diff options
Diffstat (limited to 'science')
38 files changed, 142 insertions, 129 deletions
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/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=${LOCALBASE} OPTIONS_DEFINE= DOCS LIBXC OPTIONS_DEFAULT= LIBXC diff --git a/science/atompaw/files/patch-src_input__dataset__mod.F90 b/science/atompaw/files/patch-src_input__dataset__mod.F90 new file mode 100644 index 000000000000..cca7d9e3d6ae --- /dev/null +++ b/science/atompaw/files/patch-src_input__dataset__mod.F90 @@ -0,0 +1,11 @@ +--- src/input_dataset_mod.F90.orig 2023-06-02 20:37:00 UTC ++++ src/input_dataset_mod.F90 +@@ -2097,7 +2097,7 @@ END IF + INTEGER :: input_unit,echo_unit + INTEGER :: i_all,i_dx,i_xmin,i_zmesh,i_range + LOGICAL :: has_to_echo +- CHARACTER(200) :: inputline ++ CHARACTER(256) :: inputline + TYPE(input_dataset_t),POINTER :: dataset + + !------------------------------------------------------------------ diff --git a/science/berkeleygw/Makefile b/science/berkeleygw/Makefile index 36f76867eaaa..bc988171c441 100644 --- a/science/berkeleygw/Makefile +++ b/science/berkeleygw/Makefile @@ -18,7 +18,7 @@ BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libfftw3.so:math/fftw3 RUN_DEPENDS= bash:shells/bash -USES= blaslapack:openblas gmake fortran python shebangfix +USES= blaslapack:openblas gmake fortran:gfortran python shebangfix SHEBANG_GLOB= *.sh *.py *awk diff --git a/science/cdf/Makefile b/science/cdf/Makefile index edc94cf929c9..f1b4b8b150c5 100644 --- a/science/cdf/Makefile +++ b/science/cdf/Makefile @@ -23,7 +23,6 @@ MAKE_FLAGS= INSTALLDIR=${STAGEDIR}${PREFIX} OS=freebsd ENV=gnu \ FORTRAN=yes FC_freebsd=${F77} MAKE_JOBS_UNSAFE= yes TEST_TARGET= test # XXX: test segfaults -FFLAGS+= -std=legacy WRKSRC= ${WRKDIR}/cdf${VER}-dist SUB_FILES= pkg-message @@ -37,6 +36,12 @@ OPTIONS_DEFINE= DOCS EXAMPLES MAKE_ARGS+= OS=freebsd ENV=gnu all +.include <bsd.port.pre.mk> + +.if ${FORTRAN_DEFAULT} != flang +FFLAGS= -std=legacy +.endif + post-patch: .for def in ${DEFS} @${REINPLACE_CMD} -e 's|<path>|${PREFIX}|' \ @@ -51,4 +56,4 @@ post-install: ${SED} -i '' 's,${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/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/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/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/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/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/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/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..398ade237318 100644 --- a/science/py-asdf/Makefile +++ b/science/py-asdf/Makefile @@ -1,5 +1,5 @@ PORTNAME= asdf -PORTVERSION= 4.3.0 +PORTVERSION= 4.4.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-asdf/distinfo b/science/py-asdf/distinfo index f3a2707208d2..f4e9bc88b54d 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 = 1757120806 +SHA256 (asdf-4.4.0.tar.gz) = f7146119e3d217f0b83d125e2fd657c1b2427caf6faeaf7ceedcd81db464363e +SIZE (asdf-4.4.0.tar.gz) = 899576 diff --git a/science/py-ase/Makefile b/science/py-ase/Makefile index 27c665165e36..f3e0a8056fdc 100644 --- a/science/py-ase/Makefile +++ b/science/py-ase/Makefile @@ -1,21 +1,21 @@ PORTNAME= ase -DISTVERSION= 3.23.0 -PORTREVISION= 2 +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-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-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-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-sarpy/Makefile b/science/py-sarpy/Makefile index 2319a7ca3340..f5421f78c28e 100644 --- a/science/py-sarpy/Makefile +++ b/science/py-sarpy/Makefile @@ -1,5 +1,5 @@ PORTNAME= sarpy -PORTVERSION= 1.3.60 +PORTVERSION= 1.3.61 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,8 +13,13 @@ 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} \ + ${PYTHON_PKGNAMEPREFIX}lxml5>=4.1.1:devel/py-lxml5@${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 +29,8 @@ 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/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 |