diff --git a/science/2d-rewriter/Makefile b/science/2d-rewriter/Makefile index 45fb43827c5c..56025067e62c 100644 --- a/science/2d-rewriter/Makefile +++ b/science/2d-rewriter/Makefile @@ -1,21 +1,19 @@ -# Created by: Igor Serikov - PORTNAME= 2d-rewriter PORTVERSION= 1.6 CATEGORIES= science MAINTAINER= ports@FreeBSD.org COMMENT= Cellular automata simulator USES= imake xorg USE_XORG= x11 xext USE_GITHUB= yes GH_ACCOUNT= iserikov OPTIONS_DEFINE= EXAMPLES do-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/examples/ && ${COPYTREE_SHARE} \* ${STAGEDIR}${EXAMPLESDIR}) .include diff --git a/science/ChipmunkPhysics/Makefile b/science/ChipmunkPhysics/Makefile index 1a33770fa507..f00d64f4ce5a 100644 --- a/science/ChipmunkPhysics/Makefile +++ b/science/ChipmunkPhysics/Makefile @@ -1,47 +1,45 @@ -# Created by: Tim Cas - PORTNAME= ChipmunkPhysics PORTVERSION= 7.0.1 PORTREVISION= 2 CATEGORIES= science # physics MASTER_SITES= http://chipmunk-physics.net/release/Chipmunk-7.x/ \ http://files.slembcke.net/chipmunk/release/Chipmunk-7.x/ \ http://files.libsiege.org/chipmunk/ DISTNAME= Chipmunk-${PORTVERSION} MAINTAINER= ports@stdrand.com COMMENT= 2D physics engine written in C LICENSE= MIT BROKEN_armv7= src/cpHastySpace.c:31:4: error: Cannot use CP_USE_DOUBLES on 32 bit ARM USES= cmake tar:tgz USE_LDCONFIG= yes PLIST_SUB= VERSION=${PORTVERSION} OPTIONS_DEFINE= DOCS EXAMPLES DEMOS OPTIONS_SUB= yes PORTDOCS= * PORTEXAMPLES= *.c *.h DEMOS_DESC= Install the demo program (requires GLFW and GLEW) DEMOS_USES= gl DEMOS_USE= GL=glew DEMOS_LIB_DEPENDS= libglfw.so:graphics/glfw2 DEMOS_CMAKE_OFF= -DBUILD_DEMOS=OFF post-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR} (cd ${WRKSRC} && ${COPYTREE_SHARE} "README.textile VERSION.txt" ${STAGEDIR}${DOCSDIR}) (cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}) post-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/demo && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} "-name *\.c -or -name *\.h") post-install-DEMOS-on: ${INSTALL_PROGRAM} ${WRKSRC}/demo/chipmunk_demos ${STAGEDIR}${PREFIX}/bin .include diff --git a/science/InsightToolkit/Makefile b/science/InsightToolkit/Makefile index 419af12711c5..ca5d884fbe02 100644 --- a/science/InsightToolkit/Makefile +++ b/science/InsightToolkit/Makefile @@ -1,68 +1,66 @@ -# Created by: bacon@smithers.neuro.mcw.edu - PORTNAME= InsightToolkit PORTVERSION= 5.0.1 DISTVERSIONPREFIX=v PORTREVISION= 8 CATEGORIES= science biology MASTER_SITES= https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0.1/:data DISTFILES= InsightData-5.0.1.tar.gz:data MAINTAINER= ports@FreeBSD.org COMMENT= Insight Toolkit LICENSE= APACHE20 BUILD_DEPENDS= googletest>=0:devel/googletest LIB_DEPENDS= libgdcmCommon.so:devel/gdcm \ libexpat.so:textproc/expat2 \ libfftw.so:math/fftw \ libhdf5.so:science/hdf5 \ libpng.so:graphics/png \ libsz.so:science/libaec \ libtiff.so:graphics/tiff USES= cmake compiler:c++11-lang eigen:3 jpeg pkgconfig USE_GITHUB= yes GH_ACCOUNT= InsightSoftwareConsortium GH_PROJECT= ITK CMAKE_ARGS+= -DBUILD_SHARED_LIBS:BOOL=ON \ -DITK_FORBID_DOWNLOADS:BOOL=ON \ -DITK_LEGACY_SILENT:BOOL=ON \ -DITK_USE_KWSTYLE:BOOL=OFF \ -DITK_USE_SYSTEM_EXPAT:BOOL=ON \ -DITK_USE_SYSTEM_FFTW:BOOL=ON \ -DITK_USE_SYSTEM_GDCM:BOOL=ON \ -DITK_USE_SYSTEM_HDF5:BOOL=ON \ -DITK_USE_SYSTEM_JPEG:BOOL=ON \ -DITK_USE_SYSTEM_LIBRARIES:BOOL=ON \ -DITK_USE_SYSTEM_PNG:BOOL=ON \ -DITK_USE_SYSTEM_TIFF:BOOL=ON \ -DITK_USE_SYSTEM_ZLIB:BOOL=ON \ -DModule_ITKIOMIC:BOOL=ON \ -DModule_ITKIOTransformMINC:BOOL=ON \ -DModule_ITKReview:BOOL=ON USE_LDCONFIG= ${PREFIX}/lib/InsightToolkit ITK_VER= ${PORTVERSION:R} PLIST_SUB+= ITK_VER=${ITK_VER} OPTIONS_DEFINE= EXAMPLES TESTING EXAMPLES_DESC= Build examples (very time consuming) TESTING_DESC= Build testing programs (very time consuming) EXAMPLES_CMAKE_ON= -DBUILD_EXAMPLES:BOOL=ON TESTING_CMAKE_ON= -DBUILD_TESTING:BOOL=ON .include .if ${CHOSEN_COMPILER_TYPE} == gcc PLIST_SUB+= CHOSEN_COMPILER_TYPE="GNU" .else PLIST_SUB+= CHOSEN_COMPILER_TYPE="Clang" .endif post-extract: ${MV} ${WRKDIR}/${PORTNAME}-${PORTVERSION}/.ExternalData/* ${WRKSRC}/.ExternalData/ ${RM} -r ${WRKDIR}/${PORTNAME}-${PORTVERSION} .include diff --git a/science/PETSc/Makefile b/science/PETSc/Makefile index 747748b1ab59..3969ca900932 100644 --- a/science/PETSc/Makefile +++ b/science/PETSc/Makefile @@ -1,54 +1,52 @@ -# Created by: Thierry Thomas - PORTNAME= PETSc DISTVERSION= 3.16.3 CATEGORIES= science devel MASTER_SITES= https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/ DISTNAME= ${PORTNAME:tl}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Suite of data structures and routines from Argonne National Laboratory LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= cmake:devel/cmake LIB_DEPENDS= libmpich.so:net/mpich USES= blaslapack fortran gmake python:3.7+ shebangfix xorg GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-shared-libraries=1 \ --with-mpi-dir=${LOCALBASE} \ --with-python=1 --with-python-pkg-config=${LOCALBASE}/libdata/pkgconfig \ FCFLAGS="${FCFLAGS}" FFLAGS="${FCFLAGS}" \ ${CONFIGURE_ARGS_${ARCH}} CPPFLAGS="${CPPFLAGS}" \ AR=${AR} RANLIB=${RANLIB} \ MAKEFLAGS="${MAKEFLAGS}" LDFLAGS="${LDFLAGS}" LIBS="" CONFIGURE_ARGS_amd64= CFLAGS="${CFLAGS} -msse2" CXXFLAGS="${CXXFLAGS} -msse2" CONFIGURE_ARGS_i386= CFLAGS="${CFLAGS} -msse2" CXXFLAGS="${CXXFLAGS} -msse2" CONFIGURE_LOG= configure.log USE_XORG= x11 MAKEFILE= makefile SHEBANG_FILES= lib/petsc/bin/*.py lib/petsc/bin/saws/SAWs.py lib/petsc/bin/saws/*.bash config/*.py \ lib/petsc/bin/petscnagfor lib/petsc/bin/petsc-performance-view USE_LDCONFIG= yes TEST_TARGET= test BINARY_ALIAS= python=${PYTHON_CMD} LDFLAGS+= ${LOCALBASE}/lib/libmpi.so DATADIR= ${PREFIX}/share/${PORTNAME:tl} PLIST_SUB= SHLIB=${DISTVERSION} SHL=${DISTVERSION:C/\.[0-9]$//} pre-configure: ${REINPLACE_CMD} -e 's|python3|${PYTHON_CMD}|' ${WRKSRC}/${CONFIGURE_SCRIPT} post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libpetsc.so.${DISTVERSION} @${FIND} ${STAGEDIR}${PREFIX} -name "*.html" -delete @cd ${STAGEDIR}${PREFIX} && ${RM} -r bin/win32fe lib/petsc/conf/uninstall.py @${REINPLACE_CMD} -i '' -e 's|^PYTHON = .*|PYTHON = ${PYTHON_CMD}|' ${STAGEDIR}${PREFIX}/lib/petsc/conf/petscvariables @${REINPLACE_CMD} -i '' -e 's|#!/.*|#!${PYTHON_CMD}|' ${STAGEDIR}${PREFIX}/lib/petsc/conf/reconfigure-arch-*-c-debug.py @${RM} -r ${STAGEDIR}${DATADIR}/examples # examples are a mess as installed .include diff --git a/science/R-cran-AMORE/Makefile b/science/R-cran-AMORE/Makefile index b82ad953756c..10793a0af811 100644 --- a/science/R-cran-AMORE/Makefile +++ b/science/R-cran-AMORE/Makefile @@ -1,20 +1,18 @@ -# Created by: Wen Heping - PORTNAME= AMORE PORTVERSION= 0.2.14 PORTREVISION= 7 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION:C/\./-/g:C/-/./1} MAINTAINER= wen@FreeBSD.org COMMENT= MORE flexible neural network package LICENSE= GPLv2 GPLv3 LICENSE_COMB= dual DEPRECATED= Upstream no longer maintained EXPIRATION_DATE= 2022-09-12 USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-DCluster/Makefile b/science/R-cran-DCluster/Makefile index e891318a0028..ee3d17fcd92a 100644 --- a/science/R-cran-DCluster/Makefile +++ b/science/R-cran-DCluster/Makefile @@ -1,17 +1,15 @@ -# Created by: TAKATSU Tomonari - PORTNAME= DCluster DISTVERSION= 0.2-8 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= tota@FreeBSD.org COMMENT= Functions for the detection of spatial clusters of diseases LICENSE= GPLv2+ RUN_DEPENDS= R-cran-spdep>0:math/R-cran-spdep USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-Epi/Makefile b/science/R-cran-Epi/Makefile index de9d9aedb7a3..c53e53af1db6 100644 --- a/science/R-cran-Epi/Makefile +++ b/science/R-cran-Epi/Makefile @@ -1,26 +1,24 @@ -# Created by: TAKATSU Tomonari - PORTNAME= Epi PORTVERSION= 2.47 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= tota@FreeBSD.org COMMENT= Package for statistical analysis in epidemiology LICENSE= GPLv2 CRAN_DEPENDS= R-cran-cmprsk>0:science/R-cran-cmprsk \ R-cran-etm>0:science/R-cran-etm \ R-cran-plyr>0:devel/R-cran-plyr \ R-cran-dplyr>0:math/R-cran-dplyr \ R-cran-numDeriv>0:math/R-cran-numDeriv \ R-cran-data.table>0:devel/R-cran-data.table \ R-cran-zoo>0:math/R-cran-zoo \ R-cran-magrittr>0:devel/R-cran-magrittr BUILD_DEPENDS= ${CRAN_DEPENDS} RUN_DEPENDS= ${CRAN_DEPENDS} USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-FAdist/Makefile b/science/R-cran-FAdist/Makefile index 0a219471266c..05b3f7db46e1 100644 --- a/science/R-cran-FAdist/Makefile +++ b/science/R-cran-FAdist/Makefile @@ -1,15 +1,13 @@ -# Created by: Thierry Thomas - PORTNAME= FAdist PORTVERSION= 2.4 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= thierry@FreeBSD.org COMMENT= Probability distributions that are sometimes useful in hydrology LICENSE= GPLv2 USES= cran:auto-plist .include diff --git a/science/R-cran-bayesm/Makefile b/science/R-cran-bayesm/Makefile index b7fe102dde64..c7dee09738dd 100644 --- a/science/R-cran-bayesm/Makefile +++ b/science/R-cran-bayesm/Makefile @@ -1,19 +1,17 @@ -# Created by: Wen Heping - PORTNAME= bayesm DISTVERSION= 3.1-4 PORTREVISION= 1 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= wen@FreeBSD.org COMMENT= Bayesian Inference for Marketing/Micro-econometrics LICENSE= GPLv2 GPLv3 LICENSE_COMB= dual RUN_DEPENDS= R-cran-RcppArmadillo>=0:math/R-cran-RcppArmadillo USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-cmprsk/Makefile b/science/R-cran-cmprsk/Makefile index cbbdd1fcbd13..252d7dd13e79 100644 --- a/science/R-cran-cmprsk/Makefile +++ b/science/R-cran-cmprsk/Makefile @@ -1,15 +1,13 @@ -# Created by: TAKATSU Tomonari - PORTNAME= cmprsk DISTVERSION= 2.2-11 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= tota@FreeBSD.org COMMENT= Subdistribution Analysis of Competing Risks LICENSE= GPLv2+ USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-e1071/Makefile b/science/R-cran-e1071/Makefile index 7d265382862c..4c72c1f72b0e 100644 --- a/science/R-cran-e1071/Makefile +++ b/science/R-cran-e1071/Makefile @@ -1,19 +1,17 @@ -# Created by: TAKATSU Tomonari - PORTNAME= e1071 DISTVERSION= 1.7-11 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= tota@FreeBSD.org COMMENT= Misc Functions of the Department of Statistics (e1071), TU Wien LICENSE= GPLv2+ CRAN_DEPENDS= R-cran-proxy>0:math/R-cran-proxy BUILD_DEPENDS= ${CRAN_DEPENDS} RUN_DEPENDS= ${CRAN_DEPENDS} USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-eco/Makefile b/science/R-cran-eco/Makefile index 887c5fdd62a8..c9e6f52d2b08 100644 --- a/science/R-cran-eco/Makefile +++ b/science/R-cran-eco/Makefile @@ -1,14 +1,12 @@ -# Created by: Wen Heping - PORTNAME= eco PORTVERSION= 3.1.6 PORTREVISION= 10 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION:C/\./-/g:C/-/./1} MAINTAINER= wen@FreeBSD.org COMMENT= R Package for Ecological Inference in 2x2 Tables USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-epicalc/Makefile b/science/R-cran-epicalc/Makefile index 96fcdfc585f0..b2cb3a862c28 100644 --- a/science/R-cran-epicalc/Makefile +++ b/science/R-cran-epicalc/Makefile @@ -1,14 +1,12 @@ -# Created by: Wen Heping - PORTNAME= epicalc PORTVERSION= 2.15.1.0 PORTREVISION= 11 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= wen@FreeBSD.org COMMENT= Epidemiological calculator USES= cran:auto-plist .include diff --git a/science/R-cran-etm/Makefile b/science/R-cran-etm/Makefile index 5d0980b7a3b8..932d09568631 100644 --- a/science/R-cran-etm/Makefile +++ b/science/R-cran-etm/Makefile @@ -1,21 +1,19 @@ -# Created by: TAKATSU Tomonari - PORTNAME= etm DISTVERSION= 1.1.1 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= tota@FreeBSD.org COMMENT= Empirical Transition Matrix LICENSE= MIT CRAN_DEPENDS= R-cran-data.table>0:devel/R-cran-data.table \ R-cran-Rcpp>=0.11.4:devel/R-cran-Rcpp \ R-cran-RcppArmadillo>0:math/R-cran-RcppArmadillo BUILD_DEPENDS= ${CRAN_DEPENDS} RUN_DEPENDS= ${CRAN_DEPENDS} USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-fastICA/Makefile b/science/R-cran-fastICA/Makefile index f3cf59511bd6..3062f59d9bb5 100644 --- a/science/R-cran-fastICA/Makefile +++ b/science/R-cran-fastICA/Makefile @@ -1,16 +1,14 @@ -# Created by: David Naylor - PORTNAME= fastICA DISTVERSION= 1.2-3 CATEGORIES= science math DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= ygy@FreeBSD.org COMMENT= FastICA Algorithms to Perform ICA and Projection Pursuit LICENSE= GPLv2 GPLv3 LICENSE_COMB= dual USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-kernlab/Makefile b/science/R-cran-kernlab/Makefile index e43799b76d08..19c25bc4d113 100644 --- a/science/R-cran-kernlab/Makefile +++ b/science/R-cran-kernlab/Makefile @@ -1,15 +1,13 @@ -# Created by: TAKATSU Tomonari - PORTNAME= kernlab DISTVERSION= 0.9-31 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= tota@FreeBSD.org COMMENT= Kernel-Based Machine Learning Lab LICENSE= GPLv2 USES= compiler:c++11-lang cran:auto-plist,compiles .include diff --git a/science/R-cran-ks/Makefile b/science/R-cran-ks/Makefile index 1e834c5dc4f6..88de1674754d 100644 --- a/science/R-cran-ks/Makefile +++ b/science/R-cran-ks/Makefile @@ -1,23 +1,21 @@ -# Created by: Thierry Thomas - PORTNAME= ks PORTVERSION= 1.13.5 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= thierry@FreeBSD.org COMMENT= Kernel Smoothing LICENSE= GPLv2+ RUN_DEPENDS= R-cran-FNN>0:math/R-cran-FNN \ R-cran-mclust>0:math/R-cran-mclust \ R-cran-plot3D>0:math/R-cran-plot3D \ R-cran-pracma>0:math/R-cran-pracma \ R-cran-mvtnorm>0:math/R-cran-mvtnorm \ R-cran-kernlab>0:science/R-cran-kernlab \ R-cran-multicool>0:devel/R-cran-multicool USES= cran:compiles .include diff --git a/science/R-cran-snow/Makefile b/science/R-cran-snow/Makefile index 7ee24ce2894f..28c5a33c0e0b 100644 --- a/science/R-cran-snow/Makefile +++ b/science/R-cran-snow/Makefile @@ -1,15 +1,13 @@ -# Created by: TAKATSU Tomonari - PORTNAME= snow DISTVERSION= 0.4-4 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= tota@FreeBSD.org COMMENT= Support for simple parallel computing in R LICENSE= GPLv2+ USES= cran:auto-plist .include diff --git a/science/R-cran-som/Makefile b/science/R-cran-som/Makefile index cbb5b653d457..3599001fc0ff 100644 --- a/science/R-cran-som/Makefile +++ b/science/R-cran-som/Makefile @@ -1,16 +1,14 @@ -# Created by: TAKATSU Tomonari - PORTNAME= som DISTVERSION= 0.3-5.1 PORTREVISION= 4 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= tota@FreeBSD.org COMMENT= Self-Organizing Map LICENSE= GPLv3 USES= cran:auto-plist,compiles .include diff --git a/science/R-cran-udunits2/Makefile b/science/R-cran-udunits2/Makefile index 0cd5d1df93d4..b045acac0b21 100644 --- a/science/R-cran-udunits2/Makefile +++ b/science/R-cran-udunits2/Makefile @@ -1,18 +1,16 @@ -# Created by: TAKATSU Tomonari - PORTNAME= udunits2 PORTVERSION= 0.13.2.1 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= tota@FreeBSD.org COMMENT= Udunits-2 Bindings for R LICENSE= GPLv2 LIB_DEPENDS= libudunits2.so:science/udunits \ libexpat.so:textproc/expat2 USES= cran:auto-plist,compiles .include diff --git a/science/abinit/Makefile b/science/abinit/Makefile index 9ee9180fa889..57322a7efa44 100644 --- a/science/abinit/Makefile +++ b/science/abinit/Makefile @@ -1,99 +1,97 @@ -# Created by: NAKATA Maho - PORTNAME= abinit DISTVERSION= 9.4.2 PORTREVISION= 5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Full-featured atomic-scale first-principles simulation software LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le BUILD_DEPENDS= gm4:devel/m4 \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pygments>=0:textproc/py-pygments@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}graphviz>0:graphics/py-graphviz@${PY_FLAVOR} LIB_DEPENDS= libelpa.so:math/elpa \ libsz.so:science/libaec \ libelpa.so:math/elpa \ libxc.so:science/libxc \ libfftw3.so:math/fftw3 \ libhdf5.so:science/hdf5 \ libxml2.so:textproc/libxml2 \ libnetcdf.so:science/netcdf \ libxmlf90.so:textproc/xmlf90 \ libwannier.so:science/wannier90 \ libnetcdff.so:science/netcdf-fortran RUN_DEPENDS= atompaw:science/atompaw TEST_DEPENDS= ${PYNUMPY} \ libyaml>0:textproc/libyaml USES= autoreconf:build blaslapack:netlib fortran gmake gnome localbase:ldflags \ python:3.7+ shebangfix USE_GITHUB= yes USE_GNOME= libxml2 SHEBANG_FILES= config/scripts/* doc/tutorial/paral_gspw_assets/abinit.sub.* SHEBANG_GLOB= *.py GNU_CONFIGURE= yes CONFIGURE_ENV= CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" FC_LDFLAGS="${LDFLAGS}" \ H5CC="${LOCALBASE}/bin/h5cc" \ HDF5_CFLAGS="-I${LOCALBASE}/include" \ HDF5_LDFLAGS="-L${LOCALBASE}/lib -lhdf5" \ LINALG_FCFLAGS="-I${LOCALBASE}/include/elpa-2019.05.002/modules" \ LINALG_LIBS="${BLASLIB} ${LAPACKLIB} -lelpa" \ NETCDF_FORTRAN_FCFLAGS=-I${LOCALBASE}/include \ XMLF90_FCFLAGS=-I${LOCALBASE}/include \ WANNIER90_LIBS="${BLASLIB} ${LAPACKLIB} -lwannier" CONFIGURE_ARGS= --with-fft --with-libxc --with-libxml2 --with-netcdf \ --with-netcdf-fortran --with-wannier90 --with-xmlf90 FCFLAGS+= -ffree-line-length-none TEST_TARGET= tests_abirules tests_buildsys TEST_WRKSRC= ${WRKSRC}/abichecks PORTDOCS= * OPTIONS_DEFINE= DOCS OPENMP MPI OPTIONS_DEFAULT= OPENMP MPI OPENMP_CONFIGURE_ENABLE= openmp OPENMP_LDFLAGS= -lomp MPI_CONFIGURE_WITH= mpi=yes # fftw3 not enabled because libfftw3_mpi is required but not packaged MPI_VARS= FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include \ CONFIGURE_ENV+=MPI_LIBS="`pkg-config --libs mpich` -lmpifort" \ CONFIGURE_ENV+MPI_LDFLAGS="`pkg-config --libs mpich` -lmpifort" MPI_BUILD_DEPENDS= mpich>0:net/mpich MPI_RUN_DEPENDS= mpich>0:net/mpich .if defined(WITH_LEVMAR) # --with-levmar seems deprecated LIB_DEPENDS+= liblevmar.so:math/levmar CONFIGURE_ENV+= LEVMAR_LIBS="-llevmar ${BLASLIB} ${LAPACKLIB}" CONFIGURE_ARGS+= --with-levmar .endif .include .if ${GCC_DEFAULT} >= 10 FCFLAGS+= -fallow-argument-mismatch # see https://github.com/abinit/abinit/issues/41 .endif pre-configure: (cd ${WRKSRC} && ./autogen.sh) post-install-DOCS-on: ${REINPLACE_CMD} -e 's|/usr/bin/env python|${PYTHON_CMD}|' \ ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py ${RM} ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py.bak @${MKDIR} ${STAGEDIR}${DOCSDIR} ${CP} -R ${WRKSRC}/doc/tutorial ${STAGEDIR}${DOCSDIR} pre-test: ${TOUCH} ${TEST_WRKSRC}/make.log .include diff --git a/science/bddsolve/Makefile b/science/bddsolve/Makefile index 3f7f22c2d24e..5d4bd31ee786 100644 --- a/science/bddsolve/Makefile +++ b/science/bddsolve/Makefile @@ -1,33 +1,31 @@ -# Created by: Ed Schouten - PORTNAME= bddsolve PORTVERSION= 1.04 PORTREVISION= 10 CATEGORIES= science MASTER_SITES= http://www.win.tue.nl/~wieger/bddsolve/_downloads/ DISTNAME= ${PORTNAME}-source-${PORTVERSION} MAINTAINER= ed@FreeBSD.org COMMENT= BDD-based satisfiability and reachability solver LIB_DEPENDS+= libbdd.so:science/buddy \ libboost_program_options.so:devel/boost-libs USES= compiler:c++11-lang zip NO_WRKSUBDIR= yes CFLAGS+= -I${LOCALBASE}/include -I${WRKSRC}/include LDFLAGS+= -L${LOCALBASE}/lib -lbdd -lboost_program_options OPTIONS_DEFINE= EXAMPLES do-build: ${SETENV} ${MAKE_ENV} ${CXX} ${CXXFLAGS} ${LDFLAGS} \ -o ${WRKSRC}/bddsolve ${WRKSRC}/src/bddsolve.cpp do-install: ${INSTALL_PROGRAM} ${WRKSRC}/bddsolve ${STAGEDIR}${PREFIX}/bin @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/example/reach.b ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/example/sat.b ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/bodr/Makefile b/science/bodr/Makefile index 632c5d389b45..619679e86fd7 100644 --- a/science/bodr/Makefile +++ b/science/bodr/Makefile @@ -1,28 +1,26 @@ -# Created by: Pav Lucistnik - PORTNAME= bodr PORTVERSION= 10 CATEGORIES= science MASTER_SITES= SF MAINTAINER= ports@FreeBSD.org COMMENT= Chemistry data like element and isotope properties, atomic radii, etc LICENSE= CC0-1.0 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= xsltproc:textproc/libxslt USES= gmake perl5 tar:bzip2 USE_PERL5= build GNU_CONFIGURE= yes CONFIGURE_ENV= PERL="${PERL}" NO_ARCH= yes OPTIONS_DEFINE= DOCS post-patch: @${REINPLACE_CMD} -e \ '/pkgconfig/s|{datadir}|{prefix}/libdata|' ${WRKSRC}/Makefile.in .include diff --git a/science/buddy/Makefile b/science/buddy/Makefile index eba6daa57b15..a51ac0b9f01d 100644 --- a/science/buddy/Makefile +++ b/science/buddy/Makefile @@ -1,25 +1,23 @@ -# Created by: Leland Wang - PORTNAME= buddy PORTVERSION= 2.4 PORTREVISION= 2 CATEGORIES= science MASTER_SITES= SF/${PORTNAME}/${PORTNAME}/BuDDy%20${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Binary Decision Diagram library USES= gmake libtool GNU_CONFIGURE= yes USE_LDCONFIG= yes INSTALL_TARGET= install-strip DOCS= doc/bddnotes.ps doc/buddy.ps doc/tech.txt README AUTHORS OPTIONS_DEFINE= DOCS post-install: ${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} .include diff --git a/science/cdcl/Makefile b/science/cdcl/Makefile index e3330f49b10b..58ded39c15a0 100644 --- a/science/cdcl/Makefile +++ b/science/cdcl/Makefile @@ -1,57 +1,55 @@ -# Created by: Shin'ya Murakami - PORTNAME= cdcl PORTVERSION= 5.4.8 PORTREVISION= 1 CATEGORIES= science graphics MASTER_SITES= http://www.gfd-dennou.org/arch/dcl/ \ http://dennou-h.gfd-dennou.org/arch/dcl/ \ http://dennou-q.gfd-dennou.org/arch/dcl/ DISTNAME= dcl-${PORTVERSION}-C MAINTAINER= murashin@gfd-dennou.org COMMENT= Scientific graphic library for geoscience # Converted from RESTRICTED LICENSE= cdcl LICENSE_NAME= cdcl LICENSE_TEXT= No commercial use LICENSE_PERMS= auto-accept BROKEN= fails to fetch from mastersite (newest release is 7.4.0 of 2020611) BROKEN_armv6= fails to link: final link failed: Nonrepresentable section on output BROKEN_armv7= fails to link: final link failed: Nonrepresentable section on output OPTIONS_DEFINE= DOCS EXAMPLES USES= desthack gnome pkgconfig xorg USE_XORG= x11 xext USE_GNOME= gtk20 gdkpixbuf2 GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-x --enable-shared # Fix build with clang11 CFLAGS+= -fcommon PLIST_SUB= DCL_VERSION=${PORTVERSION:S/.