diff --git a/science/avogadrolibs/Makefile b/science/avogadrolibs/Makefile index 582ad40e44c9..6ca97f1f378c 100644 --- a/science/avogadrolibs/Makefile +++ b/science/avogadrolibs/Makefile @@ -1,72 +1,72 @@ PORTNAME= avogadrolibs DISTVERSION= 1.95.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Avogadro2 libraries for chemical editor and visualization applications WWW= https://www.openchemistry.org/projects/avogadro2/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE TEST_DEPENDS= googletest>0:devel/googletest USES= cmake:testing compiler:c++17-lang eigen:3,build,run # eigen needs to be 'run' because it is written into cmake files USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= OpenChemistry GH_TUPLE= OpenChemistry:molecules:b1e16c5:molecules/../molecules \ OpenChemistry:crystals:c3e2468:crystals/../crystals CMAKE_ON= BUILD_SHARED_LIBS CMAKE_TESTING_ON= ENABLE_TESTING OPTIONS_DEFINE= HDF5 LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB VTK OPTIONS_DEFAULT= LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB OPTIONS_SUB= yes HDF5_CMAKE_BOOL= USE_HDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/libaec LIBARCHIVE_DESC= Enable optional Libarchive features LIBARCHIVE_CMAKE_BOOL= USE_LIBARCHIVE LIBARCHIVE_USES= libarchive LIBARCHIVE_IMPLIES= QT5 LIBMSYM_DESC= Enable optional features using libmsym LIBMSYM_CMAKE_BOOL= USE_LIBMSYM LIBMSYM_LIB_DEPENDS= libmsym.so:science/libmsym LIBMSYM_IMPLIES= QT5 # enables the 'symmetry' Qt plugin MMTF_DESC= Enable optional features using mmtf MMTF_CMAKE_BOOL= USE_MMTF MMTF_BUILD_DEPENDS= mmtf-cpp>0:science/mmtf-cpp OPENGL_CMAKE_BOOL= USE_OPENGL OPENGL_USES= gl OPENGL_USE= GL=gl,glew,glu QT5_CMAKE_BOOL= USE_QT QT5_USES= qt:5 QT5_USE= QT=core,concurrent,gui,network,svg,widgets,buildtools:build,qmake:build QT5_IMPLIES= OPENGL SPGLIB_DESC= Enable optional features using spglib SPGLIB_CMAKE_BOOL= USE_SPGLIB SPGLIB_CMAKE_ON= -DSPGLIB_INCLUDE_DIR=${LOCALBASE}/include/spglib SPGLIB_LIB_DEPENDS= libsymspg.so:science/spglib SPGLIB_IMPLIES= QT5 # USE_SPGLIB only installs header file without USE_QT, and also installs SpaceGroup.a with USE_QT, see https://github.com/OpenChemistry/avogadrolibs/issues/610 VTK_DESC= Enable libraries that use VTK VTK_CMAKE_BOOL= USE_VTK VTK_LIB_DEPENDS= libvtksys-8.2.so:math/vtk8 VTK_IMPLIES= QT5 VTK_BROKEN= Needs https://github.com/psavery/genXrdPattern, etc post-install: @${RM} -r ${STAGEDIR}${PREFIX}/share/doc .include diff --git a/science/octopus/Makefile b/science/octopus/Makefile index df47a8b0ff82..c8b55f7e3dbd 100644 --- a/science/octopus/Makefile +++ b/science/octopus/Makefile @@ -1,65 +1,66 @@ PORTNAME= octopus DISTVERSION= 11.4 +PORTREVISION= 1 CATEGORIES= science # chemistry MASTER_SITES= https://octopus-code.org/download/${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Scientific program aimed at the ab initio virtual experimentation WWW= https://octopus-code.org/wiki/Main_Page LICENSE= GPLv2 BROKEN_aarch64= undefined reference to `__aarch64_cas8_acq_rel' #'` BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libarpack.so:math/arpack-ng \ libblas.so:math/blas \ libfftw3.so:math/fftw3 \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libgd.so:graphics/gd \ libgmp.so:math/gmp \ libgsl.so:math/gsl \ liblapack.so:math/lapack \ libmpfr.so:math/mpfr \ libnlopt.so:math/nlopt \ libpng.so:graphics/png \ libsymspg.so:science/spglib \ libtiff.so:graphics/tiff \ libvdwxcfort.so:science/libvdwxc \ libwebp.so:graphics/webp \ libxc.so:science/libxc \ libyaml.so:textproc/libyaml USES= compiler:c++14-lang fortran gmake jpeg libtool localbase:ldflags perl5 python shebangfix USE_CXXSTD= c++14 USE_LDCONFIG= yes SHEBANG_FILES= src/fdep/fortran_dependencies.pl testsuite/performance/create_combinations.py GNU_CONFIGURE= yes CONFIGURE_SHELL= ${PREFIX}/bin/bash CONFIGURE_ARGS= --enable-shared --disable-static LDFLAGS+= -lsymspg FCFLAGS+= -I${LOCALBASE}/include -ffree-line-length-none INSTALL_TARGET= install-strip TEST_TARGET= check-short # some tests fail, see https://gitlab.com/octopus-code/octopus/-/issues/558 OPTIONS_DEFINE= OPENMP OPTIONS_DEFAULT= OPENMP OPENMP_CONFIGURE_ENABLE= openmp .include # workaround for: # Error: BOZ literal constant at (1) is neither a data-stmt-constant nor an actual argument to INT, REAL, DBLE, or CMPLX intrinsic function [see '-fno-allow-invalid-boz'] .if ${GCC_DEFAULT} >= 10 FCFLAGS+= -fallow-argument-mismatch -fallow-invalid-boz .endif post-stage: # https://gitlab.com/octopus-code/octopus/issues/108 @${RM} ${STAGEDIR}${PREFIX}/include/yaml.h .include diff --git a/science/py-spglib/Makefile b/science/py-spglib/Makefile index 1df3e0c64f6b..dfe562c64091 100644 --- a/science/py-spglib/Makefile +++ b/science/py-spglib/Makefile @@ -1,25 +1,25 @@ PORTNAME= spglib DISTVERSIONPREFIX= v -DISTVERSION= 1.16.5 +DISTVERSION= 2.0.1 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library for finding and handling crystal symmetries (python binding) WWW= https://atztogo.github.io/spglib/ LICENSE= BSD3CLAUSE BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} USES= python:3.6+ -USE_PYTHON= distutils autoplist +USE_PYTHON= distutils autoplist pytest # tests fail to run, see https://github.com/spglib/spglib/issues/192 USE_GITHUB= yes WRKSRC_SUBDIR= python post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/spglib/_spglib*.so .include diff --git a/science/py-spglib/distinfo b/science/py-spglib/distinfo index 2d505a581703..18b47482ce6a 100644 --- a/science/py-spglib/distinfo +++ b/science/py-spglib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1651985344 -SHA256 (spglib-spglib-v1.16.5_GH0.tar.gz) = 1bbde03b6b78da756c07f458bd90d84f3c253841b9b0632db5b72c5961e87aef -SIZE (spglib-spglib-v1.16.5_GH0.tar.gz) = 2032040 +TIMESTAMP = 1665187362 +SHA256 (spglib-spglib-v2.0.1_GH0.tar.gz) = d7407c0d67174a0c5e41a82ed62948c43fcaf1b5529f97238d7fadd1123ffe22 +SIZE (spglib-spglib-v2.0.1_GH0.tar.gz) = 2879617 diff --git a/science/sirius/Makefile b/science/sirius/Makefile index 0cf736524d6e..46660b6672a5 100644 --- a/science/sirius/Makefile +++ b/science/sirius/Makefile @@ -1,52 +1,52 @@ PORTNAME= sirius DISTVERSIONPREFIX= v DISTVERSION= 7.3.