.crate) = 18617 +SHA256 (rust/crates/pest_meta-2.8.0.crate) = 7f9f832470494906d1fca5329f8ab5791cc60beb230c74815dff541cbd2b5ca0 +SIZE (rust/crates/pest_meta-2.8.0.crate) = 42931 SHA256 (rust/crates/petgraph-0.6.5.crate) = b4c5cc86750666a3ed20bdaf5ca2a0344f9c67674cae0515bec2da16fbaa47db SIZE (rust/crates/petgraph-0.6.5.crate) = 710970 SHA256 (rust/crates/petgraph-0.7.1.crate) = 3672b37090dbd86368a4145bc067582552b29c27377cad4e0a306c97f9bd7772 @@ -249,8 +259,8 @@ SHA256 (rust/crates/portable-atomic-1.11.0.crate) = 350e9b48cbc6b0e028b0473b1144 SIZE (rust/crates/portable-atomic-1.11.0.crate) = 181258 SHA256 (rust/crates/portable-atomic-util-0.2.4.crate) = d8a2f0d8d040d7848a709caf78912debcc3f33ee4b3cac47d73d1e1069e83507 SIZE (rust/crates/portable-atomic-util-0.2.4.crate) = 47043 -SHA256 (rust/crates/ppv-lite86-0.2.20.crate) = 77957b295656769bb8ad2b6a6b09d897d94f05c41b069aede1fcdaa675eaea04 -SIZE (rust/crates/ppv-lite86-0.2.20.crate) = 22478 +SHA256 (rust/crates/ppv-lite86-0.2.21.crate) = 85eae3c4ed2f50dcfe72643da4befc30deadb458a9b590d720cde2f2b1e97da9 +SIZE (rust/crates/ppv-lite86-0.2.21.crate) = 22522 SHA256 (rust/crates/priority-queue-2.1.2.crate) = 090ded312ed32a928fb49cb91ab4db6523ae3767225e61fbf6ceaaec3664ed26 SIZE (rust/crates/priority-queue-2.1.2.crate) = 36557 SHA256 (rust/crates/proc-macro-error-1.0.4.crate) = da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c @@ -261,24 +271,22 @@ SHA256 (rust/crates/proc-macro2-1.0.94.crate) = a31971752e70b8b2686d7e46ec17fb38 SIZE (rust/crates/proc-macro2-1.0.94.crate) = 52391 SHA256 (rust/crates/pulp-0.18.22.crate) = a0a01a0dc67cf4558d279f0c25b0962bd08fc6dec0137699eae304103e882fe6 SIZE (rust/crates/pulp-0.18.22.crate) = 117838 -SHA256 (rust/crates/pulp-0.21.4.crate) = 95fb7a99b37aaef4c7dd2fd15a819eb8010bfc7a2c2155230d51f497316cad6d -SIZE (rust/crates/pulp-0.21.4.crate) = 135569 +SHA256 (rust/crates/pulp-0.21.5.crate) = 96b86df24f0a7ddd5e4b95c94fc9ed8a98f1ca94d3b01bdce2824097e7835907 +SIZE (rust/crates/pulp-0.21.5.crate) = 136353 SHA256 (rust/crates/pulp-macro-0.1.1.crate) = d315b3197b780e4873bc0e11251cb56a33f65a6032a3d39b8d1405c255513766 SIZE (rust/crates/pulp-macro-0.1.1.crate) = 3268 SHA256 (rust/crates/py_literal-0.4.0.crate) = 102df7a3d46db9d3891f178dcc826dc270a6746277a9ae6436f8d29fd490a8e1 SIZE (rust/crates/py_literal-0.4.0.crate) = 16747 -SHA256 (rust/crates/pyo3-0.23.5.crate) = 7778bffd85cf38175ac1f545509665d0b9b92a198ca7941f131f85f7a4f9a872 -SIZE (rust/crates/pyo3-0.23.5.crate) = 1088533 -SHA256 (rust/crates/pyo3-build-config-0.23.5.crate) = 94f6cbe86ef3bf18998d9df6e0f3fc1050a8c5efa409bf712e661a4366e010fb -SIZE (rust/crates/pyo3-build-config-0.23.5.crate) = 33885 -SHA256 (rust/crates/pyo3-build-config-0.24.0.crate) = e9b6c2b34cf71427ea37c7001aefbaeb85886a074795e35f161f5aecc7620a7a -SIZE (rust/crates/pyo3-build-config-0.24.0.crate) = 33982 -SHA256 (rust/crates/pyo3-ffi-0.23.5.crate) = e9f1b4c431c0bb1c8fb0a338709859eed0d030ff6daa34368d3b152a63dfdd8d -SIZE (rust/crates/pyo3-ffi-0.23.5.crate) = 