//g} MAKE_JOBS_UNSAFE= yes BINARIES= cdclcmap cdclclr cdcldate cdcldbs cdclexec cdclfont \ cdclpara cdcltone cdcltrf cdclver PORTDOCS= CHECK CREDITS HISTORY README PORTEXAMPLES= * post-configure: @${REINPLACE_CMD} -e 's|$$(DCLLANG)dcl$$(DCLVERNUM)|$$(DCLLANG)dcl|' ${WRKSRC}/Mkinclude post-install: .for i in ${BINARIES} ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/${i} .endfor @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/demo/ && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) @${MKDIR} ${STAGEDIR}${DOCSDIR} .for i in ${PORTDOCS} ${INSTALL_DATA} ${WRKSRC}/${i} ${STAGEDIR}${DOCSDIR}/ .endfor .include diff --git a/science/cdf/Makefile b/science/cdf/Makefile index e6fefdb446b5..04e928ebf836 100644 --- a/science/cdf/Makefile +++ b/science/cdf/Makefile @@ -1,55 +1,53 @@ -# Created by: Thierry Thomas - PORTNAME= cdf3 PORTVERSION= 3.8.0 CATEGORIES= science MASTER_SITES= https://spdf.gsfc.nasa.gov/pub/software/cdf/dist/cdf38_0/ DISTNAME= cdf${VER}-dist-cdf DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= stephen@FreeBSD.org COMMENT= Device independent view of the CDF data model LICENSE= NASA-G LICENSE_NAME= NASA/Goddard Space Flight Center LICENSE_FILE= ${WRKSRC}/CDF_copyright.txt LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BUILD_DEPENDS= bash:shells/bash USES= fortran ncurses gmake USE_LDCONFIG= yes 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 VER= ${PORTVERSION:S/.//:S/./_/} DEFS= B C K PORTDOCS= CDF_copyright.txt CHANGES.txt Release.notes Welcome.txt OPTIONS_DEFINE= DOCS EXAMPLES MAKE_ARGS+= OS=freebsd ENV=gnu all post-patch: .for def in ${DEFS} @${REINPLACE_CMD} -e 's||${PREFIX}|' \ ${WRKSRC}/src/definitions/definitions.${def} .endfor post-install: ${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${PORTDOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} ${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 diff --git a/science/cdo/Makefile b/science/cdo/Makefile index da2a1f823586..61ff1c99ed37 100644 --- a/science/cdo/Makefile +++ b/science/cdo/Makefile @@ -1,81 +1,79 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= cdo PORTVERSION= 2.0.5 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/26823/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= Climate Data Operators LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING OPTIONS_DEFINE= CGRIBEX ECCODES HDF5 JASPER NETCDF PROJ SZIP UDUNITS UUID OPTIONS_DEFAULT=CGRIBEX ECCODES HDF5 JASPER NETCDF PROJ SZIP UDUNITS UUID OPTIONS_SUB= yes CGRIBEX_DESC= Use CGRIBEX library for GRIB1 files ECCODES_DESC= Use ecCodes for GRIB files HDF5_IMPLIES= SZIP NETCDF_IMPLIES= HDF5 UUID_DESC= UUID support PORTSCOUT= site:https://code.mpimet.mpg.de/projects/cdo/files USES= compiler:c++14-lang gmake libtool localbase pathfix CONFIGURE_ARGS= --disable-data \ --disable-extra \ --disable-fortran \ --disable-ieg \ --disable-openmp \ --disable-service \ --enable-cdi-lib \ --program-transform-name="" \ --with-zlib=/usr GNU_CONFIGURE= yes INSTALL_TARGET= install-strip MAKE_JOBS_UNSAFE= yes TEST_TARGET= check USE_CXXSTD= c++14 USE_LDCONFIG= yes CGRIBEX_CONFIGURE_WITH= cgribex CGRIBEX_LIB_DEPENDS= libcgribex.so:science/cgribex ECCODES_CONFIGURE_WITH= eccodes ECCODES_LIB_DEPENDS= libeccodes.so:science/eccodes HDF5_CONFIGURE_WITH= hdf5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 JASPER_CONFIGURE_WITH= jasper JASPER_LIB_DEPENDS= libjasper.so:graphics/jasper NETCDF_CONFIGURE_WITH= netcdf NETCDF_LIB_DEPENDS= libnetcdf.so:science/netcdf PROJ_CONFIGURE_WITH= proj PROJ_LIB_DEPENDS= libproj.so:graphics/proj SZIP_CONFIGURE_WITH= szlib SZIP_LIB_DEPENDS= libsz.so:science/libaec UDUNITS_CONFIGURE_WITH= udunits2 UDUNITS_LIB_DEPENDS= libudunits2.so:science/udunits UUID_CONFIGURE_OFF= ac_cv_func_uuid_create=no ac_cv_have_decl_uuid_create=no ac_cv_have_decl_uuid_generate=no ac_cv_lib_uuid_uuid_generate=no UUID_LIB_DEPENDS= libuuid.so:misc/e2fsprogs-libuuid .include .if ${ARCH} != "sparc64" CFLAGS+= -DPTHREAD_MUTEXATTR .endif post-patch: @${REINPLACE_CMD} -e '/^SUBDIRS = / s| contrib||' ${WRKSRC}/Makefile.in @${REINPLACE_CMD} -e 's|$$(libdir)/\($$$$pkgconfigfile\)|${PREFIX}/libdata/\1|' ${WRKSRC}/libcdi/src/Makefile.in @${REINPLACE_CMD} -e 's|unsigned32 |uint32_t |' ${WRKSRC}/libcdi/src/cdilib.c ${WRKSRC}/libcdi/src/util.c post-install: ${INSTALL_DATA} ${WRKSRC}/libcdi/src/cdi.inc ${STAGEDIR}${PREFIX}/include/cdi.inc test-NETCDF-on: @cd ${WRKSRC}/ && ${SETENV} CDO_PATH=src/cdo src/cdotest .include diff --git a/science/cgnslib/Makefile b/science/cgnslib/Makefile index 0b1d574c80d8..2e7b88a982e5 100644 --- a/science/cgnslib/Makefile +++ b/science/cgnslib/Makefile @@ -1,65 +1,63 @@ -# Created by: thierry@pompo.net - PORTNAME= cgnslib PORTVERSION= 4.3.0 DISTVERSIONPREFIX= v PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= science MAINTAINER= thierry@FreeBSD.org COMMENT= CFD General Notation System library code LICENSE= AS-IS LICENSE_NAME= AS-IS LICENSE_FILE= ${WRKSRC}/license.txt LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept USES= cmake USE_GITHUB= yes GH_ACCOUNT= CGNS GH_PROJECT= CGNS USE_LDCONFIG= yes MAKE_JOBS_UNSAFE= yes #CMAKE_ARGS= -DOpenGL_GL_PREFERENCE:STRING="GLVND" CMAKE_ARGS= -DOpenGL_GL_PREFERENCE:STRING="LEGACY" FFLAGS+= -fPIC -std=legacy TEST_TARGET= test OPTIONS_DEFINE= FORTRAN HDF5 TESTS TOOLS OPTIONS_DEFAULT= FORTRAN HDF5 TESTS TOOLS OPTIONS_SUB= yes HDF5_DESC= Enable HDF5 interface TESTS_DESC= Enable test programs TOOLS_DESC= Build the CGNSTools package FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= CGNS_ENABLE_FORTRAN HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/libaec HDF5_CMAKE_BOOL= CGNS_ENABLE_HDF5 HDF5_CMAKE_ON= -DHDF5_INCLUDE_PATH:PATH="${LOCALBASE}/include" TESTS_CMAKE_BOOL= CGNS_ENABLE_TESTS TOOLS_USES= gl localbase tk xorg TOOLS_LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 TOOLS_USE= GL=egl,gl,glu \ XORG=ice,sm,x11,xau,xcomposite,xcursor,xdamage,xdmcp,xext,xfixes,xft,xi,xinerama,xkbfile,xmu,xpm,xrandr,xrender,xres,xscrnsaver,xt,xtst,xv,xxf86vm TOOLS_CMAKE_BOOL= CGNS_BUILD_CGNSTOOLS TOOLS_CMAKE_ON= -DTCL_INCLUDE_PATH:STRING="${TCL_INCLUDEDIR}" \ -DTK_INCLUDE_PATH:STRING="${TK_INCLUDEDIR}" post-install: ${RLN} ${STAGEDIR}${PREFIX}/lib/libcgns.so.${PORTVERSION:R} \ ${STAGEDIR}${PREFIX}/lib/libcgns.so.${PORTVERSION:R:R} do-test: cd ${TEST_WRKSRC} && \ ${SETENV} ${TEST_ENV} ctest -C ${CMAKE_BUILD_TYPE} .include diff --git a/science/cgribex/Makefile b/science/cgribex/Makefile index dedba8523f3e..e1ea9fa03beb 100644 --- a/science/cgribex/Makefile +++ b/science/cgribex/Makefile @@ -1,39 +1,37 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= cgribex PORTVERSION= 1.9.4 PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/21178/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= Lightweight GRIBEX in C with portable Fortran interface LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING USES= libtool CPPFLAGS+= -DgFortran GNU_CONFIGURE= yes INSTALL_TARGET= install-strip USE_LDCONFIG= yes OPTIONS_DEFINE= GRIB_API JASPER SZIP OPTIONS_DEFAULT=JASPER SZIP GRIB_API_CONFIGURE_WITH=grib_api=${LOCALBASE} GRIB_API_LIB_DEPENDS= libgrib_api.so:science/grib_api JASPER_CONFIGURE_WITH= jasper=${LOCALBASE} JASPER_LIB_DEPENDS= libjasper.so:graphics/jasper SZIP_CONFIGURE_WITH= szlib=${LOCALBASE} SZIP_LIB_DEPENDS= libsz.so:science/libaec post-configure: @${REINPLACE_CMD} -e 's|-Ino/include||g; s|-Lno/lib||g' ${WRKSRC}/Makefile ${WRKSRC}/*/Makefile post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libcgribex.so .include diff --git a/science/checkmol/Makefile b/science/checkmol/Makefile index 663967d6a6b1..8175edb8abbd 100644 --- a/science/checkmol/Makefile +++ b/science/checkmol/Makefile @@ -1,33 +1,31 @@ -# Created by: Fernan Aguero - PORTNAME= checkmol PORTVERSION= 0.5 PORTREVISION= 14 CATEGORIES= science MASTER_SITES= https://homepage.univie.ac.at/norbert.haider/download/chemistry/checkmol/ DISTFILES= ${PORTNAME} EXTRACT_SUFX= .pas MAINTAINER= acm@FreeBSD.org COMMENT= Analyze molecules for the presence of functional groups LICENSE= GPLv2+ NO_WRKSUBDIR= yes EXTRACT_CMD= ${CP} EXTRACT_BEFORE_ARGS= # EXTRACT_AFTER_ARGS= ${WRKSRC} USES= fpc PLIST_FILES= bin/checkmol bin/matchmol do-build: (cd ${WRKSRC} && ${LOCALBASE}/bin/fpc ${EXTRACT_ONLY} -S2 -O3) do-install: (cd ${WRKSRC} && ${INSTALL_PROGRAM} ${PORTNAME} ${STAGEDIR}${PREFIX}/bin/${PORTNAME}) (cd ${STAGEDIR}${PREFIX}/bin && ${LN} ${PORTNAME} matchmol) .include diff --git a/science/chemical-mime-data/Makefile b/science/chemical-mime-data/Makefile index 4f39d6b18ebb..c7481bf077df 100644 --- a/science/chemical-mime-data/Makefile +++ b/science/chemical-mime-data/Makefile @@ -1,24 +1,22 @@ -# Created by: Pav Lucistnik - PORTNAME= chemical-mime-data PORTVERSION= 0.1.94 PORTREVISION= 10 CATEGORIES= science MASTER_SITES= SF/chemical-mime/${PORTNAME}/${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Collection of chemical MIME types for UNIX desktops USES= gettext-tools gmake gnome pathfix pkgconfig shared-mime-info \ tar:bzip2 USE_GNOME= gnomemimedata intlhack librsvg2:build libxslt:build GNU_CONFIGURE= yes CONFIGURE_ARGS= --disable-update-database CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib post-patch: @${REINPLACE_CMD} -e 's|*-*-solaris*|*| ; s|rsvg|rsvg-convert|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|-f png $$< |-f png $$< > |' ${WRKSRC}/icons/hicolor/Makefile.in .include diff --git a/science/chemtool-devel/Makefile b/science/chemtool-devel/Makefile index c78ebf5259c2..39ac15ec09b2 100644 --- a/science/chemtool-devel/Makefile +++ b/science/chemtool-devel/Makefile @@ -1,39 +1,37 @@ -# Created by: NAKATA, Maho - PORTNAME= chemtool PORTVERSION= 1.7.20050716 PORTREVISION= 10 CATEGORIES= science MASTER_SITES= http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ PKGNAMESUFFIX= -devel DISTNAME= ct17a15 MAINTAINER= ports@FreeBSD.org COMMENT= Drawing organic molecules easily and store them (developer version) BROKEN_FreeBSD_13= ld: error: duplicate symbol: babelin BROKEN_FreeBSD_14= ld: error: duplicate symbol: babelin LIB_DEPENDS= libEMF.so:graphics/libemf RUN_DEPENDS= fig2dev:print/fig2dev USES= compiler:c++11-lang gettext gmake gnome pkgconfig tar:tgz xorg WRKSRC= ${WRKDIR}/${PORTNAME}-1.7alpha15/ USE_GNOME= gtk20 USE_XORG= x11 GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-emf=yes MAKE_ARGS+= MAKE=${MAKE_CMD} MAKE_JOBS_UNSAFE= yes CPPFLAGS+= -I${LOCALBASE}/include -I${LOCALBASE}/include/libEMF LIBS+= -L${LOCALBASE}/lib post-patch: @${REINPLACE_CMD} 's/-lstdc++//' ${WRKSRC}/configure @${REINPLACE_CMD} '/^SYS_LIBRARIES =/s/$$/ -lX11/' ${WRKSRC}/Makefile.in post-install: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/chemtool/Makefile b/science/chemtool/Makefile index d286cdc57a8c..55d1ce1529b8 100644 --- a/science/chemtool/Makefile +++ b/science/chemtool/Makefile @@ -1,40 +1,38 @@ -# Created by: Ying-Chieh Liao - PORTNAME= chemtool DISTVERSION= 1.6.14 PORTREVISION= 3 CATEGORIES= science MASTER_SITES= http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ MAINTAINER= yuri@FreeBSD.org COMMENT= Draw organic molecules easily and store them LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libEMF.so:graphics/libemf \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 RUN_DEPENDS= fig2dev:print/fig2dev USES= compiler:c++11-lang gmake gnome pkgconfig xorg GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-emf=yes --with-localedir=${PREFIX} USE_GNOME= cairo gdkpixbuf2 gtk20 USE_XORG= x11 CFLAGS+= -fcommon # notified the author via e-mail on Sep 20, 2020 OPTIONS_DEFINE= NLS EXAMPLES OPTIONS_SUB= yes NLS_USES= gettext NLS_CONFIGURE_ENABLE= nls PORTEXAMPLES= * do-install-EXAMPLES-on: cd ${WRKSRC}/examples && ${FIND} . | \ ${CPIO} -pdm -L -R ${SHAREOWN}:${SHAREGRP} ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/clhep/Makefile b/science/clhep/Makefile index cfb4ffec89f3..2674db91b1c6 100644 --- a/science/clhep/Makefile +++ b/science/clhep/Makefile @@ -1,29 +1,27 @@ -# Created by: will - PORTNAME= clhep PORTVERSION= 2.4.1.0 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/ MAINTAINER= bofh@FreeBSD.org COMMENT= Object-oriented toolkit for particle physics applications by CERN LICENSE= GPLv3 LGPL3 LICENSE_COMB= multi USES= cmake compiler:c++11-lang perl5 tar:tgz WRKSRC= ${WRKDIR}/${PORTVERSION}/${PORTNAME:tu} USE_PERL5= build USE_LDCONFIG= yes PLIST_SUB= VERSION="${PORTVERSION}" post-patch: @${REINPLACE_CMD} -e \ '/DESTINATION/s|lib$${LIB_SUFFIX}|libdata|' \ ${WRKSRC}/cmake/Modules/ClhepToolchain.cmake .include diff --git a/science/code_saturne/Makefile b/science/code_saturne/Makefile index 79b6c7be7272..d382e59f3481 100644 --- a/science/code_saturne/Makefile +++ b/science/code_saturne/Makefile @@ -1,129 +1,127 @@ -# Created by: thierry@pompo.net - PORTNAME= code_saturne PORTVERSION= 7.1.1 DISTVERSIONPREFIX= v CATEGORIES= science parallel MAINTAINER= thierry@FreeBSD.org COMMENT= EDF's general purpose Computational Fluid Dynamics (CFD) software LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= gsed:textproc/gsed LIB_DEPENDS= libsysinfo.so:devel/libsysinfo \ libcgns.so:science/cgnslib \ libhdf5.so:science/hdf5 \ libmedC.so:french/med RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ xmgrace:math/grace \ bash:shells/bash \ xterm:x11/xterm USE_GITHUB= yes GH_ACCOUNT= code-saturne USES= autoreconf bison compiler:c11 fortran gettext gnome gmake \ iconv localbase libtool pyqt:5 python:3.7+ shebangfix xorg USE_GNOME= libxml2 USE_PYQT= pyqt5 sip USE_XORG= x11 SHEBANG_FILES= install_saturne.py tests/unittests.py bin/*.py build-aux/*.py CFLAGS+= -D__XSI_VISIBLE CPPFLAGS+= -I${LOCALBASE}/include -I${LOCALBASE}/include/libxml2 GNU_CONFIGURE= yes CONFIGURE_ARGS= --without-salome --without-salome-yacs --without-salome-kernel \ --without-salome-gui --enable-python CONFIGURE_ENV= ac_cv_path_SED=${LOCALBASE}/bin/gsed USE_LDCONFIG= yes INSTALL_TARGET= install-strip BINARY_ALIAS= python=${PYTHON_CMD} \ pyrcc5=pyrcc5-${PYTHON_VER} \ pyuic5=pyuic5-${PYTHON_VER} OPTIONS_DEFINE= DOCS EXAMPLES BATCH BLAS HYPRE MPICH MUMPS PETSC SCOTCH OPTIONS_DEFAULT= BATCH BLAS HYPRE METIS MPICH MUMPS PETSC SCOTCH OPTIONS_RADIO= METIS OPTIONS_RADIO_METIS= METIS PARMETIS OPTIONS_SUB= yes BLAS_DESC= Support of BLAS BLAS_USES= blaslapack BLAS_CONFIGURE_ON= --with-blas=yes --with-blas-type=BLAS \ --with-blas-include=${LOCALBASE}/include/cblas \ --with-blas-lib=${LOCALBASE}/lib BLAS_LIB_DEPENDS= libcblas.so:math/cblas BATCH_DESC= Use Torque to submit batches BATCH_RUN_DEPENDS= pbs-config:sysutils/torque HYPRE_DESC= Support of HYPRE HYPRE_BUILD_DEPENDS= hypre>0:science/hypre HYPRE_RUN_DEPENDS= hypre>0:science/hypre HYPRE_CONFIGURE_ON= --with-hypre="${LOCALBASE}" MPICH_USES= mpi MPICH_BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mpi4py>0:net/py-mpi4py@${PY_FLAVOR} MPICH_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mpi4py>0:net/py-mpi4py@${PY_FLAVOR} MPICH_CONFIGURE_WITH= mpi METIS_DESC= Support of METIS METIS_LIB_DEPENDS= libmetis.so:math/metis METIS_CONFIGURE_ON= --with-metis-include="${LOCALBASE}/include" MUMPS_DESC= Support of MUMPS MUMPS_LIB_DEPENDS= libsmumps.so:math/mumps MUMPS_CONFIGURE_ON= --with-mumps="${LOCALBASE}" MUMPS_CONFIGURE_ENV= MUMPS_LIBS="-lmpiseq -llapack" PARMETIS_DESC= Support of ParMETIS PARMETIS_LIB_DEPENDS= libparmetis.so:math/parmetis PARMETIS_CONFIGURE_ON= --with-metis-include="${LOCALBASE}/include/parmetis" \ --with-metis-lib="${LOCALBASE}/lib/parmetis" PARMETIS_CONFIGURE_ENV= LIBS=-lexecinfo PETSC_DESC= Support of PETSc PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc PETSC_CONFIGURE_ON= --with-petsc="${LOCALBASE}" SCOTCH_DESC= Support of Scotch SCOTCH_LIB_DEPENDS= libscotch.so:cad/scotch SCOTCH_CONFIGURE_ON= --with-scotch-include="${LOCALBASE}/include" TEST_TARGET= check .if defined(PACKAGE_BUILDING) TERM= vt100 # Force for pointyhat to override su .else TERM?