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science PKGNAMESUFFIX= -quantum-chemistry # other software also has the name "sirius" PATCH_SITES= https://github.com/${GH_ACCOUNT}/${GH_PROJECT}/commit/ PATCHFILES= c45ef15637958885b1b299c09ec1bf9376e50ecc.patch:-p1 # https://github.com/electronic-structure/SIRIUS/pull/757 MAINTAINER= yuri@FreeBSD.org COMMENT= Domain specific library for electronic structure calculations WWW= https://github.com/electronic-structure/SIRIUS LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libcosta.so:math/costa \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ libopenblas.so:math/openblas \ libscalapack.so:math/scalapack \ libspfft.so:math/spfft \ libspla.so:math/spla \ libsymspg.so:science/spglib \ libxc.so:science/libxc USES= cmake:testing compiler:c++14-lang eigen:3,test fortran pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= electronic-structure GH_PROJECT= SIRIUS OPTIONS_DEFINE= NLCGLIB OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH # NLCGLIB NLCGLIB_DESC= Enable nlcglib NLCGLIB_CMAKE_BOOL= USE_NLCGLIB NLCGLIB_LIB_DEPENDS= libnlcglib.so:science/nlcglib \ libkokkoscore.so:devel/kokkos NLCGLIB_BROKEN= build breaks, see https://github.com/electronic-structure/SIRIUS/issues/759 MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi # many tests fail, see https://github.com/electronic-structure/SIRIUS/issues/760 .include diff --git a/science/spglib/Makefile b/science/spglib/Makefile index dd68978e04ff..a4f8a8aadddf 100644 --- a/science/spglib/Makefile +++ b/science/spglib/Makefile @@ -1,21 +1,36 @@ PORTNAME= spglib DISTVERSIONPREFIX= v -DISTVERSION= 1.16.5 +DISTVERSION= 2.0.1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= C library for finding and handling crystal symmetries WWW= https://spglib.github.io/spglib/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING USES= cmake USE_GITHUB= yes USE_LDCONFIG= yes .if !exists(/usr/include/omp.h) -CMAKE_ARGS+= -DUSE_OMP:BOOL=OFF +CMAKE_OFF+= USE_OMP .endif +OPTIONS_DEFINE= FORTRAN +OPTIONS_DEFAULT= FORTRAN +OPTIONS_SUB= yes + +FORTRAN_USES= fortran +FORTRAN_CMAKE_BOOL= WITH_Fortran +FORTRAN_LDFLAGS= -lomp # workaround for: undefined reference to `__kmpc_fork_call' + +do-test: # from test/README.md + cd ${WRKSRC}/test && \ + ${CMAKE_BIN} -S . -B build -DUSE_SANITIZER="Address" -DCMAKE_BUILD_TYPE="Debug" && \ + ${CMAKE_BIN} --build build -j ${_MAKE_JOBS} && \ + cd build && \ + ctest + .include diff --git a/science/spglib/distinfo b/science/spglib/distinfo index 30d432e2cbbd..b47dfdaee1e2 100644 --- a/science/spglib/distinfo +++ b/science/spglib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1651984887 -SHA256 (spglib-spglib-v1.16.5_GH0.tar.gz) = 1bbde03b6b78da756c07f458bd90d84f3c253841b9b0632db5b72c5961e87aef -SIZE (spglib-spglib-v1.16.5_GH0.tar.gz) = 2032040 +TIMESTAMP = 1665185311 +SHA256 (spglib-spglib-v2.0.1_GH0.tar.gz) = d7407c0d67174a0c5e41a82ed62948c43fcaf1b5529f97238d7fadd1123ffe22 +SIZE (spglib-spglib-v2.0.1_GH0.tar.gz) = 2879617 diff --git a/science/spglib/pkg-plist b/science/spglib/pkg-plist index 9964232486b8..9304ec4c4110 100644 --- a/science/spglib/pkg-plist +++ b/science/spglib/pkg-plist @@ -1,7 +1,14 @@ +%%FORTRAN%%bin/spglib_example_fortran.X include/spglib.h include/spglib_f08.f90 +%%FORTRAN%%lib/libspglib_f08.a +%%FORTRAN%%lib/libspglib_f08.so +%%FORTRAN%%lib/libspglib_f08.so.1 +%%FORTRAN%%lib/libspglib_f08.so.2.0.1 lib/libsymspg.a lib/libsymspg.so lib/libsymspg.so.1 -lib/libsymspg.so.1.16.5 +lib/libsymspg.so.2.0.1 +%%FORTRAN%%lib/spglib_f08.mod libdata/pkgconfig/spglib.pc +%%FORTRAN%%libdata/pkgconfig/spglib_f08.pc