diff options
Diffstat (limited to 'science')
33 files changed, 96 insertions, 86 deletions
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-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 \ |