diff options
Diffstat (limited to 'science')
41 files changed, 781 insertions, 107 deletions
diff --git a/science/Makefile b/science/Makefile index 12633922091d..b5866e1914e4 100644 --- a/science/Makefile +++ b/science/Makefile @@ -239,6 +239,7 @@ SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-eccodes-python + SUBDIR += py-geomet SUBDIR += py-geometer SUBDIR += py-gpaw SUBDIR += py-gsd diff --git a/science/atom/Makefile b/science/atom/Makefile index 7699cc4fa95b..d1f87676b4cd 100644 --- a/science/atom/Makefile +++ b/science/atom/Makefile @@ -14,6 +14,8 @@ EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Program for DFT calculations in atoms +BROKEN= unfetchable + LICENSE= ATOM_LICENSE LICENSE_NAME= ATOM ACADEMIC LICENCE LICENSE_FILE= ${DISTDIR}/${DIST_SUBDIR}/atom_licence.html diff --git a/science/checkmol/Makefile b/science/checkmol/Makefile index 6bab5971ddd4..976a35f366fc 100644 --- a/science/checkmol/Makefile +++ b/science/checkmol/Makefile @@ -3,16 +3,15 @@ PORTNAME= checkmol PORTVERSION= 0.5 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science MASTER_SITES= http://merian.pch.univie.ac.at/pch/download/chemistry/checkmol/ +DISTFILES= ${PORTNAME} EXTRACT_SUFX= .pas MAINTAINER= acm@FreeBSD.org COMMENT= Analyze molecules for the presence of functional groups -BROKEN= unfetchable - LICENSE= GPLv2+ NO_WRKSUBDIR= yes @@ -29,7 +28,7 @@ do-build: (cd ${WRKSRC} && ${LOCALBASE}/bin/fpc ${EXTRACT_ONLY} -S2 -O3) do-install: - (cd ${WRKSRC} && ${INSTALL_PROGRAM} ${DISTNAME} ${STAGEDIR}${PREFIX}/bin/${PORTNAME}) + (cd ${WRKSRC} && ${INSTALL_PROGRAM} ${PORTNAME} ${STAGEDIR}${PREFIX}/bin/${PORTNAME}) (cd ${STAGEDIR}${PREFIX}/bin && ${LN} ${PORTNAME} matchmol) .include <bsd.port.mk> diff --git a/science/checkmol/distinfo b/science/checkmol/distinfo index 5e9d41bb49f8..27ccd69daf38 100644 --- a/science/checkmol/distinfo +++ b/science/checkmol/distinfo @@ -1,2 +1,3 @@ -SHA256 (checkmol-0.5.pas) = 53c729ed4c2f98a19f2ede8280189d766e6107d980ba2410e98f541c0d852829 -SIZE (checkmol-0.5.pas) = 554154 +TIMESTAMP = 1577760992 +SHA256 (checkmol) = 6913ea64238a3bfe1dc9929d979e20c87fc5f40d53e300722ad18178c0dc80f2 +SIZE (checkmol) = 555927 diff --git a/science/coordgenlibs/Makefile b/science/coordgenlibs/Makefile index 90b89f9aba82..d1b4f9f3dcc6 100644 --- a/science/coordgenlibs/Makefile +++ b/science/coordgenlibs/Makefile @@ -2,8 +2,7 @@ PORTNAME= coordgenlibs DISTVERSIONPREFIX= v -DISTVERSION= 1.2.2 -PORTREVISION= 4 +DISTVERSION= 1.3.2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -20,4 +19,6 @@ USE_GITHUB= yes GH_ACCOUNT= schrodinger USE_LDCONFIG= yes +CMAKE_ARGS= -Dmaeparser_DIR=${LOCALBASE}/lib/cmake + .include <bsd.port.mk> diff --git a/science/coordgenlibs/distinfo b/science/coordgenlibs/distinfo index c715efa8549c..59fd6245869d 100644 --- a/science/coordgenlibs/distinfo +++ b/science/coordgenlibs/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1552715318 -SHA256 (schrodinger-coordgenlibs-v1.2.2_GH0.tar.gz) = e663e59c521e352d4994176b6826adf6c39a5b980291c26a68ea55f964bd88ef -SIZE (schrodinger-coordgenlibs-v1.2.2_GH0.tar.gz) = 132052 +TIMESTAMP = 1578026875 +SHA256 (schrodinger-coordgenlibs-v1.3.2_GH0.tar.gz) = 5e483f95fa4066dc13ed7db6ac3edd5ec79cc5123a3fbe0dc54e485ba9a5169d +SIZE (schrodinger-coordgenlibs-v1.3.2_GH0.tar.gz) = 134911 diff --git a/science/coordgenlibs/pkg-plist b/science/coordgenlibs/pkg-plist index e453b147c90a..2918c3bb2a02 100644 --- a/science/coordgenlibs/pkg-plist +++ b/science/coordgenlibs/pkg-plist @@ -18,7 +18,9 @@ include/coordgen/sketcherMinimizerResidue.h include/coordgen/sketcherMinimizerResidueInteraction.h include/coordgen/sketcherMinimizerRing.h include/coordgen/sketcherMinimizerStretchInteraction.h +lib/cmake/coordgen-config-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/coordgen-config.cmake lib/libcoordgen.so lib/libcoordgen.so.1 -lib/libcoordgen.so.1.2.2 +lib/libcoordgen.so.1.3.2 share/coordgen/templates.mae