diff options
Diffstat (limited to 'science')
190 files changed, 765 insertions, 758 deletions
diff --git a/science/Makefile b/science/Makefile index 0fd8eb49e6d3..7a7615c8776f 100644 --- a/science/Makefile +++ b/science/Makefile @@ -321,6 +321,7 @@ SUBDIR += py-dipy SUBDIR += py-dlib SUBDIR += py-dwave-cloud-client + SUBDIR += py-dwave-gate SUBDIR += py-dwave-greedy SUBDIR += py-dwave-hybrid SUBDIR += py-dwave-inspector diff --git a/science/abinit/Makefile b/science/abinit/Makefile index 2347581589fd..ba4df25095f7 100644 --- a/science/abinit/Makefile +++ b/science/abinit/Makefile @@ -1,5 +1,5 @@ PORTNAME= abinit -DISTVERSION= 10.4.5 +DISTVERSION= 10.4.7 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -53,7 +53,8 @@ TEST_TARGET= tests_abirules tests_buildsys # Many tests print RuntimeError, http TEST_WRKSRC= ${WRKSRC}/abichecks PORTDOCS= * -BINARY_ALIAS= git=false +BINARY_ALIAS= git=false \ + gfortran=gfortran${GCC_DEFAULT} # for tests OPTIONS_DEFINE= DOCS OPENMP OPTIONS_DEFAULT= MPICH diff --git a/science/abinit/distinfo b/science/abinit/distinfo index 3cc29d915b5d..f008b4aac551 100644 --- a/science/abinit/distinfo +++ b/science/abinit/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753132807 -SHA256 (abinit-abinit-10.4.5_GH0.tar.gz) = ccb3af00603f574208b6d5bea6f857d7040be5748e7a93a689ffad84eb6a65ce -SIZE (abinit-abinit-10.4.5_GH0.tar.gz) = 153582604 +TIMESTAMP = 1757275359 +SHA256 (abinit-abinit-10.4.7_GH0.tar.gz) = 51f91d30f8fbadf7bcc36928406188b8810ea183fd2b1b406be563bd9fcdedb7 +SIZE (abinit-abinit-10.4.7_GH0.tar.gz) = 154053477 diff --git a/science/afni/Makefile b/science/afni/Makefile index c29dbf3d85da..60a9c6179d87 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 25.2.06 +DISTVERSION= 25.2.18 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index bdb61dc7648f..86a0070395b4 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1754029956 -SHA256 (afni-afni-AFNI_25.2.06_GH0.tar.gz) = d0d67099ec86804b049d51e7e51a08076f6e60d15c00cb292626e6fe6bc3a0df -SIZE (afni-afni-AFNI_25.2.06_GH0.tar.gz) = 53316535 +TIMESTAMP = 1759213947 +SHA256 (afni-afni-AFNI_25.2.18_GH0.tar.gz) = 9f21faf0f8ed66eba8a2c1473a4c5c0421909e0f386fc699ed599bebced96003 +SIZE (afni-afni-AFNI_25.2.18_GH0.tar.gz) = 53390003 diff --git a/science/agrum/Makefile b/science/agrum/Makefile index ff6dce0acfc3..761cac949744 100644 --- a/science/agrum/Makefile +++ b/science/agrum/Makefile @@ -1,5 +1,5 @@ PORTNAME= agrum -DISTVERSION= 2.2.0 +DISTVERSION= 2.2.1 CATEGORIES= science math MAINTAINER= yuri@FreeBSD.org @@ -8,7 +8,7 @@ WWW= https://agrum.gitlab.io \ https://gitlab.com/agrumery/aGrUM LICENSE= GPLv3 -LICENSE_FILE= ${WRKSRC}/LICENSE +LICENSE_FILE= ${WRKSRC}/LICENSE.md TEST_DEPENDS= swig:devel/swig @@ -20,7 +20,7 @@ LLD_UNSAFE= yes USE_GITLAB= yes GL_ACCOUNT= agrumery GL_PROJECT= aGrUM -GL_TAGNAME= cf1283f783aa6803bafbd9a3fb4991316c1b52d9 +GL_TAGNAME= 40993102 SHEBANG_FILES= act @@ -43,16 +43,14 @@ PYTHON_CMAKE_BOOL= BUILD_PYTHON PYTHON_USES= python PYTHON_PLIST_SUB= PYTHON_VER_MAJ=${PYTHON_VER:R} PYTHON_RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}configparser>0:devel/py-configparser@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib-inline>0:math/py-matplotlib-inline@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nbconvert>0:devel/py-nbconvert@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nbformat>0:devel/py-nbformat@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pydotplus>0:graphics/py-pydotplus@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR} # see wrappers/pyAgrum/requirements.txt and wrappers/pyAgrum/testunits/optional_requirements.txt @@ -62,6 +60,6 @@ do-test: @cd ${WRKSRC} && \ ${SETENV} ${MAKE_ENV} ./act test release agrum -t all -# tests as of 2.2.0: Failed 0 of 1483 tests +# tests as of 2.2.1: Failed 0 of 1485 tests .include <bsd.port.mk> diff --git a/science/agrum/distinfo b/science/agrum/distinfo index 62c51836a6d8..03113cb380cc 100644 --- a/science/agrum/distinfo +++ b/science/agrum/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753632410 -SHA256 (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 57f7274925f64129c2f3bfcd178f75edd4cb6eaff1d06c30f20c85c41e6ca3d9 -SIZE (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 29175753 +TIMESTAMP = 1759029558 +SHA256 (aGrUM-40993102.tar.bz2) = f0a4174d7854ea4e045e79c9c6a85c40f2d017906beca221a95fba3a1f233e08 +SIZE (aGrUM-40993102.tar.bz2) = 21812219 diff --git a/science/agrum/pkg-plist b/science/agrum/pkg-plist index 9fe1f9999703..bdc68b53969c 100644 --- a/science/agrum/pkg-plist +++ b/science/agrum/pkg-plist @@ -956,9 +956,9 @@ lib/libagrumID.so.%%VERSION%% lib/libagrumMRF.so lib/libagrumMRF.so.2 lib/libagrumMRF.so.%%VERSION%% -%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE -%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE.LGPL -%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE.MIT +%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE.md +%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSES/LGPL-3.0-or-later.txt +%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSES/MIT.txt %%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/METADATA %%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/WHEEL %%PYTHON_SITELIBDIR%%/pyagrum/__init__.py diff --git a/science/atompaw/Makefile b/science/atompaw/Makefile index 61ccc526fadb..5e23ebdb9006 100644 --- a/science/atompaw/Makefile +++ b/science/atompaw/Makefile @@ -1,6 +1,6 @@ PORTNAME= atompaw DISTVERSION= 4.2.0.3 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= http://users.wfu.edu/natalie/papers/pwpaw/ @@ -16,6 +16,7 @@ LIB_DEPENDS= liblapack.so:math/lapack \ USES= fortran gmake libtool GNU_CONFIGURE= yes +CONFIGURE_ARGS= --with-linalg-prefix=${LOCALBASE} OPTIONS_DEFINE= DOCS LIBXC OPTIONS_DEFAULT= LIBXC diff --git a/science/atompaw/files/patch-src_input__dataset__mod.F90 b/science/atompaw/files/patch-src_input__dataset__mod.F90 new file mode 100644 index 000000000000..cca7d9e3d6ae --- /dev/null +++ b/science/atompaw/files/patch-src_input__dataset__mod.F90 @@ -0,0 +1,11 @@ +--- src/input_dataset_mod.F90.orig 2023-06-02 20:37:00 UTC ++++ src/input_dataset_mod.F90 +@@ -2097,7 +2097,7 @@ END IF + INTEGER :: input_unit,echo_unit + INTEGER :: i_all,i_dx,i_xmin,i_zmesh,i_range + LOGICAL :: has_to_echo +- CHARACTER(200) :: inputline ++ CHARACTER(256) :: inputline + TYPE(input_dataset_t),POINTER :: dataset + + !------------------------------------------------------------------ diff --git a/science/berkeleygw/Makefile b/science/berkeleygw/Makefile index 36f76867eaaa..bc988171c441 100644 --- a/science/berkeleygw/Makefile +++ b/science/berkeleygw/Makefile @@ -18,7 +18,7 @@ BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libfftw3.so:math/fftw3 RUN_DEPENDS= bash:shells/bash -USES= blaslapack:openblas gmake fortran python shebangfix +USES= blaslapack:openblas gmake fortran:gfortran python shebangfix SHEBANG_GLOB= *.sh *.py *awk diff --git a/science/bout++-merging-filaments/Makefile b/science/bout++-merging-filaments/Makefile index ccb4d19ed74d..be54402f7732 100644 --- a/science/bout++-merging-filaments/Makefile +++ b/science/bout++-merging-filaments/Makefile @@ -1,6 +1,6 @@ PORTNAME= bout++-merging-filaments DISTVERSION= g20200812 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/bout++/Makefile b/science/bout++/Makefile index 43b9accad186..2e49f217994d 100644 --- a/science/bout++/Makefile +++ b/science/bout++/Makefile @@ -1,7 +1,7 @@ PORTNAME= bout++ DISTVERSIONPREFIX= v DISTVERSION= 5.1.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science math # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/cantera/Makefile b/science/cantera/Makefile index 61a965965fe2..aea50ad6e4a7 100644 --- a/science/cantera/Makefile +++ b/science/cantera/Makefile @@ -1,7 +1,7 @@ PORTNAME= cantera DISTVERSIONPREFIX= v DISTVERSION= 3.1.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science # chemistry physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/cdf/Makefile b/science/cdf/Makefile index edc94cf929c9..6b516cd72448 100644 --- a/science/cdf/Makefile +++ b/science/cdf/Makefile @@ -1,9 +1,10 @@ PORTNAME= cdf3 DISTVERSION= 3.9.1 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://spdf.gsfc.nasa.gov/pub/software/cdf/dist/cdf39_1/ DISTNAME= cdf${VER}-dist-cdf -DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} +DIST_SUBDIR= ${PORTNAME}-${DISTVERSION} MAINTAINER= alven@FreeBSD.org COMMENT= Device independent view of the CDF data model @@ -16,26 +17,34 @@ LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BUILD_DEPENDS= bash:shells/bash -USES= fortran ncurses gmake - +USES= fortran gmake ncurses USE_LDCONFIG= yes + +MAKE_ARGS+= OS=freebsd ENV=gnu all MAKE_FLAGS= INSTALLDIR=${STAGEDIR}${PREFIX} OS=freebsd ENV=gnu \ FORTRAN=yes FC_freebsd=${F77} MAKE_JOBS_UNSAFE= yes -TEST_TARGET= test # XXX: test segfaults -FFLAGS+= -std=legacy +TEST_TARGET= test + +PIE_UNSAFE= yes -WRKSRC= ${WRKDIR}/cdf${VER}-dist SUB_FILES= pkg-message -VER= ${PORTVERSION:S/.//:S/./_/} -DEFS= B C K +WRKSRC= ${WRKDIR}/cdf${VER}-dist +PLIST_SUB= SOVERSION=${DISTVERSION} PORTDOCS= CDF_copyright.txt CHANGES.txt Release.notes Welcome.txt OPTIONS_DEFINE= DOCS EXAMPLES -MAKE_ARGS+= OS=freebsd ENV=gnu all +DEFS= B C K +VER= ${PORTVERSION:S/.//:S/./_/} + +.include <bsd.port.pre.mk> + +.if ${FORTRAN_DEFAULT} != flang +FFLAGS= -std=legacy +.endif post-patch: .for def in ${DEFS} @@ -44,11 +53,17 @@ post-patch: .endfor post-install: + ${SED} -i '' 's,${STAGEDIR},,g' ${STAGEDIR}${PREFIX}/bin/definitions.? + ${RM} -f ${STAGEDIR}${PREFIX}/CDFLeapSeconds.txt + cd ${STAGEDIR}${PREFIX} && \ + ${FIND} bin/* lib/* -executable -exec ${STRIP_CMD} {} \; + +post-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${PORTDOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} + +post-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/samples/* ${STAGEDIR}${EXAMPLESDIR} - ${SED} -i '' 's,${STAGEDIR},,g' ${STAGEDIR}${PREFIX}/bin/definitions.? - ${RM} -f ${STAGEDIR}${PREFIX}/CDFLeapSeconds.txt -.include <bsd.port.mk> +.include <bsd.port.post.mk> diff --git a/science/cdf/pkg-plist b/science/cdf/pkg-plist index 177ca8658467..24910333ac66 100644 --- a/science/cdf/pkg-plist +++ b/science/cdf/pkg-plist @@ -50,9 +50,9 @@ lib/cdf/help/cdfvalidatej.olh lib/cdf/help/cdfxp.ilh lib/cdf/help/skt2cdf.olh lib/cdf/help/skt2cdfj.olh -lib/libcdf.3.9.1.so lib/libcdf.a lib/libcdf.so +lib/libcdf.%%SOVERSION%%.so %%PORTEXAMPLES%%%%EXAMPLESDIR%%/OperateAttributes.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/OperateCDF.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/OperateVariables.c diff --git a/science/cdo/Makefile b/science/cdo/Makefile index 783eae420b68..43c111203c7c 100644 --- a/science/cdo/Makefile +++ b/science/cdo/Makefile @@ -1,8 +1,7 @@ PORTNAME= cdo -PORTVERSION= 2.5.2 -PORTREVISION= 1 +PORTVERSION= 2.5.3 CATEGORIES= science -MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/29938/ \ +MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/30034/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org diff --git a/science/cdo/distinfo b/science/cdo/distinfo index fea6c9bb59e8..99abd7f5e917 100644 --- a/science/cdo/distinfo +++ b/science/cdo/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1747715302 -SHA256 (cdo-2.5.2.tar.gz) = 3b28da72d75547663b1b9b08332bfe3f884d27742d0eeeb7f3c8b2c70f521fa9 -SIZE (cdo-2.5.2.tar.gz) = 13966550 +TIMESTAMP = 1755062464 +SHA256 (cdo-2.5.3.tar.gz) = 0145cdba866a02b3e9b269e2ff7728ce61e21761332888041f05dc033676fa08 +SIZE (cdo-2.5.3.tar.gz) = 14007141 diff --git a/science/cdo/files/patch-powerpc64 b/science/cdo/files/patch-powerpc64 index f903f05da1fc..5d6dd67a4dc3 100644 --- a/science/cdo/files/patch-powerpc64 +++ b/science/cdo/files/patch-powerpc64 @@ -1,4 +1,4 @@ ---- libcdi/src/cgribexlib.c.orig 2024-02-02 10:51:13 UTC +--- libcdi/src/cgribexlib.c.orig 2025-07-14 15:03:05 UTC +++ libcdi/src/cgribexlib.c @@ -10,7 +10,7 @@ #pragma GCC diagnostic warning "-Wstrict-overflow" @@ -9,31 +9,31 @@ #pragma options nostrict #include <ppu_intrinsics.h> #endif -@@ -766,21 +766,21 @@ pwr6_minmax_val_double_unrolled6(const double *restric +@@ -752,21 +752,21 @@ pwr6_minmax_val_double_unrolled6(const double *restric + { + for (size_t j = 0; j < __UNROLL_DEPTH_1; ++j) { - for (size_t j = 0; j < __UNROLL_DEPTH_1; ++j) - { -- dmin[j] = __fsel(dmin[j] - data[i + j], data[i + j], dmin[j]); -- dmax[j] = __fsel(data[i + j] - dmax[j], data[i + j], dmax[j]); -+ dmin[j] = __builtin_ppc_fsel(dmin[j] - data[i + j], data[i + j], dmin[j]); -+ dmax[j] = __builtin_ppc_fsel(data[i + j] - dmax[j], data[i + j], dmax[j]); - } +- dmin[j] = __fsel(dmin[j] - data[i + j], data[i + j], dmin[j]); +- dmax[j] = __fsel(data[i + j] - dmax[j], data[i + j], dmax[j]); ++ dmin[j] = __builtin_ppc_fsel(dmin[j] - data[i + j], data[i + j], dmin[j]); ++ dmax[j] = __builtin_ppc_fsel(data[i + j] - dmax[j], data[i + j], dmax[j]); } + } for (size_t j = 0; j < residual; ++j) - { -- dmin[j] = __fsel(dmin[j] - data[ofs + j], data[ofs + j], dmin[j]); -- dmax[j] = __fsel(data[ofs + j] - dmax[j], data[ofs + j], dmax[j]); -+ dmin[j] = __builtin_ppc_fsel(dmin[j] - data[ofs + j], data[ofs + j], dmin[j]); -+ dmax[j] = __builtin_ppc_fsel(data[ofs + j] - dmax[j], data[ofs + j], dmax[j]); - } + { +- dmin[j] = __fsel(dmin[j] - data[ofs + j], data[ofs + j], dmin[j]); +- dmax[j] = __fsel(data[ofs + j] - dmax[j], data[ofs + j], dmax[j]); ++ dmin[j] = __builtin_ppc_fsel(dmin[j] - data[ofs + j], data[ofs + j], dmin[j]); ++ dmax[j] = __builtin_ppc_fsel(data[ofs + j] - dmax[j], data[ofs + j], dmax[j]); + } for (size_t j = 0; j < __UNROLL_DEPTH_1; ++j) - { -- *fmin = __fsel(*fmin - dmin[j], dmin[j], *fmin); -- *fmax = __fsel(dmax[j] - *fmax, dmax[j], *fmax); -+ *fmin = __builtin_ppc_fsel(*fmin - dmin[j], dmin[j], *fmin); -+ *fmax = __builtin_ppc_fsel(dmax[j] - *fmax, dmax[j], *fmax); - } + { +- *fmin = __fsel(*fmin - dmin[j], dmin[j], *fmin); +- *fmax = __fsel(dmax[j] - *fmax, dmax[j], *fmax); ++ *fmin = __builtin_ppc_fsel(*fmin - dmin[j], dmin[j], *fmin); ++ *fmax = __builtin_ppc_fsel(dmax[j] - *fmax, dmax[j], *fmax); + } } #undef __UNROLL_DEPTH_1 diff --git a/science/cgnslib/Makefile b/science/cgnslib/Makefile index 471819e7794c..45a191615689 100644 --- a/science/cgnslib/Makefile +++ b/science/cgnslib/Makefile @@ -23,7 +23,7 @@ MAKE_JOBS_UNSAFE= yes #CMAKE_ARGS= -DOpenGL_GL_PREFERENCE:STRING="GLVND" CMAKE_ARGS= -DOpenGL_GL_PREFERENCE:STRING="LEGACY" -FFLAGS+= -fPIC -std=legacy +FFLAGS= -fPIC TEST_TARGET= test OPTIONS_DEFINE= FORTRAN HDF5 TESTS TOOLS @@ -59,6 +59,10 @@ TOOLS_CMAKE_ON= -DTCL_INCLUDE_PATH:STRING="${TCL_INCLUDEDIR}" \ CFLAGS+= -Wno-error=incompatible-function-pointer-types .endif +.if ${FORTRAN_DEFAULT} != flang +FFLAGS+= -std=legacy +.endif + pre-configure: ${REINPLACE_CMD} -e 's|tk-private/||' ${WRKSRC}/src/cgnstools/tkogl/tkogl.c diff --git a/science/code_saturne/Makefile b/science/code_saturne/Makefile index e1ea21b89e25..3431d8506e0c 100644 --- a/science/code_saturne/Makefile +++ b/science/code_saturne/Makefile @@ -1,6 +1,6 @@ PORTNAME= code_saturne PORTVERSION= 8.1.1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science parallel MASTER_SITES= https://www.code-saturne.org/releases/ diff --git a/science/cp2k/Makefile b/science/cp2k/Makefile index 46e7081d3302..e886894e59e5 100644 --- a/science/cp2k/Makefile +++ b/science/cp2k/Makefile @@ -5,7 +5,8 @@ CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum chemistry and solid state physics software package -WWW= https://www.cp2k.org/ +WWW= https://www.cp2k.org/ \ + https://github.com/cp2k/cp2k LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/science/csvtk/Makefile b/science/csvtk/Makefile index e4b2b99739a4..acaa471d2f00 100644 --- a/science/csvtk/Makefile +++ b/science/csvtk/Makefile @@ -1,7 +1,7 @@ PORTNAME= csvtk DISTVERSIONPREFIX= v DISTVERSION= 0.34.