= vt100 # Default value needed for tput in jail or tinderbox .endif .include .if ${ARCH} == "i386" # /wrkdirs/usr/ports/science/code_saturne/work/code_saturne-5.3.0/src/apps/.libs # /libsaturne.so: # undefined reference to `__atomic_compare_exchange' CONFIGURE_ARGS+= --disable-openmp .endif .if ${PORT_OPTIONS:MDOCS} USE_TEX= tex:build BUILD_DEPENDS+= fig2dev:print/fig2dev \ doxygen:devel/doxygen \ dot:graphics/graphviz \ dvips:print/tex-dvipsk \ ${PYTHON_PKGNAMEPREFIX}sphinx>=0,1:textproc/py-sphinx@${PY_FLAVOR} BINARY_ALIAS+= sphinx-build=sphinx-build-${PYTHON_VER} ALL_TARGET= all pdf DOCS= AUTHORS ChangeLog README .endif pre-configure: ${REINPLACE_CMD} -e 's|/usr/bin/env python|${PYTHON_CMD}|' \ ${WRKSRC}/Makefile.am post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/libexec/code_saturne/cs_solver post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DOCS:C|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/colt/Makefile b/science/colt/Makefile index e7867aea0d93..fe08d95ac773 100644 --- a/science/colt/Makefile +++ b/science/colt/Makefile @@ -1,51 +1,49 @@ -# Created by: Wen heping - PORTNAME= colt PORTVERSION= 1.2.0 PORTREVISION= 1 CATEGORIES= science java MASTER_SITES= http://acs.lbl.gov/software/colt/colt-download/releases/ MAINTAINER= ports@FreeBSD.org COMMENT= Java package for scalable scientific and technical computing USE_JAVA= yes WRKSRC= ${WRKDIR}/${PORTNAME} OPTIONS_DEFINE= DOCS COMPILE OPTIONS_DEFAULT=COMPILE COMPILE_DESC= Install the pre-compiled .jar file .include .if ${PORT_OPTIONS:MCOMPILE} USE_ANT= yes USE_LOCALE= en_US.ISO8859-1 ALL_TARGET= build .if ${PORT_OPTIONS:MDOCS} ALL_TARGET+= javadoc .endif .else NO_BUILD= yes .endif .if ${PORT_OPTIONS:MDOCS} PORTDOCS= * .endif PLIST_FILES= %%JAVAJARDIR%%/colt.jar .include do-install: .if ${PORT_OPTIONS:MDOCS} @${ECHO_MSG} -n ">> Installing documentation in ${STAGEDIR}${DOCSDIR}..." @cd ${WRKSRC}/doc && ${FIND} . -type d -exec ${MKDIR} ${STAGEDIR}${DOCSDIR}/{} \; @cd ${WRKSRC}/doc && ${FIND} . -type f -exec ${INSTALL_DATA} {} ${STAGEDIR}${DOCSDIR}/{} \; @${ECHO_MSG} " [DONE]" .endif post-install: ${INSTALL_DATA} ${WRKSRC}/lib/colt.jar ${STAGEDIR}${JAVAJARDIR} .include diff --git a/science/crf++/Makefile b/science/crf++/Makefile index 6c3467e8f00d..4d7213a3fc93 100644 --- a/science/crf++/Makefile +++ b/science/crf++/Makefile @@ -1,38 +1,36 @@ -# Created by: Cheng-Lung Sung - PORTNAME= crf++ # 0.59 as defined in # https://github.com/taku910/crfpp/commit/d78526835e4cfcc4822156724edda8a3839327c2 DISTVERSION= 0.59 PORTREVISION= 1 CATEGORIES= science math PATCH_SITES= https://patch-diff.githubusercontent.com/raw/taku910/crfpp/pull/:pr PATCHFILES= 15.patch:-p1:pr \ 16.patch:-p1:pr MAINTAINER= ports@FreeBSD.org COMMENT= Yet Another CRF toolkit LICENSE= BSD3CLAUSE LGPL21+ LICENSE_COMB= dual LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/BSD LICENSE_FILE_LGPL21+ = ${WRKSRC}/LGPL USES= libtool USE_GITHUB= yes GH_ACCOUNT= taku910 GH_PROJECT= crfpp GH_TAGNAME= 1dc92a606f874a4fe52603803364cc1d90f952fb USE_LDCONFIG= yes GNU_CONFIGURE= yes INSTALL_TARGET= install-strip PORTEXAMPLES= JapaneseNE basenp chunking seg OPTIONS_DEFINE= EXAMPLES post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAPLESDIR} (cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) .include diff --git a/science/dcl/Makefile b/science/dcl/Makefile index 19a00a448312..0f50680e6ef1 100644 --- a/science/dcl/Makefile +++ b/science/dcl/Makefile @@ -1,48 +1,46 @@ -# Created by: Shin'ya Murakami - PORTNAME= dcl PORTVERSION= 5.4.8 PORTREVISION= 9 CATEGORIES= science graphics MASTER_SITES= http://www.gfd-dennou.org/library/dcl/ \ http://dennou-h.gfd-dennou.org/library/dcl/ \ http://dennou-q.gfd-dennou.org/library/dcl/ MAINTAINER= murashin@gfd-dennou.org COMMENT= Scientific graphic library for geoscience # Converted from RESTRICTED LICENSE= dcl LICENSE_NAME= dcl LICENSE_TEXT= No commercial use LICENSE_PERMS= auto-accept BROKEN= fails to fetch from mastersite (newest release is 7.4.0 of 2020611) MAKE_JOBS_UNSAFE= yes USES= desthack fortran gnome pkgconfig xorg USE_XORG= x11 xext USE_GNOME= gtk20 gdkpixbuf2 GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-x PORTDOCS= CHECK CREDITS HISTORY README PORTEXAMPLES= * OPTIONS_DEFINE= DOCS EXAMPLES .include .if ${FORTRAN_DEFAULT} == gfortran && ${GCC_DEFAULT} >= 10 FFLAGS+= -fallow-invalid-boz .endif post-install: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/demo/ && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) @${MKDIR} ${STAGEDIR}${DOCSDIR} .for i in ${PORTDOCS} ${INSTALL_DATA} ${WRKSRC}/${i} ${STAGEDIR}${DOCSDIR}/ .endfor .include diff --git a/science/devisor/Makefile b/science/devisor/Makefile index d6bf8ef29e0e..445d4145495a 100644 --- a/science/devisor/Makefile +++ b/science/devisor/Makefile @@ -1,51 +1,49 @@ -# Created by: Pedro F. Giffuni - PORTNAME= devisor PORTVERSION= 2.1 PORTREVISION= 3 CATEGORIES= science java MASTER_SITES= http://www.featflow.de/download/ DISTNAME= devisor${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Design and Visualization Software Resource for FeatFlow USE_JAVA= yes NO_BUILD= yes # Sources are available though SUB_FILES= devisorgrid.sh DATADIR= ${JAVASHAREDIR}/${PORTNAME} DATAFILES= data images misc manual CLASSFILES= devisor2 devisorgrid.class PORTDOCS= * PLIST_FILES= bin/devisorgrid OPTIONS_DEFINE= DOCS do-install: ${INSTALL_SCRIPT} ${WRKDIR}/devisorgrid.sh ${STAGEDIR}${PREFIX}/bin/devisorgrid cd ${WRKSRC} \ && ${COPYTREE_SHARE} "${DATAFILES}" ${STAGEDIR}${DATADIR} "-not -name *\.pdf" cd ${WRKSRC} \ && ${COPYTREE_SHARE} "${CLASSFILES}" ${STAGEDIR}${DATADIR} "-name *\.class" do-install-DOCS-on: cd ${WRKSRC}/manual \ && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} "-name *\.pdf" post-install: @cd ${WRKSRC} \ && ${FIND} -s ${DATAFILES} -type f -not -name '*.pdf' \ | ${SED} -ne 's,^,${DATADIR_REL}/,p' >> ${TMPPLIST} \ && ${FIND} -s -d ${DATAFILES} -type d -empty \ | ${SED} -ne 's,^,@dir ${DATADIR_REL}/,p' >> ${TMPPLIST} @cd ${WRKSRC} \ && ${FIND} -s ${CLASSFILES} -name '*.class' -type f \ | ${SED} -ne 's,^,${DATADIR_REL}/,p' >> ${TMPPLIST} \ && ${FIND} -s -d ${CLASSFILES} -type d -empty \ | ${SED} -ne 's,^,@dir ${DATADIR_REL}/,p' >> ${TMPPLIST} .include diff --git a/science/eccodes/Makefile b/science/eccodes/Makefile index f7fa75f545c5..d918ad2429f4 100644 --- a/science/eccodes/Makefile +++ b/science/eccodes/Makefile @@ -1,57 +1,55 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= eccodes PORTVERSION= 2.26.0 DISTVERSIONSUFFIX= -Source CATEGORIES= science MASTER_SITES= https://confluence.ecmwf.int/download/attachments/45757960/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= ECMWF API for WMO FM-92 GRIB and FM-94 BUFR messages LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libnetcdf.so:science/netcdf \ libpng.so:graphics/png USES= cmake localbase perl5 shebangfix CMAKE_ARGS= -DBUILD_SHARED_LIBS=BOTH CMAKE_OFF= ENABLE_ALIGN_MEMORY \ ENABLE_ECCODES_OMP_THREADS \ ENABLE_EXTRA_TESTS \ ENABLE_FORTRAN \ ENABLE_GRIB_TIMER \ ENABLE_MEMFS \ ENABLE_MEMORY_MANAGEMENT \ ENABLE_PYTHON CMAKE_ON= ECCODES_INSTALL_EXTRA_TOOLS \ ENABLE_ECCODES_THREADS \ ENABLE_EXAMPLES \ ENABLE_INSTALL_ECCODES_DEFINITIONS \ ENABLE_NETCDF \ ENABLE_PNG USE_CSTD= c99 USE_LDCONFIG= yes CONFLICTS_INSTALL= grib_api PORTSCOUT= site:https://confluence.ecmwf.int/display/ECC/Releases SHEBANG_FILES= tools/bufr_compare_dir OPTIONS_DEFINE= AEC OPTIONS_SINGLE= JPEG OPTIONS_SINGLE_JPEG= JASPER OPENJPEG OPTIONS_DEFAULT=OPENJPEG AEC_DESC= Adaptive Entropy Coding support AEC_CMAKE_BOOL= ENABLE_AEC AEC_LIB_DEPENDS= libaec.so:science/libaec JASPER_CMAKE_BOOL= ENABLE_JPG JASPER_LIB_DEPENDS= libjasper.so:graphics/jasper OPENJPEG_LIB_DEPENDS= libopenjp2.so:graphics/openjpeg .include diff --git a/science/elmerfem/Makefile b/science/elmerfem/Makefile index 7d42a1de33cd..a2d8e8f6c219 100644 --- a/science/elmerfem/Makefile +++ b/science/elmerfem/Makefile @@ -1,114 +1,112 @@ -# Created by: Pedro Giffuni - PORTNAME= elmerfem DISTVERSIONPREFIX= release- DISTVERSION= 9.0 PORTREVISION= 2 CATEGORIES= science MAINTAINER= henrik@gulbra.net COMMENT= Multiphysical simulation software LICENSE= GPLv2 LIB_DEPENDS= libblas.so:math/blas \ libhdf5.so:science/hdf5 \ libmetis.so:math/metis \ libmpich.so:net/mpich \ libnetcdf.so:science/netcdf \ libopenblas.so:math/openblas \ libparpack.so:math/arpack-ng USES= cmake compiler:c++11-lang fortran USE_GITHUB= yes GH_ACCOUNT= ElmerCSC USE_LDCONFIG= ${PREFIX}/lib/elmersolver CMAKE_ARGS= -DELMER_FEM_REVISION:STRING=${GH_TAGNAME} ALL_TARGET= # empty LDFLAGS+= -L${LOCALBASE}/lib PORTSCOUT= limit:^release-[1-9] CMAKE_ARGS+= -DHAVE_INTTYPES_H=ON .if !defined(MAINTAINER_MODE) CMAKE_ARGS+= -Wno-dev .endif OPTIONS_DEFINE= GUI OCC OPTIONS_DEFAULT= GUI OCC OPTIONS_SUB= yes GUI_DESC= Build with ElmerGUI (Graphical User Interface) OCC_DESC= Use OpenCASCADE for CAD import in ElmerGUI GUI_LIB_DEPENDS= libqwt6.so:x11-toolkits/qwt6 GUI_USES= gl jpeg qt:5 xorg GUI_USE= gl=gl,glu xorg=ice,sm,x11,xext,xt qt=${_QT5_LIBS:ts,} GUI_CMAKE_BOOL= WITH_ELMERGUI WITH_PARAVIEW GUI_CMAKE_ON= -DQWT_LIBRARY=${QT_LIBDIR}/libqwt6.so \ -DQWT_INCLUDE_DIR=${QT_INCDIR}/qwt6 \ -DDESIRED_QT_VERSION=5 \ -DWITH_QT5:BOOL=TRUE \ -DQT_FOUND:BOOL=TRUE OCC_IMPLIES= GUI OCC_LIB_DEPENDS= libexpat.so:textproc/expat2 \ libfreetype.so:print/freetype2 \ libpng.so:graphics/png \ libpython${_PYVERSION}.so:lang/python${PYTHON_SUFFIX} \ libtiff.so:graphics/tiff \ libTKernel.so:cad/opencascade \ libvtksys-9.1.so:math/vtk9 OCC_USES= python OCC_CMAKE_BOOL= WITH_OCC OCC_CMAKE_ON= -DVTK_DIR=${LOCALBASE}/lib/cmake/vtk-9.0 _LIBSTAGEDIR= ${STAGEDIR}/${PREFIX}/lib/elmersolver _PYVERSION= ${PYTHON_VER}${PYTHON_ABIVER} _QT5_LIBS= buildtools_build concurrent core declarative gui location \ network opengl printsupport qmake_build script sensors \ sql svg webchannel webkit widgets xml .include .if ${ARCH} == "amd64" CFLAGS_${ARCH}= -fPIC CXXFLAGS_${ARCH}= -fPIC FCFLAGS+= -fPIC FFLAGS+= -fPIC .endif .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/COMPLEX(8)). # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif post-patch: @${RM} ${WRKSRC}/cmake/Modules/CMakeParseArguments.cmake @${RM} -r ${WRKSRC}/elmergrid/src/metis-5.1.0 @${REINPLACE_CMD} -e 's,"metis.*/metis\.h",,' \ ${WRKSRC}/elmergrid/src/egparallel.c post-patch-OCC-on: @${REINPLACE_CMD} -e "s|\$${VERSION}|`${PKG_QUERY} '%v' opencascade`|" \ "${WRKSRC}/cmake/Modules/FindOCE.cmake" @${REINPLACE_CMD} -e 's|$${INCLUDE}|${LOCALBASE}/include/OpenCASCADE|' \ "${WRKSRC}/cmake/Modules/FindOCE.cmake" post-install: ${LN} -sf ElmerSolver_mpi ${STAGEDIR}${PREFIX}/bin/ElmerSolver ${LN} -sf libelmersolver.so ${_LIBSTAGEDIR}/libelmersolver.so.0 ${LN} -sf libfhuti.so ${_LIBSTAGEDIR}/libfhuti.so.0 ${LN} -sf libmatc.so ${_LIBSTAGEDIR}/libmatc.so.0 ${LN} -sf libmpi_stubs.so ${_LIBSTAGEDIR}/libmpi_stubs.so.0 @${STRIP_CMD} ${STAGEDIR}/${PREFIX}/bin/ElmerGrid do-test: @cd ${TEST_WRKSRC} && ctest -C ${CMAKE_BUILD_TYPE} ${_MAKE_JOBS} .include diff --git a/science/epte/Makefile b/science/epte/Makefile index 8c859ba7519c..40138e16e187 100644 --- a/science/epte/Makefile +++ b/science/epte/Makefile @@ -1,28 +1,26 @@ -# Created by: Frederic Culot - PORTNAME= epte PORTVERSION= 2.0.8 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= http://www.toddmiller.com/epte/ MAINTAINER= ports@FreeBSD.org COMMENT= Electronic Periodic Table of the Elements USES= ncurses MAKEFILE= makefile ALL_TARGET= ${PORTNAME} WRKSRC= ${WRKDIR}/${PORTNAME} PLIST_FILES= bin/epte \ man/man1/epte.1.gz post-patch: @${REINPLACE_CMD} 's|/usr|${PREFIX}|' ${WRKSRC}/epte.1 do-install: ${INSTALL_PROGRAM} ${WRKSRC}/epte ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/epte.1 ${STAGEDIR}${MANPREFIX}/man/man1 .include diff --git a/science/fastcap/Makefile b/science/fastcap/Makefile index d08659470b86..09e81e7f07b1 100644 --- a/science/fastcap/Makefile +++ b/science/fastcap/Makefile @@ -1,66 +1,64 @@ -# Created by: Pedro Giffuni - PORTNAME= fastcap DISTVERSION= 2.0wr-011109 CATEGORIES= science cad MASTER_SITES= http://www.wrcad.com/ftp/pub/ LOCAL/bf MAINTAINER= ports@FreeBSD.org COMMENT= Three-dimensional capacitance extraction program LICENSE= FASTCAP LICENSE_NAME= fastcap license LICENSE_FILE= ${WRKSRC}/LICENSE LICENSE_PERMS= auto-accept BROKEN_aarch64= Fails to link: missing sbrk BROKEN_riscv64= Fails to link: missing sbrk HAS_CONFIGURE= yes CONFIGURE_SCRIPT= config WRKSRC= ${WRKDIR}/fastcap-2.0wr # Fix build with clang11 CFLAGS+= -fcommon BINFILES= busgen capgen cubegen fastcap pipedgen pyragen OPTIONS_DEFINE= DOCS EXAMPLES post-extract: @${HEAD} -32 ${WRKSRC}/src/direct.c | ${TAIL} +2 > ${WRKSRC}/LICENSE post-patch: @${REINPLACE_CMD} -e 's,TYPE=other,TYPE=4,' \ ${WRKSRC}/config @${REINPLACE_CMD} -Ee '/CFLAGS =/{s/=/+=/;s/-O[[:digit:]]*//;}' \ ${WRKSRC}/src/Makefile.4 # Minimal changes to fix the Clang build (there should be a more thorough # clean-up, to correct types of functions, remove implicit declarations, fix # formatting, add missing returns, etc.) @${REINPLACE_CMD} -E -e 's,^mul(Up|Down),void &,' \ ${WRKSRC}/src/mulDo.c @${REINPLACE_CMD} -e 's,^mulMatUp,void &,' \ ${WRKSRC}/src/mulMats.c @${REINPLACE_CMD} -e 's,^static getnbrs,static void getnbrs,' \ ${WRKSRC}/src/mulSetup.c # Change "cd foo ; $(MAKE)" into "$(MAKE) -C foo" to unbreak parallel builds @${REINPLACE_CMD} -E 's,cd (.+) ; (\$$\(MAKE\)),\2 -C \1,' \ ${WRKSRC}/Makefile # Avoid clashing of generated temporary files, crucial for parallel builds @${REINPLACE_CMD} -e 's,temp\.out,$$@.&,' ${WRKSRC}/src/Makefile* do-install: ${INSTALL_PROGRAM} ${BINFILES:S,^,${WRKSRC}/bin/,} ${STAGEDIR}${PREFIX}/bin do-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${CAT} ${WRKSRC}/README ${WRKSRC}/README.mit > ${STAGEDIR}${DOCSDIR}/readme ${INSTALL_DATA} ${WRKSRC}/doc/*.ps ${STAGEDIR}${DOCSDIR} ${GZIP_CMD} ${STAGEDIR}${DOCSDIR}/* .include diff --git a/science/fasthenry/Makefile b/science/fasthenry/Makefile index 8334bb1a845c..f2a8b297652b 100644 --- a/science/fasthenry/Makefile +++ b/science/fasthenry/Makefile @@ -1,71 +1,69 @@ -# Created by: Pedro Giffuni - PORTNAME= fasthenry DISTVERSION= 3.0wr-021113 CATEGORIES= science cad MASTER_SITES= http://www.wrcad.com/ftp/pub/ LOCAL/bf MAINTAINER= ports@FreeBSD.org COMMENT= Multipole-accelerated inductance analysis program BROKEN_aarch64= Fails to link: missing sbrk BROKEN_riscv64= Fails to link: missing sbrk HAS_CONFIGURE= yes CONFIGURE_SCRIPT= config WRKSRC= ${WRKDIR}/fasthenry-3.0wr # Fix build with clang11 CFLAGS+= -fcommon OPTIONS_DEFINE= DOCS EXAMPLES post-patch: @${REINPLACE_CMD} -Ee '/CFLAGS =/{s/=/+=/;s/-O[[:digit:]]*//;}' \ ${WRKSRC}/src/fasthenry/Makefile.default \ ${WRKSRC}/src/fasthenry/sparse/Makefile \ ${WRKSRC}/src/zbuf/Makefile.default #minimal changes to fix the clang build (there should be a more thorough #clean-up, to correct types of functions, remove implicit declarations, fix #formatting, add missing returns, etc.) @${REINPLACE_CMD} -e 's,return;,return 0;,' \ ${WRKSRC}/src/fasthenry/barnoldi.c \ ${WRKSRC}/src/fasthenry/contact.c \ ${WRKSRC}/src/fasthenry/findpaths.c \ ${WRKSRC}/src/fasthenry/fillM.c \ ${WRKSRC}/src/fasthenry/hole.c \ ${WRKSRC}/src/fasthenry/induct.c \ ${WRKSRC}/src/fasthenry/joelself.c \ ${WRKSRC}/src/fasthenry/mulSetup.c \ ${WRKSRC}/src/fasthenry/read_tree.c @${REINPLACE_CMD} -Ee \ '/^(AllocateBlockOfAllocationList|InitializeElementBlocks|RecordAllocation)/,/^\}/s/return;/return 0;/' \ ${WRKSRC}/src/fasthenry/sparse/spAllocate.c @${REINPLACE_CMD} -Ee \ '/^(EnlargeMatrix|ExpandTranslationArrays|spcLinkRows)/,/^\}/s/return;/return 0;/' \ ${WRKSRC}/src/fasthenry/sparse/spBuild.c @${REINPLACE_CMD} -Ee \ '/^(ComplexRowColElimination|CountMarkowitz|CreateInternalVectors|ExchangeColElements|ExchangeRowElements|ExchangeRowsAndCols|MarkowitzProducts|RealRowColElimination|UpdateMarkowitzNumbers|spcColExchange|spcRowExchange)/,/^\}/s/return;/return 0;/' \ ${WRKSRC}/src/fasthenry/sparse/spFactor.c @${REINPLACE_CMD} -Ee 's,^mul(Up|Down),void &,' \ ${WRKSRC}/src/fasthenry/mulDo.c @${REINPLACE_CMD} -e 's,^mulMatUp,void &,' \ ${WRKSRC}/src/fasthenry/mulMats.c do-install: ${INSTALL_PROGRAM} ${WRKSRC}/bin/fasthenry ${STAGEDIR}${PREFIX}/bin/ ${INSTALL_PROGRAM} ${WRKSRC}/bin/zbuf ${STAGEDIR}${PREFIX}/bin do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${CAT} ${WRKSRC}/README ${WRKSRC}/README.mit > ${STAGEDIR}${DOCSDIR}/readme ${CAT} ${WRKSRC}/doc/manual_*.ps > ${STAGEDIR}${DOCSDIR}/manual.ps ${CAT} ${WRKSRC}/doc/nonuniform_manual_*.ps > ${STAGEDIR}${DOCSDIR}/nonuniform_manual.ps ${INSTALL_DATA} ${WRKSRC}/doc/ms_thesis.ps ${STAGEDIR}${DOCSDIR} ${GZIP_CMD} ${STAGEDIR}${DOCSDIR}/* do-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/frontistr/Makefile b/science/frontistr/Makefile index b232e4f0e747..b0cff34669a0 100644 --- a/science/frontistr/Makefile +++ b/science/frontistr/Makefile @@ -1,56 +1,54 @@ -# Created by: Thierry Thomas - PORTNAME= FrontISTR PORTVERSION= 5.2 DISTVERSIONPREFIX= v CATEGORIES= science cad MAINTAINER= thierry@FreeBSD.org COMMENT= Large-Scale Parallel FEM Program for Nonlinear Structural Analysis LICENSE= MIT LIB_DEPENDS= libmetis.so:math/metis \ libscotch.so:cad/scotch \ libcmumps.so.5:math/mumps \ libscalapack.so:math/scalapack TEST_DEPENDS= bash:shells/bash \ gawk:lang/gawk USE_GITLAB= yes GL_ACCOUNT= ${PORTNAME}-Commons GL_COMMIT= c66bdc397de319ca59a0565b3f3b1a3b33f0c50c USES= blaslapack:openblas cmake:testing fortran mpi shebangfix SHEBANG_GLOB= *.sh FFLAGS+= -fallow-argument-mismatch ALL_TARGET= all OPTIONS_DEFINE= DOCS EXAMPLES DOCS_USES= python:build DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ dot:graphics/graphviz \ ${PYTHON_PKGNAMEPREFIX}mkdocs>0:textproc/py-mkdocs@${PY_FLAVOR} DOCS_CMAKE_BOOL= WITH_DOC DOCS_ALL_TARGET= doc PORTDOCS= * PORTEXAMPLES= * pre-configure: ${REINPLACE_CMD} -e 's/awk/gawk/' ${WRKSRC}/tests/test.sh do-install-DOCS-on: ${FIND} ${BUILD_WRKSRC}/doc/html -type d -empty -delete ${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${BUILD_WRKSRC}/doc/html && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} do-test: (cd ${TEST_WRKSRC} && ctest) .include diff --git a/science/gchemutils/Makefile b/science/gchemutils/Makefile index 1cc46a59ff0c..8f4f8041c31c 100644 --- a/science/gchemutils/Makefile +++ b/science/gchemutils/Makefile @@ -1,69 +1,67 @@ -# Created by: Pav Lucistnik - PORTNAME= gchemutils PORTVERSION= 0.14.16 PORTREVISION= 10 CATEGORIES= science MASTER_SITES= SAVANNAH/${PORTNAME}/${PORTVERSION:R} DISTNAME= gnome-chemistry-utils-${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= C++ classes and Gtk3 widgets related to chemistry LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/bodr.pc:science/bodr \ ${LOCALBASE}/libdata/pkgconfig/chemical-mime-data.pc:science/chemical-mime-data LIB_DEPENDS= libopenbabel.so:science/openbabel \ libgoffice-0.10.so:devel/goffice RUN_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/bodr.pc:science/bodr \ ${LOCALBASE}/libdata/pkgconfig/chemical-mime-data.pc:science/chemical-mime-data PORTSCOUT= limitw:1,even USES= compiler:c++11-lang desktop-file-utils gettext gl gmake gnome \ libtool:keepla localbase:ldflags pathfix pkgconfig \ shared-mime-info tar:xz xorg USE_XORG= x11 USE_GNOME= cairo gtk30 intlhack libgsf libxml2 USE_GL= gl USE_LDCONFIG= yes GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-omf-dir=${PREFIX}/share/omf GLIB_SCHEMAS= org.gnome.gchemutils.crystal.gschema.xml \ org.gnome.gchemutils.gschema.xml \ org.gnome.gchemutils.paint.gschema.xml \ org.gnome.gchemutils.paint.plugins.arrows.gschema.xml VER= ${PORTVERSION:R} PLIST_SUB= VER=${VER} GOFFICE=0.10 VERSION=${PORTVERSION} OPTIONS_DEFINE= GNUMERIC XUL OPTIONS_SUB= yes GNUMERIC_DESC= Build gnumeric plugin XUL_DESC= Build browser plugin (requires libxul) XUL_BROKEN= XULrunner and non-Flash plugins are no longer supported XUL_CONFIGURE_ON=--enable-mozilla-plugin \ --with-mozilla-libdir=${PREFIX}/lib/xulrunner XUL_CONFIGURE_OFF=--disable-mozilla-plugin .include .if ${PORT_OPTIONS:MGNUMERIC} || exists(${LOCALBASE}/lib/libspreadsheet.so) LIB_DEPENDS+= libspreadsheet.so:math/gnumeric PLIST_SUB+= GNUMERIC="" .else PLIST_SUB+= GNUMERIC="@comment " .endif pre-configure: ${REINPLACE_CMD} -e 's|-ldl||g' ${WRKSRC}/libs/gcp/Makefile.in ${REINPLACE_CMD} -e 's|openbabel-2.0|openbabel-3|' ${WRKSRC}/${CONFIGURE_SCRIPT} post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so.