diff --git a/science/eccodes/Makefile b/science/eccodes/Makefile index 82b0b7bb6b1c..1abbeb7bc9cb 100644 --- a/science/eccodes/Makefile +++ b/science/eccodes/Makefile @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= eccodes -PORTVERSION= 2.14.1 +PORTVERSION= 2.15.0 DISTVERSIONSUFFIX= -Source CATEGORIES= science MASTER_SITES= https://confluence.ecmwf.int/download/attachments/45757960/ \ diff --git a/science/eccodes/distinfo b/science/eccodes/distinfo index cb618c15a63f..0b4fe566e163 100644 --- a/science/eccodes/distinfo +++ b/science/eccodes/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1572806080 -SHA256 (eccodes-2.14.1-Source.tar.gz) = 16da742691c0ac81ccc378ae3f97311ef0dfdc82505aa4c652eb773e911cc9d6 -SIZE (eccodes-2.14.1-Source.tar.gz) = 11014537 +TIMESTAMP = 1577693897 +SHA256 (eccodes-2.15.0-Source.tar.gz) = 9fec8ad11f380795af632fb3105c4aa37d30f22fa70dba48fd93324cf6388d59 +SIZE (eccodes-2.15.0-Source.tar.gz) = 11255442 diff --git a/science/eccodes/pkg-plist b/science/eccodes/pkg-plist index d6e2fdf7b83a..7bc1bc7f3092 100644 --- a/science/eccodes/pkg-plist +++ b/science/eccodes/pkg-plist @@ -12732,6 +12732,490 @@ libdata/pkgconfig/eccodes.pc 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+%%DATADIR%%/definitions/bufr/tables/0/wmo/33/codetables/8082.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/codetables/8083.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/codetables/8085.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/codetables/8086.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/codetables/8087.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/codetables/8088.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/codetables/8091.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/codetables/8092.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/codetables/8093.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/element.table +%%DATADIR%%/definitions/bufr/tables/0/wmo/33/sequence.def %%DATADIR%%/definitions/bufr/tables/0/wmo/6/codetables/1003.table %%DATADIR%%/definitions/bufr/tables/0/wmo/6/codetables/10063.table %%DATADIR%%/definitions/bufr/tables/0/wmo/6/codetables/1007.table @@ -14133,6 +14617,7 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib1/local.98.1.def %%DATADIR%%/definitions/grib1/local.98.10.def %%DATADIR%%/definitions/grib1/local.98.11.def +%%DATADIR%%/definitions/grib1/local.98.12.def %%DATADIR%%/definitions/grib1/local.98.13.def %%DATADIR%%/definitions/grib1/local.98.14.def %%DATADIR%%/definitions/grib1/local.98.15.def @@ -14300,6 +14785,8 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/boot_multifield.def %%DATADIR%%/definitions/grib2/cfName.def %%DATADIR%%/definitions/grib2/cfVarName.def +%%DATADIR%%/definitions/grib2/crraLocalVersion.table +%%DATADIR%%/definitions/grib2/crra_suiteName.table %%DATADIR%%/definitions/grib2/dimension.0.table %%DATADIR%%/definitions/grib2/dimensionTableNumber.table %%DATADIR%%/definitions/grib2/dimensionType.table @@ -14318,6 +14805,7 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/local.98.0.def %%DATADIR%%/definitions/grib2/local.98.1.def %%DATADIR%%/definitions/grib2/local.98.11.def +%%DATADIR%%/definitions/grib2/local.98.12.def %%DATADIR%%/definitions/grib2/local.98.14.def %%DATADIR%%/definitions/grib2/local.98.15.def %%DATADIR%%/definitions/grib2/local.98.16.def @@ -14341,6 +14829,7 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/local.98.7.def %%DATADIR%%/definitions/grib2/local.98.9.def %%DATADIR%%/definitions/grib2/local.98.def +%%DATADIR%%/definitions/grib2/local.crra.1.def %%DATADIR%%/definitions/grib2/local.tigge.1.def %%DATADIR%%/definitions/grib2/local/1098/2.1.table %%DATADIR%%/definitions/grib2/local/1098/centres.table @@ -14408,6 +14897,8 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/parameters.def %%DATADIR%%/definitions/grib2/products_0.def %%DATADIR%%/definitions/grib2/products_1.def +%%DATADIR%%/definitions/grib2/products_10.def +%%DATADIR%%/definitions/grib2/products_11.def %%DATADIR%%/definitions/grib2/products_2.def %%DATADIR%%/definitions/grib2/products_3.def %%DATADIR%%/definitions/grib2/products_4.def @@ -14416,6 +14907,7 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/products_7.def %%DATADIR%%/definitions/grib2/products_8.def %%DATADIR%%/definitions/grib2/products_9.def +%%DATADIR%%/definitions/grib2/products_crra.def %%DATADIR%%/definitions/grib2/products_s2s.def %%DATADIR%%/definitions/grib2/products_tigge.def %%DATADIR%%/definitions/grib2/products_uerra.def @@ -16223,6 +16715,7 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/tables/21/4.233.table %%DATADIR%%/definitions/grib2/tables/21/4.234.table %%DATADIR%%/definitions/grib2/tables/21/4.236.table +%%DATADIR%%/definitions/grib2/tables/21/4.238.table %%DATADIR%%/definitions/grib2/tables/21/4.240.table %%DATADIR%%/definitions/grib2/tables/21/4.241.table %%DATADIR%%/definitions/grib2/tables/21/4.242.table @@ -16249,6 +16742,13 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/tables/21/5.7.table %%DATADIR%%/definitions/grib2/tables/21/6.0.table %%DATADIR%%/definitions/grib2/tables/21/stepType.table +%%DATADIR%%/definitions/grib2/tables/22/1.4.table +%%DATADIR%%/definitions/grib2/tables/22/3.15.table +%%DATADIR%%/definitions/grib2/tables/22/4.10.table +%%DATADIR%%/definitions/grib2/tables/22/4.230.table +%%DATADIR%%/definitions/grib2/tables/22/4.4.table +%%DATADIR%%/definitions/grib2/tables/22/4.5.table +%%DATADIR%%/definitions/grib2/tables/22/4.91.table %%DATADIR%%/definitions/grib2/tables/23/0.0.table %%DATADIR%%/definitions/grib2/tables/23/1.0.table %%DATADIR%%/definitions/grib2/tables/23/1.1.table @@ -16383,6 +16883,141 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/tables/23/5.7.table %%DATADIR%%/definitions/grib2/tables/23/6.0.table %%DATADIR%%/definitions/grib2/tables/23/stepType.table +%%DATADIR%%/definitions/grib2/tables/24/0.0.table +%%DATADIR%%/definitions/grib2/tables/24/1.0.table +%%DATADIR%%/definitions/grib2/tables/24/1.1.table +%%DATADIR%%/definitions/grib2/tables/24/1.2.table 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+%%DATADIR%%/definitions/grib2/tables/24/5.6.table +%%DATADIR%%/definitions/grib2/tables/24/5.7.table +%%DATADIR%%/definitions/grib2/tables/24/6.0.table +%%DATADIR%%/definitions/grib2/tables/24/stepType.table %%DATADIR%%/definitions/grib2/tables/3/0.0.table %%DATADIR%%/definitions/grib2/tables/3/1.0.table %%DATADIR%%/definitions/grib2/tables/3/1.1.table @@ -17349,7 +17984,15 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/template.4.71.def %%DATADIR%%/definitions/grib2/template.4.72.def %%DATADIR%%/definitions/grib2/template.4.73.def +%%DATADIR%%/definitions/grib2/template.4.76.def +%%DATADIR%%/definitions/grib2/template.4.77.def +%%DATADIR%%/definitions/grib2/template.4.78.def +%%DATADIR%%/definitions/grib2/template.4.79.def %%DATADIR%%/definitions/grib2/template.4.8.def +%%DATADIR%%/definitions/grib2/template.4.80.def +%%DATADIR%%/definitions/grib2/template.4.81.def +%%DATADIR%%/definitions/grib2/template.4.82.def +%%DATADIR%%/definitions/grib2/template.4.83.def %%DATADIR%%/definitions/grib2/template.4.9.def %%DATADIR%%/definitions/grib2/template.4.91.def %%DATADIR%%/definitions/grib2/template.4.categorical.def @@ -17361,8 +18004,11 @@ libdata/pkgconfig/eccodes.pc %%DATADIR%%/definitions/grib2/template.4.parameter_aerosol.def %%DATADIR%%/definitions/grib2/template.4.parameter_aerosol_44.def %%DATADIR%%/definitions/grib2/template.4.parameter_aerosol_optical.def +%%DATADIR%%/definitions/grib2/template.4.parameter_aerosol_optical_source.def +%%DATADIR%%/definitions/grib2/template.4.parameter_aerosol_source.def %%DATADIR%%/definitions/grib2/template.4.parameter_chemical.def %%DATADIR%%/definitions/grib2/template.4.parameter_chemical_distribution.def +%%DATADIR%%/definitions/grib2/template.4.parameter_chemical_source.def %%DATADIR%%/definitions/grib2/template.4.parameter_partition.def %%DATADIR%%/definitions/grib2/template.4.parameter_postproc.def %%DATADIR%%/definitions/grib2/template.4.parameter_tile.def diff --git a/science/esys-particle/Makefile b/science/esys-particle/Makefile index 1cd73d552144..a217597e13de 100644 --- a/science/esys-particle/Makefile +++ b/science/esys-particle/Makefile @@ -12,7 +12,7 @@ COMMENT= Particle-based numerical modelling software LICENSE= APACHE20 -BROKEN_FreeBSD_13= The upstream doesn't answer bug reports: https://bugs.launchpad.net/esys-particle/+bug/1808617 +BROKEN= The upstream doesn't answer bug reports: https://bugs.launchpad.net/esys-particle/+bug/1808617 LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libmpi.so:net/mpich diff --git a/science/gwyddion/Makefile b/science/gwyddion/Makefile index f98a77dba92b..c7b2bc5ce2a0 100644 --- a/science/gwyddion/Makefile +++ b/science/gwyddion/Makefile @@ -3,7 +3,7 @@ PORTNAME= gwyddion PORTVERSION= 2.51 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science graphics MASTER_SITES= SF diff --git a/science/hdf5/Makefile b/science/hdf5/Makefile index b55aebd5567a..dbca918901a9 100644 --- a/science/hdf5/Makefile +++ b/science/hdf5/Makefile @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= hdf5 -PORTVERSION= 1.10.5 -PORTREVISION= 2 +PORTVERSION= 1.10.6 CATEGORIES= science archivers graphics MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${PORTVERSION:R}/${DISTNAME}/src/ \ LOCAL/sunpoet diff --git a/science/hdf5/distinfo b/science/hdf5/distinfo index 7362ebc5ec46..d0018afb889b 100644 --- a/science/hdf5/distinfo +++ b/science/hdf5/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1554485971 -SHA256 (hdf5-1.10.5.tar.bz2) = 68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44 -SIZE (hdf5-1.10.5.tar.bz2) = 8706317 +TIMESTAMP = 1577693899 +SHA256 (hdf5-1.10.6.tar.bz2) = 09d6301901685201bb272a73e21c98f2bf7e044765107200b01089104a47c3bd +SIZE (hdf5-1.10.6.tar.bz2) = 8813699 diff --git a/science/hdf5/pkg-plist b/science/hdf5/pkg-plist index 92effeed59b0..f89773072942 100644 --- a/science/hdf5/pkg-plist +++ b/science/hdf5/pkg-plist @@ -51,11 +51,13 @@ include/H5Epublic.h include/H5FDcore.h include/H5FDdirect.h include/H5FDfamily.h +include/H5FDhdfs.h include/H5FDlog.h include/H5FDmpi.h include/H5FDmpio.h include/H5FDmulti.h include/H5FDpublic.h +include/H5FDros3.h include/H5FDsec2.h include/H5FDstdio.h include/H5FDwindows.h @@ -134,26 +136,26 @@ lib/libhdf5.a lib/libhdf5.settings lib/libhdf5.so lib/libhdf5.so.103 -lib/libhdf5.so.103.1.0 +lib/libhdf5.so.103.2.0 %%CXX%%lib/libhdf5_cpp.a %%CXX%%lib/libhdf5_cpp.so %%CXX%%lib/libhdf5_cpp.so.103 -%%CXX%%lib/libhdf5_cpp.so.103.1.0 +%%CXX%%lib/libhdf5_cpp.so.103.2.0 %%FORTRAN%%lib/libhdf5_fortran.a %%FORTRAN%%lib/libhdf5_fortran.so %%FORTRAN%%lib/libhdf5_fortran.so.102 -%%FORTRAN%%lib/libhdf5_fortran.so.102.0.0 +%%FORTRAN%%lib/libhdf5_fortran.so.102.0.1 lib/libhdf5_hl.a lib/libhdf5_hl.so lib/libhdf5_hl.so.100 -lib/libhdf5_hl.so.100.1.2 +lib/libhdf5_hl.so.100.1.3 %%CXX%%lib/libhdf5_hl_cpp.a %%CXX%%lib/libhdf5_hl_cpp.so %%CXX%%lib/libhdf5_hl_cpp.so.100 -%%CXX%%lib/libhdf5_hl_cpp.so.100.1.3 +%%CXX%%lib/libhdf5_hl_cpp.so.100.1.4 %%FORTRAN%%lib/libhdf5_hl_fortran.a %%FORTRAN%%lib/libhdf5_hl_fortran.so %%FORTRAN%%lib/libhdf5hl_fortran.a %%FORTRAN%%lib/libhdf5hl_fortran.so %%FORTRAN%%lib/libhdf5hl_fortran.so.100 -%%FORTRAN%%lib/libhdf5hl_fortran.so.100.0.4 +%%FORTRAN%%lib/libhdf5hl_fortran.so.100.0.5 diff --git a/science/hypre/Makefile b/science/hypre/Makefile index 45ad62a0266a..9c784879ffd0 100644 --- a/science/hypre/Makefile +++ b/science/hypre/Makefile @@ -3,15 +3,16 @@ PORTNAME= hypre DISTVERSIONPREFIX= v -DISTVERSION= 2.16.0 -PORTREVISION= 1 +DISTVERSION= 2.18.2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Scalable Linear Solvers and Multigrid Methods -LICENSE= LGPL21 -LICENSE_FILE= ${WRKSRC}/../COPYING.LESSER +LICENSE= APACHE20 MIT +LICENSE_COMB= dual +LICENSE_FILE_APACHE20= ${WRKSRC}/../LICENSE-APACHE +LICENSE_FILE_MIT= ${WRKSRC}/../LICENSE-MIT BROKEN_powerpc64= fails to compile: ./DistributedMatrixPilutSolver.h:97:20: expected ')' before '->' token diff --git a/science/hypre/distinfo b/science/hypre/distinfo index 1f4430afde92..72fe8ae29de3 100644 --- a/science/hypre/distinfo +++ b/science/hypre/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1557728492 -SHA256 (hypre-space-hypre-v2.16.0_GH0.tar.gz) = 33f8a27041e697343b820d0426e74694670f955e21bbf3fcb07ee95b22c59e90 -SIZE (hypre-space-hypre-v2.16.0_GH0.tar.gz) = 5765897 +TIMESTAMP = 1578026320 +SHA256 (hypre-space-hypre-v2.18.2_GH0.tar.gz) = 28007b5b584eaf9397f933032d8367788707a2d356d78e47b99e551ab10cc76a +SIZE (hypre-space-hypre-v2.18.2_GH0.tar.gz) = 5699792 diff --git a/science/hypre/pkg-plist b/science/hypre/pkg-plist index cbf68f79f621..36117972a461 100644 --- a/science/hypre/pkg-plist +++ b/science/hypre/pkg-plist @@ -1,10 +1,7 @@ include/HYPRE.h include/HYPRE_DistributedMatrixPilutSolver_protos.h include/HYPRE_DistributedMatrixPilutSolver_types.h -include/HYPRE_FEI.h -include/HYPRE_FEI_includes.h include/HYPRE_IJ_mv.h -include/HYPRE_LinSysCore.h include/HYPRE_MatvecFunctions.h include/HYPRE_config.h include/HYPRE_error_f.h @@ -20,11 +17,6 @@ include/HYPRE_struct_ls.h include/HYPRE_struct_mv.h include/HYPRE_utilities.h include/HYPREf.h -include/LLNL_FEI_Fei.h -include/LLNL_FEI_Impl.h -include/LLNL_FEI_LSCore.h -include/LLNL_FEI_Matrix.h -include/LLNL_FEI_Solver.h include/_hypre_IJ_mv.h include/_hypre_parcsr_ls.h include/_hypre_parcsr_mv.h @@ -33,21 +25,11 @@ include/_hypre_sstruct_mv.h include/_hypre_struct_ls.h include/_hypre_struct_mv.h include/_hypre_utilities.h -include/cfei-hypre.h -include/cfei.h -include/cfei_hypre.h include/csr_block_matrix.h include/csr_matmultivec.h include/distributed_matrix.h -include/fei_Data.hpp -include/fei_LinearSystemCore.hpp -include/fei_Lookup.hpp -include/fei_bool.h -include/fei_defs.h -include/fei_mpi.h include/fortran.h include/fortran_matrix.h -include/hypre_cfei.h include/hypre_hopscotch_hash.h include/interpreter.h include/krylov.h @@ -62,4 +44,4 @@ include/seq_mv.h include/temp_multivector.h lib/libHYPRE.so lib/libHYPRE.so.2 -lib/libHYPRE.so.2.16 +lib/libHYPRE.so.2.18 diff --git a/science/jmol/Makefile b/science/jmol/Makefile index 42639ba53d81..fe648a27b31a 100644 --- a/science/jmol/Makefile +++ b/science/jmol/Makefile @@ -14,6 +14,8 @@ EXTRACT_ONLY= ${PORTNAME}-${PORTVERSION}-full${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Java 3D viewer for chemical structures +BROKEN= unfetchable + LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/science/lm/Makefile b/science/lm/Makefile index d96246b2128f..c2a10416339e 100644 --- a/science/lm/Makefile +++ b/science/lm/Makefile @@ -11,6 +11,8 @@ PKGNAMESUFFIX= -uiuc MAINTAINER= yuri@FreeBSD.org COMMENT= Software for sampling trajectories of the reaction-diffusion equations +BROKEN= unfetchable + LICENSE= UIUC_OPEN_SOURCE_LICENSE LICENSE_NAME= University of Illinois Open Source License LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/science/mol2ps/Makefile b/science/mol2ps/Makefile index e055a86362d6..d3fb5897de84 100644 --- a/science/mol2ps/Makefile +++ b/science/mol2ps/Makefile @@ -3,7 +3,7 @@ PORTNAME= mol2ps PORTVERSION= 0.4b -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MASTER_SITES= http://merian.pch.univie.ac.at/pch/download/chemistry/${PORTNAME}/ DISTNAME= ${PORTNAME} diff --git a/science/openmx/Makefile b/science/openmx/Makefile index 8f8da2195379..713c7a5232c7 100644 --- a/science/openmx/Makefile +++ b/science/openmx/Makefile @@ -19,8 +19,6 @@ BROKEN= unfetchable LICENSE= GPLv2 BROKEN_i386= undefined reference to `__atomic_load', see bug#229605 and https://reviews.llvm.org/D42154 -DEPRECATED= Depends on expiring devel/openmp -EXPIRATION_DATE= 