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= jwb@FreeBSD.org diff --git a/science/dakota/Makefile b/science/dakota/Makefile index 96e46b04e23b..059d349e1323 100644 --- a/science/dakota/Makefile +++ b/science/dakota/Makefile @@ -1,5 +1,6 @@ PORTNAME= dakota DISTVERSION= 6.22.0 +PORTEVISION= 1 CATEGORIES= science MASTER_SITES= https://github.com/snl-dakota/dakota/releases/download/v${DISTVERSION}/ DISTNAME= ${PORTNAME}-${DISTVERSION}-public-src-cli @@ -15,7 +16,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= nanoflann>0:math/nanoflann LIB_DEPENDS= libblas.so:math/blas \ - libboost_system.so:devel/boost-libs \ + libboost_program_options.so:devel/boost-libs \ libexpat.so:textproc/expat2 \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ @@ -74,6 +75,11 @@ post-extract: @${FIND} ${WRKSRC} -name "*.orig" -delete @${ECHO} ${DISTVERSION} > ${WRKSRC}/VERSION # expected by the 'install' target +post-patch: + @${REINPLACE_CMD} -e 's| Boost::system||' \ + ${WRKSRC}/cmake/DakotaFindSystemTPLs.cmake \ + ${WRKSRC}/src/surrogates/unit/CMakeLists.txt + pre-configure: # MUQ_STANMATH_DIR is lost otherwise @${REINPLACE_CMD} 's|find_package(PkgConfig)|set(MUQ_STANMATH_DIR ${WRKSRC}/stanmath)|' ${WRKSRC}/packages/external/muq2/cmake/finds/FindSTANMATH.cmake diff --git a/science/dftd4/pkg-descr b/science/dftd4/pkg-descr index 19ae190643e6..5d459c6d9dff 100644 --- a/science/dftd4/pkg-descr +++ b/science/dftd4/pkg-descr @@ -1,2 +1,12 @@ -D4 is a generally applicable atomic-charge dependent london dispersion -correction calculator. +DFTD4 provides a generally applicable, charge-dependent London-dispersion +correction for Density Functional Theory (DFT) calculations and other +atomistic modeling methods. It addresses the missing van-der-Waals (vdW) +interactions from standard exchange-correlation functionals by approximating +them based solely on the system's structure, enabling rapid computation. + +This software can be linked as an external package to various DFT codes, +such as VASP, to add vdW energies, forces, and stresses for structure +relaxation and molecular dynamics simulations. It features functional-specific +parameters for numerous density functionals and offers API support for +Fortran, C, and Python, making it a versatile tool for computational +chemistry and physics. diff --git a/science/dimod/Makefile b/science/dimod/Makefile index f535bbdf1040..1605f697e49c 100644 --- a/science/dimod/Makefile +++ b/science/dimod/Makefile @@ -1,5 +1,5 @@ PORTNAME= dimod -DISTVERSION= 0.12.20 +DISTVERSION= 0.12.21 CATEGORIES= science python MAINTAINER= yuri@FreeBSD.org @@ -28,6 +28,6 @@ do-install: do-test: @cd ${WRKSRC}/testscpp && ${SETENV} ${MAKE_ENV} ${MAKE} -# tests as of 0.12.20: All tests passed (104295 assertions in 35 test cases) +# tests as of 0.12.21: All tests passed (104295 assertions in 35 test cases) .include <bsd.port.mk> diff --git a/science/dimod/distinfo b/science/dimod/distinfo index 8af012b9d278..93ff5101cd57 100644 --- a/science/dimod/distinfo +++ b/science/dimod/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742619271 -SHA256 (dwavesystems-dimod-0.12.20_GH0.tar.gz) = 33c06ca8a9f0ab9be5edc3ef2ea065c908fa1e3847c20a20598b1bc1674eafa6 -SIZE (dwavesystems-dimod-0.12.20_GH0.tar.gz) = 582646 +TIMESTAMP = 1758994255 +SHA256 (dwavesystems-dimod-0.12.21_GH0.tar.gz) = c7639f66a4270cc49ee2933b20ddca203e9b0e908b75ba1182fc2ff40e85f7ab +SIZE (dwavesystems-dimod-0.12.21_GH0.tar.gz) = 582916 diff --git a/science/fastjet/Makefile b/science/fastjet/Makefile index 8990a1950f62..00a5ee17b4c4 100644 --- a/science/fastjet/Makefile +++ b/science/fastjet/Makefile @@ -1,5 +1,5 @@ PORTNAME= fastjet -DISTVERSION= 3.4.3 +DISTVERSION= 3.5.1 CATEGORIES= science MASTER_SITES= https://fastjet.fr/repo/ @@ -46,7 +46,7 @@ post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/lib*.so* post-install-PYTHON-on: - @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/_fastjet.so.0.0.0 + @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/_fastjet_swig.so.0.0.0 do-test: # python tests diff --git a/science/fastjet/distinfo b/science/fastjet/distinfo index c318c545d2f6..896e7e12357e 100644 --- a/science/fastjet/distinfo +++ b/science/fastjet/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1730346663 -SHA256 (fastjet-3.4.3.tar.gz) = cc175471bfab8656b8c6183a8e5e9ad05d5f7506e46f3212a9a8230905b8f6a3 -SIZE (fastjet-3.4.3.tar.gz) = 2984798 +TIMESTAMP = 1755888400 +SHA256 (fastjet-3.5.1.tar.gz) = 9a4154163e72041dee3fdde9cb24e814625e178091a8734a6ad5375e5371b423 +SIZE (fastjet-3.5.1.tar.gz) = 3069022 diff --git a/science/fastjet/pkg-plist b/science/fastjet/pkg-plist index 35b8c8caf328..5f83019a7641 100644 --- a/science/fastjet/pkg-plist +++ b/science/fastjet/pkg-plist @@ -129,11 +129,12 @@ lib/libsiscone_spherical.so lib/libsiscone_spherical.so.0 lib/libsiscone_spherical.so.0.0.0 %%PYTHON%%%%PYTHON_SITELIBDIR%%/__pycache__/fastjet%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/__pycache__/fastjet%%PYTHON_TAG%%.opt-2.pyc %%PYTHON%%%%PYTHON_SITELIBDIR%%/__pycache__/fastjet%%PYTHON_TAG%%.pyc -%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet.a -%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet.so -%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet.so.0 -%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet.so.0.0.0 +%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet_swig.a +%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet_swig.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet_swig.so.0 +%%PYTHON%%%%PYTHON_SITELIBDIR%%/_fastjet_swig.so.0.0.0 %%PYTHON%%%%PYTHON_SITELIBDIR%%/fastjet.py %%PYTHON%%%%DATADIR%%/pyinterface/FastJetPythonExtensions.hh %%PYTHON%%%%DATADIR%%/pyinterface/fastjet-doc.i diff --git a/science/feff10/Makefile b/science/feff10/Makefile index 0eb2b3ea71bd..184eea6011ad 100644 --- a/science/feff10/Makefile +++ b/science/feff10/Makefile @@ -26,12 +26,16 @@ WRKSRC_SUBDIR= src SHEBANG_GLOB= *.script -FFLAGS+= -ffree-line-length-512 -fallow-argument-mismatch - MAKE_ARGS= FLAGS="${FFLAGS}" BINARY_ALIAS= make=${GMAKE} ifort=${FC} +.include <bsd.port.pre.mk> + +.if ${FORTRAN_DEFAULT} != flang +FFLAGS= -ffree-line-length-512 -fallow-argument-mismatch +.endif + do-install: for f in ${WRKSRC}/../bin/Seq/*; do \ if readelf -V $${f} > /dev/null 2>&1; then \ @@ -41,4 +45,4 @@ do-install: fi \ done -.include <bsd.port.mk> +.include <bsd.port.post.mk> diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile index bcc3ee4ec241..fc27b0db4de8 100644 --- a/science/gnudatalanguage/Makefile +++ b/science/gnudatalanguage/Makefile @@ -1,6 +1,6 @@ PORTNAME= gnudatalanguage PORTVERSION= 1.1.1 -PORTREVISION= 1 +PORTREVISION= 2 DISTVERSIONPREFIX= v CATEGORIES= science lang MASTER_SITES= https://github.com/${PORTNAME}/gdl/releases/download/v${PORTVERSION}/ diff --git a/science/gramps/Makefile b/science/gramps/Makefile index f261cd0a1aa4..be05bc98c53f 100644 --- a/science/gramps/Makefile +++ b/science/gramps/Makefile @@ -1,5 +1,5 @@ PORTNAME= gramps -DISTVERSION= 6.0.4 +DISTVERSION= 6.0.5 CATEGORIES= science gnome python MASTER_SITES= PYPI diff --git a/science/gramps/distinfo b/science/gramps/distinfo index 30016e379016..3e0a307bfe15 100644 --- a/science/gramps/distinfo +++ b/science/gramps/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1754945114 -SHA256 (gramps-6.0.4.tar.gz) = ebabb1cfa8dc61859ee0e9c4ad0b54c94ccff2809dd1b0895a38a46b80382692 -SIZE (gramps-6.0.4.tar.gz) = 21963080 +TIMESTAMP = 1757244514 +SHA256 (gramps-6.0.5.tar.gz) = 2160e04ec7033838e48fe3c68cfd4f383bec4e6f5398e207250b76687923e2dc +SIZE (gramps-6.0.5.tar.gz) = 22268263 diff --git a/science/isaac-cfd/Makefile b/science/isaac-cfd/Makefile index dfe1e852aff2..7ebbbae934ac 100644 --- a/science/isaac-cfd/Makefile +++ b/science/isaac-cfd/Makefile @@ -20,7 +20,6 @@ NO_WRKSUBDIR= yes MAKEFILE= makefile MAKE_ARGS= CPPFLAGS=-I. USES= fortran gmake -FFLAGS+= -std=legacy PLIST_FILES= bin/isaac PORTDOCS= man.4_2.ps.gz @@ -34,6 +33,12 @@ EXAMPLES_DISTFILES= example_cases${EXTRACT_SUFX} OPTIMIZED_FFLAGS_DESC= Use extra compiler (fortran) optimizations OPTIMIZED_FFLAGS_VARS= FFLAGS+="-O2 -ffast-math" +.include <bsd.port.pre.mk> + +.if ${FORTRAN_DEFAULT} != flang +FFLAGS= -std=legacy +.endif + pre-configure: @${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; s+%%FFLAGS%%+${FFLAGS}+;' \ ${WRKSRC}/makefile @@ -53,4 +58,4 @@ do-install-EXAMPLES-on: ${TAR} -xzf ${DISTDIR}/${DIST_SUBDIR}/example_cases${EXTRACT_SUFX} \ -C ${STAGEDIR}${EXAMPLESDIR} -.include <bsd.port.mk> +.include <bsd.port.post.mk> diff --git a/science/kalzium/distinfo b/science/kalzium/distinfo index 55a8ed08734d..2ed98aa072cd 100644 --- a/science/kalzium/distinfo +++ b/science/kalzium/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1751381644 -SHA256 (KDE/release-service/25.04.3/kalzium-25.04.3.tar.xz) = d8d76ae3d123d93fe0ddf33992d7c85292ec5560b76a634f9bf2d731c2fccada -SIZE (KDE/release-service/25.04.3/kalzium-25.04.3.tar.xz) = 22660296 +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 diff --git a/science/kalzium/pkg-plist b/science/kalzium/pkg-plist index 6d96ce611615..08dc853471f9 100644 --- a/science/kalzium/pkg-plist +++ b/science/kalzium/pkg-plist @@ -10,6 +10,9 @@ include/libkdeedu/psetables.h include/libkdeedu/science_export.h include/libkdeedu/spectrum.h include/libkdeedu/spectrumparser.h +lib/libcompoundviewer.so +lib/libcompoundviewer.so.5 +lib/libcompoundviewer.so.5.0.0 lib/libscience.so lib/libscience.so.5 lib/libscience.so.5.0.0 @@ -348,6 +351,7 @@ share/icons/hicolor/scalable/apps/kalzium.svgz %%DATADIR%%/icons/hicolor/scalable/actions/statematter.svgz %%DATADIR%%/icons/hicolor/scalable/actions/timeline.svgz %%DATADIR%%/icons/hicolor/scalable/actions/tooltip.svgz +share/knsrcfiles/kalzium.knsrc share/libkdeedu/data/elements.xml share/libkdeedu/data/isotopes.xml share/libkdeedu/data/spectra.xml @@ -383,6 +387,7 @@ share/locale/hi/LC_MESSAGES/kalzium.mo share/locale/hne/LC_MESSAGES/kalzium.mo share/locale/hr/LC_MESSAGES/kalzium.mo share/locale/hu/LC_MESSAGES/kalzium.mo +share/locale/ia/LC_MESSAGES/kalzium.mo share/locale/is/LC_MESSAGES/kalzium.mo share/locale/it/LC_MESSAGES/kalzium.mo share/locale/ja/LC_MESSAGES/kalzium.mo @@ -424,6 +429,21 @@ share/locale/uk/LC_MESSAGES/kalzium.mo share/locale/xh/LC_MESSAGES/kalzium.mo share/locale/zh_CN/LC_MESSAGES/kalzium.mo share/locale/zh_TW/LC_MESSAGES/kalzium.mo +share/man/ca/man1/kalzium.1.gz +share/man/da/man1/kalzium.1.gz +share/man/de/man1/kalzium.1.gz +share/man/es/man1/kalzium.1.gz +share/man/et/man1/kalzium.1.gz +share/man/fr/man1/kalzium.1.gz +share/man/gl/man1/kalzium.1.gz +share/man/it/man1/kalzium.1.gz share/man/man1/kalzium.1.gz +share/man/nl/man1/kalzium.1.gz +share/man/pl/man1/kalzium.1.gz +share/man/pt/man1/kalzium.1.gz +share/man/pt_BR/man1/kalzium.1.gz +share/man/ru/man1/kalzium.1.gz +share/man/sv/man1/kalzium.1.gz +share/man/uk/man1/kalzium.1.gz share/metainfo/org.kde.kalzium.appdata.xml share/qlogging-categories6/kalzium.categories diff --git a/science/kim-api/Makefile b/science/kim-api/Makefile index bcfc3fe9f454..154452adc611 100644 --- a/science/kim-api/Makefile +++ b/science/kim-api/Makefile @@ -1,12 +1,12 @@ PORTNAME= kim-api -DISTVERSION= 2.3.0 -PORTREVISION= 1 +DISTVERSION= 2.4.1 CATEGORIES= science MASTER_SITES= https://s3.openkim.org/kim-api/ MAINTAINER= yuri@FreeBSD.org COMMENT= Framework for reliable, reproducible, portable molecular simulations -WWW= https://openkim.org/ +WWW= https://openkim.org/ \ + https://github.com/openkim/kim-api LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/LICENSE.LGPL diff --git a/science/kim-api/distinfo b/science/kim-api/distinfo index 34ec678ecd72..aa9436bebfa7 100644 --- a/science/kim-api/distinfo +++ b/science/kim-api/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1647738438 -SHA256 (kim-api-2.3.0.txz) = 93673bb8fbc0625791f2ee67915d1672793366d10cabc63e373196862c14f991 -SIZE (kim-api-2.3.0.txz) = 357580 +TIMESTAMP = 1757122898 +SHA256 (kim-api-2.4.1.txz) = 225e3136d43e416a4424551e9e5f6d92cc6ecfe11389a1b6e97d6dcdfed83d44 +SIZE (kim-api-2.4.1.txz) = 364020 diff --git a/science/kim-api/pkg-plist b/science/kim-api/pkg-plist index 544dee8e567d..8ad13559dacb 100644 --- a/science/kim-api/pkg-plist +++ b/science/kim-api/pkg-plist @@ -134,8 +134,9 @@ lib/kim-api/portable-models/ex_model_Ar_SLJ_MultiCutoff/libkim-api-portable-mode lib/kim-api/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu/libkim-api-simulator-model.so lib/libkim-api.so lib/libkim-api.so.2 -lib/libkim-api.so.2.3.0 +lib/libkim-api.so.2.4.1 libdata/pkgconfig/libkim-api.pc +libexec/kim-api/kim-api-base64-encode libexec/kim-api/kim-api-collections-info libexec/kim-api/kim-api-portable-model-info libexec/kim-api/kim-api-shared-library-test diff --git a/science/libccp4/pkg-descr b/science/libccp4/pkg-descr index 8e24c34b4c17..a88f627c63b9 100644 --- a/science/libccp4/pkg-descr +++ b/science/libccp4/pkg-descr @@ -1,10 +1,13 @@ -CCP4 exists to produce and support a world-leading, integrated suite of programs -that allows researchers to determine macromolecular structures by X-ray -crystallography, and other biophysical techniques. CCP4 aims to develop and -support the development of cutting edge approaches to experimental determination -and analysis of protein structure, and integrate these approaches into the -suite. CCP4 is a community based resource that supports the widest possible -researcher community, embracing academic, not for profit, and for profit -research. CCP4 aims to play a key role in the education and training of -scientists in experimental structural biology. It encourages the wide -dissemination of new ideas, techniques and practice. +CCP4 is a world-leading, integrated software suite for macromolecular +structure determination using X-ray crystallography and other biophysical +techniques. It provides a comprehensive collection of programs covering +all stages of the process, from data processing and phasing (e.g., Crank) +to molecular replacement (e.g., Beast, AMPLE), model building (e.g., +Buccaneer), refinement (e.g., REFMAC), and validation. + +The suite features automated structure solution pipelines and modern +graphical user interfaces like CCP4i2. As a community-based resource, +CCP4 supports a wide research community and plays a key role in the +education and training of scientists in experimental structural biology. +Its modular design and Coordinate Library offer flexibility and extensive +functionality for structural biologists. diff --git a/science/libcint/Makefile b/science/libcint/Makefile index af528fdf2ec6..030c5de31ee3 100644 --- a/science/libcint/Makefile +++ b/science/libcint/Makefile @@ -1,7 +1,6 @@ PORTNAME= libcint DISTVERSIONPREFIX= v -DISTVERSION= 6.1.2 -PORTREVISION= 2 +DISTVERSION= 6.1.3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -24,7 +23,7 @@ PLIST_FILES= include/cint.h \ include/cint_funcs.h \ lib/libcint.so \ lib/libcint.so.${PORTVERSION:R:R} \ - lib/libcint.so.6.1.1 # see https://github.com/sunqm/libcint/issues/106 + lib/libcint.so.${PORTVERSION} #lib/libcint.so.${PORTVERSION} post-patch: @@ -39,4 +38,6 @@ do-test: # needs science/py-pyscf, pending https://github.com/pyscf/pyscf/issues ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test +# tests as of 6.1.3: 100% tests passed, 0 tests failed out of 2 + .include <bsd.port.mk> diff --git a/science/libcint/distinfo b/science/libcint/distinfo index 947086b18216..c2d4cf4a3f83 100644 --- a/science/libcint/distinfo +++ b/science/libcint/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1710384136 -SHA256 (sunqm-libcint-v6.1.2_GH0.tar.gz) = 8287e1eaf2b8c8e19eb7a8ea92fd73898f0884023c503b84624610400adb25c4 -SIZE (sunqm-libcint-v6.1.2_GH0.tar.gz) = 50862041 +TIMESTAMP = 1755587717 +SHA256 (sunqm-libcint-v6.1.3_GH0.tar.gz) = e4d977d4aeb4d5b87639ea57a2d2f1d5c1001f3f94e480b08c297a6cbc186f27 +SIZE (sunqm-libcint-v6.1.3_GH0.tar.gz) = 50867546 diff --git a/science/libcint/files/patch-src_c2f.h b/science/libcint/files/patch-src_c2f.h deleted file mode 100644 index b7d3deccc865..000000000000 --- a/science/libcint/files/patch-src_c2f.h +++ /dev/null @@ -1,10 +0,0 @@ ---- src/c2f.h.orig 2018-03-21 00:24:56 UTC -+++ src/c2f.h -@@ -4,6 +4,7 @@ - */ - - #include "config.h" -+#include <sys/types.h> - - #define ALL_CINT_FORTRAN_(NAME) \ - int c##NAME##_sph_(double *out, int *shls, int *atm, int *natm, \ diff --git a/science/maeparser/pkg-descr b/science/maeparser/pkg-descr index 5a07dac6de9a..f381e9c79480 100644 --- a/science/maeparser/pkg-descr +++ b/science/maeparser/pkg-descr @@ -1,5 +1,13 @@ -maeparser is a parser for Schrodinger Maestro files. +maeparser is a C++ library developed by Schrodinger for efficiently and +losslessly parsing Maestro files, which serve as Schrodinger's primary +output format for storing molecular structures and data. This parser is +crucial for any software package needing to interact with Schrodinger's +physics-based modeling outputs. -Structure files (.mae,.maegz,.mae.gz) can contain multiple structures -delimited by "f_m_ct". See MaeConstants.hpp for standard block and property -names. +It supports various applications in computational chemistry, including +molecular dynamics, ligand-protein docking, and quantum mechanics. The +library utilizes a recursive descent approach, prioritizing parsing speed +to ensure quick and accurate extraction of data from .mae, .maegz, and +.mae.gz structure files. These files can contain multiple structures, +delimited by "f_m_ct", with standard block and property names defined in +MaeConstants.hpp. diff --git a/science/mcpl/Makefile b/science/mcpl/Makefile index 7ee2ca520278..25c22bb8a36c 100644 --- a/science/mcpl/Makefile +++ b/science/mcpl/Makefile @@ -11,6 +11,9 @@ WWW= https://mctools.github.io/mcpl/ \ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE +NOT_FOR_ARCHS= armv7 powerpc i386 +NOT_FOR_ARCHS_REASON= MCPL does not support 32 bit platforms + BROKEN_i386= compilation fails, see https://github.com/mctools/mcpl/issues/88 USES= cmake:testing diff --git a/science/meep/Makefile b/science/meep/Makefile index 1c26a64c010f..a2187234803b 100644 --- a/science/meep/Makefile +++ b/science/meep/Makefile @@ -1,7 +1,7 @@ PORTNAME= meep DISTVERSIONPREFIX= v DISTVERSION= 1.29.0 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science cad MAINTAINER= yuri@FreeBSD.org diff --git a/science/molgif/Makefile b/science/molgif/Makefile index 280dc2503615..9998275f996b 100644 --- a/science/molgif/Makefile +++ b/science/molgif/Makefile @@ -1,6 +1,6 @@ PORTNAME= molgif DISTVERSION= g20180108 -PORTREVISION= 29 +PORTREVISION= 30 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/mopac/pkg-descr b/science/mopac/pkg-descr index 18229a7d331d..a510745aeb45 100644 --- a/science/mopac/pkg-descr +++ b/science/mopac/pkg-descr @@ -1,2 +1,14 @@ -MOPAC7, semi-empirical (MNDO, AM1, PM3, MINDO/3) quantum-chemical -calculation written by James J. P. Stewart and co-workers. +MOPAC (Molecular Orbital PACkage) is a powerful computational chemistry +software that employs semi-empirical quantum chemistry methods to study +molecular and periodic structures. Developed since 1981, it offers a +balance of computational speed and accuracy for a wide range of +applications in chemistry and materials