* @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*/*/*/*/*.so .include diff --git a/science/getdp/Makefile b/science/getdp/Makefile index ae16966be8cc..810aafe2b70d 100644 --- a/science/getdp/Makefile +++ b/science/getdp/Makefile @@ -1,32 +1,30 @@ -# Created by: Thierry Thomas - PORTNAME= getdp PORTVERSION= 3.5.0 CATEGORIES= science MASTER_SITES= http://www.geuz.org/getdp/src/ DISTNAME= ${PORTNAME}-${PORTVERSION}-source MAINTAINER= stephen@FreeBSD.org COMMENT= Rather general finite element solver using mixed finite elements LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libgsl.so:math/gsl \ liblapack.so:math/lapack USES= fortran tar:tgz cmake OPTIONS_DEFINE= DOCS EXAMPLES .include .if ${GCC_DEFAULT} >= 10 # workaround for Rank mismatch in argument 'lines' at (1) (rank-1 and scalar) FFLAGS+= -fallow-argument-mismatch .endif do-test: cd ${WRKSRC}/demos && yes "" | ${STAGEDIR}${PREFIX}/bin/${PORTNAME} magnet.pro -solve MagSta_phi .include diff --git a/science/ghemical/Makefile b/science/ghemical/Makefile index 950e8fda6549..8e56f8898907 100644 --- a/science/ghemical/Makefile +++ b/science/ghemical/Makefile @@ -1,46 +1,44 @@ -# Created by: Nakata Maho - PORTNAME= ghemical PORTVERSION= 3.0.0 PORTREVISION= 23 CATEGORIES= science MASTER_SITES= http://bioinformatics.org/ghemical/download/%SUBDIR%/ MASTER_SITE_SUBDIR= release20111012 current MAINTAINER= yuri@FreeBSD.org COMMENT= Computational chemistry software package LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libblas.so:math/blas \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libghemical.so:science/libghemical \ libgtkglext-x11-1.0.so:x11-toolkits/gtkglext \ libint.so:science/libint \ liblapack.so:math/lapack \ liboglappth.so:science/liboglappth \ libmopac7.so:science/mopac \ libmpqc.so:science/mpqc RUN_DEPENDS= xdg-open:devel/xdg-utils USES= compiler:c++11-lang fortran gettext gl gmake gnome pathfix \ pkgconfig xorg GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-gtk --enable-threads --disable-openbabel # not compatible with OpenBabel-3 so it is disabled USE_GNOME= cairo gdkpixbuf2 gtk20 libglade2 intltool pangox-compat USE_GL= gl glu USE_XORG= x11 CPPFLAGS+= -I${LOCALBASE}/include CXXFLAGS+= -Wno-c++11-narrowing # prevent build errors: non-constant-expression cannot be narrowed from type 'double' to 'fGL' (aka 'float') PLIST_SUB= GHEMICAL_VERSION="${PORTVERSION}" post-patch: @${REINPLACE_CMD} -e \ 's|"mozilla "|"xdg-open "|' ${WRKSRC}/src/gtk_app.cpp @${REINPLACE_CMD} -e 's|openbabel-2.0|openbabel-3|' ${WRKSRC}/configure # attempt at OpenBabel-3 compatibility .include diff --git a/science/ghmm/Makefile b/science/ghmm/Makefile index c226cfd921b3..ad0d5e6c5521 100644 --- a/science/ghmm/Makefile +++ b/science/ghmm/Makefile @@ -1,26 +1,24 @@ -# Created by: Cheng-Lung Sung - PORTNAME= ghmm DISTVERSION= 0.9-rc3 PORTREVISION= 2 CATEGORIES= science math MASTER_SITES= SF/${PORTNAME}/${PORTNAME}/${PORTNAME}%20${DISTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= General Hidden Markov Model Library in C LICENSE= GPLv3 #BUILD_DEPENDS= swig:devel/swig13 GNU_CONFIGURE= yes INSTALL_TARGET= install-strip USE_GNOME= libxml2 USES= autoreconf gnome libtool pkgconfig CONFIGURE_ARGS+= --without-python USE_LDCONFIG= yes CONFLICTS_INSTALL= graphviz # bin/cluster .include diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile index 1be2972fbe74..adf3433f1b03 100644 --- a/science/gnudatalanguage/Makefile +++ b/science/gnudatalanguage/Makefile @@ -1,154 +1,152 @@ -# Created by: thierry@pompo.net - PORTNAME= gnudatalanguage PORTVERSION= 1.0.1 DISTVERSIONPREFIX= v PORTREVISION= 3 CATEGORIES= science lang .if defined(BUILD_PYTHON_MODULE) PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} .endif MAINTAINER= thierry@FreeBSD.org COMMENT?= Free IDL-compatible incremental compiler LICENSE= GPLv2 LIB_DEPENDS+= libgeotiff.so:graphics/libgeotiff\ libexpat.so:textproc/expat2 \ libplplot.so:math/plplot \ libtiff.so:graphics/tiff \ libshp.so:devel/shapelib \ libpng.so:graphics/png \ libsz.so:science/libaec \ libps.so:print/pslib \ libgsl.so:math/gsl USE_GITHUB= yes GH_PROJECT= gdl USES= cmake compiler:c++11-lang fortran ncurses pkgconfig readline \ xorg USE_WX= 3.0+ USE_XORG= x11 sm ice xext # Disable ncurses and readline from ports # TODO: create a port for Astron http://idlastro.gsfc.nasa.gov/ftp/astron.tar.gz # TODO: create a port for TexToIdl http://physics.mnstate.edu/mcraig/textoidl/textoidl-2-1-2.tar CMAKE_ARGS= -DREADLINEDIR:STRING="/usr" \ -DOPENMP:BOOL=ON \ -DNCURSESDIR:STRING="/usr" \ -DPYTHON:BOOL=NO CPPFLAGS+= ${CFLAGS} -fno-inline -DNPY_NO_DEPRECATED_API -DNPY_1_7_API_VERSION CXXFLAGS+= -std=gnu++11 LDFLAGS+= -lpthread -L${LOCALBASE}/lib TEST_TARGET= test SLAVEDIRS= science/py-gnudatalanguage # Upstream prefer GraphicsMagick over ImageMackick # see https://github.com/gnudatalanguage/gdl/issues/611 # and https://github.com/gnudatalanguage/gdl/issues/1044 for ImageMagick 7 OPTIONS_DEFINE= EIGEN EXAMPLES FFTW GLPK GRAPHICSMAGICK GRIB HDF5 LIBPROJ4 MPI NETCDF PYTHON UDUNITS OPTIONS_DEFAULT=EIGEN FFTW GLPK GRAPHICSMAGICK GRIB HDF5 LIBPROJ4 NETCDF PYTHON UDUNITS EIGEN_DESC= Eigen3 support (boost performance) EIGEN_USES= eigen:3 EIGEN_CMAKE_ON= -DEIGEN3:BOOL=YES EIGEN_CMAKE_OFF= -DEIGEN3:BOOL=NO FFTW_LIB_DEPENDS= libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float FFTW_CMAKE_ON= -DFFTW:BOOL=YES FFTW_CMAKE_OFF= -DFFTW:BOOL=NO GLPK_DESC= Support GLPK for Simplex (Linear programming) GLPK_LIB_DEPENDS= libglpk.so:math/glpk GLPK_CMAKE_ON= -DGLPK=ON:BOOL=YES GLPK_CMAKE_OFF= -DGLPK=OFF:BOOL=NO GRAPHICSMAGICK_DESC= Support GraphicsMagick GRAPHICSMAGICK_LIB_DEPENDS= libGraphicsMagick.so:graphics/GraphicsMagick GRAPHICSMAGICK_CMAKE_ON= -DGRAPHICSMAGICK:BOOL=YES GRAPHICSMAGICK_CMAKE_OFF= -DGRAPHICSMAGICK:BOOL=NO # Temporary swith to ImageMagick #IMAGEMAGICK_DESC= Support ImageMagick #IMAGEMAGICK_LIB_DEPENDS=libMagick++-7.so:graphics/ImageMagick7 #IMAGEMAGICK_CMAKE_ON= -DGRAPHICSMAGICK:BOOL=NO -DMAGICK:BOOL=YES -DMAGICKDIR=${LOCALBASE} #IMAGEMAGICK_CMAKE_OFF= -DMAGICK:BOOL=NO GRIB_DESC= Support GRIB messages GRIB_LIB_DEPENDS= libeccodes.so:science/eccodes GRIB_CMAKE_ON= -DGRIB:BOOL=YES GRIB_CMAKE_OFF= -DGRIB:BOOL=NO HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_CMAKE_ON= -DHDF5:BOOL=YES HDF5_CMAKE_OFF= -DHDF5:BOOL=NO -DHDF:BOOL=NO LIBPROJ4_DESC= Support cartographic processes LIBPROJ4_LIB_DEPENDS= libproj.so:graphics/proj LIBPROJ4_CMAKE_ON= -DLIBPROJ:BOOL=YES LIBPROJ4_CMAKE_OFF= -DLIBPROJ:BOOL=NO MPI_LIB_DEPENDS= libmpich.so:net/mpich MPI_CMAKE_ON= -DMPI:BOOL=ON MPI_CMAKE_OFF= -DMPI:BOOL=OFF -DMPIDIR=/none NETCDF_LIB_DEPENDS= libnetcdf.so:science/netcdf NETCDF_CMAKE_ON= -DNETCDF:BOOL=YES -DHDF:BOOL=NO NETCDF_CMAKE_OFF= -DNETCDF:BOOL=NO PYTHON_USES= python:3.7+ PYTHON_BUILD_DEPENDS= ${PYNUMPY} PYTHON_RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} PYTHON_CMAKE_ON= -DPYTHON:BOOL=YES -DPYTHONVERSION:STRING="${PYTHON_VER}" PYTHON_CMAKE_OFF= -DPYTHON:BOOL=NO # QHULL IS NOT NEEDED YET! #QHULL_DESC= Enable Triangulate and Qhull support #QHULL_LIB_DEPENDS= libqhull.so:math/qhull #QHULL_CMAKE_ON= -DQHULL:BOOL=YES #QHULL_CMAKE_OFF= -DQHULL:BOOL=NO UDUNITS_LIB_DEPENDS= libudunits2.so:science/udunits UDUNITS_CMAKE_ON= -DUDUNITS2:BOOL=YES UDUNITS_CMAKE_OFF= -DUDUNITS2:BOOL=NO .if defined(BUILD_PYTHON_MODULE) CATEGORIES+= python CMAKE_ARGS+= -DPYTHON_MODULE:BOOL=YES PLIST= ${.CURDIR}/pkg-plist.pymod .else CMAKE_ARGS+= -DPYTHON_MODULE:BOOL=NO .endif .if defined(BUILD_PYTHON_MODULE) do-install: ${MKDIR} ${STAGEDIR}${PYTHON_SITELIBDIR} ${INSTALL_DATA} ${INSTALL_WRKSRC}/src/GDL.so ${STAGEDIR}${PYTHON_SITELIBDIR}/ .endif .if !defined(BUILD_PYTHON_MODULE) post-install: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR}/testsuite (cd ${WRKSRC}/testsuite && ${COPYTREE_SHARE} \* ${STAGEDIR}${EXAMPLESDIR}/testsuite/) .endif .if defined(MAINTAINER_MODE) regression-test: install . if defined(BUILD_PYTHON_MODULE) @${ECHO_CMD} 'import GDL' > ${WRKDIR}/testgdl.py @${ECHO_CMD} 'print GDL.function("sin",(1,))' >> ${WRKDIR}/testgdl.py ${PYTHON_CMD} ${WRKDIR}/testgdl.py . else @${ECHO_CMD} ".RUN ${EXAMPLESDIR}/testsuite/test_suite.pro" \ > ${WRKDIR}/testgdl @${ECHO_CMD} "exit" >> ${WRKDIR}/testgdl ${PREFIX}/bin/gdl < ${WRKDIR}/testgdl . endif .endif .include diff --git a/science/gramps/Makefile b/science/gramps/Makefile index c0aef62a5569..bcff87280490 100644 --- a/science/gramps/Makefile +++ b/science/gramps/Makefile @@ -1,49 +1,47 @@ -# Created by: Andreas Fehlner - PORTNAME= gramps PORTVERSION= 5.1.5 DISTVERSIONPREFIX= v PORTREVISION= 3 CATEGORIES= science gnome python MAINTAINER= ports@FreeBSD.org COMMENT= GTK3-based genealogy program LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libgeocode-glib.so:net/geocode-glib \ libosmgpsmap-1.0.so:x11-toolkits/osm-gps-map RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pygraphviz>=0:graphics/py-pygraphviz@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyicu>=1.8:devel/py-pyicu@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlite3>=0:databases/py-sqlite3@${PY_FLAVOR} \ xdg-open:devel/xdg-utils USES= desktop-file-utils gettext gnome python:3.3+ shared-mime-info USE_GITHUB= yes GH_ACCOUNT= gramps-project USE_GNOME= cairo gtk30 intltool librsvg2 pango pygobject3 USE_PYTHON= autoplist distutils noflavors CONFIGURE_ARGS= --disable-mime-install NO_ARCH= yes OPTIONS_DEFINE= GEXIV GTKSPELL PIL RCS TTFFREEFONT OPTIONS_DEFAULT= GEXIV GTKSPELL GEXIV_DESC= Manage Exif metadata embedded in media GTKSPELL_DESC= Spell checking support via gtkspell PIL_DESC= Crop/convert images with Python Imaging Library (Pillow) RCS_DESC= Manage revisions of family trees with with GNU RCS TTFFREEFONT_DESC= More font support in reports GEXIV_LIB_DEPENDS= libgexiv2.so:graphics/gexiv2 GTKSPELL_LIB_DEPENDS= libgtkspell3-3.so:textproc/gtkspell3 PIL_RUN_DEPENDS= ${PY_PILLOW} RCS_RUN_DEPENDS= rcsdiff:devel/rcs TTFFREEFONT_RUN_DEPENDS=${LOCALBASE}/share/fonts/freefont-ttf/FreeMono.ttf:x11-fonts/freefont-ttf post-install: ${ECHO_CMD} -n ${PREFIX}/share > ${STAGEDIR}${PYTHON_SITELIBDIR}/gramps/gen/utils/resource-path .include diff --git a/science/grib_api/Makefile b/science/grib_api/Makefile index 3d3832f212d3..7e834c9d519d 100644 --- a/science/grib_api/Makefile +++ b/science/grib_api/Makefile @@ -1,44 +1,42 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= grib_api PORTVERSION= 1.28.0 DISTVERSIONSUFFIX= -Source PORTREVISION= 5 CATEGORIES= science MASTER_SITES= https://confluence.ecmwf.int/download/attachments/3473437/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= ECMWF API for WMO FM-92 GRIB messages LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libnetcdf.so:science/netcdf \ libpng.so:graphics/png CONFLICTS_INSTALL= eccodes OPTIONS_SINGLE= JPEG OPTIONS_SINGLE_JPEG= JASPER OPENJPEG OPTIONS_DEFAULT=OPENJPEG PORTSCOUT= site:https://software.ecmwf.int/wiki/display/GRIB/Releases USES= libtool pathfix CONFIGURE_ARGS= --enable-pthread --with-netcdf=${LOCALBASE} --with-png-support GNU_CONFIGURE= yes INSTALL_TARGET= install-strip USE_LDCONFIG= yes JASPER_CONFIGURE_ON= --with-jasper=${LOCALBASE} JASPER_LIB_DEPENDS= libjasper.so:graphics/jasper OPENJPEG_CFLAGS= -I${LOCALBASE}/include/openjpeg-1.5 OPENJPEG_CONFIGURE_ON= --with-openjpeg=${LOCALBASE} OPENJPEG_LIB_DEPENDS= libopenjpeg.so:graphics/openjpeg15 post-install: ${INSTALL_SCRIPT} ${WRKSRC}/tools/grib1to2 ${STAGEDIR}${PREFIX}/bin/grib1to2 .include diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile index 1a89d9c50873..57ee048beaca 100644 --- a/science/gromacs/Makefile +++ b/science/gromacs/Makefile @@ -1,100 +1,98 @@ -# Created by: Stephen Montgomery-Smith - PORTNAME= gromacs DISTVERSION= 2022.2 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ MAINTAINER= yuri@FreeBSD.org COMMENT= Compute molecular dynamics LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_i386= undefined reference to `__atomic_load' and `__atomic_compare_exchange' #` BUILD_DEPENDS= boost-libs>=1.44:devel/boost-libs LIB_DEPENDS= libhwloc.so:devel/hwloc2 USES= cmake compiler:c++17-lang fortran gnome perl5 pkgconfig python:build shebangfix xorg USE_GNOME= libxml2 USE_LDCONFIG= yes SHEBANG_FILES= admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh bash_CMD= ${SH} CMAKE_OFF= GMX_USE_RDTSCP \ USE_PYTHON_SCRIPTS CMAKE_ARGS= -DPython3_EXECUTABLE=${PYTHON_CMD} OPTIONS_DEFINE= ATLAS FLOAT LEGACY OPENCL OPENMP SIMD X11 OPTIONS_SINGLE= MP OPTIONS_SINGLE_MP= NOMP MPICH OPENMPI THREAD_MPI OPTIONS_DEFAULT= LEGACY OPENMP THREAD_MPI X11 # FLOAT should not a default because science/votca needs double precision. This is likely the same for many other uses. OPTIONS_SUB= yes ATLAS_DESC= Use ATLAS for BLAS and LAPACK ATLAS_USES= blaslapack:atlas ATLAS_USES_OFF= blaslapack ATLAS_CMAKE_ON= -DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libcblas.so;${LOCALBASE}/lib/libf77blas.so" \ -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libalapack.so" ATLAS_CMAKE_OFF= -DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libblas.so" \ -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/liblapack.so" FLOAT_DESC= Use single instead of double precision FLOAT_BUILD_DEPENDS= fftw3>0:math/fftw3 FLOAT_LIB_DEPENDS= libfftw3f.so:math/fftw3-float FLOAT_LIB_DEPENDS_OFF= libfftw3.so:math/fftw3 FLOAT_CMAKE_ON= -DGMX_DOUBLE:BOOL=OFF FLOAT_CMAKE_OFF= -DGMX_DOUBLE:BOOL=ON FLOAT_PLIST_SUB= SUFFIX_D="" FLOAT_PLIST_SUB_OFF= SUFFIX_D="_d" LEGACY_DESC= Install legacy API # expected by science/votca LEGACY_CMAKE_BOOL= GMX_INSTALL_LEGACY_API OPENCL_CMAKE_BOOL= GMX_USE_OPENCL OPENCL_CMAKE_ON= -DGMX_GPU:STRING=OpenCL # one of: OFF, CUDA, OpenCL, SYCL OPENCL_CMAKE_OFF= -DGMX_GPU:STRING=OFF OPENCL_LIB_DEPENDS= libOpenCL.so:devel/ocl-icd OPENMP_CMAKE_ON= -DGMX_CXX11:BOOL=OFF OPENMP_CMAKE_OFF= -DGMX_OPENMP:BOOL=OFF SIMD_CMAKE_OFF= -DGMX_SIMD:STRING="None" X11_USE= XORG=ice,sm,xext,x11 X11_CMAKE_BOOL= GMX_X11 MP_DESC= Multiprocessing NOMP_DESC= No multiprocessing support NOMP_PLIST_SUB= SUFFIX_MPI="" MPICH_LIB_DEPENDS= libmpich.so:net/mpich MPICH_CMAKE_ON= -DGMX_MPI:BOOL=ON \ -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc" MPICH_PLIST_SUB= SUFFIX_MPI="_mpi" OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi OPENMPI_CMAKE_ON= -DGMX_MPI:BOOL=ON \ -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" OPENMPI_PLIST_SUB= SUFFIX_MPI="_mpi" THREAD_MPI_DESC= Build a thread-MPI-based multithreaded version of GROMACS THREAD_MPI_CMAKE_BOOL= GMX_THREAD_MPI THREAD_MPI_PLIST_SUB= SUFFIX_MPI="" post-patch: @${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \ ${REINPLACE_CMD} -e \ 's|share/man|man| ; \ /pkgconfig/s|LIB_INSTALL_DIR}|CMAKE_INSTALL_PREFIX}/libdata|' @${FIND} ${WRKSRC} -name "GMXRC.*" | ${XARGS} ${REINPLACE_CMD} -e \ 's|LDLIB/pkgconfig|LDLIB/../libdata/pkgconfig| ; \ s|LDLIB}/pkgconfig|LDLIB}/../libdata/pkgconfig|' @${REINPLACE_CMD} -e '/CMAKE_REQUIRED_LIBRARIES/d' \ ${WRKSRC}/cmake/gmxTestdlopen.cmake .include diff --git a/science/gsmc/Makefile b/science/gsmc/Makefile index b8a1a46abb26..158ce25bae7c 100644 --- a/science/gsmc/Makefile +++ b/science/gsmc/Makefile @@ -1,22 +1,20 @@ -# Created by: db - PORTNAME= gsmc PORTVERSION= 1.1 PORTREVISION= 5 CATEGORIES= science hamradio MASTER_SITES= http://www.qsl.net/ik5nax/ MAINTAINER= hamradio@FreeBSD.org COMMENT= Smith chart program for impedance matching LICENSE= GPLv2 USE_GNOME= gtk20 GNU_CONFIGURE= yes USES= autoreconf gmake gnome pkgconfig PLIST_FILES= bin/gsmc man/man1/gsmc.1.gz post-patch: @${REINPLACE_CMD} '/^LIBS=/s/$$/ -lm/' ${WRKSRC}/Makefile.am .include diff --git a/science/gtamsanalyzer/Makefile b/science/gtamsanalyzer/Makefile index 277c5ded25f9..d8b39bedd0d9 100644 --- a/science/gtamsanalyzer/Makefile +++ b/science/gtamsanalyzer/Makefile @@ -1,28 +1,26 @@ -# Created by: gurkan@phys.ethz.ch - PORTNAME= gtamsanalyzer PORTVERSION= 0.42 PORTREVISION= 11 CATEGORIES= science gnustep MASTER_SITES= SF/tamsys/gnustep%20tams/GTAMSAnalyzer%2${PORTVERSION} DISTNAME= GTAMSAnalyzer.src.${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Qualitative Research Software for the Free World for GNUstep LICENSE= GPLv2 USES= gnustep USE_GNUSTEP= back build WRKSRC= ${WRKDIR}/${DISTNAME}/Source post-patch: ${RM} "${WRKSRC}/obj" @${REINPLACE_CMD} '/^GNUSTEP_INSTALLATION_DIR/ s|=|=$$(DESTDIR)|' \ ${WRKSRC}/GNUmakefile post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/GNUstep/System/Applications/GTAMSAnalyzer.app/GTAMSAnalyzer .include diff --git a/science/h5utils/Makefile b/science/h5utils/Makefile index ae288bbdbf1c..5dd206ca3a16 100644 --- a/science/h5utils/Makefile +++ b/science/h5utils/Makefile @@ -1,40 +1,38 @@ -# Created by: Klaus Aehlig - PORTNAME= h5utils DISTVERSION= 1.13.1 PORTREVISION= 5 CATEGORIES= science MAINTAINER= aehlig@linta.de COMMENT= Set of utilities for visualization and conversion of HDF5 format LICENSE= MIT GPLv2 LICENSE_COMB= multi LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= gawk:lang/gawk LIB_DEPENDS= libhdf5.so:science/hdf5 \ libpng.so:graphics/png \ libmatheval.so:devel/libmatheval USES= autoreconf compiler:c++11-lang GNU_CONFIGURE= yes USE_GITHUB= yes GH_ACCOUNT= stevengj CFLAGS+= -L${LOCALBASE}/lib -I${LOCALBASE}/include -lpthread CXXFLAGS+= -std=c++11 OPTIONS_DEFINE= OCTAVE OPTIONS_SUB= yes OCTAVE_DESC= With Octave support OCTAVE_CONFIGURE_WITH= octave OCTAVE_BUILD_DEPENDS= ${LOCALBASE}/include/octave-${OCTAVE_VERSION}/octave/octave.h:math/octave OCTAVE_VARS= PLIST_SUB+="OCTAVE_VERSION=${OCTAVE_VERSION} CONFIGURE_TARGET=${CONFIGURE_TARGET}" post-install-OCTAVE-on: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/octave/${OCTAVE_VERSION}/site/oct/${CONFIGURE_TARGET}/h5read.oct .include "../../math/octave/Makefile.version" .include diff --git a/science/harminv/Makefile b/science/harminv/Makefile index e15cb170ef44..100ce6ba334b 100644 --- a/science/harminv/Makefile +++ b/science/harminv/Makefile @@ -1,23 +1,21 @@ -# Created by: Stas Timokhin - PORTNAME= harminv PORTVERSION= 1.3.1 PORTREVISION= 19 CATEGORIES= science MASTER_SITES= http://ab-initio.mit.edu/harminv/ MAINTAINER= devel@stasyan.com COMMENT= Solver of harmonic inversion LIB_DEPENDS= libguile-2.2.so:lang/guile2 USES= blaslapack fortran gmake libtool pathfix GNU_CONFIGURE= yes USE_GCC= yes CPPFLAGS+= -I${LOCALBASE}/include -fPIC LD_LIBRARY_PATH= -L${LOCALBASE}/lib -L/usr/lib LDFLAGS+= -L${LOCALBASE}/lib CONFIGURE_ENV+= LD_LIBRARY_PATH="${LD_LIBRARY_PATH}" USE_LDCONFIG= yes .include diff --git a/science/hdf/Makefile b/science/hdf/Makefile index 6dab0d3ef722..5ae3d901793f 100644 --- a/science/hdf/Makefile +++ b/science/hdf/Makefile @@ -1,56 +1,54 @@ -# Created by: mi - PORTNAME= hdf PORTVERSION= 4.2.15 PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= science archivers graphics MASTER_SITES= http://www.hdfgroup.org/ftp/HDF/releases/HDF${PORTVERSION}/src/ \ ftp://ftp.hdfgroup.org/HDF/releases/HDF${PORTVERSION}/src/ MAINTAINER= ports@FreeBSD.org COMMENT= Hierarchical Data Format library (from NCSA) NOT_FOR_ARCHS= aarch64 armv6 armv7 NOT_FOR_ARCHS_REASON= fails to compile: no machine type has been defined LIB_DEPENDS= libsz.so:science/libaec CONFLICTS_INSTALL= netcdf-4.[0-9]* USES= fortran jpeg libtool GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared --with-jpeg=${LOCALBASE} \ --with-szlib=${LOCALBASE} USE_LDCONFIG= yes INSTALL_TARGET= install-strip TEST_TARGET= check PORTDATA= * PORTEXAMPLES= * OPTIONS_DEFINE= EXAMPLES .include .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (CHARACTER(0)/INTEGER(4)). # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif post-patch: @${REINPLACE_CMD} -e '/PROD_/ s|=.*|=""|' ${WRKSRC}/config/freebsd @${REINPLACE_CMD} -e 's/ || (__APPLE__.*//' \ ${WRKSRC}/hdf/test/fortest.c post-install: ${INSTALL_MAN} ${WRKSRC}/man/hdfunpac.1 \ ${STAGEDIR}${MAN1PREFIX}/man/man1 # Allow to build on PowerPC @${REINPLACE_CMD} -e '/if defined (__APPLE__)/ \ s,),) || defined(__powerpc__),' ${WRKSRC}/hdf/src/hdfi.h ${INSTALL_MAN} ${WRKSRC}/man/gr_chunk.3 \ ${STAGEDIR}${MAN3PREFIX}/man/man3 .include diff --git a/science/hdf5-110/Makefile b/science/hdf5-110/Makefile index ccff2103c287..458ad98fd309 100644 --- a/science/hdf5-110/Makefile +++ b/science/hdf5-110/Makefile @@ -1,79 +1,77 @@ -# Created by: ijliao - PORTNAME= hdf5 PORTVERSION= 1.10.9 CATEGORIES= science archivers graphics MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${PORTVERSION:R}/${DISTNAME}/src/ \ LOCAL/sunpoet PKGNAMESUFFIX= -110 MAINTAINER= sunpoet@FreeBSD.org COMMENT= Hierarchical Data Format library (from NCSA) 1.10.x LICENSE= BSD4CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING USES= compiler:c11 cpe libtool localbase tar:bzip2 CONFIGURE_ARGS= --enable-hl \ --enable-instrument \ --enable-strict-format-checks \ --includedir=${PREFIX}/include/hdf5${PKGNAMESUFFIX} \ --program-suffix=${PKGNAMESUFFIX} \ --with-default-api-version=v110 GNU_CONFIGURE= yes INSTALL_TARGET= install-strip MAKE_JOBS_UNSAFE= yes TEST_TARGET= check USE_LDCONFIG= yes EXAMPLESDIR= ${PREFIX}/share/examples/hdf5${PKGNAMESUFFIX} CONFLICTS_INSTALL= hdf CPE_VENDOR= hdfgroup PORTSCOUT= limit:^1\.10\. OPTIONS_DEFINE= DEBUG EXAMPLES FORTRAN SZIP OPTIONS_RADIO= SUPPORT OPTIONS_RADIO_SUPPORT= CXX PARALLEL OPTIONS_DEFAULT=CXX SZIP OPTIONS_SUB= yes PARALLEL_DESC= Parallel support CXX_CONFIGURE_ENABLE= cxx DEBUG_CONFIGURE_OFF= --enable-build-mode=production DEBUG_CONFIGURE_ON= --enable-build-mode=debug FORTRAN_CONFIGURE_ENABLE= fortran FORTRAN_CONFIGURE_ENV= F9X=${FC} FORTRAN_USES= fortran PARALLEL_CONFIGURE_ENABLE= parallel PARALLEL_LDFLAGS= -L${LOCALBASE}/lib -lmpi PARALLEL_LIB_DEPENDS= libmpi.so:net/mpich SZIP_CONFIGURE_ON= --with-szlib=${LOCALBASE} SZIP_LIB_DEPENDS= libsz.so:science/libaec post-patch: @${REINPLACE_CMD} -e 's|hdf5_examples|examples/hdf5${PKGNAMESUFFIX}|' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/config/gnu-flags @${REINPLACE_CMD} \ -e '/LD_LIBRARY_PATH/ s|^|#|' \ -e 's|(INSTALL)|(INSTALL_DATA)|' \ `${FIND} ${WRKSRC} -regex '.