2019-12-31 LIB_DEPENDS= libblas.so:math/blas \ libfftw3.so:math/fftw3 \ diff --git a/science/py-PyFR/Makefile b/science/py-PyFR/Makefile index 390cae9d4f54..e0c3485d17fb 100644 --- a/science/py-PyFR/Makefile +++ b/science/py-PyFR/Makefile @@ -1,8 +1,7 @@ # $FreeBSD$ PORTNAME= PyFR -DISTVERSION= 1.8.0 -PORTREVISION= 5 +DISTVERSION= 1.9.0 CATEGORIES= science python MASTER_SITES= http://www.pyfr.org/download/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,9 +12,6 @@ COMMENT= Framework for solving advection-diffusion type problems LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE -DEPRECATED= Depends on expiring devel/openmp -EXPIRATION_DATE= 2019-12-31 - RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}appdirs>=1.4.0:devel/py-appdirs@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}gimmik>=2.0:math/py-gimmik@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>=2.6:science/py-h5py@${PY_FLAVOR} \ diff --git a/science/py-PyFR/distinfo b/science/py-PyFR/distinfo index 98242d6a65e7..0bd8b96669d7 100644 --- a/science/py-PyFR/distinfo +++ b/science/py-PyFR/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1539760102 -SHA256 (PyFR-1.8.0.zip) = 6b2b71886cea1bade16b3c8cd5bc681b2a9a22b7388a6aa4e69c934be69f3c23 -SIZE (PyFR-1.8.0.zip) = 829366 +TIMESTAMP = 1578023973 +SHA256 (PyFR-1.9.0.zip) = 032cff5e21e708f2b0e157aa4eabf6dfe1bd1c615cd92e62fa4a75a5453ff7d1 +SIZE (PyFR-1.9.0.zip) = 837264 diff --git a/science/py-asdf/Makefile b/science/py-asdf/Makefile index 02bf12275d8a..aa496c1ff43c 100644 --- a/science/py-asdf/Makefile +++ b/science/py-asdf/Makefile @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= asdf -PORTVERSION= 2.4.2 -PORTREVISION= 1 +PORTVERSION= 2.5.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -18,7 +17,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools_scm>=0:devel/py-setuptools_scm@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}jsonschema>=2.3<4:devel/py-jsonschema@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lz4>=0.10:archivers/py-lz4@${PY_FLAVOR} \ ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}semantic_version26>=2.3.1<2.6.1:devel/py-semantic_version26@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}semantic_version>=2.8:devel/py-semantic_version@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>=1.9.0:devel/py-six@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>=3.10:devel/py-yaml@${PY_FLAVOR} diff --git a/science/py-asdf/distinfo b/science/py-asdf/distinfo index 4250f754934d..d7c0665caeb8 100644 --- a/science/py-asdf/distinfo +++ b/science/py-asdf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1567510040 -SHA256 (asdf-2.4.2.tar.gz) = 6ff3557190c6a33781dae3fd635a8edf0fa0c24c6aca27d8679af36408ea8ff2 -SIZE (asdf-2.4.2.tar.gz) = 448618 +TIMESTAMP = 1577523916 +SHA256 (asdf-2.5.0.tar.gz) = 32a54815304b7d2cc4b42fb96f0ead0d49bdf3ac7c195e7f858bc25df267ade1 +SIZE (asdf-2.5.0.tar.gz) = 447425 diff --git a/science/py-geomet/Makefile b/science/py-geomet/Makefile new file mode 100644 index 000000000000..d9cc7592449c --- /dev/null +++ b/science/py-geomet/Makefile @@ -0,0 +1,24 @@ +# Created by: Po-Chuan Hsieh <sunpoet@FreeBSD.org> +# $FreeBSD$ + +PORTNAME= geomet +PORTVERSION= 0.2.1 +CATEGORIES= science python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= sunpoet@FreeBSD.org +COMMENT= GeoJSON <-> WKT/WKB conversion utilities + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/LICENSE + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}six>=0:devel/py-six@${PY_FLAVOR} + +USES= python +USE_PYTHON= autoplist concurrent distutils + +NO_ARCH= yes + +.include <bsd.port.mk> diff --git a/science/py-geomet/distinfo b/science/py-geomet/distinfo new file mode 100644 index 000000000000..2685adc972a0 --- /dev/null +++ b/science/py-geomet/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1577523846 +SHA256 (geomet-0.2.1.tar.gz) = adfafeac8d0b6ccc509f67c61ce6db7feb27a3eca40eaad93b2e29669e3c0297 +SIZE (geomet-0.2.1.tar.gz) = 19527 diff --git a/science/py-geomet/files/patch-setup.py b/science/py-geomet/files/patch-setup.py new file mode 100644 index 000000000000..806bca1fc493 --- /dev/null +++ b/science/py-geomet/files/patch-setup.py @@ -0,0 +1,9 @@ +--- setup.py.orig 2019-08-20 22:39:12 UTC ++++ setup.py +@@ -61,5 +61,5 @@ setup( + ], + zip_safe=False, + install_requires=['click', 'six'], +- python_requires=">2.6, !