science. + +MOPAC implements various semi-empirical models, including AM1, PM3, PM6, +and PM7. It performs geometry optimization, transition-state optimization, +and vibrational analysis. Key features include solvation models (COSMO), +support for periodic boundary conditions, and the unique MOZYME solver +for rapid calculations on large systems, such as biomolecules and +materials. MOPAC also calculates gas-phase thermodynamics, molecular +polarizability, and integrates with numerous graphical user interfaces +and other chemistry software. It supports 83 elements of the periodic table. diff --git a/science/openmodelica/Makefile b/science/openmodelica/Makefile index dafafc57c8da..20193cb276c9 100644 --- a/science/openmodelica/Makefile +++ b/science/openmodelica/Makefile @@ -1,7 +1,6 @@ PORTNAME= openmodelica DISTVERSIONPREFIX= v -DISTVERSION= 1.25.1 -PORTREVISION= 1 +DISTVERSION= 1.25.4 CATEGORIES= science cad java DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} @@ -54,15 +53,15 @@ GH_PROJECT= OpenModelica SHEBANG_GLOB= *.sh *.in *.ac GH_TUPLE= \ - OpenModelica:OMOptim:f1036f43db18c5015da259771004cfb80e08a110:OpenModelica_OMOptim/OMOptim \ - OpenModelica:OMSimulator:46fa40f:OpenModelica_OMSimulator/OMSimulator \ + OpenModelica:OMOptim:d53288b:OpenModelica_OMOptim/OMOptim \ + OpenModelica:OMSimulator:e3a3aeb:OpenModelica_OMSimulator/OMSimulator \ OpenModelica:OMSimulator-3rdParty:5c10de1648d1134a577d9284b58580a72383d89f:OpenModelica_OMSimulator_3rdParty/OMSimulator/3rdParty \ OpenModelica:OMCompiler-3rdParty:520663f:OpenModelica_OMCompiler_3rdParty/OMCompiler/3rdParty \ OpenModelica:OMSens:093ad11:OpenModelica_OMSens/OMSens \ OpenModelica:OMSens_Qt:bab329a:OpenModelica_OMSens_Qt/OMSens_Qt \ OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMOptim/common \ OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMSens_Qt/common -GH_TUPLE+= OpenModelica:OMBootstrapping:91938f0acbdc6e9ba91114376e3640ca6147b579:bootstrapping/OMCompiler/Compiler/boot/bomc # downloaded by cmake +GH_TUPLE+= OpenModelica:OMBootstrapping:04d16f7461e5401321f0f72613daf466ae2f76be:bootstrapping/OMCompiler/Compiler/boot/bomc # downloaded by cmake # this should change make program everywhere, but it doesn't, # hence the patches in OMCompiler/Compiler/runtime/CMakeLists.txt, OMEdit/OMEditLIB/Simulation/SimulationOutputWidget.cpp diff --git a/science/openmodelica/distinfo b/science/openmodelica/distinfo index 66b481d27d53..2597c4be9261 100644 --- a/science/openmodelica/distinfo +++ b/science/openmodelica/distinfo @@ -1,19 +1,19 @@ -TIMESTAMP = 1750120788 -SHA256 (openmodelica-1.25.1/OpenModelica-OpenModelica-v1.25.1_GH0.tar.gz) = f7d819fd7b838bad5ddbbd9ee585e49053464db68c0b9a406b2f9fea400ac2e5 -SIZE (openmodelica-1.25.1/OpenModelica-OpenModelica-v1.25.1_GH0.tar.gz) = 148275827 -SHA256 (openmodelica-1.25.1/OpenModelica-OMOptim-f1036f43db18c5015da259771004cfb80e08a110_GH0.tar.gz) = 11189c8ab3fb9d22ed805271ef53b9698b0d41007a1708d7a77ef074a5b20447 -SIZE (openmodelica-1.25.1/OpenModelica-OMOptim-f1036f43db18c5015da259771004cfb80e08a110_GH0.tar.gz) = 4022842 -SHA256 (openmodelica-1.25.1/OpenModelica-OMSimulator-46fa40f_GH0.tar.gz) = eb5fbb88b2cf6a3556c43ee4c0b446fb26a70be06ddfb4031e50636dc1af1048 -SIZE (openmodelica-1.25.1/OpenModelica-OMSimulator-46fa40f_GH0.tar.gz) = 92370094 -SHA256 (openmodelica-1.25.1/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d -SIZE (openmodelica-1.25.1/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 -SHA256 (openmodelica-1.25.1/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 37c82357fc1e862eb13d79cf1ff2d143f263502472db9bb2c350c0c551022954 -SIZE (openmodelica-1.25.1/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 50256095 -SHA256 (openmodelica-1.25.1/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 335512c08f94902bb07e75278cea791370a551336272f7bebef8c707ef5e5e2b -SIZE (openmodelica-1.25.1/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 8871049 -SHA256 (openmodelica-1.25.1/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 2f2dcba4defd7f13e9fd5e0c26bb4951b9f1fcc7da64960a6ad1cee32a628efa -SIZE (openmodelica-1.25.1/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 211270 -SHA256 (openmodelica-1.25.1/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = fdb5bb442da0375373ef221cf26195114bf149511c1c2be051caad6301c21c9a -SIZE (openmodelica-1.25.1/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = 36148 -SHA256 (openmodelica-1.25.1/OpenModelica-OMBootstrapping-91938f0acbdc6e9ba91114376e3640ca6147b579_GH0.tar.gz) = 1a0327dabedd09dab3aa872af194b6d4e79bacc45659ea3154076e7f1f54b2cc -SIZE (openmodelica-1.25.1/OpenModelica-OMBootstrapping-91938f0acbdc6e9ba91114376e3640ca6147b579_GH0.tar.gz) = 3328929 +TIMESTAMP = 1757658835 +SHA256 (openmodelica-1.25.4/OpenModelica-OpenModelica-v1.25.4_GH0.tar.gz) = b9d50f8321f4537735d70368b2ca105e35ad118797d71b0107b24eb660387ad4 +SIZE (openmodelica-1.25.4/OpenModelica-OpenModelica-v1.25.4_GH0.tar.gz) = 148278628 +SHA256 (openmodelica-1.25.4/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = d5012951f43e90dce03d7866d221278ee11ddfbdac4db20fe43d93adbc3748e7 +SIZE (openmodelica-1.25.4/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = 4024177 +SHA256 (openmodelica-1.25.4/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 6192d933c258950fb0171f5d0ddac0353632d17ee99f6974ba53dd654f547e49 +SIZE (openmodelica-1.25.4/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 95557541 +SHA256 (openmodelica-1.25.4/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d +SIZE (openmodelica-1.25.4/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 +SHA256 (openmodelica-1.25.4/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 37c82357fc1e862eb13d79cf1ff2d143f263502472db9bb2c350c0c551022954 +SIZE (openmodelica-1.25.4/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 50256095 +SHA256 (openmodelica-1.25.4/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 335512c08f94902bb07e75278cea791370a551336272f7bebef8c707ef5e5e2b +SIZE (openmodelica-1.25.4/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 8871049 +SHA256 (openmodelica-1.25.4/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 2f2dcba4defd7f13e9fd5e0c26bb4951b9f1fcc7da64960a6ad1cee32a628efa +SIZE (openmodelica-1.25.4/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 211270 +SHA256 (openmodelica-1.25.4/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = fdb5bb442da0375373ef221cf26195114bf149511c1c2be051caad6301c21c9a +SIZE (openmodelica-1.25.4/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = 36148 +SHA256 (openmodelica-1.25.4/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 9ac6d28be6a331dfb61a57b033f2bcf984448cd63bc1a4cd140d60c2f5c64a79 +SIZE (openmodelica-1.25.4/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 3346859 diff --git a/science/openmodelica/pkg-plist b/science/openmodelica/pkg-plist index 2f3a85526399..9c08ba4f8e0a 100644 --- a/science/openmodelica/pkg-plist +++ b/science/openmodelica/pkg-plist @@ -778,12 +778,15 @@ share/OMSimulator/schema/fmi3/fmi3Type.xsd share/OMSimulator/schema/fmi3/fmi3Unit.xsd share/OMSimulator/schema/fmi3/fmi3Variable.xsd share/OMSimulator/schema/fmi3/fmi3VariableDependency.xsd +share/OMSimulator/schema/ssp/SSPTraceabilityCommon.xsd +share/OMSimulator/schema/ssp/SimulationResourceMetaData.xsd share/OMSimulator/schema/ssp/SystemStructureCommon.xsd share/OMSimulator/schema/ssp/SystemStructureDescription.xsd share/OMSimulator/schema/ssp/SystemStructureDescription11.xsd share/OMSimulator/schema/ssp/SystemStructureParameterMapping.xsd share/OMSimulator/schema/ssp/SystemStructureParameterValues.xsd share/OMSimulator/schema/ssp/SystemStructureSignalDictionary.xsd +share/OMSimulator/schema/ssp/xlink.xsd share/OMSimulator/scripts/OMSimulatorServer.py share/cmake/ZeroMQ/ZeroMQConfig.cmake share/cmake/ZeroMQ/ZeroMQConfigVersion.cmake diff --git a/science/opsin/pkg-descr b/science/opsin/pkg-descr index f49b9052d4ca..efc128011b63 100644 --- a/science/opsin/pkg-descr +++ b/science/opsin/pkg-descr @@ -1,4 +1,13 @@ -OPSIN is a Java library for IUPAC name-to-structure conversion offering high -recall and precision on organic chemical nomenclature. -Supported outputs are SMILES, CML (Chemical Markup Language) and InChI (IUPAC -International Chemical Identifier). +OPSIN (Open Parser for Systematic IUPAC Nomenclature) is a freely +available, open-source Java library designed to accurately interpret +systematic IUPAC chemical nomenclature and convert it into chemical +structures. It offers high precision and recall for organic chemical +names, including complex heterocycles and stereochemistry. + +OPSIN supports multiple output formats such as SMILES, InChI, and CML, +and can also generate PNG, SVG, and JSON. It can be deployed as a web +service, a local command-line application for bulk conversion, or +integrated into other systems via third-party Python libraries. Its +extensible design and robust parsing mechanism make it a valuable tool +for chemical information extraction from scientific literature and +patents, research and development, and populating chemical databases. diff --git a/science/packmol/Makefile b/science/packmol/Makefile index 627188fa12eb..5f2d5ae0c487 100644 --- a/science/packmol/Makefile +++ b/science/packmol/Makefile @@ -1,6 +1,6 @@ PORTNAME= packmol DISTVERSIONPREFIX= v -DISTVERSION= 21.0.4 +DISTVERSION= 21.1.1 CATEGORIES= science MAINTAINER= eduardo@FreeBSD.org diff --git a/science/packmol/distinfo b/science/packmol/distinfo index 1e7f2f2c9e84..a48cfe0d0a3d 100644 --- a/science/packmol/distinfo +++ b/science/packmol/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1752317019 -SHA256 (m3g-packmol-v21.0.4_GH0.tar.gz) = ca2398a6f8f2a326f52cda8e45a8818ea430a1b195fd3801d017e1a18f38fde8 -SIZE (m3g-packmol-v21.0.4_GH0.tar.gz) = 630743 +TIMESTAMP = 1759409929 +SHA256 (m3g-packmol-v21.1.1_GH0.tar.gz) = 4bad785e6e1b91d8b80934eeebf91013e940c577693bbecd7ec56eb563f5d97f +SIZE (m3g-packmol-v21.1.1_GH0.tar.gz) = 634943 diff --git a/science/paraview/Makefile b/science/paraview/Makefile index 4e69796ed499..e657e04d7f84 100644 --- a/science/paraview/Makefile +++ b/science/paraview/Makefile @@ -1,6 +1,6 @@ PORTNAME= paraview DISTVERSION= ${PARAVIEW_VER}.3 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science graphics MASTER_SITES= http://www.paraview.org/files/v${PARAVIEW_VER}/ DISTNAME= ParaView-v${PORTVERSION} diff --git a/science/plumed/pkg-descr b/science/plumed/pkg-descr index a4e5b42106c3..9d390c7b6028 100644 --- a/science/plumed/pkg-descr +++ b/science/plumed/pkg-descr @@ -1,6 +1,13 @@ -PLUMED is an open-source, community-developed library that provides a wide -range of different methods, which include: -* enhanced-sampling algorithms -* free-energy methods -* tools to analyze the vast amounts of data produced by molecular dynamics (MD) - simulations. +PLUMED is an open-source, community-developed library designed to work +with molecular dynamics (MD) simulations. It provides a comprehensive +toolbox of methods, including enhanced-sampling algorithms, free-energy +methods, and advanced tools for analyzing the vast amounts of data +produced by MD simulations. + +This versatile library offers a wide range of collective variables, +making it suitable for studying complex processes across various scientific +disciplines such as physics, chemistry, material science, and biology. +PLUMED seamlessly integrates with popular MD engines like GROMACS and +LAMMPS, as well as analysis tools such as VMD. Its API supports multiple +programming languages (C, C++, Fortran, Python) and its L-GPL license +ensures compatibility with proprietary software. diff --git a/science/pnetcdf/Makefile b/science/pnetcdf/Makefile index 05829ebeef97..e131d647de3b 100644 --- a/science/pnetcdf/Makefile +++ b/science/pnetcdf/Makefile @@ -1,5 +1,5 @@ PORTNAME= pnetcdf -PORTVERSION= 1.14.0 +PORTVERSION= 1.14.1 CATEGORIES= science parallel MASTER_SITES= https://parallel-netcdf.github.io/Release/ \ LOCAL/sunpoet diff --git a/science/pnetcdf/distinfo b/science/pnetcdf/distinfo index c6351e3b6792..17dd83110f2f 100644 --- a/science/pnetcdf/distinfo +++ b/science/pnetcdf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1736671217 -SHA256 (pnetcdf-1.14.0.tar.gz) = 575f189fb01c53f93b3d6ae0e506f46e19694807c81af0b9548e947995acf704 -SIZE (pnetcdf-1.14.0.tar.gz) = 2419346 +TIMESTAMP = 1757120530 +SHA256 (pnetcdf-1.14.1.tar.gz) = 6f0f7221006c211fce9ddd2c008796b8c69dd717b2ad1be0b4027fc328fd3220 +SIZE (pnetcdf-1.14.1.tar.gz) = 2512984 diff --git a/science/pnetcdf/files/patch-src-packaging-Makefile.in b/science/pnetcdf/files/patch-src-packaging-Makefile.in deleted file mode 100644 index 6b5360cc75d6..000000000000 --- a/science/pnetcdf/files/patch-src-packaging-Makefile.in +++ /dev/null @@ -1,11 +0,0 @@ ---- src/packaging/Makefile.in.orig 2024-11-11 22:32:47 UTC -+++ src/packaging/Makefile.in -@@ -637,7 +637,7 @@ install-data-hook: - # GNU autoconf allows DESTDIR variable when running 'make install' which will - # prepend it before all installation names. - install-data-hook: -- $(SED_I) -e 's|INSTALL_PREFIX|$(DESTDIR)$(prefix)|g ; s|INSTALL_EXEC_PREFIX|$(DESTDIR)$(exec_prefix)|g' $(DESTDIR)$(prefix)/libdata/pkgconfig/pnetcdf.pc -+ $(SED_I) -e 's|INSTALL_PREFIX|$(prefix)|g ; s|INSTALL_EXEC_PREFIX|$(exec_prefix)|g' $(DESTDIR)$(prefix)/libdata/pkgconfig/pnetcdf.pc - - # Tell versions [3.59,3.63) of GNU make to not export all variables. - # Otherwise a system limit (for SysV at least) may be exceeded. diff --git a/science/pnetcdf/files/patch-src-utils-Makefile.in b/science/pnetcdf/files/patch-src-utils-Makefile.in deleted file mode 100644 index f91866b7caab..000000000000 --- a/science/pnetcdf/files/patch-src-utils-Makefile.in +++ /dev/null @@ -1,11 +0,0 @@ ---- src/utils/Makefile.in.orig 2024-11-11 22:32:47 UTC -+++ src/utils/Makefile.in -@@ -856,7 +856,7 @@ install-exec-hook: - # GNU autoconf allows DESTDIR variable when running 'make install' which will - # prepend it before all installation names. - install-exec-hook: -- $(SED_I) -e 's|INSTALL_PREFIX|$(DESTDIR)$(prefix)|g ; s|INSTALL_EXEC_PREFIX|$(DESTDIR)$(exec_prefix)|g' $(DESTDIR)$(bindir)/pnetcdf-config -+ $(SED_I) -e 's|INSTALL_PREFIX|$(prefix)|g ; s|INSTALL_EXEC_PREFIX|$(exec_prefix)|g' $(DESTDIR)$(bindir)/pnetcdf-config - chmod +x $(DESTDIR)$(bindir)/pnetcdf-config - - # Tell versions [3.59,3.63) of GNU make to not export all variables. diff --git a/science/pnetcdf/pkg-plist b/science/pnetcdf/pkg-plist index a99ef4d0e02d..303359f6614a 100644 --- a/science/pnetcdf/pkg-plist +++ b/science/pnetcdf/pkg-plist @@ -12,8 +12,8 @@ include/pnetcdf.inc include/pnetcdf.mod lib/libpnetcdf.a lib/libpnetcdf.so -lib/libpnetcdf.so.6 -lib/libpnetcdf.so.6.0.0 +lib/libpnetcdf.so.7 +lib/libpnetcdf.so.7.0.0 libdata/pkgconfig/pnetcdf.pc share/man/man1/cdfdiff.1.gz share/man/man1/ncmpidiff.1.gz diff --git a/science/psi4/Makefile b/science/psi4/Makefile index 4670af321999..dcdbd6077751 100644 --- a/science/psi4/Makefile +++ b/science/psi4/Makefile @@ -1,7 +1,7 @@ PORTNAME= psi4 DISTVERSIONPREFIX= v DISTVERSION= 1.9.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science # quantum-chemistry EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} diff --git a/science/py-HofstadterTools/Makefile b/science/py-HofstadterTools/Makefile index fd8636f491cb..44bd350e5745 100644 --- a/science/py-HofstadterTools/Makefile +++ b/science/py-HofstadterTools/Makefile @@ -1,5 +1,6 @@ PORTNAME= HofstadterTools DISTVERSION= 1.0.4 +PORTREVISION= 1 CATEGORIES= science python # physics MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-MDAnalysis/Makefile b/science/py-MDAnalysis/Makefile index c43d93a3447a..3df1c2089e7c 100644 --- a/science/py-MDAnalysis/Makefile +++ b/science/py-MDAnalysis/Makefile @@ -1,6 +1,6 @@ PORTNAME= MDAnalysis DISTVERSION= 2.7.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-MDAnalysisTests/Makefile b/science/py-MDAnalysisTests/Makefile index 87eb1f4ade49..4150fad1fa25 100644 --- a/science/py-MDAnalysisTests/Makefile +++ b/science/py-MDAnalysisTests/Makefile @@ -1,6 +1,6 @@ PORTNAME= MDAnalysisTests DISTVERSION= 2.7.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-OpenFermion-Dirac/Makefile b/science/py-OpenFermion-Dirac/Makefile index f2c3ee0a9746..290577d9a3fb 100644 --- a/science/py-OpenFermion-Dirac/Makefile +++ b/science/py-OpenFermion-Dirac/Makefile @@ -1,6 +1,6 @@ PORTNAME= OpenFermion-Dirac DISTVERSION= g20220812 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python # chemistry, quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-OpenFermion-PySCF/Makefile b/science/py-OpenFermion-PySCF/Makefile index f16589ecc951..8cc4e8dab201 100644 --- a/science/py-OpenFermion-PySCF/Makefile +++ b/science/py-OpenFermion-PySCF/Makefile @@ -1,7 +1,7 @@ PORTNAME= py-OpenFermion-PySCF DISTVERSIONPREFIX= v DISTVERSION= 0.5 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python # chemistry, quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-OpenFermion/Makefile b/science/py-OpenFermion/Makefile index 6505d132d2ad..7ba275fab7f0 100644 --- a/science/py-OpenFermion/Makefile +++ b/science/py-OpenFermion/Makefile @@ -1,6 +1,7 @@ PORTNAME= OpenFermion DISTVERSIONPREFIX= v DISTVERSION= 1.7.1 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-OpenMC/Makefile b/science/py-OpenMC/Makefile index 77f10b2454d9..32fa25a62689 100644 --- a/science/py-OpenMC/Makefile +++ b/science/py-OpenMC/Makefile @@ -1,7 +1,7 @@ PORTNAME= OpenMC DISTVERSIONPREFIX= v DISTVERSION= 0.15.0 -PORTREVISION= 2 +PORTREVISION= 4 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} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${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-PyNE/Makefile b/science/py-PyNE/Makefile index 8fc222236634..ea9dd4c53a1e 100644 --- a/science/py-PyNE/Makefile +++ b/science/py-PyNE/Makefile @@ -1,6 +1,6 @@ PORTNAME= PyNE DISTVERSION= 0.7.8 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science # physics MASTER_SITES= https://raw.githubusercontent.com/pyne/data/master/:decay \ https://raw.githubusercontent.com/pyne/data/master/:cram \ diff --git a/science/py-abipy/Makefile b/science/py-abipy/Makefile index b4c9c5f1ce34..06e725dae361 100644 --- a/science/py-abipy/Makefile +++ b/science/py-abipy/Makefile @@ -1,6 +1,6 @@ PORTNAME= abipy DISTVERSION= 0.9.8 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-asap3/Makefile b/science/py-asap3/Makefile index bd7ad5f687d7..421b77a892db 100644 --- a/science/py-asap3/Makefile +++ b/science/py-asap3/Makefile @@ -1,6 +1,6 @@ PORTNAME= asap3 DISTVERSION= 3.12.8 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-asdf-standard/Makefile b/science/py-asdf-standard/Makefile index 9283d803ac3f..b2b41ce32e12 100644 --- a/science/py-asdf-standard/Makefile +++ b/science/py-asdf-standard/Makefile @@ -1,5 +1,5 @@ PORTNAME= asdf-standard -PORTVERSION= 1.3.0 +PORTVERSION= 1.4.