74867 -SHA256 (rust/crates/pyo3-macros-0.23.5.crate) = fbc2201328f63c4710f68abdf653c89d8dbc2858b88c5d88b0ff38a75288a9da -SIZE (rust/crates/pyo3-macros-0.23.5.crate) = 8856 -SHA256 (rust/crates/pyo3-macros-backend-0.23.5.crate) = fca6726ad0f3da9c9de093d6f116a93c1a38e417ed73bf138472cf4064f72028 -SIZE (rust/crates/pyo3-macros-backend-0.23.5.crate) = 70938 +SHA256 (rust/crates/pyo3-0.25.0.crate) = f239d656363bcee73afef85277f1b281e8ac6212a1d42aa90e55b90ed43c47a4 +SIZE (rust/crates/pyo3-0.25.0.crate) = 1120850 +SHA256 (rust/crates/pyo3-build-config-0.25.0.crate) = 755ea671a1c34044fa165247aaf6f419ca39caa6003aee791a0df2713d8f1b6d +SIZE (rust/crates/pyo3-build-config-0.25.0.crate) = 34122 +SHA256 (rust/crates/pyo3-ffi-0.25.0.crate) = fc95a2e67091e44791d4ea300ff744be5293f394f1bafd9f78c080814d35956e +SIZE (rust/crates/pyo3-ffi-0.25.0.crate) = 77991 +SHA256 (rust/crates/pyo3-macros-0.25.0.crate) = a179641d1b93920829a62f15e87c0ed791b6c8db2271ba0fd7c2686090510214 +SIZE (rust/crates/pyo3-macros-0.25.0.crate) = 8876 +SHA256 (rust/crates/pyo3-macros-backend-0.25.0.crate) = 9dff85ebcaab8c441b0e3f7ae40a6963ecea8a9f5e74f647e33fcf5ec9a1e89e +SIZE (rust/crates/pyo3-macros-backend-0.25.0.crate) = 75089 SHA256 (rust/crates/quote-1.0.39.crate) = c1f1914ce909e1658d9907913b4b91947430c7d9be598b15a1912935b8c04801 SIZE (rust/crates/quote-1.0.39.crate) = 31206 SHA256 (rust/crates/ra_ap_limit-0.0.188.crate) = 92d33758724f997689f84146e5401e28d875a061804f861f113696f44f5232aa @@ -323,12 +331,14 @@ SHA256 (rust/crates/regex-syntax-0.8.5.crate) = 2b15c43186be67a4fd63bee50d0303af SIZE (rust/crates/regex-syntax-0.8.5.crate) = 357541 SHA256 (rust/crates/rowan-0.15.15.crate) = 32a58fa8a7ccff2aec4f39cc45bf5f985cec7125ab271cf681c279fd00192b49 SIZE (rust/crates/rowan-0.15.15.crate) = 39971 +SHA256 (rust/crates/rstar-0.12.2.crate) = 421400d13ccfd26dfa5858199c30a5d76f9c54e0dba7575273025b43c5175dbb +SIZE (rust/crates/rstar-0.12.2.crate) = 43756 SHA256 (rust/crates/rustc-hash-1.1.0.crate) = 08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2 SIZE (rust/crates/rustc-hash-1.1.0.crate) = 9331 SHA256 (rust/crates/rustc-hash-2.1.1.crate) = 357703d41365b4b27c590e3ed91eabb1b663f07c4c084095e60cbed4362dff0d SIZE (rust/crates/rustc-hash-2.1.1.crate) = 14154 -SHA256 (rust/crates/rustiq-core-0.0.10.crate) = 666b580cb45b60a39f5a17b284bbe8343cfcd67929931729b4afee19ec94d308 -SIZE (rust/crates/rustiq-core-0.0.10.crate) = 40292 +SHA256 (rust/crates/rustiq-core-0.0.11.crate) = 51bfa802a80a4fa591941e4caaf2d6d7793ae3ffd307022afe0739453fae07a6 +SIZE (rust/crates/rustiq-core-0.0.11.crate) = 41963 SHA256 (rust/crates/rustix-0.38.44.crate) = fdb5bc1ae2baa591800df16c9ca78619bf65c0488b41b96ccec5d11220d8c154 SIZE (rust/crates/rustix-0.38.44.crate) = 379347 SHA256 (rust/crates/rustversion-1.0.20.crate) = eded382c5f5f786b989652c49544c4877d9f015cc22e145a5ea8ea66c2921cd2 @@ -343,10 +353,10 @@ SHA256 (rust/crates/same-file-1.0.6.crate) = 93fc1dc3aaa9bfed95e02e6eadabb4baf7e SIZE (rust/crates/same-file-1.0.6.crate) = 10183 SHA256 (rust/crates/seq-macro-0.3.6.crate) = 1bc711410fbe7399f390ca1c3b60ad0f53f80e95c5eb935e52268a0e2cd49acc SIZE (rust/crates/seq-macro-0.3.6.crate) = 16031 -SHA256 (rust/crates/serde-1.0.218.crate) = e8dfc9d19bdbf6d17e22319da49161d5d0108e4188e8b680aef6299eed22df60 -SIZE (rust/crates/serde-1.0.218.crate) = 78968 -SHA256 (rust/crates/serde_derive-1.0.218.crate) = f09503e191f4e797cb8aac08e9a4a4695c5edf6a2e70e376d961ddd5c969f82b -SIZE (rust/crates/serde_derive-1.0.218.crate) = 57782 +SHA256 (rust/crates/serde-1.0.219.crate) = 5f0e2c6ed6606019b4e29e69dbaba95b11854410e5347d525002456dbbb786b6 +SIZE (rust/crates/serde-1.0.219.crate) = 78983 +SHA256 (rust/crates/serde_derive-1.0.219.crate) = 5b0276cf7f2c73365f7157c8123c21cd9a50fbbd844757af28ca1f5925fc2a00 +SIZE (rust/crates/serde_derive-1.0.219.crate) = 57798 SHA256 (rust/crates/serde_json-1.0.140.crate) = 20068b6e96dc6c9bd23e01df8827e6c7e1f2fddd43c21810382803c136b99373 SIZE (rust/crates/serde_json-1.0.140.crate) = 154852 SHA256 (rust/crates/serde_spanned-0.6.8.crate) = 87607cb1398ed59d48732e575a4c28a7a8ebf2454b964fe3f224f2afc07909e1 @@ -355,10 +365,12 @@ SHA256 (rust/crates/sha2-0.10.8.crate) = 793db75ad2bcafc3ffa7c68b215fee268f53798 SIZE (rust/crates/sha2-0.10.8.crate) = 26357 SHA256 (rust/crates/simba-0.9.0.crate) = b3a386a501cd104797982c15ae17aafe8b9261315b5d07e3ec803f2ea26be0fa SIZE (rust/crates/simba-0.9.0.crate) = 52680 -SHA256 (rust/crates/smallvec-1.14.0.crate) = 7fcf8323ef1faaee30a44a340193b1ac6814fd9b7b4e88e9d4519a3e4abe1cfd -SIZE (rust/crates/smallvec-1.14.0.crate) = 35561 +SHA256 (rust/crates/smallvec-1.15.0.crate) = 8917285742e9f3e1683f0a9c4e6b57960b7314d0b08d30d1ecd426713ee2eee9 +SIZE (rust/crates/smallvec-1.15.0.crate) = 38113 SHA256 (rust/crates/smol_str-0.2.2.crate) = dd538fb6910ac1099850255cf94a94df6551fbdd602454387d0adb2d1ca6dead SIZE (rust/crates/smol_str-0.2.2.crate) = 15840 +SHA256 (rust/crates/stable_deref_trait-1.2.0.crate) = a8f112729512f8e442d81f95a8a7ddf2b7c6b8a1a6f509a95864142b30cab2d3 +SIZE (rust/crates/stable_deref_trait-1.2.0.crate) = 8054 SHA256 (rust/crates/strsim-0.11.1.crate) = 7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f SIZE (rust/crates/strsim-0.11.1.crate) = 14266 SHA256 (rust/crates/syn-1.0.109.crate) = 72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237 @@ -407,6 +419,8 @@ SHA256 (rust/crates/unindent-0.2.4.crate) = 7264e107f553ccae879d21fbea1d6724ac78 SIZE (rust/crates/unindent-0.2.4.crate) = 7422 SHA256 (rust/crates/utf8parse-0.2.2.crate) = 06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821 SIZE (rust/crates/utf8parse-0.2.2.crate) = 13499 +SHA256 (rust/crates/uuid-1.17.0.crate) = 3cf4199d1e5d15ddd86a694e4d0dffa9c323ce759fea589f00fef9d81cc1931d +SIZE (rust/crates/uuid-1.17.0.crate) = 59014 SHA256 (rust/crates/version_check-0.9.5.crate) = 0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a SIZE (rust/crates/version_check-0.9.5.crate) = 15554 SHA256 (rust/crates/walkdir-2.5.0.crate) = 