=3.3.*, <3.8", ++ python_requires=">2.6, !=3.3.*, <4", + ) diff --git a/science/py-geomet/pkg-descr b/science/py-geomet/pkg-descr new file mode 100644 index 000000000000..e467502084a3 --- /dev/null +++ b/science/py-geomet/pkg-descr @@ -0,0 +1,8 @@ +GeoMet converts GeoJSON to WKT/WKB (Well-Known Text/Binary), and vice versa. +Extended WKB/WKT are also supported. Conversion functions are exposed through +idiomatic load/loads/dump/dumps interfaces. + +GeoMet is intended to cover all common use cases for dealing with 2D, 3D, and 4D +geometries (including 'Z', 'M', and 'ZM'). + +WWW: https://github.com/geomet/geomet diff --git a/science/py-gsd/Makefile b/science/py-gsd/Makefile index b438174372a8..330fea63ea28 100644 --- a/science/py-gsd/Makefile +++ b/science/py-gsd/Makefile @@ -2,7 +2,7 @@ PORTNAME= gsd DISTVERSIONPREFIX= v -DISTVERSION= 1.9.3 +DISTVERSION= 1.10.0 CATEGORIES= science python MASTER_SITES= http://glotzerlab.engin.umich.edu/Downloads/gsd/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -17,6 +17,6 @@ RUN_DEPENDS= ${PYNUMPY} BUILD_DEPENDS= ${PYNUMPY} USES= python -USE_PYTHON= distutils autoplist +USE_PYTHON= distutils cython autoplist .include <bsd.port.mk> diff --git a/science/py-gsd/distinfo b/science/py-gsd/distinfo index 6c3d1aeb9b37..35cfc22d5024 100644 --- a/science/py-gsd/distinfo +++ b/science/py-gsd/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1570898731 -SHA256 (gsd-v1.9.3.tar.gz) = 89db85565b87d7a167ecf01881382ec4bc7280f07fe0295c2cf74af5db949231 -SIZE (gsd-v1.9.3.tar.gz) = 177157 +TIMESTAMP = 1578023096 +SHA256 (gsd-v1.10.0.tar.gz) = 6c121775106ee9073787fd3ea7c5608710f62a041d5e82b171247b057410aec3 +SIZE (gsd-v1.10.0.tar.gz) = 86383 diff --git a/science/py-phono3py/Makefile b/science/py-phono3py/Makefile index 53196db17f85..9b776a9e42a3 100644 --- a/science/py-phono3py/Makefile +++ b/science/py-phono3py/Makefile @@ -13,9 +13,6 @@ COMMENT= Software to calculate phonon-phonon interaction and related properties LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE -DEPRECATED= Depends on expiring devel/openmp -EXPIRATION_DATE= 2019-12-31 - BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ diff --git a/science/quantum-espresso/Makefile b/science/quantum-espresso/Makefile index 8c9d0ee49ff8..245c155a0281 100644 --- a/science/quantum-espresso/Makefile +++ b/science/quantum-espresso/Makefile @@ -2,8 +2,7 @@ PORTNAME= quantum-espresso DISTVERSIONPREFIX= qe- -DISTVERSION= 6.4.1 -PORTREVISION= 2 +DISTVERSION= 6.5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/quantum-espresso/distinfo b/science/quantum-espresso/distinfo index f2ae994285d2..ebd83b1dbc72 100644 --- a/science/quantum-espresso/distinfo +++ b/science/quantum-espresso/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1554789366 -SHA256 (QEF-q-e-qe-6.4.1_GH0.tar.gz) = b0d7e9f617b848753ad923d8c6ca5490d5d82495f82b032b71a0ff2f2e9cfa08 -SIZE (QEF-q-e-qe-6.4.1_GH0.tar.gz) = 83100337 +TIMESTAMP = 1577781248 +SHA256 (QEF-q-e-qe-6.5_GH0.tar.gz) = 258b2a8a6280e86dad779e5c56356d8b35dc96d12ff33dabeee914bc03d6d602 +SIZE (QEF-q-e-qe-6.5_GH0.tar.gz) = 81656121 diff --git a/science/quantum-espresso/pkg-plist b/science/quantum-espresso/pkg-plist index 9624f00b4cc1..a193ea4f32de 100644 --- a/science/quantum-espresso/pkg-plist +++ b/science/quantum-espresso/pkg-plist @@ -1,16 +1,19 @@ bin/alpha2f.x bin/average.x bin/bands.x +bin/benchmark_libxc.x bin/bse_main.x bin/casino2upf.x bin/cell2ibrav.x bin/cp.x bin/cpmd2upf.x +bin/cppp.x bin/dos.x bin/dynmat.x bin/epa.x bin/epsilon.x bin/ev.x +bin/extract_core.x bin/fd.x bin/fd_ef.x bin/fd_ifc.x @@ -21,8 +24,6 @@ bin/fix_upf.x bin/fpmd2upf.x bin/fqha.x bin/fs.x -bin/generate_rVV10_kernel_table.x -bin/generate_vdW_kernel_table.x bin/gww.x bin/gww_fit.x bin/head.x diff --git a/science/rmf/files/patch-src-hdf5_wrapper.cpp b/science/rmf/files/patch-src-hdf5_wrapper.cpp new file mode 100644 index 000000000000..0b784ecb1081 --- /dev/null +++ b/science/rmf/files/patch-src-hdf5_wrapper.cpp @@ -0,0 +1,11 @@ +--- src/hdf5_wrapper.cpp.orig 2019-10-16 16:05:15 UTC ++++ src/hdf5_wrapper.cpp +@@ -138,7 +138,7 @@ hid_t get_parameters() { + RMF_HDF5_CALL(H5Pset_cache(plist, 0, 10000, 10000000, 0.0)); + #if defined(H5_VERS_MAJOR) && H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && \ + H5_VERS_RELEASE >= 6 +- RMF_HDF5_CALL(H5Pset_libver_bounds(plist, H5F_LIBVER_18, H5F_LIBVER_LATEST)); ++ RMF_HDF5_CALL(H5Pset_libver_bounds(plist, H5F_LIBVER_V18, H5F_LIBVER_LATEST)); + #endif + return plist; + } diff --git a/science/vipster/Makefile b/science/vipster/Makefile index b4b518a8a2ef..ea227c0e2c61 100644 --- a/science/vipster/Makefile +++ b/science/vipster/Makefile @@ -2,15 +2,13 @@ PORTNAME= vipster DISTVERSIONPREFIX= v -DISTVERSION= 1.16b -PORTREVISION= 1 +DISTVERSION= 1.18b-75 +DISTVERSIONSUFFIX= -gfa5853f CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Crystalline and molecular structure visualisation program -BROKEN= unfetchable - LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/science/vipster/distinfo b/science/vipster/distinfo index cf8f587ccfdd..bfc52605a4fa 100644 --- a/science/vipster/distinfo +++ b/science/vipster/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1554132408 -SHA256 (sgsaenger-vipster-v1.16b_GH0.tar.gz) = edcc92f1dd6c2b665fb0a25e205504f86ebd784dc67b99f3ba9a5a34820f3845 -SIZE (sgsaenger-vipster-v1.16b_GH0.tar.gz) = 1181194 +TIMESTAMP = 1577938644 +SHA256 (sgsaenger-vipster-v1.18b-75-gfa5853f_GH0.tar.gz) = f8796af4e85db5e176222fb1c5f28d71f4b64557681cbb50109c5e929beeda29 +SIZE (sgsaenger-vipster-v1.18b-75-gfa5853f_GH0.tar.gz) = 1205340 diff --git a/science/vipster/files/patch-libvipster_configfile.h b/science/vipster/files/patch-libvipster_configfile.h deleted file mode 100644 index 26dd67a6dfba..000000000000 --- a/science/vipster/files/patch-libvipster_configfile.h +++ /dev/null @@ -1,11 +0,0 @@ ---- libvipster/configfile.h.orig 2018-12-21 06:15:43 UTC -+++ libvipster/configfile.h -@@ -27,7 +27,7 @@ bool saveConfig(); - #ifdef __EMSCRIPTEN__ - const std::string user_path{}; // not used - const std::string user_config{}; // not used --#elif __linux__ -+#elif __linux__ || defined(__FreeBSD__) - const std::string user_path = [](){ - auto tmp = std::getenv("XDG_CONFIG_HOME"); - return tmp == nullptr ? std::string{std::getenv("HOME")}+"/.config" : tmp; diff --git a/science/vipster/pkg-plist b/science/vipster/pkg-plist index 648b3b6f72ea..8624d290ab78 100644 --- a/science/vipster/pkg-plist +++ b/science/vipster/pkg-plist @@ -20,6 +20,8 @@ include/vipster/io/orca/param.h include/vipster/io/orca/plugin.h include/vipster/io/parameters.h include/vipster/io/plugin.h +include/vipster/io/poscar/config.h +include/vipster/io/poscar/plugin.h include/vipster/io/pwinput/config.h include/vipster/io/pwinput/param.h include/vipster/io/pwinput/plugin.h @@ -30,7 +32,7 @@ include/vipster/io/xyz/config.h include/vipster/io/xyz/plugin.h include/vipster/kpoints.h include/vipster/molecule.h -include/vipster/pse.h +include/vipster/periodictable.h include/vipster/pyvipster.h include/vipster/settings.h include/vipster/step.h @@ -41,7 +43,7 @@ include/vipster/vec.h include/vipster/version.h lib/libvipster.so lib/libvipster.so.1 -lib/libvipster.so.1.15 +lib/libvipster.so.1.18 %%DESKTOP%%share/applications/vipster.desktop %%DESKTOP%%share/icons/hicolor/128x128/apps/vipster.png %%DESKTOP%%share/metainfo/vipster.appdata.xml |