*/examples/Makefile.in'` @${REINPLACE_CMD} -e 's|\[ -a|\[ -f|g' `${FIND} ${WRKSRC} -name \*.sh\*` @${FIND} ${WRKSRC} -name Makefile.in | ${XARGS} \ ${REINPLACE_CMD} -e 's|libhdf5|libhdf5${PKGNAMESUFFIX}|g' \ -e 's|libhdf5${PKGNAMESUFFIX}.settings|libhdf5.settings|g' @${REINPLACE_CMD} -e 's|libhdf5|libhdf5${PKGNAMESUFFIX}|g' ${WRKSRC}/test/testlibinfo.sh.in post-install: ${MV} ${STAGEDIR}${PREFIX}/lib/libhdf5.settings ${STAGEDIR}${PREFIX}/lib/libhdf5${PKGNAMESUFFIX}.settings post-install-CXX-on: ${MV} ${STAGEDIR}${PREFIX}/bin/h5cc ${STAGEDIR}${PREFIX}/bin/h5cc${PKGNAMESUFFIX} post-install-FORTRAN-on: ${MV} ${STAGEDIR}${PREFIX}/bin/h5fc ${STAGEDIR}${PREFIX}/bin/h5fc${PKGNAMESUFFIX} .include diff --git a/science/hdf5-18/Makefile b/science/hdf5-18/Makefile index bb5f149f01ec..5f38edacd307 100644 --- a/science/hdf5-18/Makefile +++ b/science/hdf5-18/Makefile @@ -1,92 +1,90 @@ -# Created by: Wen Heping - PORTNAME= hdf5 PORTVERSION= 1.8.21 # When PORTVERSION changes, please update french/med/files/patch-configure PORTREVISION= 4 CATEGORIES= science archivers graphics MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/ \ http://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/ \ ftp://ftp.hdfgroup.org/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/ PKGNAMESUFFIX= -18 MAINTAINER= thierry@FreeBSD.org COMMENT= Hierarchical Data Format library (from NCSA) 1.8 LICENSE= BSD4CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING OPTIONS_DEFINE= DEBUG EXAMPLES FORTRAN SZIP USES= cpe libtool:keepla localbase tar:bzip2 CPE_VENDOR= hdfgroup USE_LDCONFIG= yes GNU_CONFIGURE= yes PORTSUFF= ${PORTNAME}${PKGNAMESUFFIX} CONFIGURE_ARGS= --enable-cxx \ --enable-instrument \ --enable-strict-format-checks \ --with-pthread=/usr \ --with-zlib=/usr \ --program-suffix=${PKGNAMESUFFIX} \ --includedir=${PREFIX}/include/${PORTSUFF} EXAMPLESDIR= ${PREFIX}/share/examples/${PORTSUFF} SUFF2FIX= tools/misc/h5cc.in tools/misc/h5redeploy.in \ c++/src/h5c++.in fortran/src/h5fc.in .include .if ${PORT_OPTIONS:MDEBUG} CONFIGURE_ARGS+=--disable-production --enable-debug=all .endif .if ${PORT_OPTIONS:MFORTRAN} USES+= fortran CONFIGURE_ARGS+=--enable-fortran CONFIGURE_ENV+= F9X=${FC} PLIST_SUB+= FORTRAN="" FCFLAGS_f90= ${FCFLAGS} LIBS+= -lstdc++ .else PLIST_SUB+= FORTRAN="@comment " .endif .if ${PORT_OPTIONS:MSZIP} LIB_DEPENDS+= libsz.so:science/libaec CONFIGURE_ARGS+=--with-szlib=${LOCALBASE} .endif pre-configure: ${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure ${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/config/gnu-flags ${REINPLACE_CMD} \ -e '/LD_LIBRARY_PATH/ s|^|#|' \ -e 's|/share/hdf5_examples|/${EXAMPLESDIR_REL}|' \ -e 's|(INSTALL)|(INSTALL_DATA)|' \ `${FIND} ${WRKSRC} -regex '.*/examples/Makefile.in'` ${REINPLACE_CMD} -e 's|\[ -a|\[ -f|g' `${FIND} ${WRKSRC} -name \*.sh\*` .if !${PORT_OPTIONS:MEXAMPLES} ${REINPLACE_CMD} -e '/^install:/ s|install-examples||' ${WRKSRC}/Makefile.in .endif ${FIND} ${WRKSRC} -name Makefile.in | ${XARGS} \ ${REINPLACE_CMD} -e 's|libhdf5|libhdf5${PKGNAMESUFFIX}|g' ${REINPLACE_CMD} -e 's|libhdf5|libhdf5${PKGNAMESUFFIX}|g' \ ${WRKSRC}/test/testlibinfo.sh.in .for pf in ${SUFF2FIX} ${REINPLACE_CMD} -e 's|%%SUFF%%|${PKGNAMESUFFIX}|g' ${WRKSRC}/${pf} .endfor post-configure: ${CP} -p ${WRKSRC}/src/libhdf5.settings.in \ ${WRKSRC}/src/libhdf5${PKGNAMESUFFIX}.settings.in ${CP} -p ${WRKSRC}/src/libhdf5.settings \ ${WRKSRC}/src/libhdf5${PKGNAMESUFFIX}.settings post-stage: .if ${PORT_OPTIONS:MFORTRAN} ${MV} ${STAGEDIR}${PREFIX}/bin/h5fc ${STAGEDIR}${PREFIX}/bin/h5fc${PKGNAMESUFFIX} .endif regression-test test: build cd ${WRKSRC}/ && ${SETENV} ${MAKE_ENV} ${MAKE} check .include diff --git a/science/hdf5/Makefile b/science/hdf5/Makefile index 4fd8a52f4743..5782b8649294 100644 --- a/science/hdf5/Makefile +++ b/science/hdf5/Makefile @@ -1,77 +1,75 @@ -# Created by: ijliao - PORTNAME= hdf5 PORTVERSION= 1.12.2 PORTEPOCH= 1 CATEGORIES= science archivers graphics MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${PORTVERSION:R}/hdf5-${PORTVERSION}/src/ DISTNAME= CMake-hdf5-${PORTVERSION} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Hierarchical Data Format library (from NCSA) (latest) LICENSE= BSD4CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING USES= cmake compiler:c11 localbase perl5 USE_PERL5= build CFLAGS+= -D__LONG_LONG_SUPPORTED CMAKE_ARGS= -DDEFAULT_API_VERSION=v112 \ -DHDF5_INSTALL_CMAKE_DIR=lib/cmake/hdf5 \ -DHDF5_INSTALL_INCLUDE_DIR=${PREFIX}/include CMAKE_ON= HDF5_BUILD_HL_LIB HDF5_BUILD_TOOLS HDF5_ENABLE_INSTRUMENT HDF5_ENABLE_Z_LIB_SUPPORT HDF5_STRICT_FORMAT_CHECKS TEST_TARGET= test USE_LDCONFIG= yes PLIST_SUB= PORTVERSION=${PORTVERSION} WRKSRC_SUBDIR= hdf5-${PORTVERSION} CONFLICTS_INSTALL= hdf CPE_VENDOR= hdfgroup OPTIONS_DEFINE= DEBUG EXAMPLES FORTRAN SZIP OPTIONS_RADIO= SUPPORT OPTIONS_RADIO_SUPPORT= CXX PARALLEL OPTIONS_DEFAULT=CXX SZIP OPTIONS_SUB= yes PARALLEL_DESC= Parallel support PARALLEL_IMPLIES= FORTRAN CXX_CMAKE_BOOL= HDF5_BUILD_CPP_LIB EXAMPLES_CMAKE_BOOL= HDF5_BUILD_EXAMPLES HDF5_TEST_EXAMPLES HDF5_PACK_EXAMPLES FORTRAN_CMAKE_BOOL= HDF5_BUILD_FORTRAN FORTRAN_CONFIGURE_ENV= F9X=${FC} FORTRAN_USES= fortran PARALLEL_CMAKE_BOOL= HDF5_ENABLE_PARALLEL PARALLEL_USES= localbase:ldflags mpi:mpich PARALLEL_VARS= FCFLAGS+=-I${LOCALBASE}/include SZIP_CMAKE_BOOL= HDF5_ENABLE_SZIP_SUPPORT SZIP_LIB_DEPENDS= libsz.so:science/libaec post-patch-EXAMPLES-on: @${MKDIR} ${WRKDIR}/.build @${TAR} -C ${WRKDIR}/.build -xf ${WRKSRC}/../HDF5Examples-1.12.9-Source.tar.gz post-install: ${MKDIR} ${STAGEDIR}${DATADIR} ${RM} ${STAGEDIR}${PREFIX}/share/COPYING ${RM} ${STAGEDIR}${DATADIR}/COPYING cd ${STAGEDIR}${PREFIX}/share && ${MV} RELEASE.txt USING_HDF5_CMake.txt ${STAGEDIR}${DATADIR}/ ${LN} -fs hdf5.pc ${STAGEDIR}${PREFIX}/libdata/pkgconfig/hdf5-${PORTVERSION}.pc ${LN} -fs hdf5_hl.pc ${STAGEDIR}${PREFIX}/libdata/pkgconfig/hdf5_hl-${PORTVERSION}.pc post-install-CXX-on: ${LN} -fs hdf5_cpp.pc ${STAGEDIR}${PREFIX}/libdata/pkgconfig/hdf5_cpp-${PORTVERSION}.pc ${LN} -fs hdf5_hl_cpp.pc ${STAGEDIR}${PREFIX}/libdata/pkgconfig/hdf5_hl_cpp-${PORTVERSION}.pc post-install-EXAMPLES-on: cd ${STAGEDIR}${PREFIX}/share && ${MV} CTestScript.cmake HDF5_Examples.cmake HDF5_Examples_options.cmake USING_CMake_Examples.txt ${STAGEDIR}${DATADIR}/ ${MV} ${STAGEDIR}${PREFIX}/share/HDF5Examples ${STAGEDIR}${EXAMPLESDIR} post-install-FORTRAN-on: ${LN} -fs hdf5_fortran.pc ${STAGEDIR}${PREFIX}/libdata/pkgconfig/hdf5_fortran-${PORTVERSION}.pc ${LN} -fs hdf5_hl_fortran.pc ${STAGEDIR}${PREFIX}/libdata/pkgconfig/hdf5_hl_fortran-${PORTVERSION}.pc .include diff --git a/science/hypre/Makefile b/science/hypre/Makefile index 2b066733a8e1..de09efd1086f 100644 --- a/science/hypre/Makefile +++ b/science/hypre/Makefile @@ -1,49 +1,47 @@ -# Created by: Pedro Giffuni - PORTNAME= hypre DISTVERSIONPREFIX= v DISTVERSION= 2.25.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Scalable Linear Solvers and Multigrid Methods LICENSE= APACHE20 MIT LICENSE_COMB= dual LICENSE_FILE_APACHE20= ${WRKSRC}/../LICENSE-APACHE LICENSE_FILE_MIT= ${WRKSRC}/../LICENSE-MIT USES= blaslapack cmake:testing fortran localbase USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= hypre-space WRKSRC_SUBDIR= src CMAKE_ON= HYPRE_ENABLE_SHARED HYPRE_WITH_OPENMP CMAKE_TESTING_ON= HYPRE_BUILD_TESTS # tests are only built and not run, see https://github.com/hypre-space/hypre/issues/502 OPTIONS_DEFINE= DOCS OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH NOMPI_DESC= Build without parallel processing support NOMPI_CMAKE_ON= -DHYPRE_WITH_MPI=OFF MPICH_LIB_DEPENDS= libmpich.so:net/mpich MPICH_CONFIGURE_ENV= CC=${LOCALBASE}/bin/mpicc CXX=${LOCALBASE}/bin/mpicxx OPENMPI_LIB_DEPENDS= libmpi.so:net/openmpi OPENMPI_CONFIGURE_ENV= CC=${LOCALBASE}/mpi/openmpi/bin/mpicc \ CXX=${LOCALBASE}/mpi/openmpi/bin/mpicxx OPENMPI_BROKEN= doesn't switch to openmpi in cmake build PORTDOCS= * post-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${WRKSRC}/docs && ${COPYTREE_SHARE} usr-manual ${STAGEDIR}${DOCSDIR} .include diff --git a/science/iboview/Makefile b/science/iboview/Makefile index 5d16a3fe9b75..4285973723c8 100644 --- a/science/iboview/Makefile +++ b/science/iboview/Makefile @@ -1,30 +1,28 @@ -# Created by: Johannes Dieterich - PORTNAME= iboview PORTVERSION= 20150427 PORTREVISION= 23 CATEGORIES= science MASTER_SITES= http://www.iboview.org/bin/ DISTNAME= ibo-view.20150427 MAINTAINER= jmd@FreeBSD.org COMMENT= Program for analyzing molecular electronic structure LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= boost-libs>=0:devel/boost-libs RUN_DEPENDS= boost-libs>=0:devel/boost-libs ONLY_FOR_ARCHS= amd64 USES= blaslapack:openblas fortran gl qmake:outsource qt:5 tar:bz2 USE_GL= gl glu USE_QT= buildtools_build core gui widgets opengl script svg PLIST_FILES= bin/iboview do-install: ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/iboview ${STAGEDIR}${PREFIX}/bin .include diff --git a/science/isaac-cfd/Makefile b/science/isaac-cfd/Makefile index d2d3d65d2dee..0fa304df5cc4 100644 --- a/science/isaac-cfd/Makefile +++ b/science/isaac-cfd/Makefile @@ -1,57 +1,55 @@ -# Created by: Pedro F. Giffuni - PORTNAME= isaac PORTVERSION= 4.2 PORTREVISION= 16 CATEGORIES= science MASTER_SITES= SF/${PORTNAME}-cfd/${PORTNAME}-cfd/ISAAC%20Version%20${PORTVERSION} DISTFILES= ${PORTNAME}src.4_2${EXTRACT_SUFX} ${PORTNAME}mk.4_2${EXTRACT_SUFX} DIST_SUBDIR= isaac-cfd EXTRACT_ONLY= ${PORTNAME}src.4_2${EXTRACT_SUFX} ${PORTNAME}mk.4_2${EXTRACT_SUFX} MAINTAINER= ports@FreeBSD.org COMMENT= Integrated Solution Algorithm for Arbitrary Configuration LICENSE= ISAAC LICENSE_NAME= ISAAC_LICENSE LICENSE_FILE= ${WRKSRC}/license.txt LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept NO_WRKSUBDIR= yes MAKEFILE= makefile MAKE_ARGS= CPPFLAGS=-I. USES= fortran gmake FFLAGS+= -std=legacy PLIST_FILES= bin/isaac PORTDOCS= man.4_2.ps.gz PORTEXAMPLES= * OPTIONS_DEFINE= DOCS EXAMPLES OPTIMIZED_FFLAGS DOCS_DISTFILES= man.4_2.ps.gz EXAMPLES_DISTFILES= example_cases${EXTRACT_SUFX} OPTIMIZED_FFLAGS_DESC= Use extra compiler (fortran) optimizations OPTIMIZED_FFLAGS_VARS= FFLAGS+="-O2 -ffast-math" pre-configure: @${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; s+%%FFLAGS%%+${FFLAGS}+;' \ ${WRKSRC}/makefile @${FIND} ${WRKSRC} -name "*.mk" -exec \ ${REINPLACE_CMD} -e 's|SRC= $$(HOME)/ISAAC/src|SRC= ${WRKSRC}|; \ s|$$(FFLAGS)|${FFLAGS} -I.|' {} \; do-install: ${INSTALL_PROGRAM} ${WRKSRC}/isaac ${STAGEDIR}${PREFIX}/bin/isaac do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${CP} ${DISTDIR}/${DIST_SUBDIR}/${PORTDOCS} ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${TAR} -xzf ${DISTDIR}/${DIST_SUBDIR}/example_cases${EXTRACT_SUFX} \ -C ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/jmol/Makefile b/science/jmol/Makefile index 562326f9f359..3c0420fefe41 100644 --- a/science/jmol/Makefile +++ b/science/jmol/Makefile @@ -1,65 +1,63 @@ -# Created by: Wen heping - PORTNAME= Jmol DISTVERSION= 14.32.63 CATEGORIES= science java MASTER_SITES= SF/${PORTNAME:tl}/${PORTNAME}/Version%20${DISTVERSION:R}/${PORTNAME}%20${DISTVERSION}/ DISTFILES= ${PORTNAME}-${DISTVERSION}-full${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Java 3D viewer for chemical structures LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE.txt USE_JAVA= yes USE_ANT= yes NO_ARCH= yes WRKSRC= ${WRKDIR}/${PORTNAME:tl}-${DISTVERSION} SIGN_DIR= ${WRKSRC}/selfSignedCertificate SUB_FILES= ${EXES} SUB_LIST= JAVA=${JAVA} EXES= ${PORTNAME:tl} ${PORTNAME:tl}data JARS= ${PORTNAME}.jar Jvxl.jar ${PORTNAME}Data.jar # ${PORTNAME}Lib.jar PLIST_FILES= ${EXES:S/^/bin\//} \ ${JARS:S/^/${JAVAJARDIR}\//} OPTIONS_DEFINE= DOCS JSMOL OPTIONS_DEFAULT= JSMOL JSMOL_DESC= Install JSmol JSMOL_BUILD_DEPENDS= unzip>0:archivers/unzip JSMOL_VARS= WWWDIR=${PREFIX}/www/JSmol PLIST=${.CURDIR}/pkg-plist-jsmol PORTDOCS= * DESKTOP_ENTRIES="${PORTNAME}" "" "" "${PORTNAME:tl}" "" false post-patch: @${REINPLACE_CMD} 's| diff --git a/science/kst2/Makefile b/science/kst2/Makefile index 65850e2294f1..7b34f1ad08d1 100644 --- a/science/kst2/Makefile +++ b/science/kst2/Makefile @@ -1,60 +1,58 @@ -# Created by: Markus Brueffer - PORTNAME= kst DISTVERSION= ${KST_VERSION}.${KST_DATE} CATEGORIES= science MAINTAINER= makc@FreeBSD.org COMMENT= Data viewing and plotting tool LICENSE= GPLv2 GFDL LGPL20 LICENSE_COMB= multi LICENSE_FILE_GPLv2= ${WRKSRC}/COPYING LICENSE_FILE_GFDL= ${WRKSRC}/COPYING-DOCS LICENSE_FILE_LGPL20= ${WRKSRC}/COPYING.LGPL LIB_DEPENDS= libgsl.so:math/gsl \ libtiff.so:graphics/tiff USES= cmake compiler:c++11-lang desktop-file-utils kde:5 pkgconfig \ qt:5 shared-mime-info USE_QT= concurrent core gui network printsupport svg widgets xml \ buildtools_build linguisttools_build qmake_build USE_LDCONFIG= yes KST_VERSION= 2.0.8 KST_DATE= 20220216 KST_COMMIT= 40cdf2d3 KDE_INVENT= 40cdf2d397e4277ee7226188ef89ae3e0f12d884 graphics kst-plot CMAKE_ARGS= -Dkst_install_prefix=${PREFIX} \ -Dkst_pch=off \ -Dkst_version_string=${KST_VERSION} \ -Dkst_revision="${KST_COMMIT} ${KST_DATE}" \ -DCMAKE_DISABLE_FIND_PACKAGE_Getdata=ON \ -Dkst_qt5=on PLIST_SUB= SHLIB_VER=${KST_VERSION} OPTIONS_DEFINE= FITS HDF5 MATLAB NETCDF OPTIONS_DEFAULT= FITS HDF5 MATLAB OPTIONS_SUB= yes FITS_DESC= Support for data in FITS format FITS_LIB_DEPENDS= libcfitsio.so:astro/cfitsio FITS_CMAKE_OFF= -DCMAKE_DISABLE_FIND_PACKAGE_CFITSIO=ON HDF5_DESC= Support for data in HDF5 format HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_CMAKE_OFF= -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=ON MATLAB_DESC= Support for data in MATLAB format MATLAB_LIB_DEPENDS= libmatio.so:math/matio MATLAB_CMAKE_OFF= -DCMAKE_DISABLE_FIND_PACKAGE_Matio=ON NETCDF_DESC= Support for data in NetCDF format (broken) NETCDF_LIB_DEPENDS= libnetcdf.so:science/netcdf NETCDF_IGNORE= does not support NetCDF 4 NETCDF_CMAKE_OFF= -DCMAKE_DISABLE_FIND_PACKAGE_Netcdf=ON .include diff --git a/science/libaec/Makefile b/science/libaec/Makefile index e7f2b4fc046b..0ad0705cf2e3 100644 --- a/science/libaec/Makefile +++ b/science/libaec/Makefile @@ -1,22 +1,20 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= libaec PORTVERSION= 1.0.6 CATEGORIES= science MASTER_SITES= https://gitlab.dkrz.de/k202009/libaec/uploads/45b10e42123edd26ab7b3ad92bcf7be2/ MAINTAINER= sunpoet@FreeBSD.org COMMENT= Adaptive entropy coding library LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt USES= libtool GNU_CONFIGURE= yes INSTALL_TARGET= install-strip USE_LDCONFIG= yes CONFLICTS_INSTALL= hdf-szip .include diff --git a/science/libctl/Makefile b/science/libctl/Makefile index 201715c27ac3..2c924658be97 100644 --- a/science/libctl/Makefile +++ b/science/libctl/Makefile @@ -1,39 +1,37 @@ -# Created by: ijliao - PORTNAME= libctl DISTVERSION= 4.5.0 CATEGORIES= science math MASTER_SITES= https://github.com/NanoComp/libctl/releases/download/v${DISTVERSION}/ MAINTAINER= devel@stasyan.com COMMENT= Control Language Library LICENSE= GPLv2 BROKEN_sparc64= does not build LIB_DEPENDS= libgc-threaded.so:devel/boehm-gc-threaded \ libguile-2.2.so:lang/guile2 USES= fortran libtool pkgconfig GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared USE_LDCONFIG= yes LDFLAGS+= -L${LOCALBASE}/lib -lm OPTIONS_DEFINE= NLOPT DOCS EXAMPLES OPTIONS_DEFAULT= NLOPT NLOPT_DESC= Use NLopt, an external NonLinear OPTimizer NLOPT_LIB_DEPENDS= libnlopt.so:math/nlopt post-install: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${CP} -R ${WRKSRC}/doc/ ${STAGEDIR}${DOCSDIR} @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${CP} -R ${WRKSRC}/examples/ ${STAGEDIR}${EXAMPLESDIR} @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libctl.so.7.3.0 @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libctlgeom.so.7.3.0 @${STRIP_CMD} ${STAGEDIR}${EXAMPLESDIR}/.libs/example .include diff --git a/science/libgeodecomp/Makefile b/science/libgeodecomp/Makefile index fb054a64a891..be522c25b2ed 100644 --- a/science/libgeodecomp/Makefile +++ b/science/libgeodecomp/Makefile @@ -1,42 +1,40 @@ -# Created by: Kurt Kanzenbach - PORTNAME= libgeodecomp PORTVERSION= 0.4.0 PORTREVISION= 22 CATEGORIES= science devel MASTER_SITES= http://www.libgeodecomp.org/archive/ MAINTAINER= kurt@kmk-computers.de COMMENT= Auto-parallelizing library for computer simulations LICENSE= BSL LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libboost_system.so:devel/boost-libs libboost_date_time.so:devel/boost-libs \ libboost_filesystem.so:devel/boost-libs BROKEN= error: incomplete type 'LibFlatArray::detail::flat_array::offset, LibGeoDecomp::TopologiesHelpers::Topology<3, false, false, false>, LibGeoDecomp::TestCellHelpers::SoAAPI>, -1>' used in nested name specifier USES= cmake compiler:c++11-lib USE_GCC= yes USE_LDCONFIG= yes CMAKE_ARGS= -DWITH_CUDA:BOOL=FALSE -DWITH_VISIT:BOOL=FALSE \ -DWITH_HPX:BOOL=FALSE -DWITH_OPENCL:BOOL=FALSE \ -DWITH_OPENCV:BOOL=FALSE -DWITH_TYPEMAPS=FALSE OPTIONS_DEFINE= MPI SILO SCOTCH OPTIONS_DEFAULT= MPI SILO SCOTCH MPI_LIB_DEPENDS= libmpich.so:net/mpich MPI_CMAKE_BOOL= WITH_MPI SILO_DESC= Enable Silo dependend output SILO_LIB_DEPENDS= libsiloh5.so:science/silo SILO_CMAKE_BOOL= WITH_SILO SCOTCH_DESC= Enable graph partitioning based on Scotch/Scotch-PT SCOTCH_LIB_DEPENDS= libscotch.so:cad/scotch SCOTCH_CMAKE_BOOL= WITH_SCOTCH .include diff --git a/science/libghemical/Makefile b/science/libghemical/Makefile index 639a919e199c..0b48e3e803db 100644 --- a/science/libghemical/Makefile +++ b/science/libghemical/Makefile @@ -1,40 +1,38 @@ -# Created by: Nakata Maho - PORTNAME= libghemical PORTVERSION= 3.0.0 PORTREVISION= 17 CATEGORIES= science MASTER_SITES= http://bioinformatics.org/ghemical/download/release20111012/ \ http://bioinformatics.org/ghemical/download/current/ MAINTAINER= yuri@FreeBSD.org COMMENT= Support libraries of science/ghemical port LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= obabel:science/openbabel \ intltool-update:textproc/intltool \ ld:devel/binutils LIB_DEPENDS= libblas.so:math/blas \ libint.so:science/libint \ libf2c.so:lang/f2c \ liblapack.so:math/lapack \ libmpqc.so:science/mpqc USES= fortran gettext gl gmake libtool localbase pathfix pkgconfig USE_CXXSTD= c++98 USE_GL= gl GNU_CONFIGURE= yes USE_LDCONFIG= yes CONFIGURE_ARGS+= --enable-mpqc LDFLAGS+= -lSCbasis -lSCcints -lSCclass -lSCcontainer -lSCdft -lSCgroup \ -lSCintv3 -lSCisosurf -lSCkeyval -lSCmbpt -lSCmbptr12 -lSCmisc \ -lSCmolecule -lSCoint3 -lSCoptimize -lSCoptions -lSCpsi \ -lSCref -lSCrender -lSCscf -lSCscmat -lSCsolvent -lSCstate \ -lSCsymmetry -lSCwfn -lgfortran -lpthread -lblas -llapack PLIST_SUB= LIBGHEMICAL_VERSION="${PORTVERSION}" INSTALL_TARGET= install-strip .include diff --git a/science/libint/Makefile b/science/libint/Makefile index b302dfbec74c..f04b13024f75 100644 --- a/science/libint/Makefile +++ b/science/libint/Makefile @@ -1,43 +1,41 @@ -# Created by: NAKATA, Maho - PORTNAME= libint DISTVERSIONPREFIX= release- DISTVERSION= 1-2-1-15 DISTVERSIONSUFFIX= -gb349524 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Evaluate the integrals in modern atomic