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-asdf-standard/distinfo b/science/py-asdf-standard/distinfo index b0cc521e77a1..af5e997fab1e 100644 --- a/science/py-asdf-standard/distinfo +++ b/science/py-asdf-standard/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1750188132 -SHA256 (asdf_standard-1.3.0.tar.gz) = 5958961f399dead2000a78724da37f5aeeb0499a780bbd9ae4fc3ecbe3eaed64 -SIZE (asdf_standard-1.3.0.tar.gz) = 273495 +TIMESTAMP = 1757120808 +SHA256 (asdf_standard-1.4.0.tar.gz) = 0c5f121d0db87cb7780d61a087f392c5104ce208016cfb2a130c9cea912cfddc +SIZE (asdf_standard-1.4.0.tar.gz) = 275426 diff --git a/science/py-asdf/Makefile b/science/py-asdf/Makefile index 3986edee3d15..150580aa2496 100644 --- a/science/py-asdf/Makefile +++ b/science/py-asdf/Makefile @@ -1,5 +1,5 @@ PORTNAME= asdf -PORTVERSION= 4.3.0 +PORTVERSION= 4.5.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-asdf/distinfo b/science/py-asdf/distinfo index f3a2707208d2..cf61646370fe 100644 --- a/science/py-asdf/distinfo +++ b/science/py-asdf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753265788 -SHA256 (asdf-4.3.0.tar.gz) = 961d75fb1f1c4868b4533f885655b7ea9a3f0d257c65b49d728da53fe6df087d -SIZE (asdf-4.3.0.tar.gz) = 897816 +TIMESTAMP = 1757436539 +SHA256 (asdf-4.5.0.tar.gz) = 1f37979263cac53b8f7b078c521fda8aa9a08cd5d2badb9aacec34d6badd2dc1 +SIZE (asdf-4.5.0.tar.gz) = 900039 diff --git a/science/py-ase/Makefile b/science/py-ase/Makefile index 5ac43a3541ee..f3e0a8056fdc 100644 --- a/science/py-ase/Makefile +++ b/science/py-ase/Makefile @@ -1,21 +1,21 @@ PORTNAME= ase -DISTVERSION= 3.23.0 -PORTREVISION= 1 +DISTVERSION= 3.26.0 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Atomic simulation environment -WWW= https://wiki.fysik.dtu.dk/ase/ +WWW= https://ase-lib.org/ \ + https://gitlab.com/ase/ase LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING.LESSER RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.1.0:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=1.1.0:science/py-scipy@${PY_FLAVOR} \ - nwchem:science/nwchem + ${PYTHON_PKGNAMEPREFIX}scipy>=1.1.0:science/py-scipy@${PY_FLAVOR} +# nwchem:science/nwchem TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest-mock>0:devel/py-pytest-mock@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-xdist>=1.30.0:devel/py-pytest-xdist@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}asap3>0:science/py-asap3@${PY_FLAVOR} \ @@ -29,4 +29,6 @@ USE_PYTHON= distutils concurrent autoplist pytest NO_ARCH= yes +# tests as of 3.26.0: 25 failed, 3036 passed, 538 skipped, 5 xfailed, 49 warnings, 10 errors in 2377.98s (0:39:37), see https://gitlab.com/ase/ase/-/issues/1746, https://gitlab.com/ase/ase/-/issues/1747 + .include <bsd.port.mk> diff --git a/science/py-ase/distinfo b/science/py-ase/distinfo index 856920eb9664..eb2ad2c0fbb6 100644 --- a/science/py-ase/distinfo +++ b/science/py-ase/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1720836089 -SHA256 (ase-3.23.0.tar.gz) = 91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae -SIZE (ase-3.23.0.tar.gz) = 2336462 +TIMESTAMP = 1757118068 +SHA256 (ase-3.26.0.tar.gz) = a071a355775b0a8062d23e9266e9d811b19d9f6d9ec5215e8032f7d93dc65075 +SIZE (ase-3.26.0.tar.gz) = 2405567 diff --git a/science/py-ase/files/patch-pyproject.toml b/science/py-ase/files/patch-pyproject.toml new file mode 100644 index 000000000000..f1ffc89d09c4 --- /dev/null +++ b/science/py-ase/files/patch-pyproject.toml @@ -0,0 +1,11 @@ +--- pyproject.toml.orig 2025-09-06 00:22:04 UTC ++++ pyproject.toml +@@ -7,8 +7,6 @@ readme = 'README.rst' + description='Atomic Simulation Environment' + dynamic = ['version'] + readme = 'README.rst' +-license = 'LGPL-2.1-or-later' +-license-files = ['LICENSE'] + maintainers = [{ name = 'ASE Community', email = 'ase-users@listserv.fysik.dtu.dk' }] + classifiers = [ + 'Development Status :: 6 - Mature', diff --git a/science/py-boutdata/Makefile b/science/py-boutdata/Makefile index 472e48f39589..ae4f47733575 100644 --- a/science/py-boutdata/Makefile +++ b/science/py-boutdata/Makefile @@ -1,6 +1,6 @@ PORTNAME= boutdata DISTVERSION= 0.1.10 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science education MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-boututils/Makefile b/science/py-boututils/Makefile index c6a3ec8e7c5b..c03168492951 100644 --- a/science/py-boututils/Makefile +++ b/science/py-boututils/Makefile @@ -1,6 +1,6 @@ PORTNAME= boututils DISTVERSION= 0.1.9 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science education MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-chainer-chemistry/Makefile b/science/py-chainer-chemistry/Makefile index fe6795f67cb8..43b43174b0e8 100644 --- a/science/py-chainer-chemistry/Makefile +++ b/science/py-chainer-chemistry/Makefile @@ -1,6 +1,6 @@ PORTNAME= chainer-chemistry DISTVERSION= 0.7.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science biology # machine-learning MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-chempy/Makefile b/science/py-chempy/Makefile index 1d24deab4e11..f8038dcc66d8 100644 --- a/science/py-chempy/Makefile +++ b/science/py-chempy/Makefile @@ -1,6 +1,6 @@ PORTNAME= chempy DISTVERSION= 0.9.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-aqt/Makefile b/science/py-cirq-aqt/Makefile index 1092c6dc5212..e283bf48ecdf 100644 --- a/science/py-cirq-aqt/Makefile +++ b/science/py-cirq-aqt/Makefile @@ -1,6 +1,7 @@ PORTNAME= cirq-aqt DISTVERSIONPREFIX= v DISTVERSION= 1.5.0 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-core/Makefile b/science/py-cirq-core/Makefile index e44380d38e2e..61e40b03c471 100644 --- a/science/py-cirq-core/Makefile +++ b/science/py-cirq-core/Makefile @@ -1,6 +1,7 @@ PORTNAME= cirq-core DISTVERSIONPREFIX= v DISTVERSION= 1.5.0 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-ionq/Makefile b/science/py-cirq-ionq/Makefile index 44ea65f06987..ea3fc7ffc5c6 100644 --- a/science/py-cirq-ionq/Makefile +++ b/science/py-cirq-ionq/Makefile @@ -1,6 +1,7 @@ PORTNAME= cirq-ionq DISTVERSIONPREFIX= v DISTVERSION= 1.5.0 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-pasqal/Makefile b/science/py-cirq-pasqal/Makefile index 2c7c3405af84..c279a6440d3f 100644 --- a/science/py-cirq-pasqal/Makefile +++ b/science/py-cirq-pasqal/Makefile @@ -1,6 +1,7 @@ PORTNAME= cirq-pasqal DISTVERSIONPREFIX= v DISTVERSION= 1.5.0 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cirq-rigetti/Makefile b/science/py-cirq-rigetti/Makefile index e63bae3bff48..9f32d20ceff5 100644 --- a/science/py-cirq-rigetti/Makefile +++ b/science/py-cirq-rigetti/Makefile @@ -1,6 +1,7 @@ PORTNAME= cirq-rigetti DISTVERSIONPREFIX= v DISTVERSION= 1.5.0 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-dimod/Makefile b/science/py-dimod/Makefile index 74fe1a102445..7d5302b9ef4f 100644 --- a/science/py-dimod/Makefile +++ b/science/py-dimod/Makefile @@ -1,5 +1,5 @@ PORTNAME= dimod -DISTVERSION= 0.12.20 +DISTVERSION= 0.12.21 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -27,6 +27,6 @@ TEST_WRKSRC= ${WRKSRC}/tests post-install: @${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME} -name "*${PYTHON_TAG}.so" | ${XARGS} ${STRIP_CMD} -# tests as of 0.12.20: Ran 2913 tests in 34.742s +# tests as of 0.12.21: Ran 2914 tests in 35.706s .include <bsd.port.mk> diff --git a/science/py-dimod/distinfo b/science/py-dimod/distinfo index e0aa99e8e9ee..b3ff37953dd7 100644 --- a/science/py-dimod/distinfo +++ b/science/py-dimod/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742619329 -SHA256 (dwavesystems-dimod-0.12.20_GH0.tar.gz) = 33c06ca8a9f0ab9be5edc3ef2ea065c908fa1e3847c20a20598b1bc1674eafa6 -SIZE (dwavesystems-dimod-0.12.20_GH0.tar.gz) = 582646 +TIMESTAMP = 1758994821 +SHA256 (dwavesystems-dimod-0.12.21_GH0.tar.gz) = c7639f66a4270cc49ee2933b20ddca203e9b0e908b75ba1182fc2ff40e85f7ab +SIZE (dwavesystems-dimod-0.12.21_GH0.tar.gz) = 582916 diff --git a/science/py-dwave-cloud-client/Makefile b/science/py-dwave-cloud-client/Makefile index 97095c32e14d..6a79a590dca2 100644 --- a/science/py-dwave-cloud-client/Makefile +++ b/science/py-dwave-cloud-client/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-cloud-client -DISTVERSION= 0.12.0 -PORTREVISION= 1 +DISTVERSION= 0.14.0 CATEGORIES= science python www # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,19 +11,21 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}authlib>=1.2:security/py-authlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}click>=7:devel/py-click@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}click>=7.0:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}python-dateutil>=2.7:devel/py-python-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}diskcache>=5.2.1:devel/py-diskcache@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.9:science/py-dwave-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}homebase>=1.0:devel/py-homebase@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}http-sf>=1.0.4:www/py-http-sf@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}importlib-metadata>=5.0.0:devel/py-importlib-metadata@${PY_FLAVOR} \ ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}orjson>=3.10:devel/py-orjson@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>=19:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plucky>=0.4.3:devel/py-plucky@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pydantic2>=2:devel/py-pydantic2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.25:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.5.0:devel/py-typing-extensions@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}urllib3>=1.26,1<3.0,1:net/py-urllib3@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}urllib3>=1.26:net/py-urllib3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}werkzeug>=2.2:www/py-werkzeug@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} diff --git a/science/py-dwave-cloud-client/distinfo b/science/py-dwave-cloud-client/distinfo index b26ca956e0e1..b69fa4d5c43d 100644 --- a/science/py-dwave-cloud-client/distinfo +++ b/science/py-dwave-cloud-client/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721011778 -SHA256 (dwavesystems-dwave-cloud-client-0.12.0_GH0.tar.gz) = 392a65fdeead193bd5e018b408a1379259297950e23b5706f44ab14afd0a3796 -SIZE (dwavesystems-dwave-cloud-client-0.12.0_GH0.tar.gz) = 215318 +TIMESTAMP = 1759002074 +SHA256 (dwavesystems-dwave-cloud-client-0.14.0_GH0.tar.gz) = 1bb21f5c65f598b6aefff4bc1dfafc698572428501d60267b6f5ea19e4e23614 +SIZE (dwavesystems-dwave-cloud-client-0.14.0_GH0.tar.gz) = 257192 diff --git a/science/py-dwave-gate/Makefile b/science/py-dwave-gate/Makefile new file mode 100644 index 000000000000..cd726d2113cb --- /dev/null +++ b/science/py-dwave-gate/Makefile @@ -0,0 +1,25 @@ +PORTNAME= dwave-gate +DISTVERSION= 0.3.4 +CATEGORIES= science python # quantum-computing +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= DWave: Gate model library +WWW= https://github.com/dwavesystems/dwave-gate + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} +RUN_DEPENDS= ${PYNUMPY} + +USES= python +USE_PYTHON= pep517 cython3 autoplist pytest + +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} + +.include <bsd.port.mk> diff --git a/science/py-dwave-gate/distinfo b/science/py-dwave-gate/distinfo new file mode 100644 index 000000000000..aeb63b7147d2 --- /dev/null +++ b/science/py-dwave-gate/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1758999333 +SHA256 (dwave_gate-0.3.4.tar.gz) = 17e193da453724c427448e3d7beeb8260c804404ac0ab43ed2d0abcbb0d55b5e +SIZE (dwave_gate-0.3.4.tar.gz) = 367210 diff --git a/science/py-dwave-gate/files/example.py b/science/py-dwave-gate/files/example.py new file mode 100644 index 000000000000..1148e23e9b0a --- /dev/null +++ b/science/py-dwave-gate/files/example.py @@ -0,0 +1,3 @@ +from tabu import TabuSampler +response = TabuSampler().sample_ising({'a': -0.5, 'b': 1.0}, {('a', 'b'): -1}) +print(response) diff --git a/science/py-dwave-gate/files/patch-pyproject.toml b/science/py-dwave-gate/files/patch-pyproject.toml new file mode 100644 index 000000000000..02f8f28f6143 --- /dev/null +++ b/science/py-dwave-gate/files/patch-pyproject.toml @@ -0,0 +1,11 @@ +--- pyproject.toml.orig 2025-09-27 18:57:44 UTC ++++ pyproject.toml +@@ -3,7 +3,7 @@ requires = [ + "setuptools>=46.4.0", # PEP-420 support, PEP-517/518 support + "wheel>=0.30.0", # limited python api support + "cython~=3.0", +- "numpy~=2.0", ++ "numpy", + ] + build-backend = "setuptools.build_meta" + diff --git a/science/py-dwave-gate/pkg-descr b/science/py-dwave-gate/pkg-descr new file mode 100644 index 000000000000..929fb4be2268 --- /dev/null +++ b/science/py-dwave-gate/pkg-descr @@ -0,0 +1,2 @@ +dwave-gate is a software package for constructing, modifying and running quantum +circuits on the provided state-vector simulator. diff --git a/science/py-dwave-greedy/Makefile b/science/py-dwave-greedy/Makefile index da45962c8a45..9aa61e5b3d74 100644 --- a/science/py-dwave-greedy/Makefile +++ b/science/py-dwave-greedy/Makefile @@ -1,6 +1,6 @@ PORTNAME= dwave-greedy DISTVERSION= 0.3.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-dwave-hybrid/Makefile b/science/py-dwave-hybrid/Makefile index 4d0b1cbdbe67..e4f3e04da77e 100644 --- a/science/py-dwave-hybrid/Makefile +++ b/science/py-dwave-hybrid/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-hybrid -DISTVERSION= 0.6.11 -PORTREVISION= 1 +DISTVERSION= 0.6.14 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,17 +11,15 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>5:devel/py-click@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dimod>=0.10.13:science/py-dimod@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.2:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.10.6:science/py-dwave-cloud-client@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-greedy>=0.1.0:science/py-dwave-greedy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.8:science/py-dwave-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-neal>=0.5.4:science/py-dwave-neal@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>0:science/py-dwave-preprocessing@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.13.0:science/py-dwave-system@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-tabu>=0.2.0:science/py-dwave-tabu@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.5.4:science/py-dwave-preprocessing@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.0.0:science/py-dwave-samplers@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.16.0:science/py-dwave-system@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.7:math/py-minorminer@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}minorminer>=0.1.7:math/py-minorminer@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plucky>=0.4.3:devel/py-plucky@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} diff --git a/science/py-dwave-hybrid/distinfo b/science/py-dwave-hybrid/distinfo index 28edf5d6a7c0..3ca4e02ba017 100644 --- a/science/py-dwave-hybrid/distinfo +++ b/science/py-dwave-hybrid/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1709582741 -SHA256 (dwavesystems-dwave-hybrid-0.6.11_GH0.tar.gz) = 3f0bff143bd43039c81108b5a78bcd91e306ce98313107915e391b8b4266ac97 -SIZE (dwavesystems-dwave-hybrid-0.6.11_GH0.tar.gz) = 21334393 +TIMESTAMP = 1758900792 +SHA256 (dwavesystems-dwave-hybrid-0.6.14_GH0.tar.gz) = 48592f46150bc863de6fd50a2a80589f1184e54dc0f4a310f613340108b13f0d +SIZE (dwavesystems-dwave-hybrid-0.6.14_GH0.tar.gz) = 21327352 diff --git a/science/py-dwave-inspector/Makefile b/science/py-dwave-inspector/Makefile index bebfb624a90a..b583ab95b573 100644 --- a/science/py-dwave-inspector/Makefile +++ b/science/py-dwave-inspector/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-inspector -DISTVERSION= 0.5.1 -PORTREVISION= 1 +DISTVERSION= 0.5.5 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,7 +11,7 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.10.0:science/py-dimod@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.11.0:science/py-dwave-cloud-client@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.13.0:science/py-dwave-cloud-client@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.3.0:science/py-dwave-system@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}flask>=2.2:www/py-flask@${PY_FLAVOR} \ ${PYNUMPY} \ diff --git a/science/py-dwave-inspector/distinfo b/science/py-dwave-inspector/distinfo index 46a2556a8d09..fe7ec0bf2296 100644 --- a/science/py-dwave-inspector/distinfo +++ b/science/py-dwave-inspector/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1725082475 -SHA256 (dwavesystems-dwave-inspector-0.5.1_GH0.tar.gz) = cfc67472572e4dffd3ab40bae9b000a0efbf4f147a477ee7f2df39c4c11f7b9f -SIZE (dwavesystems-dwave-inspector-0.5.1_GH0.tar.gz) = 1551148 +TIMESTAMP = 1758901017 +SHA256 (dwavesystems-dwave-inspector-0.5.5_GH0.tar.gz) = 9426ba5515079b7d704c1ae951f602ef67119add3ab2f811a1e1901a40f3ea6b +SIZE (dwavesystems-dwave-inspector-0.5.5_GH0.tar.gz) = 1474496 diff --git a/science/py-dwave-neal/Makefile b/science/py-dwave-neal/Makefile index 7374bd2fd4cf..1f22837bcbb3 100644 --- a/science/py-dwave-neal/Makefile +++ b/science/py-dwave-neal/Makefile @@ -1,6 +1,6 @@ PORTNAME= dwave-neal DISTVERSION= 0.6.