29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b @@ -467,13 +481,9 @@ SHA256 (rust/crates/xshell-macros-0.2.7.crate) = 32ac00cd3f8ec9c1d33fb3e7958a82d SIZE (rust/crates/xshell-macros-0.2.7.crate) = 2890 SHA256 (rust/crates/yansi-0.5.1.crate) = 09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec SIZE (rust/crates/yansi-0.5.1.crate) = 16525 -SHA256 (rust/crates/zerocopy-0.7.35.crate) = 1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0 -SIZE (rust/crates/zerocopy-0.7.35.crate) = 152645 -SHA256 (rust/crates/zerocopy-0.8.21.crate) = dcf01143b2dd5d134f11f545cf9f1431b13b749695cb33bcce051e7568f99478 -SIZE (rust/crates/zerocopy-0.8.21.crate) = 238506 -SHA256 (rust/crates/zerocopy-derive-0.7.35.crate) = fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e -SIZE (rust/crates/zerocopy-derive-0.7.35.crate) = 37829 -SHA256 (rust/crates/zerocopy-derive-0.8.21.crate) = 712c8386f4f4299382c9abee219bee7084f78fb939d88b6840fcc1320d5f6da2 -SIZE (rust/crates/zerocopy-derive-0.8.21.crate) = 83886 -SHA256 (Qiskit-qiskit-2.0.0_GH0.tar.gz) = 563938d0f2c353b0a79ea8b7a1c9a3d7d915972b282ddad48e0ffd1079edaeaa -SIZE (Qiskit-qiskit-2.0.0_GH0.tar.gz) = 7911127 +SHA256 (rust/crates/zerocopy-0.8.25.crate) = a1702d9583232ddb9174e01bb7c15a2ab8fb1bc6f227aa1233858c351a3ba0cb +SIZE (rust/crates/zerocopy-0.8.25.crate) = 252714 +SHA256 (rust/crates/zerocopy-derive-0.8.25.crate) = 28a6e20d751156648aa063f3800b706ee209a32c0b4d9f24be3d980b01be55ef +SIZE (rust/crates/zerocopy-derive-0.8.25.crate) = 87671 +SHA256 (Qiskit-qiskit-2.1.1_GH0.tar.gz) = 96cd5725ea5f99a6527885e9ef4436bcb34e6388c6ab1bf43d48b9dab80f429f +SIZE (Qiskit-qiskit-2.1.1_GH0.tar.gz) = 7095152 diff --git a/science/py-quantities/Makefile b/science/py-quantities/Makefile index 74a45beef3b2..dddaaa22df9e 100644 --- a/science/py-quantities/Makefile +++ b/science/py-quantities/Makefile @@ -1,6 +1,5 @@ PORTNAME= quantities -DISTVERSION= 0.16.1 -PORTREVISION= 1 +DISTVERSION= 0.16.2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -21,6 +20,6 @@ TEST_WRKSRC= ${WRKSRC}/quantities/tests NO_ARCH= yes -# tests: 173 passed, 3 xfailed in 33.50s +# tests as of 0.16.2: 175 passed, 3 xfailed in 30.81s .include <bsd.port.mk> diff --git a/science/py-quantities/distinfo b/science/py-quantities/distinfo index 26529773f059..eb191c3bbb35 100644 --- a/science/py-quantities/distinfo +++ b/science/py-quantities/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1731110912 -SHA256 (quantities-0.16.1.tar.gz) = c9d688e8719720654187a6a83425e7d54f427d7465e03c49f3da53befd20074b -SIZE (quantities-0.16.1.tar.gz) = 101045 +TIMESTAMP = 1753137018 +SHA256 (quantities-0.16.2.tar.gz) = 1f7c24f10d9ff57ddf751a358ea2fdfa9914516722f06a788ef4a2924c77d21c +SIZE (quantities-0.16.2.tar.gz) = 101862 diff --git a/science/py-rmf/Makefile b/science/py-rmf/Makefile index 1d13d19df62c..dbe6e2950396 100644 --- a/science/py-rmf/Makefile +++ b/science/py-rmf/Makefile @@ -6,7 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library to support