and molecular theory LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE PORTSCOUT= limit:^1 USES= autoreconf:build gmake libtool USE_GITHUB= yes GH_ACCOUNT= evaleev USE_LDCONFIG= yes ALL_TARGET= default GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared --with-cc-optflags="${CFLAGS}" \ --with-cxx-optflags="${CXXFLAGS}" OPTIONS_DEFINE= STATIC # osa@ requested to keep static libs on 2018/08/28 OPTIONS_SUB= yes STATIC_CONFIGURE_ENABLE= static post-patch: @${REINPLACE_CMD} -e 's| -rpath|${LDFLAGS} -rpath|g' \ ${WRKSRC}/src/lib/MakeVars.in pre-configure: # Cannot run autoheader so cannot use autoreconf. @cd ${WRKSRC} && ${LOCALBASE}/bin/libtoolize -c -f \ && ${LOCALBASE}/bin/aclocal && ${LOCALBASE}/bin/autoconf post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so .include diff --git a/science/libint2/Makefile b/science/libint2/Makefile index 4d0d72e919df..6d8b39aadd75 100644 --- a/science/libint2/Makefile +++ b/science/libint2/Makefile @@ -1,47 +1,45 @@ -# Created by: NAKATA, Maho - PORTNAME= libint DISTVERSIONPREFIX= v DISTVERSION= 2.7.2 CATEGORIES= science PKGNAMESUFFIX= 2 MAINTAINER= yuri@FreeBSD.org COMMENT= Evaluate the integrals in modern atomic and molecular theory LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libgmpxx.so:math/gmp USES= autoreconf:build compiler:c++11-lang gmake libtool localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= evaleev USE_LDCONFIG= yes ALL_TARGET= default GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared \ --enable-1body=1 --enable-eri=1 --enable-eri3=1 --enable-eri2=1 --enable-contracted-ints \ --with-cc-optflags="${CFLAGS}" --with-cxx-optflags="${CXXFLAGS}" OPTIONS_DEFINE= STATIC # osa@ requested to keep static libs on 2018/08/28 OPTIONS_SUB= yes STATIC_CONFIGURE_ENABLE= static PLIST_SUB= VER=${DISTVERSION} post-patch: @${REINPLACE_CMD} -e 's| -rpath|${LDFLAGS} -rpath|g' \ ${WRKSRC}/src/lib/MakeVars.in pre-configure: # Cannot run autoheader so cannot use autoreconf. @cd ${WRKSRC} && ${LOCALBASE}/bin/libtoolize -c -f \ && ${LOCALBASE}/bin/aclocal && ${LOCALBASE}/bin/autoconf post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so .include diff --git a/science/libkml/Makefile b/science/libkml/Makefile index b6c9063636c2..e023853fd322 100644 --- a/science/libkml/Makefile +++ b/science/libkml/Makefile @@ -1,35 +1,33 @@ -# Created by: Wen Heping - PORTNAME= libkml PORTVERSION= 1.3.0 PORTREVISION= 21 CATEGORIES= science MAINTAINER= sunpoet@FreeBSD.org COMMENT= Reference implementation of OGC KML 2.2 LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= boost-libs>=1.44.0:devel/boost-libs \ googletest>=1.7.0:devel/googletest LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libexpat.so:textproc/expat2 \ libgtest.so:devel/googletest \ liburiparser.so:net/uriparser OPTIONS_DEFINE= EXAMPLES USES= cmake compiler:c11 minizip pathfix CMAKE_OFF= WITH_JAVA WITH_PYTHON WITH_SWIG USE_CXXSTD= gnu++98 USE_LDCONFIG= yes USE_GITHUB= yes EXAMPLES_CMAKE_BOOL= BUILD_EXAMPLES INSTALL_EXAMPLES EXAMPLES_CMAKE_ON= -DKML_EXAMPLES_DIR=${EXAMPLESDIR} EXAMPLES_LIB_DEPENDS= libcurl.so:ftp/curl .include diff --git a/science/liblinear/Makefile b/science/liblinear/Makefile index 365d574ceb2a..a02c172e3046 100644 --- a/science/liblinear/Makefile +++ b/science/liblinear/Makefile @@ -1,20 +1,18 @@ -# Created by: Rong-En Fan - PORTNAME= liblinear PORTVERSION= 2.44 CATEGORIES= science math MASTER_SITES= https://www.csie.ntu.edu.tw/~cjlin/liblinear/ \ https://www.csie.ntu.edu.tw/~cjlin/liblinear/oldfiles/ MAINTAINER= sunpoet@FreeBSD.org COMMENT= Library for Large Linear Classification LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYRIGHT PLIST_FILES= bin/predict bin/train do-install: ${INSTALL_PROGRAM} ${WRKSRC}/predict ${WRKSRC}/train ${STAGEDIR}${PREFIX}/bin .include diff --git a/science/liboglappth/Makefile b/science/liboglappth/Makefile index 409830616c90..2022902e442a 100644 --- a/science/liboglappth/Makefile +++ b/science/liboglappth/Makefile @@ -1,20 +1,18 @@ -# Created by: Nakata Maho - PORTNAME= liboglappth PORTVERSION= 1.0.0 PORTREVISION= 5 CATEGORIES= science MASTER_SITES= http://bioinformatics.org/ghemical/download/release20111012/ \ http://bioinformatics.org/ghemical/download/current MAINTAINER= ports@FreeBSD.org COMMENT= Support libraries of science/ghemical port GNU_CONFIGURE= yes INSTALL_TARGET= install-strip USES= gl libtool pathfix USE_GL= glu CPPFLAGS+= -I${LOCALBASE}/include .include diff --git a/science/libquantum/Makefile b/science/libquantum/Makefile index fc1817393607..40d6993ec10a 100644 --- a/science/libquantum/Makefile +++ b/science/libquantum/Makefile @@ -1,28 +1,26 @@ -# Created by: Wen Heping - PORTNAME= libquantum PORTVERSION= 1.1.1 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= http://www.libquantum.de/files/ MAINTAINER= ports@FreeBSD.org COMMENT= C library for quantum computing and quantum simulation LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/COPYING GNU_CONFIGURE= yes USES= gmake libtool USE_LDCONFIG= yes PLIST_FILES= include/quantum.h \ lib/libquantum.a \ lib/libquantum.so \ lib/libquantum.so.8 \ lib/libquantum.so.8.0.0 post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libquantum.so .include diff --git a/science/libsvm-python/Makefile b/science/libsvm-python/Makefile index 511a4315831c..9452d69e76aa 100644 --- a/science/libsvm-python/Makefile +++ b/science/libsvm-python/Makefile @@ -1,12 +1,10 @@ -# Created by: rafan@infor.org - PORTREVISION= 1 PKGNAMESUFFIX= -python MAINTAINER= ports@FreeBSD.org MASTERDIR= ${.CURDIR}/../../science/libsvm PLIST= ${.CURDIR}/pkg-plist .include "${MASTERDIR}/Makefile" diff --git a/science/libsvm/Makefile b/science/libsvm/Makefile index bd24f5eaf149..c1635bea7d98 100644 --- a/science/libsvm/Makefile +++ b/science/libsvm/Makefile @@ -1,78 +1,76 @@ -# Created by: Chia-Hsing Yu - PORTNAME= libsvm PORTVERSION= 3.23 CATEGORIES= science math MASTER_SITES= http://www.csie.ntu.edu.tw/~cjlin/libsvm/ \ http://www.csie.ntu.edu.tw/~cjlin/libsvm/oldfiles/ MAINTAINER?= iblis@hs.ntnu.edu.tw COMMENT= Library for Support Vector Machines LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYRIGHT USES= zip USE_LDCONFIG= yes ALL_TARGET= all lib OPTIONS_DEFINE= DOCS .if defined(PKGNAMESUFFIX) && ${PKGNAMESUFFIX} == "-python" CATEGORIES+= python USES+= python MAKE_ARGS= PYTHON_INCLUDEDIR=${PYTHON_INCLUDEDIR} PORTDOCS= README.python NO_BUILD= yes NO_ARCH= yes .else PORTDOCS= README FAQ.html README.tools TOOLS= tools/checkdata.py tools/easy.py tools/grid.py tools/subset.py SUB_FILES= pkg-message SUB_LIST= DATADIR=${DATADIR} OPTIONS_DEFINE+= OPTIMIZED_CFLAGS OPTIONS_DEFAULT+= OPTIMIZED_CFLAGS OPTIMIZED_CFLAGS_CFLAGS= -Wall -Wconversion -O3 .endif post-patch: .if defined(PKGNAMESUFFIX) && ${PKGNAMESUFFIX} == "-python" @${CP} ${WRKSRC}/python/README ${WRKSRC}/README.python .else @${CP} ${WRKSRC}/tools/README ${WRKSRC}/README.tools .endif do-install: .if defined(PKGNAMESUFFIX) && ${PKGNAMESUFFIX} == "-python" @${MKDIR} ${STAGEDIR}${PYTHON_SITELIBDIR} ${INSTALL_DATA} ${WRKSRC}/python/svm.py ${STAGEDIR}${PYTHON_SITELIBDIR} ${INSTALL_DATA} ${WRKSRC}/python/svmutil.py ${STAGEDIR}${PYTHON_SITELIBDIR} .else ${INSTALL_PROGRAM} ${WRKSRC}/svm-train ${STAGEDIR}${PREFIX}/bin/ ${INSTALL_PROGRAM} ${WRKSRC}/svm-predict ${STAGEDIR}${PREFIX}/bin/ ${INSTALL_PROGRAM} ${WRKSRC}/svm-scale ${STAGEDIR}${PREFIX}/bin/ ${INSTALL_DATA} ${WRKSRC}/svm.h ${STAGEDIR}${PREFIX}/include/ ${INSTALL_LIB} ${WRKSRC}/libsvm.so.2 ${STAGEDIR}${PREFIX}/lib/ ${LN} -sf libsvm.so.2 ${STAGEDIR}${PREFIX}/lib/libsvm.so @${MKDIR} ${STAGEDIR}${DATADIR} for f in ${TOOLS}; do \ ${INSTALL_DATA} ${WRKSRC}/$$f ${STAGEDIR}${DATADIR}; \ done .endif do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} .for f in ${PORTDOCS} ${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DOCSDIR} .endfor .include diff --git a/science/libxc/Makefile b/science/libxc/Makefile index 583161552055..944edb156e14 100644 --- a/science/libxc/Makefile +++ b/science/libxc/Makefile @@ -1,22 +1,20 @@ -# Created by: Johannes Dieterich - PORTNAME= libxc DISTVERSION= 5.2.3 CATEGORIES= science MASTER_SITES= https://www.tddft.org/programs/${PORTNAME}/down/${DISTVERSION}/ MAINTAINER= jmd@FreeBSD.org COMMENT= Library of exchange-correlation functionals for DFT LICENSE= LGPL3+ LICENSE_FILE= ${WRKSRC}/COPYING USES= fortran gmake libtool perl5 USE_LDCONFIG= yes GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared --disable-static INSTALL_TARGET= install-strip .include diff --git a/science/massxpert/Makefile b/science/massxpert/Makefile index 289a32633b4d..cf46abf5111f 100644 --- a/science/massxpert/Makefile +++ b/science/massxpert/Makefile @@ -1,29 +1,27 @@ -# Created by: Veniamin Gvozdikov - PORTNAME= massxpert DISTVERSION= 6.0.3 CATEGORIES= science MAINTAINER= salvadore@FreeBSD.org COMMENT= Software suite for (bio)chemists LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/pthread-stubs.pc:devel/libpthread-stubs LIB_DEPENDS= libexpat.so:textproc/expat2 \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libpng.so:graphics/png USES= cmake compiler:c++17-lang gnome qt:5 xorg USE_GITLAB= yes GL_SITE= https://salsa.debian.org/ GL_ACCOUNT= debichem-team GL_COMMIT= a21ad33eee0314df202146392023dfb3868b7d84 USE_GNOME= glib20 USE_QT= core gui printsupport svg widgets xml buildtools_build \ qmake_build USE_XORG= ice sm x11 xau xcb xdmcp xext xrender .include diff --git a/science/mbdyn/Makefile b/science/mbdyn/Makefile index 00691d9627c9..adc7ddb2d5aa 100644 --- a/science/mbdyn/Makefile +++ b/science/mbdyn/Makefile @@ -1,75 +1,73 @@ -# Created by: Kay Lehmann - PORTNAME= mbdyn DISTVERSION= 1.7.3 PORTREVISION= 3 CATEGORIES= science MASTER_SITES= https://www.mbdyn.org/userfiles/downloads/ MAINTAINER= yuri@FreeBSD.org COMMENT= MultiBody Dynamics analysis system LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_powerpc= Does not compile on powerpc BUILD_DEPENDS= libatomic_ops>0:devel/libatomic_ops LIB_DEPENDS= libltdl.so:devel/libltdl \ libarpack.so:math/arpack-ng \ libumfpack.so:math/suitesparse-umfpack USES= compiler:c++11-lib fortran gmake libtool:build localbase USE_LDCONFIG= yes CPPFLAGS+= -fpermissive -I${LOCALBASE}/include/suitesparse GNU_CONFIGURE= yes CONFIGURE_ARGS= --program-prefix='' --enable-multithread --with-mpi=no \ --with-ginac=no INSTALL_TARGET= install-strip OPTIONS_DEFINE= METIS CHACO OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= REFERENCE GOTOBLAS ATLAS OPTIONS_DEFAULT= REFERENCE ATLAS_DESC= ATLAS CHACO_DESC= Enable chaco-support GOTOBLAS_DESC= GotoBLAS2 METIS_DESC= Enable metis-support REFERENCE_DESC= Blas / Lapack ATLAS_CONFIGURE_ON= --with-blas=atlas ATLAS_USES= blaslapack:atlas CHACO_BUILD_DEPENDS= ${LOCALBASE}/lib/libchaco.a:math/chaco CHACO_CONFIGURE_ON= --with-chaco=yes CHACO_CONFIGURE_OFF= --with-chaco=no GOTOBLAS_CONFIGURE_ON= --with-blas=goto --with-goto=goto2 GOTOBLAS_USES= blaslapack:gotoblas METIS_CONFIGURE_ON= --with-metis=yes METIS_CONFIGURE_OFF= --with-metis=no METIS_CPPFLAGS= -I${LOCALBASE}/include/metis METIS_LIB_DEPENDS= libmetis.so:math/metis REFERENCE_CONFIGURE_ON= --with-blas=blas REFERENCE_USES= blaslapack:netlib .include .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch in argument 't' at (1); passed REAL(4) to INTEGER(4) # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif pre-configure: ${REINPLACE_CMD} -e '/try_lapack_LIBS=/s/-llapack/${LAPACKLIB}/' \ -e 's/ -lxerbla//; s/-lcholmod/-lcholmod ${BLASLIB} ${LAPACKLIB} -lsuitesparseconfig/' \ ${WRKSRC}/configure .include diff --git a/science/mcstas-comps/Makefile b/science/mcstas-comps/Makefile index c4b9aecfb1c3..1f461f178f44 100644 --- a/science/mcstas-comps/Makefile +++ b/science/mcstas-comps/Makefile @@ -1,30 +1,28 @@ -# Created by: Erik B Knudsen - PORTNAME= mcstas-comps PORTVERSION= 2.5 PORTREVISION= 2 CATEGORIES= science MASTER_SITES= http://download.mcstas.org/${PORTNAME:C/-comps\$//}-${PORTVERSION}/unix/ DISTNAME= ${PORTNAME}-${PORTVERSION}-src MAINTAINER= erkn@fysik.dtu.dk COMMENT= Component Library for the McStas neutron ray tracing package LICENSE= GPLv2 RUN_DEPENDS= mcstas:science/mcstas USES= cmake:noninja fortran shebangfix SHEBANG_FILES= samples/sasview_generator.py PLIST_SUB= PORTVERSION=${PORTVERSION} MCEXECS= cif2hkl mcpl2ssw mcpltool ssw2mcpl post-install: .for e in ${MCEXECS} ${STRIP_CMD} ${STAGEDIR}${PREFIX}/mcstas/${PORTVERSION}/bin/${e} ${RLN} ${STAGEDIR}${PREFIX}/mcstas/${PORTVERSION}/bin/${e} ${STAGEDIR}${PREFIX}/bin/${e} .endfor .include diff --git a/science/medit/Makefile b/science/medit/Makefile index 1c0fd1100333..a2f1dad0dcad 100644 --- a/science/medit/Makefile +++ b/science/medit/Makefile @@ -1,66 +1,64 @@ -# Created by: Thierry Thomas - PORTNAME= medit PORTVERSION= 2012.02.05 PORTREVISION= 5 CATEGORIES= science graphics MASTER_SITES= https://www.ljll.math.upmc.fr/~frey/ftp/archives/ DISTFILES= ${SOURCETARB} ${LIBTARBALL} EXTRACT_ONLY= ${SOURCETARB} MAINTAINER= thierry@FreeBSD.org COMMENT= Interactive meshes visualization LICENSE= None LICENSE_NAME= Special grant LICENSE_TEXT= Special grant from the author LICENSE_PERMS= dist-mirror pkg-mirror auto-accept BUILD_DEPENDS= ${LOCALBASE}/include/cfortran.h:lang/cfortran USES= gl gmake tar:tgz xorg USE_XORG= x11 xmu xext USE_GL= gl glu glut MAKEFILE= makefile ALL_TARGET= ${OPSYS} MAKE_ENV= WRKSRC="${WRKSRC}" ARCHI=${OPSYS} ARCH=${ARCH} OSREL=${OSREL} NO_WRKSUBDIR= yes MAKE_JOBS_UNSAFE= yes LLD_UNSAFE= yes LIBVERSION= ${PORTVERSION} SOURCETARB= ${PORTNAME}.${PORTVERSION}${EXTRACT_SUFX} LIBTARBALL= library.${LIBVERSION}${EXTRACT_SUFX} PLIST_FILES= bin/${PORTNAME} OPTIONS_DEFINE= EXAMPLES .include . if ${PORT_OPTIONS:MEXAMPLES} || make(makesum) DISTFILES+= meshes.tar.gz EXTRACT_ONLY+= meshes.tar.gz MESHES= DEFAULT.medit ozark.gis part.bb part.mesh thepart.mesh PLIST_FILES+= ${MESHES:S|^|%%EXAMPLESDIR%%/|} . endif post-extract: cd ${WRKSRC} && \ ${EXTRACT_CMD} ${EXTRACT_BEFORE_ARGS} ${_DISTDIR}/${LIBTARBALL} ${EXTRACT_AFTER_ARGS} --exclude ${MAKEFILE} ${CP} ${FILESDIR}/gttime.c ${WRKSRC}/sources/ .for l in lplib2.c lplib2.h ${MV} ${WRKSRC}/sources/${l} ${WRKSRC}/sources/${l}.old .endfor pre-build: ${MKDIR} ${WRKSRC}/bin/${ARCH}/${OSREL} do-install: ${INSTALL_PROGRAM} ${WRKSRC}/bin/${PORTNAME} ${STAGEDIR}${PREFIX}/bin do-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${MESHES:S|^|${WRKSRC}/INRIA.dir/|} ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/minc2/Makefile b/science/minc2/Makefile index 31d6b638c888..dceb3f1afd72 100644 --- a/science/minc2/Makefile +++ b/science/minc2/Makefile @@ -1,47 +1,45 @@ -# Created by: jbacon - PORTNAME= minc PORTVERSION= 2.2.00 DISTVERSIONPREFIX= release- PORTREVISION= 11 PORTEPOCH= 1 CATEGORIES= science biology PKGNAMESUFFIX= 2 MAINTAINER= ports@FreeBSD.org COMMENT= Medical Imaging NetCDF LICENSE= MIT LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_FreeBSD_13= ld: error: duplicate symbol: matrix_errno BROKEN_FreeBSD_14= ld: error: duplicate symbol: matrix_errno LIB_DEPENDS= libhdf5.so:science/hdf5 \ libnetcdf.so:science/netcdf RUN_DEPENDS= bash:shells/bash USE_GITHUB= yes GH_ACCOUNT= BIC-MNI MAKE_JOBS_UNSAFE= yes USES= autoreconf bison gmake libtool perl5 shebangfix SHEBANG_FILES= progs/mincview/mincview GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared=yes --enable-static=yes INSTALL_TARGET= install-strip USE_LDCONFIG= yes CFLAGS+= -Wno-error=return-type CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib CONFLICTS= minc-1* zh-tk pre-patch: @${RM} ${WRKSRC}/ac_config_aux/* @${RM} ${WRKSRC}/progs/minccalc/gram.[ch] @${RM} ${WRKSRC}/progs/mincgen/ncgentab.[ch] .include diff --git a/science/mol2ps/Makefile b/science/mol2ps/Makefile index 900ba3fff3c1..2f923f30eddf 100644 --- a/science/mol2ps/Makefile +++ b/science/mol2ps/Makefile @@ -1,38 +1,36 @@ -# Created by: Fernan Aguero - PORTNAME= mol2ps PORTVERSION= 0.4b PORTREVISION= 12 CATEGORIES= science MASTER_SITES= https://homepage.univie.ac.at/norbert.haider/download/chemistry/mol2ps/ DISTNAME= ${PORTNAME} EXTRACT_SUFX= .pas DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= acm@FreeBSD.org COMMENT= Read molecular structure files and generate Postscript output LICENSE= GPLv2+ NO_WRKSUBDIR= yes EXTRACT_CMD= ${CP} EXTRACT_BEFORE_ARGS= # EXTRACT_AFTER_ARGS= ${WRKSRC} USES= fpc USE_FPC= rtl-objpas PLIST_FILES= bin/mol2eps bin/mol2ps bin/mol2svg %%DATADIR%%/color.conf do-build: (cd ${WRKSRC} && ${LOCALBASE}/bin/fpc mol2ps -S2 -O3) do-install: (cd ${WRKSRC} && ${INSTALL_PROGRAM} mol2ps ${STAGEDIR}${PREFIX}/bin) (cd ${STAGEDIR}${PREFIX}/bin && \ ${LN} mol2ps mol2eps && ${LN} mol2ps mol2svg) @${MKDIR} ${STAGEDIR}${DATADIR} (cd ${FILESDIR} && ${INSTALL_DATA} color.conf ${STAGEDIR}${DATADIR}) .include diff --git a/science/mopac/Makefile b/science/mopac/Makefile index 4e6be1cf82e1..307831a7c800 100644 --- a/science/mopac/Makefile +++ b/science/mopac/Makefile @@ -1,44 +1,42 @@ -# Created by: Ryo MIYAMOTO - PORTNAME= mopac PORTVERSION= 7.