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python # quantum-computing MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-dwave-networkx/Makefile b/science/py-dwave-networkx/Makefile index d58f9f11857b..ea480887bd30 100644 --- a/science/py-dwave-networkx/Makefile +++ b/science/py-dwave-networkx/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-networkx -DISTVERSION= 0.8.15 -PORTREVISION= 1 +DISTVERSION= 0.8.18 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} @@ -13,7 +12,8 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.0:science/py-dimod@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} \ + ${PYNUMPY} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}parameterized>0:devel/py-parameterized@${PY_FLAVOR} \ diff --git a/science/py-dwave-networkx/distinfo b/science/py-dwave-networkx/distinfo index 9bf974558485..9ac31a859a25 100644 --- a/science/py-dwave-networkx/distinfo +++ b/science/py-dwave-networkx/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1718437530 -SHA256 (dwavesystems-dwave-networkx-0.8.15_GH0.tar.gz) = 101eb8179c27fc3c95f7759922c295004063b06de673a17a3f7dae15c83be806 -SIZE (dwavesystems-dwave-networkx-0.8.15_GH0.tar.gz) = 1414577 +TIMESTAMP = 1759003300 +SHA256 (dwavesystems-dwave-networkx-0.8.18_GH0.tar.gz) = c136b4c30dbb1f4d7baa435627fa1043dfa0faca44ff4a2c7a04f5e9ed69ad99 +SIZE (dwavesystems-dwave-networkx-0.8.18_GH0.tar.gz) = 1416959 diff --git a/science/py-dwave-ocean-sdk/Makefile b/science/py-dwave-ocean-sdk/Makefile index 285638c3a620..c7dd59b5b1bb 100644 --- a/science/py-dwave-ocean-sdk/Makefile +++ b/science/py-dwave-ocean-sdk/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-ocean-sdk -DISTVERSION= 6.9.0 -PORTREVISION= 1 +DISTVERSION= 9.0.0 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,26 +10,26 @@ WWW= https://docs.ocean.dwavesys.com/en/stable/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE -PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.14:science/py-dimod@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.11.3:science/py-dwave-cloud-client@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-greedy>=0.3.0:science/py-dwave-greedy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-hybrid>=0.6.11:science/py-dwave-hybrid@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-inspector>=0.4.4:science/py-dwave-inspector@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-neal>=0.6.0:science/py-dwave-neal@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.14:science/py-dwave-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.6.5:science/py-dwave-preprocessing@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.2.0:science/py-dwave-samplers@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.23.0:science/py-dwave-system@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-tabu>=0.5.0:science/py-dwave-tabu@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwavebinarycsp>=0.3.0:science/py-dwavebinarycsp@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.13:math/py-minorminer@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}penaltymodel>=1.1.0:science/py-penaltymodel@${PY_FLAVOR} +PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.21:science/py-dimod@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.14.0:science/py-dwave-cloud-client@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-gate>=0.3.4:science/py-dwave-gate@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-hybrid>=0.6.14:science/py-dwave-hybrid@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-inspector>=0.5.5:science/py-dwave-inspector@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.18:science/py-dwave-networkx@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-optimization>=0.6.4:science/py-dwave-optimization@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.6.10:science/py-dwave-preprocessing@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.6.0:science/py-dwave-samplers@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.33.0:science/py-dwave-system@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.19:math/py-minorminer@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}penaltymodel>=1.3.0:science/py-penaltymodel@${PY_FLAVOR} #${PYTHON_PKGNAMEPREFIX}pyqubo>=1.4.0:science/py-pyqubo@${PY_FLAVOR} # exclude pyqubo until it supports py312 -BUILD_DEPENDS= ${PY_DEPENDS} +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PY_DEPENDS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} USES= python -USE_PYTHON= distutils autoplist unittest +USE_PYTHON= pep517 autoplist unittest USE_GITHUB= yes GH_ACCOUNT= dwavesystems diff --git a/science/py-dwave-ocean-sdk/distinfo b/science/py-dwave-ocean-sdk/distinfo index cbd8a9aa1a24..c9e61347cfb0 100644 --- a/science/py-dwave-ocean-sdk/distinfo +++ b/science/py-dwave-ocean-sdk/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1709591130 -SHA256 (dwavesystems-dwave-ocean-sdk-6.9.0_GH0.tar.gz) = 369170b1f92248f97621098f19647649bec14f1b407fa8861d0ef0407d6f6fdc -SIZE (dwavesystems-dwave-ocean-sdk-6.9.0_GH0.tar.gz) = 12689356 +TIMESTAMP = 1758900842 +SHA256 (dwavesystems-dwave-ocean-sdk-9.0.0_GH0.tar.gz) = 84af7387adf9f9fa63f506daa00b381450542d6bb0967d5186d66e45bdda303c +SIZE (dwavesystems-dwave-ocean-sdk-9.0.0_GH0.tar.gz) = 43904011 diff --git a/science/py-dwave-optimization/Makefile b/science/py-dwave-optimization/Makefile index 9afc4936d88d..116210d8c460 100644 --- a/science/py-dwave-optimization/Makefile +++ b/science/py-dwave-optimization/Makefile @@ -1,8 +1,9 @@ PORTNAME= dwave-optimization -DISTVERSION= 0.1.0 +DISTVERSION= 0.6.6 CATEGORIES= science python # quantum-computing MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= DWave: Nonlinear models for industrial optimization problems @@ -12,31 +13,19 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}setuptools-dso>=2.10:devel/py-setuptools-dso@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}reno>=4.1.0:textproc/py-reno@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}meson-python>=0.18.0:devel/meson-python@${PY_FLAVOR} +RUN_DEPENDS= ${PYNUMPY} USES= python -USE_PYTHON= autoplist cython3 pep517 - -POST_PLIST= fix-plist +USE_PYTHON= pep517 cython3 autoplist pytest post-install: # strip binaries @${STRIP_CMD} \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/_model${PYTHON_TAG}.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/_utilities${PYTHON_TAG}.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/libdwave-optimization.so \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/model${PYTHON_TAG}.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/states${PYTHON_TAG}.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/symbols${PYTHON_TAG}.so - # remove conflicting __init__.py, see https://github.com/dwavesystems/dwave-system/issues/462 - @${RM} -r \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__init__.py \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__pycache__ - -fix-plist: - @${REINPLACE_CMD} -e " \ - s|.*dwave/__init__\.py||; \ - s|.*dwave/__pycache__/.*|| \ - " ${TMPPLIST} .include <bsd.port.mk> diff --git a/science/py-dwave-optimization/distinfo b/science/py-dwave-optimization/distinfo index f0f7d3875377..02983f9df619 100644 --- a/science/py-dwave-optimization/distinfo +++ b/science/py-dwave-optimization/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721017559 -SHA256 (dwave-optimization-0.1.0.tar.gz) = 585b69026d26e9f99b9c8552a68dae794960cd94582ccdf973d2eb30a6303b9e -SIZE (dwave-optimization-0.1.0.tar.gz) = 725660 +TIMESTAMP = 1759005736 +SHA256 (dwave_optimization-0.6.6.tar.gz) = f50fd9cff71b259487212f88c793348e26ebe785e6c2a50ec2b62486c2060ee4 +SIZE (dwave_optimization-0.6.6.tar.gz) = 341092 diff --git a/science/py-dwave-optimization/files/patch-pyproject.toml b/science/py-dwave-optimization/files/patch-pyproject.toml index 266f645a6998..3ee77e1a76e5 100644 --- a/science/py-dwave-optimization/files/patch-pyproject.toml +++ b/science/py-dwave-optimization/files/patch-pyproject.toml @@ -1,13 +1,11 @@ ---- pyproject.toml.orig 2024-07-15 16:16:29 UTC +--- pyproject.toml.orig 2025-09-27 21:16:33 UTC +++ pyproject.toml -@@ -1,8 +1,8 @@ requires = [ +@@ -1,7 +1,7 @@ requires = [ [build-system] requires = [ -- "cython==3.0.8", -+ "cython>=3.0.8", - 'numpy==1.19.0;python_version<"3.9"', # C API for numpy.random -- 'oldest-supported-numpy;python_version>="3.9"', -+ 'numpy;python_version>="3.9"', - "setuptools>=46.4.0", - "setuptools_dso>=2.10,<3.0;platform_system != 'Windows'", # On Windows we don't distribute a dynamic library - "wheel>=0.30.0", + "cython~=3.1.0", +- "meson-python~=0.18.0", ++ "meson-python", + ] + build-backend = 'mesonpy' + diff --git a/science/py-dwave-preprocessing/Makefile b/science/py-dwave-preprocessing/Makefile index a7fc27a649bb..c9a03c027f18 100644 --- a/science/py-dwave-preprocessing/Makefile +++ b/science/py-dwave-preprocessing/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-preprocessing -DISTVERSION= 0.6.6 -PORTREVISION= 1 +DISTVERSION= 0.6.10 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,7 +11,7 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.6:science/py-dimod@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.6:science/py-dimod@${PY_FLAVOR} \ +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.20:science/py-dimod@${PY_FLAVOR} \ ${PYNUMPY} USES= localbase:ldflags python diff --git a/science/py-dwave-preprocessing/distinfo b/science/py-dwave-preprocessing/distinfo index da8873cbb9b2..281af1f3ac64 100644 --- a/science/py-dwave-preprocessing/distinfo +++ b/science/py-dwave-preprocessing/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721009063 -SHA256 (dwavesystems-dwave-preprocessing-0.6.6_GH0.tar.gz) = 3ffbf8694997f2527380e6080f7f6fa7501a85927ca98ace87672e9b0d251438 -SIZE (dwavesystems-dwave-preprocessing-0.6.6_GH0.tar.gz) = 126646 +TIMESTAMP = 1758901068 +SHA256 (dwavesystems-dwave-preprocessing-0.6.10_GH0.tar.gz) = 95c1f7a0508c11fe17d37461cf27d267592dbc4a5233194fe5ac645539ab81f0 +SIZE (dwavesystems-dwave-preprocessing-0.6.10_GH0.tar.gz) = 128447 diff --git a/science/py-dwave-samplers/Makefile b/science/py-dwave-samplers/Makefile index e7ec7a9d766c..26518e9c6501 100644 --- a/science/py-dwave-samplers/Makefile +++ b/science/py-dwave-samplers/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-samplers -DISTVERSION= 1.3.0 -PORTREVISION= 1 +DISTVERSION= 1.6.0 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,7 +11,7 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.13:science/py-dimod@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>=2.6.3:math/py-networkx@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}reno>0:textproc/py-reno@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} @@ -20,7 +19,7 @@ RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}parameterized>0:devel/py-parameterized@${PY_FLAVOR} USES= python -USE_PYTHON= cython3 distutils unittest # 2 tests fail, see https://github.com/dwavesystems/dwave-samplers/issues/66 +USE_PYTHON= cython3 distutils autoplist unittest # 2 tests fail, see https://github.com/dwavesystems/dwave-samplers/issues/66 USE_GITHUB= yes GH_ACCOUNT= dwavesystems @@ -46,4 +45,6 @@ post-install: post-test: @${SETENV} ${TEST_ENV} ${PYTHON_CMD} ${FILESDIR}/example.py +# tests as of 1.6.0: Ran 522 tests in 102.085s + .include <bsd.port.mk> diff --git a/science/py-dwave-samplers/distinfo b/science/py-dwave-samplers/distinfo index 17abea740f3f..cc7fd1115361 100644 --- a/science/py-dwave-samplers/distinfo +++ b/science/py-dwave-samplers/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721009758 -SHA256 (dwavesystems-dwave-samplers-1.3.0_GH0.tar.gz) = ed4b3a4e3da76c35dfb3d70e4bb45fe3c0b5eb277115d41894381cf8c9cd5999 -SIZE (dwavesystems-dwave-samplers-1.3.0_GH0.tar.gz) = 147340 +TIMESTAMP = 1758900891 +SHA256 (dwavesystems-dwave-samplers-1.6.0_GH0.tar.gz) = 4d16e1262e8a93adbf27d8a2bcab48f5f53927396c751cec0ecc1b38a7a3c269 +SIZE (dwavesystems-dwave-samplers-1.6.0_GH0.tar.gz) = 193371 diff --git a/science/py-dwave-samplers/pkg-plist b/science/py-dwave-samplers/pkg-plist deleted file mode 100644 index d9aa3ff38972..000000000000 --- a/science/py-dwave-samplers/pkg-plist +++ /dev/null @@ -1,105 +0,0 @@ -%%PYTHON_SITELIBDIR%%/dwave/samplers/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/composite%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/composite%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/composite.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/decl.pxd -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent%%PYTHON_TAG%%.so -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent.pyx -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/sampler.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/src/descent.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/src/descent.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/planar%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/planar%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/util%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/util%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/planar.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/sampler.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/util.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__pycache__/sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__pycache__/sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/cyrandom.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/cyrandom%%PYTHON_TAG%%.so -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/cyrandom.pyx -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/sampler.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/sa/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/sa/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/sa/__pycache__/__init__%%PYTHON_TAG%%.pyc 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-%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/utils%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/utils%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/sampler.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/bqp.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/bqp.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/common.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/tabu_search.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/tabu_search.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/tabu_utils.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/tabu_utils.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/tabu.pxd -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/tabu_search.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/tabu_search%%PYTHON_TAG%%.so -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/tabu_search.pyx -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/utils.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/samplers%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/__pycache__/samplers%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/orang.pxd -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/sample.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/sample%%PYTHON_TAG%%.so -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/sample.pyx -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/samplers.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve%%PYTHON_TAG%%.so -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve.pyx -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/base.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/buckettree.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/combine.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/exception.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/graph.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/marginalizer.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/merger.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/operations/count.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/operations/dummy.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/operations/logsumprod.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/operations/min.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/orang.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/sample.hpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/solve.hpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/table.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/task.