reading and writing of Rich Molecular Format files WWW= https://integrativemodeling.org/rmf/ \ - https://github.com/open-rmf/rmf + https://github.com/salilab/rmf LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/science/py-spglib/Makefile b/science/py-spglib/Makefile index 14ad98f6aa4a..01e37fba4057 100644 --- a/science/py-spglib/Makefile +++ b/science/py-spglib/Makefile @@ -1,7 +1,6 @@ PORTNAME= spglib DISTVERSIONPREFIX= v -DISTVERSION= 2.5.0 -PORTREVISION= 1 +DISTVERSION= 2.6.0 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -19,10 +18,12 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@$ ${PYNUMPY} \ ${PY_SETUPTOOLS} LIB_DEPENDS= libsymspg.so:science/spglib -RUN_DEPENDS= ${PYNUMPY} +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.9.0:devel/py-typing-extensions@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest-benchmark>0:devel/py-pytest-benchmark@${PY_FLAVOR} USES= python -USE_PYTHON= pep517 autoplist pytest # tests fail to run, see https://github.com/spglib/spglib/issues/192 +USE_PYTHON= pep517 autoplist pytest USE_GITHUB= yes CMAKE_ARGS= -DPython3_EXECUTABLE=${PYTHON_CMD} @@ -32,4 +33,6 @@ MAKE_ENV= SETUPTOOLS_SCM_PRETEND_VERSION=${DISTVERSION} TEST_WRKSRC= ${WRKSRC} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +# tests as of 2.6.0: 3024 passed in 149.52s (0:02:29) + .include <bsd.port.mk> diff --git a/science/py-spglib/distinfo b/science/py-spglib/distinfo index 48711790a26d..b88216427863 100644 --- a/science/py-spglib/distinfo +++ b/science/py-spglib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1720768210 -SHA256 (spglib-spglib-v2.5.0_GH0.tar.gz) = b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914 -SIZE (spglib-spglib-v2.5.0_GH0.tar.gz) = 2926427 +TIMESTAMP = 1753137266 +SHA256 (spglib-spglib-v2.6.0_GH0.tar.gz) = c65af71136c915352eb82444b165ec83289877eb8e46593033f199801b43dbf7 +SIZE (spglib-spglib-v2.6.0_GH0.tar.gz) = 2438640 diff --git a/science/py-spglib/files/patch-pyproject.toml b/science/py-spglib/files/patch-pyproject.toml index 38d350736f4d..d7417075f4d6 100644 --- a/science/py-spglib/files/patch-pyproject.toml +++ b/science/py-spglib/files/patch-pyproject.toml @@ -1,21 +1,21 @@ - removal of license-files is a workaround for https://github.com/spglib/spglib/issues/560 ---- pyproject.toml.orig 2024-07-11 08:36:56 UTC +--- pyproject.toml.orig 2025-03-06 12:33:46 UTC +++ pyproject.toml @@ -1,7 +1,7 @@ [build-system] # Numpy build and runtime dependencies are linked to ABI compatibility # A new wheel rebuild is needed when changing these --requires = ["scikit-build-core", "numpy~=2.0"] -+requires = ["scikit-build-core", "numpy"] +-requires = ["scikit-build-core>=0.11", "numpy~=2.0"] ++requires = ["scikit-build-core>=0.11", "numpy"] build-backend = "scikit_build_core.build" [project] -@@ -9,7 +9,6 @@ license = { text = "BSD-3-Clause" } +@@ -9,7 +9,6 @@ license = "BSD-3-Clause" requires-python = ">=3.9" description = "This is the spglib module." - license = { text = "BSD-3-Clause" } --license-files = { paths = ["COPYING"] } + license = "BSD-3-Clause" +-license-files = ["COPYING"] readme = "python/README.rst" dynamic = ["version"] dependencies = [ diff --git a/science/rmf/Makefile b/science/rmf/Makefile index 5d09f287b9f7..9a1b1c673a5d 100644 --- a/science/rmf/Makefile +++ b/science/rmf/Makefile @@ -6,7 +6,7 @@ CATEGORIES= science graphics MAINTAINER= yuri@FreeBSD.org COMMENT= Library to support reading and writing of Rich Molecular Format files WWW= https://integrativemodeling.org/rmf/ \ - https://github.com/open-rmf/rmf + https://github.com/salilab/rmf LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/science/spglib/Makefile b/science/spglib/Makefile index 4615c4db21ff..d12f56544466 100644 --- a/science/spglib/Makefile +++ b/science/spglib/Makefile @@ -1,6 +1,6 @@ PORTNAME= spglib DISTVERSIONPREFIX= v -DISTVERSION= 2.5.0 +DISTVERSION= 2.6.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -32,4 +32,6 @@ OPTIONS_SUB= yes FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= SPGLIB_WITH_Fortran +# tests as of 2.6.0: 100% tests passed, 0 tests failed out of 59 + .include <bsd.port.mk> diff --git a/science/spglib/distinfo b/science/spglib/distinfo index 07218b207bc7..85fbb27635db 100644 --- a/science/spglib/distinfo +++ b/science/spglib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1720768091 -SHA256 (spglib-spglib-v2.5.0_GH0.tar.gz) = b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914 -SIZE (spglib-spglib-v2.5.0_GH0.tar.gz) = 2926427 +TIMESTAMP = 1753138641 +SHA256 (spglib-spglib-v2.6.0_GH0.tar.gz) = c65af71136c915352eb82444b165ec83289877eb8e46593033f199801b43dbf7 +SIZE (spglib-spglib-v2.6.0_GH0.tar.gz) = 2438640 diff --git a/science/spglib/pkg-plist b/science/spglib/pkg-plist index c3b5f01c8d33..5315006f0e5c 100644 --- a/science/spglib/pkg-plist +++ b/science/spglib/pkg-plist @@ -11,9 +11,9 @@ lib/cmake/Spglib/SpglibTargets_shared.cmake %%FORTRAN%%lib/cmake/Spglib/try_compile.f90 %%FORTRAN%%lib/libspglib_f08.so %%FORTRAN%%lib/libspglib_f08.so.2 -%%FORTRAN%%lib/libspglib_f08.so.2.5.0 +%%FORTRAN%%lib/libspglib_f08.so.2.6.0 lib/libsymspg.so lib/libsymspg.so.2 -lib/libsymspg.so.2.5.0 +lib/libsymspg.so.2.6.0 libdata/pkgconfig/spglib.pc %%FORTRAN%%libdata/pkgconfig/spglib_f08.pc diff --git a/science/votca/Makefile b/science/votca/Makefile index 24ce596890b3..f12745e528a9 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -1,21 +1,22 @@ PORTNAME= votca DISTVERSIONPREFIX= v DISTVERSION= 2025 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= CSG and XTP: libraries for atomistic simulations -WWW= https://github.com/votca/votca +WWW= https://www.votca.org/ \ + https://github.com/votca/votca LICENSE= APACHE20 -BROKEN_i386= undefined reference to `__atomic_load' +BROKEN_i386= undefined reference to `__atomic_load' # ' PY_DEPENDS= \ ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xmltodict>0:devel/py-xmltodict@${PY_FLAVOR} \ rdkit>0:science/rdkit BUILD_DEPENDS= bash:shells/bash \ |