${MOPAC_SUBVERSION} PORTREVISION= 8 PORTEPOCH= 1 CATEGORIES= science # chemistry MASTER_SITES= http://bioinformatics.org/ghemical/download/%SUBDIR%/ MASTER_SITE_SUBDIR= release20111012 current DISTNAME= mopac7-${MOPAC_SUBVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Semi-empirical (MNDO, etc.) molecular orbital calculation LICENSE= GPLv2+ USES= fortran gmake libtool pathfix GNU_CONFIGURE= yes INSTALL_TARGET= install-strip USE_LDCONFIG= yes CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib PORTEXAMPLES= * OPTIONS_DEFINE= EXAMPLES MOPAC_SUBVERSION= 1.15 post-patch: @${REINPLACE_CMD} -e '/usage/s|run_||g' \ -e 's|./src/mopac7|${PREFIX}/libexec/mopac7|g' \ ${WRKSRC}/run_${PORTNAME}7 post-install: ${INSTALL_SCRIPT} ${WRKSRC}/run_${PORTNAME}7 \ ${STAGEDIR}${PREFIX}/bin/${PORTNAME}7 ${INSTALL_PROGRAM} ${WRKSRC}/fortran/.libs/${PORTNAME}7 \ ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}7 @${MKDIR} ${STAGEDIR}${EXAMPLESDIR}/test ${INSTALL_DATA} ${WRKSRC}/tests/*.dat ${STAGEDIR}${EXAMPLESDIR}/test .include diff --git a/science/mpb/Makefile b/science/mpb/Makefile index b7ea472db418..5ea360fcb5ce 100644 --- a/science/mpb/Makefile +++ b/science/mpb/Makefile @@ -1,49 +1,47 @@ -# Created by: ijliao - PORTNAME= mpb DISTVERSION= 1.11.1 CATEGORIES= science MASTER_SITES= https://github.com/NanoComp/mpb/releases/download/v${DISTVERSION}/ MAINTAINER= rhurlin@FreeBSD.org COMMENT= MIT Photonic-Bands LICENSE= GPLv2 BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libctl.so:science/libctl \ libfftw3.so:math/fftw3 \ libgc-threaded.so:devel/boehm-gc-threaded \ libguile-2.2.so:lang/guile2 \ libhdf5.so:science/hdf5 USES= fortran libtool pkgconfig readline GNU_CONFIGURE= yes USE_GCC= yes # Do not use --with-mpi, because it is not guaranted # that science/hdf5 also built with option PARALLEL CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib MAKE_JOBS_UNSAFE= yes OPTIONS_DEFINE= ATLAS NLOPT OPENMP OPTIONS_DEFAULT= NLOPT ATLAS_DESC= Use math/atlas instead of math/openblas NLOPT_DESC= Use math/nlopt (enable also in science/libctl) OPENMP_DESC= Use OpenMP (enable also in math/fftw3) ATLAS_LIB_DEPENDS= libatlas.so:math/atlas ATLAS_USES_OFF= blaslapack:openblas ATLAS_CONFIGURE_ON= --with-lapack=-lalapack ATLAS_CONFIGURE_OFF= --with-blas=openblas --with-lapack=-lopenblas NLOPT_LIB_DEPENDS= libnlopt.so:math/nlopt OPENMP_CONFIGURE_ON= --with-openmp post-install: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/examples && \ ${COPYTREE_SHARE} "*.ctl *.scm" ${STAGEDIR}${EXAMPLESDIR}) .include diff --git a/science/mpqc/Makefile b/science/mpqc/Makefile index aa433ac13a2a..3bc3f040ae34 100644 --- a/science/mpqc/Makefile +++ b/science/mpqc/Makefile @@ -1,114 +1,112 @@ -# Created by: batman - PORTNAME= mpqc PORTVERSION= 2.3.1 PORTREVISION= 47 CATEGORIES= science parallel MASTER_SITES= SF MAINTAINER= yuri@FreeBSD.org COMMENT= Massively Parallel Quantum Chemistry Program LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= dot:graphics/graphviz LIB_DEPENDS= libint.so:science/libint RUN_DEPENDS= wish:x11-toolkits/tk-wrapper \ dot:graphics/graphviz USES= fortran gmake libtool localbase perl5 shebangfix tar:bzip2 CONFLICTS_BUILD= ga # devel/ga: it links to libarmci.so, has HAVE_ARMCI defined, and hits some bug GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-production \ --enable-shared \ --with-cc-optflags="${CFLAGS}" \ --with-cxx-optflags="${CXXFLAGS}" \ --with-sc-datadir=${DATADIR} ALL_TARGET= default INSTALL_TARGET= install install_devel DESTDIRNAME= installroot SHEBANG_FILES= src/bin/mpqc/ccarunproc src/bin/mpqc/mpqcrunproc USE_LDCONFIG= yes USE_CXXSTD= c++98 # workaround https://github.com/ValeevGroup/mpqc/issues/57 OPTIONS_DEFINE= ATLAS DOXYGEN EXAMPLES ICC MPI OPTIFLAGS OPTIONS_DEFAULT= DOXYGEN MPI OPTIONS_SUB= yes ICC_DESC= Build with ICC compiler instead ATLAS_DESC= Link with ATLAS instead of BLAS OPTIFLAGS_DESC= Build with optimized flags ATLAS_USES= blaslapack:atlas ATLAS_USES_OFF= blaslapack:netlib DOXYGEN_CONFIGURE_ENABLE= doxygen-man DOXYGEN_BUILD_DEPENDS= doxygen:devel/doxygen \ dot:graphics/graphviz DOXYGEN_USE= TEX=base,dvipsk,pdftex ICC_BUILD_DEPENDS= ${LOCALBASE}/intel_cc_80/bin/icc:lang/icc MPI_CONFIGURE_ENABLE= parallel MPI_LIB_DEPENDS= libmpich.so:net/mpich MPI_LDFLAGS= -lmpich # build fails to supply libmpich.so to link OPTIFLAGS_CFLAGS= -ffast-math OPTIFLAGS_CXXFLAGS= -ffast-math .include .if ${PORT_OPTIONS:MICC} CC= ${LOCALBASE}/intel_cc_80/bin/icc CXX= ${LOCALBASE}/intel_cc_80/bin/icpc CFLAGS= -O3 -tpp7 -xMKW -Vaxlib CXXFLAGS= -O3 -tpp7 -xMKW -Vaxlib LIBS+= -lsvml .endif post-patch: @${REINPLACE_CMD} \ -e 's/-lblas/${BLASLIB}/' -e 's/-llapack/${LAPACKLIB}/' \ -e 's/pthread_join(0,0)/pthread_create(0,0,0,0)/' \ -e 's|/usr/bin/wish|${LOCALBASE}/bin/wish|' \ ${WRKSRC}/configure @${REINPLACE_CMD} \ 's|#include |#include <${WRKSRC}/src/lib/chemistry/qc/mbptr12/f77sym.h>|' \ ${WRKSRC}/src/lib/chemistry/qc/mbptr12/blas.h \ ${WRKSRC}/src/lib/chemistry/qc/mbptr12/lapack.h post-configure: # workaround: https://github.com/ValeevGroup/mpqc/issues/56 @${REINPLACE_CMD} -e ' \ s|/\* #undef USING_NAMESPACE_STD \*/|#define USING_NAMESPACE_STD 1|; \ s|/\* #undef HAVE_SGETN \*/|#define HAVE_SGETN 1|' \ ${WRKSRC}/src/lib/scconfig.h do-build-DOXYGEN-on: @(cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS}) ${RM} ${WRKSRC}/doc/man/man1/_* ${WRKSRC}/doc/man/man3/_* do-install-DOXYGEN-on: @(cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} \ install install_man) ${MV} ${STAGEDIR}${PREFIX}/html ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: @(cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} \ install_samples) ${MV} ${STAGEDIR}${PREFIX}/examples/mp2 ${STAGEDIR}${EXAMPLESDIR} ${RMDIR} ${STAGEDIR}${PREFIX}/examples post-install: (cd ${STAGEDIR}${PREFIX}/bin && ${STRIP_CMD} scpr molrender mpqc scls) ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so validate: (cd ${WRKSRC}/src/bin/mpqc/validate && \ ${MAKE_CMD} check0 && \ ${MAKE_CMD} check0_run && \ ${MAKE_CMD} check0_chk) .include diff --git a/science/netcdf-cxx/Makefile b/science/netcdf-cxx/Makefile index 0e7766353090..5795531b5c42 100644 --- a/science/netcdf-cxx/Makefile +++ b/science/netcdf-cxx/Makefile @@ -1,29 +1,27 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= netcdf-cxx PORTVERSION= 4.3.1 PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://downloads.unidata.ucar.edu/netcdf-cxx/${PORTVERSION}/ \ LOCAL/sunpoet DISTNAME= ${PORTNAME}4-${PORTVERSION} MAINTAINER= sunpoet@FreeBSD.org COMMENT= C++ library for machine-independent, array-oriented data access LICENSE= UCAR_UNIDATA LICENSE_FILE= ${WRKSRC}/COPYRIGHT LICENSE_NAME= University Corporation for Atmospheric Research/Unidata LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept LIB_DEPENDS= libnetcdf.so:science/netcdf USES= libtool localbase pathfix CPPFLAGS+= -fPIC -DPIC GNU_CONFIGURE= yes INSTALL_TARGET= install-strip TEST_TARGET= check USE_LDCONFIG= yes .include diff --git a/science/netcdf-fortran/Makefile b/science/netcdf-fortran/Makefile index 5dbf56ae543b..6ca685a29093 100644 --- a/science/netcdf-fortran/Makefile +++ b/science/netcdf-fortran/Makefile @@ -1,30 +1,28 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= netcdf-fortran PORTVERSION= 4.5.4 CATEGORIES= science MASTER_SITES= https://downloads.unidata.ucar.edu/netcdf-fortran/${PORTVERSION}/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= Fortran library for machine-independent, array-oriented data access LICENSE= UCAR_UNIDATA LICENSE_FILE= ${WRKSRC}/COPYRIGHT LICENSE_NAME= University Corporation for Atmospheric Research/Unidata LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BUILD_DEPENDS= netcdf>=4.7.4:science/netcdf LIB_DEPENDS= libnetcdf.so:science/netcdf USES= fortran gmake libtool localbase makeinfo pathfix CPPFLAGS+= -fPIC -DPIC -DgFortran GNU_CONFIGURE= yes INSTALL_TARGET= install-strip MAKE_ENV= MAKEINFOFLAGS=--no-split MAKE_JOBS_UNSAFE= yes TEST_TARGET= check USE_LDCONFIG= yes .include diff --git a/science/netcdf/Makefile b/science/netcdf/Makefile index 74f42c5bd372..d95c30afa90f 100644 --- a/science/netcdf/Makefile +++ b/science/netcdf/Makefile @@ -1,54 +1,52 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= netcdf PORTVERSION= 4.9.0 DISTVERSIONPREFIX= c- CATEGORIES= science MASTER_SITES= https://downloads.unidata.ucar.edu/netcdf-c/${PORTVERSION}/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= C library for machine-independent, array-oriented data access LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYRIGHT LIB_DEPENDS= libcurl.so:ftp/curl \ libhdf5.so:science/hdf5 USES= gmake libtool localbase ncurses pathfix pkgconfig:run CONFIGURE_ARGS= --disable-filter-testing --disable-libxml2 \ --enable-byterange --enable-dap --enable-netcdf-4 CPPFLAGS+= -fPIC -DPIC GNU_CONFIGURE= yes INSTALL_TARGET= install-strip LIBS+= -lexecinfo TEST_TARGET= check USE_LDCONFIG= yes CONFLICTS_INSTALL= hdf-4.[0-9]* netcdf-3.[0-9]* netcdf3-3.[0-9]* OPTIONS_DEFINE= DOCS DOXYGEN SZIP OPTIONS_DEFAULT=SZIP OPTIONS_SUB= yes DOXYGEN_IMPLIES=DOCS SZIP_DESC= SZIP support (required if HDF5 was built with SZIP) DOXYGEN_BUILD_DEPENDS= doxygen:devel/doxygen DOXYGEN_CONFIGURE_ENABLE= doxygen SZIP_LIB_DEPENDS= libsz.so:science/libaec SZIP_LIBS= -lsz post-patch: @${REINPLACE_CMD} -e 's|-ldl ||g' ${WRKSRC}/configure @${REINPLACE_CMD} -e '/ int fileno(FILE\*);/d' ${WRKSRC}/libdispatch/d*.c ${WRKSRC}/ncgen/ncgen* ${WRKSRC}/ncgen3/ncgen* ${WRKSRC}/oc2/ocdump.c post-build-DOXYGEN-on: cd ${WRKSRC}/docs/ && ${LOCALBASE}/bin/doxygen . post-install-DOXYGEN-on: ${MKDIR} ${STAGEDIR}${DOCSDIR}/ cd ${WRKSRC}/docs/html/ && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} .include diff --git a/science/openbabel/Makefile b/science/openbabel/Makefile index 11573707f916..26fafdc08e74 100644 --- a/science/openbabel/Makefile +++ b/science/openbabel/Makefile @@ -1,66 +1,64 @@ -# Created by: ijliao - PORTNAME= openbabel DISTVERSION= 3.1.1 PORTREVISION= 5 DISTVERSIONSUFFIX= -source CATEGORIES= science MASTER_SITES= https://github.com/openbabel/openbabel/releases/download/openbabel-${PORTVERSION:C/\./-/g}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Chemical toolbox designed to speak the many languages of chemical data LICENSE= GPLv2+ BUILD_DEPENDS= rapidjson>0:devel/rapidjson LIB_DEPENDS= libmaeparser.so:science/maeparser \ libcoordgen.so:science/coordgenlibs \ libboost_thread.so:devel/boost-libs CONFLICTS_INSTALL= babel USES= cmake compiler:c++11-lang eigen:3 gnome pkgconfig tar:bz2 USE_CXXSTD= gnu++98 USE_GNOME= libxml2 USE_LDCONFIG= yes CMAKE_ON= WITH_COORDGEN WITH_JSON OPENBABEL_USE_SYSTEM_RAPIDJSON WITH_MAEPARSER WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} PLIST_SUB= VERSION=3.1.0 # To be replaced by ${PORTVERSION} nexttime! OPTIONS_DEFINE= CAIRO PYTHON GUI OPTIONS_DEFAULT= CAIRO PYTHON GUI OPTIONS_SUB= yes CAIRO_DESC= PNG support via cairo library CAIRO_USE= GNOME=cairo PYTHON_USES= python PYTHON_CMAKE_BOOL= PYTHON_BINDINGS GUI_CMAKE_BOOL= BUILD_GUI GUI_CMAKE_ON= -DwxWidgets_CONFIG_EXECUTABLE:STRING=${WX_CONFIG} GUI_USE= WX=3.0 .include .if ${CHOSEN_COMPILER_TYPE} == gcc CXXFLAGS+= -Wno-narrowing USE_CXXSTD= c++11 .endif pre-configure: ${REINPLACE_CMD} -e '/pkgconfig/s,$${LIB_INSTALL_DIR},libdata,' \ ${WRKSRC}/CMakeLists.txt pre-configure-CAIRO-off: ${REINPLACE_CMD} -e '/find_package(Cairo)/d' \ ${WRKSRC}/CMakeLists.txt post-install-PYTHON-on: (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) .include diff --git a/science/orthanc-dicomweb/Makefile b/science/orthanc-dicomweb/Makefile index 8802e0598ceb..468a40c7c946 100644 --- a/science/orthanc-dicomweb/Makefile +++ b/science/orthanc-dicomweb/Makefile @@ -1,64 +1,62 @@ -# Created by: maintainer.freebsd@xpoundit.com - PORTNAME= orthanc-dicomweb DISTVERSION= 1.8 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-dicom-web/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ https://orthanc.osimis.io/ThirdPartyDownloads/:thirdparty \ https://orthanc.osimis.io/ThirdPartyDownloads/dicom-web/:thirdpartydicomweb DISTFILES= OrthancDicomWeb-${PORTVERSION}.tar.gz:main EXTRADISTFILES= Orthanc-1.11.0.tar.gz:framework \ e2fsprogs-1.44.5.tar.gz:thirdparty \ bootstrap-4.3.1.zip:thirdpartydicomweb \ vuejs-2.6.10.tar.gz:thirdpartydicomweb \ axios-0.19.0.tar.gz:thirdpartydicomweb \ Font-Awesome-4.7.0.tar.gz:thirdpartydicomweb \ bootstrap-vue-2.0.0-rc.24-dist.tar.gz:thirdpartydicomweb \ babel-polyfill-6.26.0.min.js.gz:thirdpartydicomweb DISTFILES+= ${EXTRADISTFILES} DIST_SUBDIR= orthanc EXTRACT_ONLY= OrthancDicomWeb-${PORTVERSION}.tar.gz MAINTAINER= maintainer.freebsd@xpoundit.com COMMENT= Orthanc plugin to bring support of the DICOMweb standard into Orthanc LICENSE= AGPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCPlugin.h:science/orthanc LIB_DEPENDS= libboost_atomic.so:devel/boost-libs \ libexpat.so:textproc/expat2 \ libgdcmCommon.so:devel/gdcm \ libicudata.so:devel/icu \ libjsoncpp.so:devel/jsoncpp \ libopenjp2.so:graphics/openjpeg \ libpugixml.so:textproc/pugixml RUN_DEPENDS= Orthanc:science/orthanc USES= cmake localbase python:build USE_LDCONFIG= yes CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/ThirdPartyDownloads/Orthanc-1.11.0/OrthancFramework/Sources \ -DORTHANC_FRAMEWORK_SOURCE=path CMAKE_OFF= USE_SYSTEM_UUID CFLAGS+= -DORTHANC_ENABLE_LOGGING_PLUGIN -DNDEBUG CXXFLAGS+= -DNDEBUG WRKSRC= ${WRKDIR}/OrthancDicomWeb-${PORTVERSION} PLIST_SUB= DISTVERSION=${DISTVERSION} post-extract: ${MKDIR} ${WRKSRC}/ThirdPartyDownloads .for f in ${EXTRADISTFILES:C/:[^:]*//} ${CP} ${DISTDIR}/${DIST_SUBDIR}/${f} ${WRKSRC}/ThirdPartyDownloads .endfor ${TAR} -C ${WRKSRC}/ThirdPartyDownloads -xf ${WRKSRC}/ThirdPartyDownloads/Orthanc-1.11.0.tar.gz do-test: @cd ${BUILD_WRKSRC} && ./UnitTests .include diff --git a/science/orthanc-mysql/Makefile b/science/orthanc-mysql/Makefile index ef9fe4478cea..265329cb62b8 100644 --- a/science/orthanc-mysql/Makefile +++ b/science/orthanc-mysql/Makefile @@ -1,51 +1,49 @@ -# Created by: maintainer.freebsd@xpoundit.com - PORTNAME= orthanc-mysql DISTVERSION= 4.3 PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-mysql/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ https://orthanc.osimis.io/ThirdPartyDownloads/:thirdparty DISTFILES= OrthancMySQL-${PORTVERSION}.tar.gz:main \ Orthanc-1.9.3.tar.gz:framework \ e2fsprogs-1.44.5.tar.gz:thirdparty DIST_SUBDIR= orthanc EXTRACT_ONLY= OrthancMySQL-${PORTVERSION}.tar.gz MAINTAINER= maintainer.freebsd@xpoundit.com COMMENT= Orthanc plugin to use MySQL/MariaDB for indexing or storage LICENSE= AGPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCDatabasePlugin.h:science/orthanc LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ libcurl.so:ftp/curl \ libgdcmCommon.so:devel/gdcm \ libjsoncpp.so:devel/jsoncpp \ libpugixml.so:textproc/pugixml RUN_DEPENDS= Orthanc:science/orthanc USES= cmake localbase mysql:client python:build ssl USE_LDCONFIG= yes WRKSRC= ${WRKDIR}/OrthancMySQL-${PORTVERSION} CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancFramework/Sources \ -DORTHANC_FRAMEWORK_SOURCE=path CMAKE_OFF= DBUILD_UNIT_TESTS USE_SYSTEM_ORTHANC_SDK USE_SYSTEM_UUID CMAKE_SOURCE_PATH= ${WRKSRC}/MySQL CFLAGS+= -DORTHANC_ENABLE_LOGGING_PLUGIN -DNDEBUG CXXFLAGS+= -I${LOCALBASE}/include -DNDEBUG PLIST_SUB= DISTVERSION=${DISTVERSION} post-extract: ${MKDIR} ${WRKSRC}/MySQL/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/e2fsprogs-1.44.5.tar.gz ${WRKSRC}/MySQL/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-1.9.3.tar.gz ${WRKSRC}/MySQL/ThirdPartyDownloads ${TAR} -C ${WRKSRC}/MySQL/ThirdPartyDownloads -xf ${WRKSRC}/MySQL/ThirdPartyDownloads/Orthanc-1.9.3.tar.gz .include diff --git a/science/orthanc-postgresql/Makefile b/science/orthanc-postgresql/Makefile index aa8ed33f5e32..ed32c5d0a54d 100644 --- a/science/orthanc-postgresql/Makefile +++ b/science/orthanc-postgresql/Makefile @@ -1,50 +1,48 @@ -# Created by: maintainer.freebsd@xpoundit.com - PORTNAME= orthanc-postgresql DISTVERSION= 4.0 PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-postgresql/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ https://orthanc.osimis.io/ThirdPartyDownloads/:thirdparty DISTFILES= OrthancPostgreSQL-${PORTVERSION}.tar.gz:main \ Orthanc-1.9.3.tar.gz:framework \ e2fsprogs-1.44.5.tar.gz:thirdparty DIST_SUBDIR= orthanc EXTRACT_ONLY= OrthancPostgreSQL-${PORTVERSION}.tar.gz MAINTAINER= maintainer.freebsd@xpoundit.com COMMENT= Orthanc plugin to use PostgreSQL for indexing or storage LICENSE= AGPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCDatabasePlugin.h:science/orthanc LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ libgdcmCommon.so:devel/gdcm \ libjsoncpp.so:devel/jsoncpp \ libpugixml.so:textproc/pugixml RUN_DEPENDS= Orthanc:science/orthanc USES= cmake compiler:c11 localbase pgsql:11+ python:build ssl USE_LDCONFIG= yes WRKSRC= ${WRKDIR}/OrthancPostgreSQL-${PORTVERSION} CMAKE_SOURCE_PATH= ${WRKSRC}/PostgreSQL CMAKE_OFF= BUILD_UNIT_TESTS USE_SYSTEM_ORTHANC_SDK USE_SYSTEM_UUID CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancFramework/Sources \ -DORTHANC_FRAMEWORK_SOURCE=path CXXFLAGS+= -I${LOCALBASE}/include -DNDEBUG LDFLAGS+= -L${LOCALBASE}/lib CFLAGS+= -DORTHANC_ENABLE_LOGGING_PLUGIN -DNDEBUG PLIST_SUB= DISTVERSION=${DISTVERSION} post-extract: ${MKDIR} ${WRKSRC}/PostgreSQL/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/e2fsprogs-1.44.5.tar.gz ${WRKSRC}/PostgreSQL/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-1.9.3.tar.gz ${WRKSRC}/PostgreSQL/ThirdPartyDownloads ${TAR} -C ${WRKSRC}/PostgreSQL/ThirdPartyDownloads -xf ${WRKSRC}/PostgreSQL/ThirdPartyDownloads/Orthanc-1.9.3.tar.gz .include diff --git a/science/orthanc-webviewer/Makefile b/science/orthanc-webviewer/Makefile index bf2904b5fa3c..e6604d8ebee4 100644 --- a/science/orthanc-webviewer/Makefile +++ b/science/orthanc-webviewer/Makefile @@ -1,66 +1,64 @@ -# Created by: maintainer.freebsd@xpoundit.com - PORTNAME= orthanc-webviewer DISTVERSION= 2.8 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-webviewer/:main \ https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ http://orthanc.osimis.io/ThirdPartyDownloads/WebViewer/:thirdpartywebviewer \ http://orthanc.osimis.io/ThirdPartyDownloads/:thirdparty DISTFILES= OrthancWebViewer-${PORTVERSION}.tar.gz:main \ jsPanel-2.3.3-fixed.zip:thirdpartywebviewer \ cornerstone-0.11.0.zip:thirdpartywebviewer \ jquery-ui-1.11.3.zip:thirdpartywebviewer \ pako-0.2.5.zip:thirdpartywebviewer \ js-url-1.8.6.zip:thirdpartywebviewer \ Orthanc-1.11.0.tar.gz:framework \ e2fsprogs-1.44.5.tar.gz:thirdparty DIST_SUBDIR= orthanc EXTRACT_ONLY= OrthancWebViewer-${PORTVERSION}.tar.gz MAINTAINER= maintainer.freebsd@xpoundit.com COMMENT= Orthanc plugin to extend Orthanc with a Web viewer of medical images LICENSE= AGPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCPlugin.h:science/orthanc LIB_DEPENDS= libboost_atomic.so:devel/boost-libs \ libexpat.so:textproc/expat2 \ libgdcmCommon.so:devel/gdcm \ libicudata.so:devel/icu \ libjsoncpp.so:devel/jsoncpp \ libopenjp2.so:graphics/openjpeg \ libsqlite3.so:databases/sqlite3 RUN_DEPENDS= Orthanc:science/orthanc USES= cmake localbase python:build USE_LDCONFIG= yes CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/ThirdPartyDownloads/Orthanc-1.11.0/OrthancFramework/Sources \ -DORTHANC_FRAMEWORK_SOURCE=path CMAKE_OFF= USE_SYSTEM_UUID CFLAGS+= -I${LOCALBASE}/include -DORTHANC_ENABLE_LOGGING_PLUGIN -DNDEBUG CXXFLAGS+= -DNDEBUG WRKSRC= ${WRKDIR}/OrthancWebViewer-${PORTVERSION} PLIST_SUB= DISTVERSION=${DISTVERSION} post-extract: ${MKDIR} ${WRKSRC}/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/jsPanel-2.3.3-fixed.zip ${WRKSRC}/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/cornerstone-0.11.0.zip ${WRKSRC}/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/jquery-ui-1.11.3.zip ${WRKSRC}/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/pako-0.2.5.zip ${WRKSRC}/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/js-url-1.8.6.zip ${WRKSRC}/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/e2fsprogs-1.44.5.tar.gz ${WRKSRC}/ThirdPartyDownloads ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-1.11.0.tar.gz ${WRKSRC}/ThirdPartyDownloads ${TAR} -C ${WRKSRC}/ThirdPartyDownloads -xf ${WRKSRC}/ThirdPartyDownloads/Orthanc-1.11.0.tar.gz post-build: @cd ${BUILD_WRKSRC} && ./UnitTests .include diff --git a/science/orthanc/Makefile b/science/orthanc/Makefile index efec4059c63c..b604253f3f03 100644 --- a/science/orthanc/Makefile +++ b/science/orthanc/Makefile @@ -1,59 +1,57 @@ -# Created by: maintainer.freebsd@xpoundit.com - PORTNAME= orthanc DISTVERSION= 1.11.0 PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/orthanc/ DISTNAME= Orthanc-${PORTVERSION} MAINTAINER= maintainer.freebsd@xpoundit.com COMMENT= Lightweight DICOM server for healthcare and medical research LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libboost_atomic.so:devel/boost-libs \ libcivetweb.so:www/civetweb \ libcurl.so:ftp/curl \ libdcmtkcharls.so:graphics/dcmtk \ libgtest.so:devel/googletest \ libicuuc.so:devel/icu \ libjsoncpp.so:devel/jsoncpp \ libpng16.so:graphics/png \ libpugixml.so:textproc/pugixml \ libtiff.so:graphics/tiff \ libuuid.so:misc/e2fsprogs-libuuid USES= cmake gnome iconv jpeg lua python:build sqlite ssl USE_GNOME= libxml2 USE_LDCONFIG= yes USE_RC_SUBR= orthanc CMAKE_ON= USE_SYSTEM_BOOST USE_SYSTEM_CIVETWEB USE_SYSTEM_DCMTK \ USE_SYSTEM_GOOGLE_TEST USE_SYSTEM_JSONCPP USE_SYSTEM_LIBICONV \ USE_SYSTEM_LIBJPEG USE_SYSTEM_LIBPNG USE_SYSTEM_LUA \ USE_SYSTEM_OPENSSL USE_SYSTEM_PUGIXML USE_SYSTEM_SQLITE \ USE_SYSTEM_UUID USE_SYSTEM_ZLIB CMAKE_OFF= BUILD_CONNECTIVITY_CHECKS UNIT_TESTS_WITH_HTTP_CONNEXIONS CMAKE_SOURCE_PATH= ${WRKSRC}/OrthancServer CFLAGS+= -DNDEBUG CXXFLAGS+= -DNDEBUG WRKSRC= ${WRKDIR}/Orthanc-${PORTVERSION} USERS= orthanc GROUPS= orthanc PLIST_SUB+= DISTVERSION=${DISTVERSION} post-install: ${MKDIR} ${STAGEDIR}/var/db/orthanc/db/db-v5 ${MKDIR} ${STAGEDIR}${DATADIR}/plugins ${MKDIR} ${STAGEDIR}${ETCDIR} ${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|g' ${CMAKE_SOURCE_PATH}/Resources/Configuration.json ${CP} ${CMAKE_SOURCE_PATH}/Resources/Configuration.json ${STAGEDIR}${ETCDIR}/orthanc.json.sample .include diff --git a/science/p5-Algorithm-SVMLight/Makefile b/science/p5-Algorithm-SVMLight/Makefile index 2b6f1710446e..2bdfd14c8ca1 100644 --- a/science/p5-Algorithm-SVMLight/Makefile +++ b/science/p5-Algorithm-SVMLight/Makefile @@ -1,23 +1,21 @@ -# Created by: Gea-Suan Lin - PORTNAME= Algorithm-SVMLight PORTVERSION= 0.09 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Perl interface to SVMLight Machine-Learning Package BUILD_DEPENDS= svmlight>=6.01_2:science/svmlight