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/treedecomp.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/utils.hpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/varorder.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities%%PYTHON_TAG%%.so -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities.pyx diff --git a/science/py-dwave-system/Makefile b/science/py-dwave-system/Makefile index 45b9e9b43d56..0039e8028bfb 100644 --- a/science/py-dwave-system/Makefile +++ b/science/py-dwave-system/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-system -DISTVERSION= 1.25.0 -PORTREVISION= 1 +DISTVERSION= 1.33.0 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,23 +10,21 @@ WWW= https://github.com/dwavesystems/dwave-system LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE -PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.13:science/py-dimod@${PY_FLAVOR} \ +PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.20:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.12.0:science/py-dwave-cloud-client@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-greedy>=0.2.5:science/py-dwave-greedy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.10:science/py-dwave-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-optimization>=0.1.0:science/py-dwave-optimization@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-optimization>=0.6.6:science/py-dwave-optimization@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.5.0:science/py-dwave-preprocessing@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.0.0:science/py-dwave-samplers@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}homebase>=1.0.0:devel/py-homebase@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.8:math/py-minorminer@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>=2.8.8:math/py-networkx@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.19:math/py-minorminer@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.3:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python -USE_PYTHON= distutils unittest # 1 test fails because the closed source dwave.drivers optional dependency is missing +USE_PYTHON= distutils unittest autoplist # 1 test fails because the closed source dwave.drivers optional dependency is missing USE_GITHUB= yes GH_ACCOUNT= dwavesystems diff --git a/science/py-dwave-system/distinfo b/science/py-dwave-system/distinfo index 10c14a5f509b..9024afa5cadc 100644 --- a/science/py-dwave-system/distinfo +++ b/science/py-dwave-system/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721015341 -SHA256 (dwavesystems-dwave-system-1.25.0_GH0.tar.gz) = ab33c625f588f7197ce82bcee634305717afe537ba4a8662e41ffc659dc8e775 -SIZE (dwavesystems-dwave-system-1.25.0_GH0.tar.gz) = 685604 +TIMESTAMP = 1759022035 +SHA256 (dwavesystems-dwave-system-1.33.0_GH0.tar.gz) = e34f9df6d48140ac2a3f8e73457991b783ae47f34d8fb41478ac5b6540734920 +SIZE (dwavesystems-dwave-system-1.33.0_GH0.tar.gz) = 707773 diff --git a/science/py-dwave-system/pkg-plist b/science/py-dwave-system/pkg-plist deleted file mode 100644 index b55d9993ee26..000000000000 --- a/science/py-dwave-system/pkg-plist +++ /dev/null @@ -1,108 +0,0 @@ -%%PYTHON_SITELIBDIR%%/dwave/embedding/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chain_breaks%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chain_breaks%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chain_strength%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chain_strength%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chimera%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chimera%%PYTHON_TAG%%.pyc 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-%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/cache_manager%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/database_manager%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/database_manager%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/schema%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/schema%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/cache_manager.py -%%PYTHON_SITELIBDIR%%/dwave/system/cache/database_manager.py -%%PYTHON_SITELIBDIR%%/dwave/system/cache/schema.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/cutoffcomposite%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/cutoffcomposite%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/embedding%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/embedding%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/reversecomposite%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/reversecomposite%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/tiling%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/tiling%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/virtual_graph%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/virtual_graph%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/cutoffcomposite.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/embedding.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/reversecomposite.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/tiling.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/virtual_graph.py -%%PYTHON_SITELIBDIR%%/dwave/system/coupling_groups.py -%%PYTHON_SITELIBDIR%%/dwave/system/exceptions.py -%%PYTHON_SITELIBDIR%%/dwave/system/flux_bias_offsets.py -%%PYTHON_SITELIBDIR%%/dwave/system/package_info.py -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/clique%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/clique%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/dwave_sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/dwave_sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/leap_hybrid_sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/leap_hybrid_sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/clique.py -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/dwave_sampler.py -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/leap_hybrid_sampler.py -%%PYTHON_SITELIBDIR%%/dwave/system/schedules.py -%%PYTHON_SITELIBDIR%%/dwave/system/temperatures.py -%%PYTHON_SITELIBDIR%%/dwave/system/testing.py -%%PYTHON_SITELIBDIR%%/dwave/system/utilities.py -%%PYTHON_SITELIBDIR%%/dwave/system/warnings.py diff --git a/science/py-dwave-tabu/Makefile b/science/py-dwave-tabu/Makefile index c9174437cfe8..fa6651f47ae6 100644 --- a/science/py-dwave-tabu/Makefile +++ b/science/py-dwave-tabu/Makefile @@ -1,6 +1,6 @@ PORTNAME= dwave-tabu DISTVERSION= 0.5.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python # quantum-computing MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-dwavebinarycsp/Makefile b/science/py-dwavebinarycsp/Makefile index 67c4982371de..d32f01053748 100644 --- a/science/py-dwavebinarycsp/Makefile +++ b/science/py-dwavebinarycsp/Makefile @@ -1,6 +1,6 @@ PORTNAME= dwavebinarycsp DISTVERSION= 0.3.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-earthpy/Makefile b/science/py-earthpy/Makefile index 25b1bd5d131a..8717fb174349 100644 --- a/science/py-earthpy/Makefile +++ b/science/py-earthpy/Makefile @@ -1,6 +1,6 @@ PORTNAME= earthpy PORTVERSION= 0.9.4 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science geography python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-emmet-core/Makefile b/science/py-emmet-core/Makefile index 5a90f8182102..6ae7bcd00050 100644 --- a/science/py-emmet-core/Makefile +++ b/science/py-emmet-core/Makefile @@ -14,7 +14,7 @@ LICENSE= BSD3CLAUSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools_scm7>0:devel/py-setuptools_scm7@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}monty>=2021.3:devel/py-monty@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pybtex>=0.24:textproc/py-pybtex@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pydantic>=1.10.2:devel/py-pydantic@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pydantic2>=1.10.2:devel/py-pydantic2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spglib>=2.0.1:science/py-spglib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}typing-extensions>=3.7<5.0:devel/py-typing-extensions@${PY_FLAVOR} #RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}pymatgen>=2023.5.8:science/py-pymatgen@${PY_FLAVOR} # break dependency circle: pymatgen -> mp-api -> emmet-core, see https://github.com/materialsproject/api/issues/825 diff --git a/science/py-geometric/Makefile b/science/py-geometric/Makefile index 3dc948298d35..186198e8badf 100644 --- a/science/py-geometric/Makefile +++ b/science/py-geometric/Makefile @@ -1,6 +1,6 @@ PORTNAME= geometric DISTVERSION= 1.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-gpaw/Makefile b/science/py-gpaw/Makefile index 7adec17183e7..d849a0d2021b 100644 --- a/science/py-gpaw/Makefile +++ b/science/py-gpaw/Makefile @@ -1,6 +1,6 @@ PORTNAME= gpaw DISTVERSION= 24.6.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-hiphive/Makefile b/science/py-hiphive/Makefile index def7bb28a62c..f81c2e5085a0 100644 --- a/science/py-hiphive/Makefile +++ b/science/py-hiphive/Makefile @@ -1,6 +1,6 @@ PORTNAME= hiphive DISTVERSION= 1.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-icet/Makefile b/science/py-icet/Makefile index 44a8eb096d13..2a01864fa3b9 100644 --- a/science/py-icet/Makefile +++ b/science/py-icet/Makefile @@ -1,5 +1,5 @@ PORTNAME= icet -DISTVERSION= 3.0 +DISTVERSION= 3.1 CATEGORIES= science # chemistry, physics #MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -28,7 +28,7 @@ USE_PYTHON= pep517 autoplist pytest USE_GITLAB= yes GL_ACCOUNT= materials-modeling -GL_TAGNAME= 769b5db248baa5146bdb294e963e061cf2dfd228 +GL_TAGNAME= 3.1 TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} diff --git a/science/py-icet/distinfo b/science/py-icet/distinfo index bcff29135073..27b719b500bf 100644 --- a/science/py-icet/distinfo +++ b/science/py-icet/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737766451 -SHA256 (materials-modeling-icet-769b5db248baa5146bdb294e963e061cf2dfd228_GL0.tar.gz) = bec8c2a34bc8343e7e075460964c997228a1a8fe1a12ba449503c7e80b2b653a -SIZE (materials-modeling-icet-769b5db248baa5146bdb294e963e061cf2dfd228_GL0.tar.gz) = 3928095 +TIMESTAMP = 1758905344 +SHA256 (icet-3.1.tar.bz2) = b942fa3001fd53095cca9e19f4fdcea7c3716a69cf0bb2f4e735c8b997f1de5b +SIZE (icet-3.1.tar.bz2) = 3740838 diff --git a/science/py-icet/files/patch-pyproject.toml b/science/py-icet/files/patch-pyproject.toml new file mode 100644 index 000000000000..f1953b314896 --- /dev/null +++ b/science/py-icet/files/patch-pyproject.toml @@ -0,0 +1,10 @@ +--- pyproject.toml.orig 2025-09-28 03:59:57 UTC ++++ pyproject.toml +@@ -1,6 +1,6 @@ requires = [ + [build-system] + requires = [ +- "setuptools>=77.0", ++ "setuptools", + "wheel", + "pybind11>=2.10", + ] diff --git a/science/py-inequality/Makefile b/science/py-inequality/Makefile index 76fde967a827..cc8f4eea51b7 100644 --- a/science/py-inequality/Makefile +++ b/science/py-inequality/Makefile @@ -1,5 +1,6 @@ PORTNAME= inequality PORTVERSION= 1.1.1 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-kimpy/Makefile b/science/py-kimpy/Makefile index 442b5c9a82d3..0c537ae18c1e 100644 --- a/science/py-kimpy/Makefile +++ b/science/py-kimpy/Makefile @@ -1,6 +1,5 @@ PORTNAME= kimpy -DISTVERSION= 2.1.1 -PORTREVISION= 1 +DISTVERSION= 2.1.3 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -19,7 +18,11 @@ RUN_DEPENDS= ${PYNUMPY} USES= compiler:c++20-lang pkgconfig python USE_PYTHON= distutils autoplist pytest # tests fail to run, see https://github.com/openkim/kimpy/issues/16 +TEST_WRKSRC= ${WRKSRC}/tests + post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/kimpy/*${PYTHON_TAG}.so +# tests as of 2.1.3: 21 passed in 2.91s + .include <bsd.port.mk> diff --git a/science/py-kimpy/distinfo b/science/py-kimpy/distinfo index e7d3c6deaef7..6d692faf3795 100644 --- a/science/py-kimpy/distinfo +++ b/science/py-kimpy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1726458544 -SHA256 (kimpy-2.1.1.tar.gz) = 3ab9ab64179cdf8b7d41704330d12bbb78461792664354e9e9144098709bc636 -SIZE (kimpy-2.1.1.tar.gz) = 50141 +TIMESTAMP = 1757123909 +SHA256 (kimpy-2.1.3.tar.gz) = 2a4a4455dfc5aeb5b8379a96b7c1e7a3f34bfe6bd3c077e23a3e27b8829c2aed +SIZE (kimpy-2.1.3.tar.gz) = 49856 diff --git a/science/py-kliff/Makefile b/science/py-kliff/Makefile index c5a5995637ee..b346f87c3fbe 100644 --- a/science/py-kliff/Makefile +++ b/science/py-kliff/Makefile @@ -1,5 +1,6 @@ PORTNAME= kliff DISTVERSION= 0.4.4 +PORTREVISION= 1 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-kpLib/Makefile b/science/py-kpLib/Makefile index bc5206c29439..5cb720714515 100644 --- a/science/py-kpLib/Makefile +++ b/science/py-kpLib/Makefile @@ -1,6 +1,6 @@ PORTNAME= kpLib DISTVERSION= 1.1.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-lifelines/Makefile b/science/py-lifelines/Makefile index 57a070d0c9be..7e2307e559b6 100644 --- a/science/py-lifelines/Makefile +++ b/science/py-lifelines/Makefile @@ -1,6 +1,6 @@ PORTNAME= lifelines DISTVERSION= 0.19.5 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-mp-api/Makefile b/science/py-mp-api/Makefile index fb894efd1196..cda39e1cd11d 100644 --- a/science/py-mp-api/Makefile +++ b/science/py-mp-api/Makefile @@ -1,5 +1,6 @@ PORTNAME= mp-api DISTVERSION= 0.34.0 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -20,7 +21,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}boto3>0:www/py-boto3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}monty>=2022.3.12:devel/py-monty@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mpcontribs-client>=5.0.10:science/py-mpcontribs-client@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}msgpack>0:devel/py-msgpack@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pydantic>=1.8.2:devel/py-pydantic@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pydantic2>=1.8.2:devel/py-pydantic2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pymatgen-analysis-alloys>=0.0.3:science/py-pymatgen-analysis-alloys@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pymatgen>=2022.3.7:science/py-pymatgen@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.27.1:www/py-requests@${PY_FLAVOR} \ diff --git a/science/py-mpcontribs-client/Makefile b/science/py-mpcontribs-client/Makefile index 98a049cfe2b2..50a04843eab8 100644 --- a/science/py-mpcontribs-client/Makefile +++ b/science/py-mpcontribs-client/Makefile @@ -1,6 +1,6 @@ PORTNAME= mpcontribs-client DISTVERSION= 5.10.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-mplhep/Makefile b/science/py-mplhep/Makefile index 27fc7bf6b658..d1b5c9b1af24 100644 --- a/science/py-mplhep/Makefile +++ b/science/py-mplhep/Makefile @@ -1,5 +1,6 @@ PORTNAME= mplhep DISTVERSION= 0.3.59 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-obspy/Makefile b/science/py-obspy/Makefile index b0a3b8b4c973..a61d0fd9a229 100644 --- a/science/py-obspy/Makefile +++ b/science/py-obspy/Makefile @@ -1,6 +1,6 @@ PORTNAME= obspy PORTVERSION= 1.4.2 -PORTREVISION= 1 +PORTREVISION= 3 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,7 +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} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>=2.2:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>=2.2:devel/py-lxml@${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-openpiv/Makefile b/science/py-openpiv/Makefile index 66e447b465d5..4243feff9291 100644 --- a/science/py-openpiv/Makefile +++ b/science/py-openpiv/Makefile @@ -1,6 +1,6 @@ PORTNAME= openpiv PORTVERSION= 0.23.8 -PORTREVISION= 3 +PORTREVISION= 4 DISTVERSIONPREFIX= v CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-optking/Makefile b/science/py-optking/Makefile index d1ab10707dfa..8c71b977a3be 100644 --- a/science/py-optking/Makefile +++ b/science/py-optking/Makefile @@ -1,6 +1,6 @@ PORTNAME= optking DISTVERSION= 0.3.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python # chemistry PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-penaltymodel/Makefile b/science/py-penaltymodel/Makefile index 09203698bbcf..a99d122fbb4e 100644 --- a/science/py-penaltymodel/Makefile +++ b/science/py-penaltymodel/Makefile @@ -1,6 +1,5 @@ PORTNAME= penaltymodel -DISTVERSION= 1.1.0 -PORTREVISION= 1 +DISTVERSION= 1.3.0 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,7 +14,6 @@ PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.13:science/py-dimod@${PY_FLAVOR} ${PYTHON_PKGNAMEPREFIX}homebase>=1.0.1:devel/py-homebase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}reno>=3.3.0:textproc/py-reno@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.3:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} diff --git a/science/py-penaltymodel/distinfo b/science/py-penaltymodel/distinfo index f636f3095631..884d08c6d13f 100644 --- a/science/py-penaltymodel/distinfo +++ b/science/py-penaltymodel/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1705599914 -SHA256 (dwavesystems-penaltymodel-1.1.0_GH0.tar.gz) = cdcfeac4b9682fed6118f28459d33acb6c302850e9c2952a413fe17378d8f640 -SIZE (dwavesystems-penaltymodel-1.1.0_GH0.tar.gz) = 38244 +TIMESTAMP = 1759022813 +SHA256 (dwavesystems-penaltymodel-1.3.0_GH0.tar.gz) = bb8874b2ca46c2250e3093abd2e531516b6304556f850ec280be43ec7b18d653 +SIZE (dwavesystems-penaltymodel-1.3.0_GH0.tar.gz) = 36574 diff --git a/science/py-phono3py/Makefile b/science/py-phono3py/Makefile index 44d7932674ed..31ebec85b93d 100644 --- a/science/py-phono3py/Makefile +++ b/science/py-phono3py/Makefile @@ -1,6 +1,6 @@ PORTNAME= phono3py DISTVERSION= 3.9.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile index b298e416ecf5..3ec6ed90d710 100644 --- a/science/py-phonopy/Makefile +++ b/science/py-phonopy/Makefile @@ -1,5 +1,6 @@ PORTNAME= phonopy DISTVERSION= 2.42.0 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pnetcdf/Makefile b/science/py-pnetcdf/Makefile index 3bede6cc5d26..6162f6f155ef 100644 --- a/science/py-pnetcdf/Makefile +++ b/science/py-pnetcdf/Makefile @@ -1,5 +1,6 @@ PORTNAME= pnetcdf PORTVERSION= 1.0.0 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pycsw/Makefile b/science/py-pycsw/Makefile index 0e08e20fb106..0438efb397ae 100644 --- a/science/py-pycsw/Makefile +++ b/science/py-pycsw/Makefile @@ -1,6 +1,6 @@ PORTNAME= pycsw PORTVERSION= 2.6.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -16,7 +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} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${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 df12a82e2163..e5edb487276c 100644 --- a/science/py-pygeometa/Makefile +++ b/science/py-pygeometa/Makefile @@ -1,6 +1,6 @@ PORTNAME= pygeometa PORTVERSION= 0.15.3 -PORTREVISION= 4 +PORTREVISION= 5 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} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${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-pygmo2/Makefile b/science/py-pygmo2/Makefile index a7ed3634ffd4..869cc90d53f7 100644 --- a/science/py-pygmo2/Makefile +++ b/science/py-pygmo2/Makefile @@ -1,7 +1,7 @@ PORTNAME= pygmo2 DISTVERSIONPREFIX= v DISTVERSION= 2.19.7 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science graphics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pymatgen-analysis-alloys/Makefile b/science/py-pymatgen-analysis-alloys/Makefile index 88142b17b01f..3252f214eceb 100644 --- a/science/py-pymatgen-analysis-alloys/Makefile +++ b/science/py-pymatgen-analysis-alloys/Makefile @@ -1,5 +1,6 @@ PORTNAME= pymatgen-analysis-alloys DISTVERSION= 0.0.7 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pymatgen/Makefile b/science/py-pymatgen/Makefile index dc428fc53ede..666ba10e005f 100644 --- a/science/py-pymatgen/Makefile +++ b/science/py-pymatgen/Makefile @@ -1,6 +1,7 @@ PORTNAME= pymatgen DISTVERSIONPREFIX= v DISTVERSION= 2025.6.14 +PORTREVISION= 1 CATEGORIES= science python #MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pyqubo/Makefile b/science/py-pyqubo/Makefile index 86582cb6a231..f7b37bace0fa 100644 --- a/science/py-pyqubo/Makefile +++ b/science/py-pyqubo/Makefile @@ -1,6 +1,6 @@ PORTNAME= pyqubo DISTVERSION= 1.4.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pyteomics/Makefile b/science/py-pyteomics/Makefile index 6ef21f18727d..546b78099722 100644 --- a/science/py-pyteomics/Makefile +++ b/science/py-pyteomics/Makefile @@ -1,6 +1,6 @@ PORTNAME= pyteomics PORTVERSION= 4.7.5 -PORTREVISION= 1 +PORTREVISION= 3 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -31,9 +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= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ +UNIMOD_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlalchemy14>=0:databases/py-sqlalchemy14@${PY_FLAVOR} -XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ +XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} .include <bsd.port.mk> diff --git a/science/py-qcelemental/Makefile b/science/py-qcelemental/Makefile index 5547c73f62a2..b1a5efde166b 100644 --- a/science/py-qcelemental/Makefile +++ b/science/py-qcelemental/Makefile @@ -1,5 +1,6 @@ PORTNAME= qcelemental DISTVERSION= 0.28.0 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-qcengine/Makefile b/science/py-qcengine/Makefile index a868cf47203a..92e077639ffb 100644 --- a/science/py-qcengine/Makefile +++ b/science/py-qcengine/Makefile @@ -1,6 +1,6 @@ PORTNAME= qcengine DISTVERSION= 0.30.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-qiskit/Makefile b/science/py-qiskit/Makefile index c55d7b2e49e3..9e1c3667b27d 100644 --- a/science/py-qiskit/Makefile +++ b/science/py-qiskit/Makefile @@ -1,5 +1,6 @@ PORTNAME= qiskit -DISTVERSION= 2.1.1 +DISTVERSION= 2.1.2 +PORTREVISION= 1 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-qiskit/distinfo b/science/py-qiskit/distinfo index f1f98a1c4ce5..40086a88e8e1 100644 --- a/science/py-qiskit/distinfo +++ b/science/py-qiskit/distinfo @@ -1,4 +1,4 @@ -TIMESTAMP = 1753430083 +TIMESTAMP = 1757578345 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 @@ -485,5 +485,5 @@ SHA256 (rust/crates/zerocopy-0.8.25.crate) = a1702d9583232ddb9174e01bb7c15a2ab8f 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 +SHA256 (Qiskit-qiskit-2.1.2_GH0.tar.gz) = 23559ca58042d263152b233843af24f6753d591500de5a84df14a68a54f4a7db +SIZE (Qiskit-qiskit-2.1.2_GH0.tar.gz) = 7100760 diff --git a/science/py-sarpy/Makefile b/science/py-sarpy/Makefile index 2319a7ca3340..84ec18c8ecee 100644 --- a/science/py-sarpy/Makefile +++ b/science/py-sarpy/Makefile @@ -1,5 +1,6 @@ PORTNAME= sarpy -PORTVERSION= 1.3.60 +PORTVERSION= 1.3.61 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,8 +14,13 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.19.0,1:math/py-numpy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=0:science/py-scipy@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}h5py>=0:science/py-h5py@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>=4.1.1:devel/py-lxml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.19.0,1:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pillow>=0:graphics/py-pillow@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}shapely>=1.6.4:devel/py-shapely@${PY_FLAVOR} USES= python USE_PYTHON= autoplist concurrent pep517 @@ -24,13 +30,8 @@ NO_ARCH= yes OPTIONS_DEFINE= ALL ALL_DESC= All optional dependencies -ALL_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}h5py>=0:science/py-h5py@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>=4.1.1:devel/py-lxml5@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>=2.5:math/py-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pillow>=0:graphics/py-pillow@${PY_FLAVOR} \ +ALL_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}networkx>=2.5:math/py-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest>=3.3.2,1:devel/py-pytest@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}shapely>=1.6.4:devel/py-shapely@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}smart-open>=0:net/py-smart-open@${PY_FLAVOR} .include <bsd.port.mk> diff --git a/science/py-sarpy/distinfo b/science/py-sarpy/distinfo index ff475cd5792a..bf135760549a 100644 --- a/science/py-sarpy/distinfo +++ b/science/py-sarpy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1738089136 -SHA256 (sarpy-1.3.60.tar.gz) = cf9ef0359419b1e69dfc3ea9eed5507ad6bd1479da386d1b513d8e5d904dfcda -SIZE (sarpy-1.3.60.tar.gz) = 1282348 +TIMESTAMP = 1757120810 +SHA256 (sarpy-1.3.61.tar.gz) = 85c94a91990b7aacf8cf552d61c0065f827e28b33a42160daafb3668f73b647a +SIZE (sarpy-1.3.61.tar.gz) = 1283179 diff --git a/science/py-scikit-fuzzy/Makefile b/science/py-scikit-fuzzy/Makefile index e6fcb0ff80c4..658380d01336 100644 --- a/science/py-scikit-fuzzy/Makefile +++ b/science/py-scikit-fuzzy/Makefile @@ -1,5 +1,6 @@ PORTNAME= scikit-fuzzy DISTVERSION= 0.5.0 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-sdf/Makefile b/science/py-sdf/Makefile index a4827b68afe5..8e4670177f9d 100644 --- a/science/py-sdf/Makefile +++ b/science/py-sdf/Makefile @@ -1,6 +1,6 @@ PORTNAME= sdf PORTVERSION= 0.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science cad python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-segregation/Makefile b/science/py-segregation/Makefile index f145f800c94a..88bd0223be01 100644 --- a/science/py-segregation/Makefile +++ b/science/py-segregation/Makefile @@ -1,6 +1,6 @@ PORTNAME= segregation PORTVERSION= 2.5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-xbout/Makefile b/science/py-xbout/Makefile index d1424ca01695..1afc7238febc 100644 --- a/science/py-xbout/Makefile +++ b/science/py-xbout/Makefile @@ -1,6 +1,6 @@ PORTNAME= xbout DISTVERSION= 0.3.5 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science education MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/qt6-quick3dphysics/distinfo b/science/qt6-quick3dphysics/distinfo index 03a1722c995d..a1a299cb31b7 100644 --- a/science/qt6-quick3dphysics/distinfo +++ b/science/qt6-quick3dphysics/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1749162772 -SHA256 (KDE/Qt/6.9.1/qtquick3dphysics-everywhere-src-6.9.1.tar.xz) = 66e8365eb8c409a8426dec13a83203879f31845d555bf7632ce0728e8ddca24f -SIZE (KDE/Qt/6.9.1/qtquick3dphysics-everywhere-src-6.9.1.tar.xz) = 4683360 +TIMESTAMP = 1759303916 +SHA256 (KDE/Qt/6.9.3/qtquick3dphysics-everywhere-src-6.9.3.tar.xz) = dcd7b22d745d249eb602c5d4d8af8a8e9d11217ccb42b3dd611bb047153b5a6e +SIZE (KDE/Qt/6.9.3/qtquick3dphysics-everywhere-src-6.9.3.tar.xz) = 4668392 diff --git a/science/qwalk/pkg-descr b/science/qwalk/pkg-descr index f0e473e2929f..d3ad2e3f8fb3 100644 --- a/science/qwalk/pkg-descr +++ b/science/qwalk/pkg-descr @@ -1,4 +1,12 @@ -QWalk is a program developed to perform high accuracy quantum Monte Carlo -calculations of electronic structure in molecules and solids. It is specifically -designed as a research vehicle for new algorithms and method developments, as -well as being able to scale up to large system sizes. +QWalk is a high-accuracy quantum Monte Carlo (QMC) program designed for +electronic structure calculations in molecules and solids. It serves as a +research vehicle for developing new algorithms and methods, capable of +scaling up to large system sizes and finding very accurate solutions to +the stationary Schrodinger equation for atoms, molecules, solids, and +various model systems. + +Its primary application lies in computational condensed-matter physics +and chemistry, particularly for studying correlated electron systems and +determining both ground-state and excited-state properties of quantum +systems. QWalk provides a robust platform for advanced research in +quantum chemistry and materials science. diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index d4caaecd8c66..dd2255f3a900 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ DISTVERSION= 2025_03_1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font DISTFILES= ComicNeue-Regular.ttf:font diff --git a/science/salome-configuration/Makefile b/science/salome-configuration/Makefile index e9e82543ac64..de2ea9312b27 100644 --- a/science/salome-configuration/Makefile +++ b/science/salome-configuration/Makefile @@ -1,40 +1,28 @@ PORTNAME= salome-configuration DISTVERSIONPREFIX= V -DISTVERSION= 9_11_0 +DISTVERSION= 9_15_0 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Salome Project: Multi-physics simulations: Configuration -WWW= https://www.salome-platform.org/ +WWW= https://www.salome-platform.org/ \ + https://github.com/SalomePlatform/configuration/ -BROKEN= Unfetchable -DEPRECATED= Fails to fetch -EXPIRATION_DATE=2025-06-30 +LICENSE= LGPL21+ +LICENSE_FILE= ${WRKSRC}/COPYING -FETCH_DEPENDS= git:devel/git - -GIT_URL= https://git.salome-platform.org/gitpub/tools/configuration.git # all Salome repositories: https://git.salome-platform.org/gitweb/ +USE_GITHUB= yes +GH_ACCOUNT= SalomePlatform +GH_PROJECT= configuration DATADIR= ${PREFIX}/share/salome - -NO_BUILD= yes NO_ARCH= yes - -do-fetch: - @if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \ - ${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \ - cd ${DISTDIR}/${DIST_SUBDIR} && \ - git clone -q ${GIT_URL} ${PORTNAME}-${DISTVERSIONFULL} && \ - (cd ${PORTNAME}-${DISTVERSIONFULL} && git reset -q --hard ${DISTVERSIONFULL} && ${RM} -r .git) && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -print0 | LC_ALL=C ${SORT} -z | \ - ${TAR} czf ${PORTNAME}-${DISTVERSIONFULL}${EXTRACT_SUFX} --format=ustar --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \ - ${RM} -r ${PORTNAME}-${DISTVERSIONFULL}; \ - fi +NO_BUILD= yes do-install: ${MKDIR} ${STAGEDIR}${DATADIR}/configuration - cd ${WRKSRC} && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/configuration + cd ${WRKSRC} && \ + ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/configuration ${RM} ${STAGEDIR}${DATADIR}/configuration/.gitignore .include <bsd.port.mk> diff --git a/science/salome-configuration/distinfo b/science/salome-configuration/distinfo index 18910f5ff474..d3b5c510e961 100644 --- a/science/salome-configuration/distinfo +++ b/science/salome-configuration/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1688414005 -SHA256 (salome-configuration-V9_11_0.tar.gz) = 5f19f22ea595e7f7e5cffc97386dc89ad8c0ed597e86c94f03924386a56815e4 -SIZE (salome-configuration-V9_11_0.tar.gz) = 90716 +TIMESTAMP = 1758452949 +SHA256 (SalomePlatform-configuration-V9_15_0_GH0.tar.gz) = 01dd367a167383fbc03ca8de47e127c87f4a9d4c826c68768ac3a2bfd5f998f7 +SIZE (SalomePlatform-configuration-V9_15_0_GH0.tar.gz) = 101578 diff --git a/science/salome-configuration/pkg-plist b/science/salome-configuration/pkg-plist index 3408d0ae8100..8a94f255db5d 100644 --- a/science/salome-configuration/pkg-plist +++ b/science/salome-configuration/pkg-plist @@ -1,3 +1,4 @@ +%%DATADIR%%/configuration/COPYING %%DATADIR%%/configuration/autotools/m4/ac_check_sizeof_fortran.m4 %%DATADIR%%/configuration/autotools/m4/ac_cxx_depend_flag.m4 %%DATADIR%%/configuration/autotools/m4/ac_cxx_have_sstream.m4 @@ -70,11 +71,14 @@ %%DATADIR%%/configuration/cmake/FindSIP.cmake %%DATADIR%%/configuration/cmake/FindSMESH.cmake %%DATADIR%%/configuration/cmake/FindSalomeBLSURFPLUGIN.cmake +%%DATADIR%%/configuration/cmake/FindSalomeBasicIterativeStatistics.cmake %%DATADIR%%/configuration/cmake/FindSalomeBoost.cmake +%%DATADIR%%/configuration/cmake/FindSalomeBootstrap.cmake %%DATADIR%%/configuration/cmake/FindSalomeCALCULATOR.cmake %%DATADIR%%/configuration/cmake/FindSalomeCAS.cmake %%DATADIR%%/configuration/cmake/FindSalomeCGNS.cmake %%DATADIR%%/configuration/cmake/FindSalomeCOMPONENT.cmake +%%DATADIR%%/configuration/cmake/FindSalomeCommonGeomLib.cmake %%DATADIR%%/configuration/cmake/FindSalomeCppUnit.cmake %%DATADIR%%/configuration/cmake/FindSalomeDoxygen.cmake %%DATADIR%%/configuration/cmake/FindSalomeFIELDS.cmake @@ -97,6 +101,7 @@ %%DATADIR%%/configuration/cmake/FindSalomeLibXml2.cmake %%DATADIR%%/configuration/cmake/FindSalomeMEDCoupling.cmake %%DATADIR%%/configuration/cmake/FindSalomeMEDFile.cmake +%%DATADIR%%/configuration/cmake/FindSalomeMEDFileWindows.cmake %%DATADIR%%/configuration/cmake/FindSalomeMESHGEMS.cmake %%DATADIR%%/configuration/cmake/FindSalomeMPI.cmake %%DATADIR%%/configuration/cmake/FindSalomeMetis.cmake @@ -157,3 +162,4 @@ %%DATADIR%%/configuration/copyright/modules.info %%DATADIR%%/configuration/tests/ListOfSalomeTestLabelsToBeOK %%DATADIR%%/configuration/tests/README.txt +%%DATADIR%%/configuration/tests/sod_test_config.json diff --git a/science/salome-kernel/Makefile b/science/salome-kernel/Makefile index 490e715aab60..11413201242a 100644 --- a/science/salome-kernel/Makefile +++ b/science/salome-kernel/Makefile @@ -1,64 +1,49 @@ PORTNAME= salome-kernel DISTVERSIONPREFIX= V DISTVERSION= 9_11_0 -PORTREVISION= 4 -CATEGORIES= science +PORTREVISION= 5 +CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Salome Project: Multi-physics simulations: Kernel -WWW= https://www.salome-platform.org/ +WWW= https://www.salome-platform.org/ \ + https://github.com/SalomePlatform/kernel/ -LICENSE= LGPL21 +LICENSE= LGPL21+ LICENSE_FILE= ${WRKSRC}/COPYING -DEPRECATED= Depends on expired science/salome-configuration -EXPIRATION_DATE=2025-09-30 - -FETCH_DEPENDS= git:devel/git PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}omniorb>0:devel/py-omniorb \ ${PYTHON_PKGNAMEPREFIX}psutil>0:sysutils/py-psutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} -BUILD_DEPENDS= salome-configuration>0:science/salome-configuration \ - swig:devel/swig \ - ${PY_DEPENDS} +BUILD_DEPENDS= ${PY_DEPENDS} \ + salome-configuration>0:science/salome-configuration \ + swig:devel/swig LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ libomniORB4.so:devel/omniORB -RUN_DEPENDS= bash:shells/bash \ - ${PY_DEPENDS} +RUN_DEPENDS= ${PY_DEPENDS} \ + bash:shells/bash USES= cmake compiler:c++11-lang gnome python shebangfix +USE_GITHUB= yes +GH_ACCOUNT= SalomePlatform +GH_PROJECT= kernel USE_GNOME= libxml2 USE_LDCONFIG= yes +SHEBANG_FILES= bin/appliskel/.bashrc bin/appliskel/.salome_run \ + bin/appliskel/salome bin/appliskel/salome_mesa SHEBANG_GLOB= *.py *.sh -SHEBANG_FILES= bin/appliskel/salome \ - bin/appliskel/salome_mesa \ - bin/appliskel/.salome_run \ - bin/appliskel/.bashrc - -GIT_URL= https://git.salome-platform.org/gitpub/modules/kernel # all Salome repositories: https://git.salome-platform.org/gitweb/ CMAKE_ARGS= -DCONFIGURATION_ROOT_DIR=${LOCALBASE}/share/salome/configuration \ -DOMNIORBPY_ROOT_DIR=${LOCALBASE} \ -DPython_EXECUTABLE=${PYTHON_CMD} -CMAKE_OFF= SALOME_BUILD_TESTS SALOME_BUILD_DOC +CMAKE_OFF= SALOME_BUILD_DOC SALOME_BUILD_TESTS + CFLAGS+= -DSIZEOF_INT=4 -DSIZEOF_LONG=4 LDFLAGS+= -lexecinfo DATADIR= ${PREFIX}/share/salome -do-fetch: - @if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \ - ${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \ - cd ${DISTDIR}/${DIST_SUBDIR} && \ - git clone -q ${GIT_URL} ${PORTNAME}-${DISTVERSIONFULL} && \ - (cd ${PORTNAME}-${DISTVERSIONFULL} && git reset -q --hard ${DISTVERSIONFULL} && ${RM} -r .git) && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -print0 | LC_ALL=C ${SORT} -z | \ - ${TAR} czf ${PORTNAME}-${DISTVERSIONFULL}${EXTRACT_SUFX} --format=ustar --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \ - ${RM} -r ${PORTNAME}-${DISTVERSIONFULL}; \ - fi - .include <bsd.port.mk> diff --git a/science/salome-kernel/distinfo b/science/salome-kernel/distinfo index 91a1299e3225..f80643ecdf7c 100644 --- a/science/salome-kernel/distinfo +++ b/science/salome-kernel/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1688418727 -SHA256 (salome-kernel-V9_11_0.tar.gz) = ab1ba2be6f48adc97497266f2b6db3b6878aceb8ce8732e496130bc4924ccb3d -SIZE (salome-kernel-V9_11_0.tar.gz) = 3435113 +TIMESTAMP = 1758456327 +SHA256 (SalomePlatform-kernel-V9_11_0_GH0.tar.gz) = cdbc752b1dc093f3a9d9509e68fe70437bb195baf37f9653f0e33a21ce75b935 +SIZE (SalomePlatform-kernel-V9_11_0_GH0.tar.gz) = 3437694 diff --git a/science/smoldyn/Makefile b/science/smoldyn/Makefile index 965707c3adac..55178cea9aca 100644 --- a/science/smoldyn/Makefile +++ b/science/smoldyn/Makefile @@ -1,5 +1,5 @@ PORTNAME= smoldyn -DISTVERSION= 2.74 +DISTVERSION= 2.75 CATEGORIES= science MASTER_SITES= https://www.smoldyn.org/ @@ -32,8 +32,8 @@ PYTHON_CMAKE_BOOL= OPTION_PYTHON PYTHON_USES= python PYTHON_CMAKE_ON= -DPython3_EXECUTABLE=${PYTHON_CMD} PYTHON_BUILD_DEPENDS= ${PY_SETUPTOOLS} -PYTHON_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biosimulators-utils>0:biology/py-biosimulators-utils@${PY_FLAVOR} -PYTHON_BROKEN= pending biology/py-biosimulators-utils completion +#PYTHON_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biosimulators-utils>0:biology/py-biosimulators-utils@${PY_FLAVOR} +PYTHON_BROKEN= some python dependencies aren't ported post-extract: # see https://github.com/ssandrews/Smoldyn/issues/127 @${CHMOD} +x ${WRKSRC}/scripts/run_pyscript.py.in diff --git a/science/smoldyn/distinfo b/science/smoldyn/distinfo index 61749de73a7f..5083a957430a 100644 --- a/science/smoldyn/distinfo +++ b/science/smoldyn/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737604798 -SHA256 (smoldyn-2.74.tgz) = 1abae836ac515092be14e2058af58a25981d7872c3a002fbff67bde0f64fa28a -SIZE (smoldyn-2.74.tgz) = 34348669 +TIMESTAMP = 1755906394 +SHA256 (smoldyn-2.75.tgz) = f7116e207d6ba91d3f709b6839d8054a622383ac6e0c5f81108015d083a2a094 +SIZE (smoldyn-2.75.tgz) = 34008076 diff --git a/science/step/distinfo b/science/step/distinfo index d0003f376b70..5db7278905a9 100644 --- a/science/step/distinfo +++ b/science/step/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1751381646 -SHA256 (KDE/release-service/25.04.3/step-25.04.3.tar.xz) = 0aa86e2dd0bebbd9da8b8b77d0da3cd924e25be7084accaf11850d51857fba3e -SIZE (KDE/release-service/25.04.3/step-25.04.3.tar.xz) = 987244 +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 diff --git a/science/step/pkg-plist b/science/step/pkg-plist index f0365a2c6bf1..4186212eb37b 100644 --- a/science/step/pkg-plist +++ b/science/step/pkg-plist @@ -133,6 +133,8 @@ share/locale/lt/LC_MESSAGES/step_example_files.mo share/locale/lt/LC_MESSAGES/step_objinfo_files.mo share/locale/lt/LC_MESSAGES/step_qt.qm share/locale/lv/LC_MESSAGES/step.mo +share/locale/lv/LC_MESSAGES/step_example_files.mo +share/locale/lv/LC_MESSAGES/step_objinfo_files.mo share/locale/lv/LC_MESSAGES/step_qt.qm share/locale/mai/LC_MESSAGES/step_qt.qm share/locale/ml/LC_MESSAGES/step.mo @@ -561,6 +563,23 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/examples/lt/solar.step %%DATADIR%%/examples/lt/springs.step %%DATADIR%%/examples/lt/wave.step +%%DATADIR%%/examples/lv/brownian.step +%%DATADIR%%/examples/lv/doublependulum.step +%%DATADIR%%/examples/lv/eightpendula.step +%%DATADIR%%/examples/lv/first.step +%%DATADIR%%/examples/lv/fourpendula.step +%%DATADIR%%/examples/lv/gas.step +%%DATADIR%%/examples/lv/graph.step +%%DATADIR%%/examples/lv/liquid.step +%%DATADIR%%/examples/lv/lissajous.step +%%DATADIR%%/examples/lv/motor.step +%%DATADIR%%/examples/lv/motor1.step +%%DATADIR%%/examples/lv/note.step +%%DATADIR%%/examples/lv/resonance.step +%%DATADIR%%/examples/lv/softbody.step +%%DATADIR%%/examples/lv/solar.step +%%DATADIR%%/examples/lv/springs.step +%%DATADIR%%/examples/lv/wave.step %%DATADIR%%/examples/ml/brownian.step %%DATADIR%%/examples/ml/doublependulum.step %%DATADIR%%/examples/ml/eightpendula.step @@ -1198,6 +1217,25 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/objinfo/l10n/lt/spring.html %%DATADIR%%/objinfo/l10n/lt/weightforce.html %%DATADIR%%/objinfo/l10n/lt/world.html +%%DATADIR%%/objinfo/l10n/lv/anchor.html +%%DATADIR%%/objinfo/l10n/lv/box.html +%%DATADIR%%/objinfo/l10n/lv/chargedparticle.html +%%DATADIR%%/objinfo/l10n/lv/coulombforce.html +%%DATADIR%%/objinfo/l10n/lv/disk.html +%%DATADIR%%/objinfo/l10n/lv/gas.html +%%DATADIR%%/objinfo/l10n/lv/gasljforce.html +%%DATADIR%%/objinfo/l10n/lv/gasparticle.html +%%DATADIR%%/objinfo/l10n/lv/gravitationforce.html +%%DATADIR%%/objinfo/l10n/lv/linearmotor.html +%%DATADIR%%/objinfo/l10n/lv/meter.html +%%DATADIR%%/objinfo/l10n/lv/note.html +%%DATADIR%%/objinfo/l10n/lv/particle.html +%%DATADIR%%/objinfo/l10n/lv/pin.html +%%DATADIR%%/objinfo/l10n/lv/polygon.html +%%DATADIR%%/objinfo/l10n/lv/softbody.html +%%DATADIR%%/objinfo/l10n/lv/spring.html +%%DATADIR%%/objinfo/l10n/lv/weightforce.html +%%DATADIR%%/objinfo/l10n/lv/world.html %%DATADIR%%/objinfo/l10n/ml/anchor.html %%DATADIR%%/objinfo/l10n/ml/box.html %%DATADIR%%/objinfo/l10n/ml/chargedparticle.html @@ -1555,6 +1593,11 @@ share/mime/packages/org.kde.step.xml %%DATADIR%%/tutorials/lt/tutorial3.step %%DATADIR%%/tutorials/lt/tutorial4.step %%DATADIR%%/tutorials/lt/tutorial5.step +%%DATADIR%%/tutorials/lv/tutorial1.step +%%DATADIR%%/tutorials/lv/tutorial2.step +%%DATADIR%%/tutorials/lv/tutorial3.step +%%DATADIR%%/tutorials/lv/tutorial4.step +%%DATADIR%%/tutorials/lv/tutorial5.step %%DATADIR%%/tutorials/ml/tutorial1.step %%DATADIR%%/tutorials/ml/tutorial2.step %%DATADIR%%/tutorials/ml/tutorial3.step diff --git a/science/sz3/Makefile b/science/sz3/Makefile index e65b8ad06873..fe01a0279dc0 100644 --- a/science/sz3/Makefile +++ b/science/sz3/Makefile @@ -1,5 +1,5 @@ PORTNAME= sz3 -PORTVERSION= 3.2.1 +PORTVERSION= 3.3.0 DISTVERSIONPREFIX= v CATEGORIES= science @@ -13,15 +13,18 @@ LICENSE_FILE= ${WRKSRC}/copyright-and-BSD-license.txt LIB_DEPENDS= libgsl.so:math/gsl \ libzstd.so:archivers/zstd +TEST_DEPENDS= googletest>=0:devel/googletest -USES= cmake pkgconfig +USES= cmake:testing pkgconfig CMAKE_OFF= BUILD_H5Z_FILTER \ BUILD_MDZ \ + BUILD_TESTING \ SZ3_DEBUG_TIMINGS \ SZ3_USE_BUNDLED_ZSTD CMAKE_ON= BUILD_SHARED_LIBS \ - BUILD_STATIC_LIBS + BUILD_STATIC_LIBS \ + SZ3_USE_SKA_HASH DATADIR= ${PREFIX}/share/SZ3 diff --git a/science/sz3/distinfo b/science/sz3/distinfo index 638b3b67e6a1..29921144bbbb 100644 --- a/science/sz3/distinfo +++ b/science/sz3/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1738088812 -SHA256 (szcompressor-SZ3-v3.2.1_GH0.tar.gz) = 24ed1c8159832734a241df66b857eca64d18a2e8e949ef583a2d0bfe01c6b7e1 -SIZE (szcompressor-SZ3-v3.2.1_GH0.tar.gz) = 4474033 +TIMESTAMP = 1757120532 +SHA256 (szcompressor-SZ3-v3.3.0_GH0.tar.gz) = c6b9e114e5849911e14334fca14eaf30f9a84d4bbe681a1f32d3be62ec68fb52 +SIZE (szcompressor-SZ3-v3.3.0_GH0.tar.gz) = 128524 diff --git a/science/sz3/pkg-plist b/science/sz3/pkg-plist index cbe94507605e..44a0f55e5e88 100644 --- a/science/sz3/pkg-plist +++ b/science/sz3/pkg-plist @@ -1,4 +1,5 @@ bin/sz3 +bin/sz3_customized_demo bin/sz3_smoke_test include/SZ3/api/impl/SZAlgoInterp.hpp include/SZ3/api/impl/SZAlgoLorenzoReg.hpp @@ -9,13 +10,11 @@ include/SZ3/api/impl/SZImplOMP.hpp include/SZ3/api/sz.hpp include/SZ3/compressor/Compressor.hpp include/SZ3/compressor/SZGenericCompressor.hpp -include/SZ3/compressor/SZIterateCompressor.hpp -include/SZ3/compressor/specialized/SZBlockInterpolationCompressor.hpp include/SZ3/compressor/specialized/SZExaaltCompressor.hpp include/SZ3/compressor/specialized/SZTruncateCompressor.hpp +include/SZ3/decomposition/BlockwiseDecomposition.hpp include/SZ3/decomposition/Decomposition.hpp include/SZ3/decomposition/InterpolationDecomposition.hpp -include/SZ3/decomposition/LorenzoRegressionDecomposition.hpp include/SZ3/decomposition/NoPredictionDecomposition.hpp include/SZ3/decomposition/TimeSeriesDecomposition.hpp include/SZ3/def.hpp @@ -29,11 +28,6 @@ include/SZ3/lossless/Lossless_bypass.hpp include/SZ3/lossless/Lossless_zstd.hpp include/SZ3/predictor/ComposedPredictor.hpp include/SZ3/predictor/LorenzoPredictor.hpp -include/SZ3/predictor/MetaLorenzoPredictor.hpp -include/SZ3/predictor/MetaRegressionPredictor.hpp -include/SZ3/predictor/PolyRegressionCoeffAux.hpp -include/SZ3/predictor/PolyRegressionCoeffAux.m -include/SZ3/predictor/PolyRegressionPredictor.hpp include/SZ3/predictor/Predictor.hpp include/SZ3/predictor/RegressionPredictor.hpp include/SZ3/preprocessor/PreFilter.hpp @@ -42,6 +36,7 @@ include/SZ3/preprocessor/Transpose.hpp include/SZ3/preprocessor/Wavelet.hpp include/SZ3/quantizer/LinearQuantizer.hpp include/SZ3/quantizer/Quantizer.hpp +include/SZ3/utils/BlockwiseIterator.hpp include/SZ3/utils/ByteUtil.hpp include/SZ3/utils/Config.hpp include/SZ3/utils/Extraction.hpp @@ -50,12 +45,10 @@ include/SZ3/utils/Interpolators.hpp include/SZ3/utils/Iterator.hpp include/SZ3/utils/KmeansUtil.hpp include/SZ3/utils/MemoryUtil.hpp -include/SZ3/utils/MetaDef.hpp include/SZ3/utils/QuantOptimizatioin.hpp +include/SZ3/utils/Sample.hpp include/SZ3/utils/Statistic.hpp include/SZ3/utils/Timer.hpp -include/SZ3/utils/inih/INIReader.h -include/SZ3/utils/inih/LICENSE.txt include/SZ3/utils/ska_hash/LICENSE.txt include/SZ3/utils/ska_hash/bytell_hash_map.hpp include/SZ3/utils/ska_hash/flat_hash_map.hpp diff --git a/science/tinker/Makefile b/science/tinker/Makefile index a62f2268609b..5723eb9b39db 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,5 +1,6 @@ PORTNAME= tinker -DISTVERSION= 25.3 +DISTVERSION= 25.5 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ diff --git a/science/tinker/distinfo b/science/tinker/distinfo index 7ca60014bed4..b452890259c0 100644 --- a/science/tinker/distinfo +++ b/science/tinker/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753634645 -SHA256 (tinker-25.3.tar.gz) = d536f1d4d0d7d4394b3b3d88a52cf12ed3489312ac2ad9c6ce4d198bd681e36c -SIZE (tinker-25.3.tar.gz) = 80772142 +TIMESTAMP = 1759481421 +SHA256 (tinker-25.5.tar.gz) = 10e24742d262a09a4b191eb73ef994cc8987e1e5e18ac7759420b36f07a02036 +SIZE (tinker-25.5.tar.gz) = 81137927 diff --git a/science/tinker/files/patch-cmake_CMakeLists.txt b/science/tinker/files/patch-cmake_CMakeLists.txt new file mode 100644 index 000000000000..e4d2d621ed7f --- /dev/null +++ b/science/tinker/files/patch-cmake_CMakeLists.txt @@ -0,0 +1,15 @@ +--- cmake/CMakeLists.txt.orig 2025-10-03 08:52:37 UTC ++++ cmake/CMakeLists.txt +@@ -68,12 +68,6 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + + # Set compiler flags + +-if(APPLE) +- set(ARCH_FLAGS "-mtune=native") +-else() +- set(ARCH_FLAGS "-march=native") +-endif() +- + if(WIN32) + if(CMAKE_Fortran_COMPILER_ID MATCHES "Intel") + set(CMAKE_Fortran_FLAGS_RELEASE "/O3 /QxHost /Qip- /Qprec-div- /w") diff --git a/science/tinker/files/patch-make_Makefile b/science/tinker/files/patch-make_Makefile index 4b7b308532ab..7e1f679a86a0 100644 --- a/science/tinker/files/patch-make_Makefile +++ b/science/tinker/files/patch-make_Makefile @@ -1,15 +1,6 @@ ---- make/Makefile.orig 2024-05-04 16:08:28 UTC +--- make/Makefile.orig 2025-09-30 16:25:57 UTC +++ make/Makefile -@@ -68,7 +68,7 @@ F77FLAGS = -c - - F77 = gfortran - F77FLAGS = -c --OPTFLAGS = -Ofast -march=native -fopenmp -+OPTFLAGS = -Ofast $(PORT_SIMD_FLAGS) -fopenmp - OPTFLAGS = -Ofast -fopenmp - OPTFLAGS = -Og -g -fbacktrace -fcheck=bounds -Wunused -Wmaybe-uninitialized - LIBDIR = -L. -L$(TINKER_LIBDIR)/linux -Wl,--no-as-needed -ldl -@@ -829,138 +829,138 @@ rename_bin: +@@ -813,138 +813,138 @@ rename_bin: cat *.f *.c > tinker.txt rename_bin: diff --git a/science/tinker/pkg-descr b/science/tinker/pkg-descr index bd18a27c4744..1cd6d0590002 100644 --- a/science/tinker/pkg-descr +++ b/science/tinker/pkg-descr @@ -1,14 +1,15 @@ -Tinker is a set of small programs for doing general purpose molecular -modeling calculations. Tools are included for energy minimizations, -geometry calculations, simulated annealing, molecular dynamics, and -molecular analysis calculations. Tools for converting coordinate sets -are also provided. Tinker employs several force fields and minimization -techniques. +Tinker is a comprehensive and versatile molecular modeling software package +designed for molecular mechanics and dynamics simulations, with specialized +capabilities for biopolymers. It provides a complete set of tools for +energy minimizations, geometry calculations, simulated annealing, and +molecular dynamics. -This port sets the maxatm value to 2500 atoms. This should be -sufficient for most molecular systems. Should you need to work with -larger systems you can set the maxatm parameter in the sizes.i file -located in the tinker/source directory and recompile. Note that if it -is set too large that tinker programs will abort and core dump. - -For more information about Tinker see: +Tinker supports a wide array of force fields, including Amber, CHARMM, +OPLS, MMFF94, and advanced polarizable models like AMOEBA. It features +atomic multipole-based electrostatics with explicit dipole polarizability +and various continuum solvation treatments. The software offers efficient +truncated Newton optimization, normal mode vibrational analysis, and +free energy calculations. It also includes algorithms for conformational +searches, global optimization, and transition state location. Written in +Fortran 95, Tinker is a modular and extensible system, widely used in +computational chemistry and biophysics. diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist index b0f9367ade44..723615e476ff 100644 --- a/science/tinker/pkg-plist +++ b/science/tinker/pkg-plist @@ -96,7 +96,9 @@ bin/xyzpdb %%DATADIR%%/params/mmff94.prm %%DATADIR%%/params/mmff94s.prm %%DATADIR%%/params/oplsaa08.prm +%%DATADIR%%/params/oplsaa24.prm %%DATADIR%%/params/oplsaal.prm +%%DATADIR%%/params/oplsaam.prm %%DATADIR%%/params/oplsua.prm %%DATADIR%%/params/smoothaa.prm %%DATADIR%%/params/smoothua.prm diff --git a/science/ttk/Makefile b/science/ttk/Makefile index 825079819c86..1b1d123f5933 100644 --- a/science/ttk/Makefile +++ b/science/ttk/Makefile @@ -1,5 +1,6 @@ PORTNAME= ttk DISTVERSION= 1.3.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/v_sim/Makefile b/science/v_sim/Makefile index 68f706f4fb08..5108a9903564 100644 --- a/science/v_sim/Makefile +++ b/science/v_sim/Makefile @@ -1,6 +1,6 @@ PORTNAME= v_sim DISTVERSION= 3.8.0 -PORTREVISION= 13 +PORTREVISION= 14 CATEGORIES= science MAINTAINER= thierry@FreeBSD.org diff --git a/science/vmd/pkg-descr b/science/vmd/pkg-descr index 82404ecc97d5..a62978d88d97 100644 --- a/science/vmd/pkg-descr +++ b/science/vmd/pkg-descr @@ -1,2 +1,13 @@ -VMD is a molecular visualization program for displaying, animating, and -analyzing large biomolecular systems using 3-D graphics and built-in scripting. +VMD (Visual Molecular Dynamics) is a molecular visualization program for +displaying, animating, and analyzing large biomolecular systems. It +utilizes 3D graphics and built-in scripting (Tcl and Python) for +interactive exploration. + +Key features include: +- Visualization of molecular dynamics simulations. +- Support for over 60 molecular file formats and data types. +- Various rendering styles (licorice, ribbons, van der Waals spheres). +- High-quality rendering, animation, and stereo display. +- Integrated analysis tools and custom scripting for advanced analysis. +- GPU acceleration and no inherent limits on molecular size. +- Cross-platform availability (Windows, macOS, and Linux). diff --git a/science/votca/Makefile b/science/votca/Makefile index f12745e528a9..07f97264f4bb 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -1,7 +1,7 @@ PORTNAME= votca DISTVERSIONPREFIX= v DISTVERSION= 2025 -PORTREVISION= 2 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -16,7 +16,7 @@ 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} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xmltodict>0:devel/py-xmltodict@${PY_FLAVOR} \ rdkit>0:science/rdkit BUILD_DEPENDS= bash:shells/bash \ diff --git a/science/wannier90/pkg-descr b/science/wannier90/pkg-descr index b1bce64c43cd..9aa0b87cae34 100644 --- a/science/wannier90/pkg-descr +++ b/science/wannier90/pkg-descr @@ -1,2 +1,15 @@ -The computer program that calculates maximally-localized Wannier functions -(MLWFs) and Wannier90 for quantum chemistry and physics fields. +Wannier90 is an open-source software package for generating maximally- +localized Wannier functions (MLWFs) and utilizing them to calculate +advanced electronic properties of materials with high efficiency and +accuracy. It is widely used in computational materials science and +interfaced with numerous popular electronic structure codes such as +Quantum ESPRESSO, ABINIT, VASP, and Siesta. + +The program exploits the real-space localization of MLWFs for efficient +Wannier interpolation of spectral and Fermi-surface properties. Its +applications include calculating electronic band structures, densities +of states, Fermi surfaces, and various transport properties. Wannier90 +also supports advanced functionalities like symmetry-adapted MLWFs, +calculation of shift currents, and Berry-curvature dipole, making it a +versatile tool for analyzing chemical bonding, dielectric properties, +and topological features in materials. diff --git a/science/wwplot/Makefile b/science/wwplot/Makefile index bfab3e211939..ab33bcd5f63e 100644 --- a/science/wwplot/Makefile +++ b/science/wwplot/Makefile @@ -1,6 +1,7 @@ PORTNAME= wwplot DISTVERSIONPREFIX= v DISTVERSION= 1.0.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org |