LIB_DEPENDS= libsvmlight.so:science/svmlight USES= perl5 USE_PERL5= modbuild post-patch: @${REINPLACE_CMD} -e "s,%%LOCALBASE%%,${LOCALBASE},g" \ ${WRKSRC}/Build.PL .include diff --git a/science/p5-Chemistry-3DBuilder/Makefile b/science/p5-Chemistry-3DBuilder/Makefile index 87176687dc91..48aa4090a819 100644 --- a/science/p5-Chemistry-3DBuilder/Makefile +++ b/science/p5-Chemistry-3DBuilder/Makefile @@ -1,30 +1,28 @@ -# Created by: Steve Wills =0:science/p5-Chemistry-Mol \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES \ p5-Chemistry-File-SMARTS>=0:science/p5-Chemistry-File-SMARTS \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring \ p5-Chemistry-InternalCoords>=0:science/p5-Chemistry-InternalCoords \ p5-Math-VectorReal>=0:math/p5-Math-VectorReal RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES \ p5-Chemistry-File-SMARTS>=0:science/p5-Chemistry-File-SMARTS \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring \ p5-Chemistry-InternalCoords>=0:science/p5-Chemistry-InternalCoords \ p5-Math-VectorReal>=0:math/p5-Math-VectorReal USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-Bond-Find/Makefile b/science/p5-Chemistry-Bond-Find/Makefile index d6a11052a904..327c7c5c2bb4 100644 --- a/science/p5-Chemistry-Bond-Find/Makefile +++ b/science/p5-Chemistry-Bond-Find/Makefile @@ -1,24 +1,22 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-Bond-Find PORTVERSION= 0.23 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Detect bonds in a molecule and assign formal bond orders LICENSE= ART10 GPLv1+ LICENSE_COMB= dual BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol USES= perl5 USE_PERL5= configure NO_ARCH= yes .include diff --git a/science/p5-Chemistry-Canonicalize/Makefile b/science/p5-Chemistry-Canonicalize/Makefile index cd2580c39fb9..b24c03812722 100644 --- a/science/p5-Chemistry-Canonicalize/Makefile +++ b/science/p5-Chemistry-Canonicalize/Makefile @@ -1,23 +1,21 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-Canonicalize PORTVERSION= 0.11 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Number the atoms in a molecule in a unique way LICENSE= ART10 GPLv1+ LICENSE_COMB= dual BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-Elements/Makefile b/science/p5-Chemistry-Elements/Makefile index 607eaa3e9b0d..3bf26eedbc7c 100644 --- a/science/p5-Chemistry-Elements/Makefile +++ b/science/p5-Chemistry-Elements/Makefile @@ -1,20 +1,18 @@ -# Created by: Seamus Venasse - PORTNAME= Chemistry-Elements PORTVERSION= 1.075 CATEGORIES= science perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Perl extension for working with Chemical Elements LICENSE= ART20 LICENSE_FILE= ${WRKSRC}/LICENSE USES= perl5 USE_PERL5= configure NO_ARCH= yes .include diff --git a/science/p5-Chemistry-File-MDLMol/Makefile b/science/p5-Chemistry-File-MDLMol/Makefile index 93cd7380bd28..2affdd0cfa77 100644 --- a/science/p5-Chemistry-File-MDLMol/Makefile +++ b/science/p5-Chemistry-File-MDLMol/Makefile @@ -1,22 +1,20 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-File-MDLMol PORTVERSION= 0.21 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= MDL molfile reader/write BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-File-Mopac/Makefile b/science/p5-Chemistry-File-Mopac/Makefile index e6507949c8a8..c5524c69d81b 100644 --- a/science/p5-Chemistry-File-Mopac/Makefile +++ b/science/p5-Chemistry-File-Mopac/Makefile @@ -1,22 +1,20 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-File-Mopac PORTVERSION= 0.15 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= MOPAC 6 input file reader/writer BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-InternalCoords>=0:science/p5-Chemistry-InternalCoords RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-InternalCoords>=0:science/p5-Chemistry-InternalCoords USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-File-PDB/Makefile b/science/p5-Chemistry-File-PDB/Makefile index 9b20cb2fc165..5bec922be47f 100644 --- a/science/p5-Chemistry-File-PDB/Makefile +++ b/science/p5-Chemistry-File-PDB/Makefile @@ -1,20 +1,18 @@ -# Created by: Wen Heping - PORTNAME= Chemistry-File-PDB PORTVERSION= 0.23 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Perl module to read and write PDB files BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= p5-Chemistry-Mol>=0.37:science/p5-Chemistry-Mol \ p5-Chemistry-MacroMol>=0.06:science/p5-Chemistry-MacroMol USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-File-SLN/Makefile b/science/p5-Chemistry-File-SLN/Makefile index aa43134c93bf..f28450afcebe 100644 --- a/science/p5-Chemistry-File-SLN/Makefile +++ b/science/p5-Chemistry-File-SLN/Makefile @@ -1,28 +1,26 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-File-SLN PORTVERSION= 0.11 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= SLN linear notation parser/writer BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring \ p5-Chemistry-Canonicalize>=0:science/p5-Chemistry-Canonicalize \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Parse-Yapp>=0:devel/p5-Parse-Yapp RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring \ p5-Chemistry-Canonicalize>=0:science/p5-Chemistry-Canonicalize \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Parse-Yapp>=0:devel/p5-Parse-Yapp USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-File-SMARTS/Makefile b/science/p5-Chemistry-File-SMARTS/Makefile index acb61e7b9216..e6280d27e04f 100644 --- a/science/p5-Chemistry-File-SMARTS/Makefile +++ b/science/p5-Chemistry-File-SMARTS/Makefile @@ -1,26 +1,24 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-File-SMARTS PORTVERSION= 0.22 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= SMARTS chemical substructure pattern linear notation parser BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-File-SMILES/Makefile b/science/p5-Chemistry-File-SMILES/Makefile index 26c096c96138..e9e5d7e94647 100644 --- a/science/p5-Chemistry-File-SMILES/Makefile +++ b/science/p5-Chemistry-File-SMILES/Makefile @@ -1,29 +1,27 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-File-SMILES PORTVERSION= 0.47 PORTREVISION= 2 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= SMILES linear notation parser/writer BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Chemistry-Canonicalize>=0:science/p5-Chemistry-Canonicalize \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Chemistry-Canonicalize>=0:science/p5-Chemistry-Canonicalize \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring USES= perl5 shebangfix SHEBANG_FILES= write.pl perl_OLD_CMD= /home/ivan/bin/perl USE_PERL5= configure NO_ARCH= yes .include diff --git a/science/p5-Chemistry-File-VRML/Makefile b/science/p5-Chemistry-File-VRML/Makefile index 8fe4b8ba365f..8fc1a7515500 100644 --- a/science/p5-Chemistry-File-VRML/Makefile +++ b/science/p5-Chemistry-File-VRML/Makefile @@ -1,20 +1,18 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-File-VRML PORTVERSION= 0.10 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Generate VRML models for molecules BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-File-XYZ/Makefile b/science/p5-Chemistry-File-XYZ/Makefile index a3050aabedca..cd9d941e46dc 100644 --- a/science/p5-Chemistry-File-XYZ/Makefile +++ b/science/p5-Chemistry-File-XYZ/Makefile @@ -1,20 +1,18 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-File-XYZ PORTVERSION= 0.11 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= XYZ molecule format reader/writer BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-FormulaPattern/Makefile b/science/p5-Chemistry-FormulaPattern/Makefile index 5c8b8f1de9b4..943b87918e6d 100644 --- a/science/p5-Chemistry-FormulaPattern/Makefile +++ b/science/p5-Chemistry-FormulaPattern/Makefile @@ -1,22 +1,20 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-FormulaPattern PORTVERSION= 0.10 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Match molecule by formula BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-InternalCoords/Makefile b/science/p5-Chemistry-InternalCoords/Makefile index 1d44c2bec5f9..782709a76968 100644 --- a/science/p5-Chemistry-InternalCoords/Makefile +++ b/science/p5-Chemistry-InternalCoords/Makefile @@ -1,24 +1,22 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-InternalCoords PORTVERSION= 0.18 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Represent the position of an atom using internal coordinates BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Chemistry-Canonicalize>=0:science/p5-Chemistry-Canonicalize RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Chemistry-Canonicalize>=0:science/p5-Chemistry-Canonicalize USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-Isotope/Makefile b/science/p5-Chemistry-Isotope/Makefile index 3e8157446c6d..fbc338edf82d 100644 --- a/science/p5-Chemistry-Isotope/Makefile +++ b/science/p5-Chemistry-Isotope/Makefile @@ -1,17 +1,15 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-Isotope PORTVERSION= 0.11 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Table of the isotopes exact mass data USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-MacroMol/Makefile b/science/p5-Chemistry-MacroMol/Makefile index 14e246623b1f..9823e36e4a79 100644 --- a/science/p5-Chemistry-MacroMol/Makefile +++ b/science/p5-Chemistry-MacroMol/Makefile @@ -1,19 +1,17 @@ -# Created by: Wen Heping - PORTNAME= Chemistry-MacroMol PORTVERSION= 0.06 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Perl toolkit to describe macromolecules BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= p5-Chemistry-Mol>=0.37:science/p5-Chemistry-Mol USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-MidasPattern/Makefile b/science/p5-Chemistry-MidasPattern/Makefile index e10f609d8eba..16a82d62328b 100644 --- a/science/p5-Chemistry-MidasPattern/Makefile +++ b/science/p5-Chemistry-MidasPattern/Makefile @@ -1,26 +1,24 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-MidasPattern PORTVERSION= 0.11 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Select atoms in macromolecules BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-File-PDB>=0:science/p5-Chemistry-File-PDB \ p5-Chemistry-MacroMol>=0:science/p5-Chemistry-MacroMol \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-File-PDB>=0:science/p5-Chemistry-File-PDB \ p5-Chemistry-MacroMol>=0:science/p5-Chemistry-MacroMol \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-Mok/Makefile b/science/p5-Chemistry-Mok/Makefile index 20774f0d6fdb..b0e9917699da 100644 --- a/science/p5-Chemistry-Mok/Makefile +++ b/science/p5-Chemistry-Mok/Makefile @@ -1,26 +1,24 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-Mok PORTVERSION= 0.25 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Molecular awk interpreter BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-Mol/Makefile b/science/p5-Chemistry-Mol/Makefile index a0570339c65e..096fd30cfacb 100644 --- a/science/p5-Chemistry-Mol/Makefile +++ b/science/p5-Chemistry-Mol/Makefile @@ -1,25 +1,23 @@ -# Created by: Wen Heping - PORTNAME= Chemistry-Mol PORTVERSION= 0.39 CATEGORIES= science perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Perl toolkit to describe molecules LICENSE= ART10 GPLv1+ LICENSE_COMB= dual BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= p5-IO-String>=0:devel/p5-IO-String \ p5-Math-VectorReal>=1.0:math/p5-Math-VectorReal TEST_DEPENDS= p5-Clone>=0:devel/p5-Clone USES= perl5 USE_PERL5= configure NO_ARCH= yes .include diff --git a/science/p5-Chemistry-Pattern/Makefile b/science/p5-Chemistry-Pattern/Makefile index dd3359aaabf5..5fb0112ad1c9 100644 --- a/science/p5-Chemistry-Pattern/Makefile +++ b/science/p5-Chemistry-Pattern/Makefile @@ -1,20 +1,18 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-Pattern PORTVERSION= 0.27 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Chemical substructure pattern matching BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-Reaction/Makefile b/science/p5-Chemistry-Reaction/Makefile index b32e73112eb1..d5fcc4f1e580 100644 --- a/science/p5-Chemistry-Reaction/Makefile +++ b/science/p5-Chemistry-Reaction/Makefile @@ -1,29 +1,27 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-Reaction PORTVERSION= 0.02 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Represent a ring as a substructure of a molecule LICENSE= ART10 GPLv1+ LICENSE_COMB= dual BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES \ p5-Statistics-Regression>=0:math/p5-Statistics-Regression \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES \ p5-Statistics-Regression>=0:math/p5-Statistics-Regression \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Chemistry-Ring/Makefile b/science/p5-Chemistry-Ring/Makefile index 235506523188..f53cb51a9e8c 100644 --- a/science/p5-Chemistry-Ring/Makefile +++ b/science/p5-Chemistry-Ring/Makefile @@ -1,22 +1,20 @@ -# Created by: Steve Wills - PORTNAME= Chemistry-Ring PORTVERSION= 0.20 PORTREVISION= 1 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Represent a ring as a substructure of a molecule BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Statistics-Regression>=0:math/p5-Statistics-Regression RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Statistics-Regression>=0:math/p5-Statistics-Regression USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Geo-BUFR/Makefile b/science/p5-Geo-BUFR/Makefile index 50f89251aeb8..9cb303d0a31a 100644 --- a/science/p5-Geo-BUFR/Makefile +++ b/science/p5-Geo-BUFR/Makefile @@ -1,23 +1,21 @@ -# Created by: Wen Heping - PORTNAME= Geo-BUFR PORTVERSION= 1.38 CATEGORIES= science perl5 geography MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= Perl extension for handling of WMO BUFR files LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENCE USES= perl5 shebangfix USE_PERL5= configure SHEBANG_FILES= *.pl post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/${SITE_ARCH_REL}/auto/Geo/BUFR/BUFR.so .include diff --git a/science/p5-Geo-Coordinates-Converter-iArea/Makefile b/science/p5-Geo-Coordinates-Converter-iArea/Makefile index d303ce0b750b..d36d07b3b72e 100644 --- a/science/p5-Geo-Coordinates-Converter-iArea/Makefile +++ b/science/p5-Geo-Coordinates-Converter-iArea/Makefile @@ -1,26 +1,24 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= Geo-Coordinates-Converter-iArea PORTVERSION= 0.14 PORTREVISION= 1 CATEGORIES= science geography perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= Some utility functions around iArea LICENSE= ART10 GPLv1+ LICENSE_COMB= dual BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= p5-CDB_File>=0.96:databases/p5-CDB_File \ p5-File-ShareDir>=1.02:devel/p5-File-ShareDir \ p5-Geo-Coordinates-Converter>=0.09:science/p5-Geo-Coordinates-Converter USES= perl5 USE_PERL5= configure NO_ARCH= yes .include diff --git a/science/p5-Geo-Coordinates-Converter/Makefile b/science/p5-Geo-Coordinates-Converter/Makefile index 59037665bfd7..8509e9e9e0fb 100644 --- a/science/p5-Geo-Coordinates-Converter/Makefile +++ b/science/p5-Geo-Coordinates-Converter/Makefile @@ -1,27 +1,25 @@ -# Created by: Wen Heping - PORTNAME= Geo-Coordinates-Converter PORTVERSION= 0.13 PORTREVISION= 1 CATEGORIES= science geography perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Simple converter of geo coordinates LICENSE= ART10 GPLv1+ LICENSE_COMB= dual BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= p5-Class-Accessor-Lite>=0.05:devel/p5-Class-Accessor-Lite \ p5-String-CamelCase>0:textproc/p5-String-CamelCase \ p5-YAML>0:textproc/p5-YAML TEST_DEPENDS= p5-Test-Base>0:devel/p5-Test-Base USES= perl5 USE_PERL5= configure NO_ARCH= yes .include diff --git a/science/p5-Geo-WebService-Elevation-USGS/Makefile b/science/p5-Geo-WebService-Elevation-USGS/Makefile index 2bd6a2a44799..feadd04716ed 100644 --- a/science/p5-Geo-WebService-Elevation-USGS/Makefile +++ b/science/p5-Geo-WebService-Elevation-USGS/Makefile @@ -1,29 +1,27 @@ -# Created by: Wen Heping - PORTNAME= Geo-WebService-Elevation-USGS PORTVERSION= 0.120 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:WYANT PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Perl extension for elevation queries against USGS web services LICENSE= ART10 GPLv1+ LICENSE_COMB= dual BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= p5-HTTP-Message>=0:www/p5-HTTP-Message \ p5-JSON>=0:converters/p5-JSON \ p5-LWP-Protocol-https>=0:www/p5-LWP-Protocol-https \ p5-libwww>=0:www/p5-libwww USES= perl5 USE_PERL5= configure NO_ARCH= yes PORTSCOUT= limit:^[0-9\.]*$$ .include diff --git a/science/p5-PerlMol/Makefile b/science/p5-PerlMol/Makefile index 56be0747ebb7..c416ea22bced 100644 --- a/science/p5-PerlMol/Makefile +++ b/science/p5-PerlMol/Makefile @@ -1,64 +1,62 @@ -# Created by: Steve Wills - PORTNAME= PerlMol PORTVERSION= 0.3500 PORTREVISION= 2 CATEGORIES= science perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:ITUB PKGNAMEPREFIX= p5- MAINTAINER= swills@FreeBSD.org COMMENT= Perl modules for molecular chemistry BUILD_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-MacroMol>=0:science/p5-Chemistry-MacroMol \ p5-Parse-Yapp>=0:devel/p5-Parse-Yapp \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES \ p5-Chemistry-File-SMARTS>=0:science/p5-Chemistry-File-SMARTS \ p5-Chemistry-InternalCoords>=0:science/p5-Chemistry-InternalCoords \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring \ p5-Chemistry-Isotope>=0:science/p5-Chemistry-Isotope \ p5-Chemistry-3DBuilder>=0:science/p5-Chemistry-3DBuilder \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Chemistry-Canonicalize>=0:science/p5-Chemistry-Canonicalize \ p5-Chemistry-File-PDB>=0:science/p5-Chemistry-File-PDB \ p5-Chemistry-File-XYZ>=0:science/p5-Chemistry-File-XYZ \ p5-Chemistry-File-VRML>=0:science/p5-Chemistry-File-VRML \ p5-Chemistry-File-SLN>=0:science/p5-Chemistry-File-SLN \ p5-Chemistry-File-Mopac>=0:science/p5-Chemistry-File-Mopac \ p5-Chemistry-File-MDLMol>=0:science/p5-Chemistry-File-MDLMol \ p5-Chemistry-Reaction>=0:science/p5-Chemistry-Reaction \ p5-Chemistry-FormulaPattern>=0:science/p5-Chemistry-FormulaPattern \ p5-Chemistry-MidasPattern>=0:science/p5-Chemistry-MidasPattern \ p5-Chemistry-Mok>=0:science/p5-Chemistry-Mok \ p5-Statistics-Regression>=0:math/p5-Statistics-Regression RUN_DEPENDS= p5-Chemistry-Mol>=0:science/p5-Chemistry-Mol \ p5-Chemistry-MacroMol>=0:science/p5-Chemistry-MacroMol \ p5-Parse-Yapp>=0:devel/p5-Parse-Yapp \ p5-Chemistry-File-SMILES>=0:science/p5-Chemistry-File-SMILES \ p5-Chemistry-File-SMARTS>=0:science/p5-Chemistry-File-SMARTS \ p5-Chemistry-InternalCoords>=0:science/p5-Chemistry-InternalCoords \ p5-Chemistry-Pattern>=0:science/p5-Chemistry-Pattern \ p5-Chemistry-Ring>=0:science/p5-Chemistry-Ring \ p5-Chemistry-Isotope>=0:science/p5-Chemistry-Isotope \ p5-Chemistry-3DBuilder>=0:science/p5-Chemistry-3DBuilder \ p5-Chemistry-Bond-Find>=0:science/p5-Chemistry-Bond-Find \ p5-Chemistry-Canonicalize>=0:science/p5-Chemistry-Canonicalize \ p5-Chemistry-File-PDB>=0:science/p5-Chemistry-File-PDB \ p5-Chemistry-File-XYZ>=0:science/p5-Chemistry-File-XYZ \ p5-Chemistry-File-VRML>=0:science/p5-Chemistry-File-VRML \ p5-Chemistry-File-SLN>=0:science/p5-Chemistry-File-SLN \ p5-Chemistry-File-Mopac>=0:science/p5-Chemistry-File-Mopac \ p5-Chemistry-File-MDLMol>=0:science/p5-Chemistry-File-MDLMol \ p5-Chemistry-Reaction>=0:science/p5-Chemistry-Reaction \ p5-Chemistry-FormulaPattern>=0:science/p5-Chemistry-FormulaPattern \ p5-Chemistry-MidasPattern>=0:science/p5-Chemistry-MidasPattern \ p5-Chemistry-Mok>=0:science/p5-Chemistry-Mok \ p5-Statistics-Regression>=0:math/p5-Statistics-Regression USES= perl5 USE_PERL5= configure .include diff --git a/science/p5-Physics-Unit/Makefile b/science/p5-Physics-Unit/Makefile index 21d0dd026eb1..1384119e73b3 100644 --- a/science/p5-Physics-Unit/Makefile +++ b/science/p5-Physics-Unit/Makefile @@ -1,29 +1,27 @@ -# Created by: Frederic Culot - PORTNAME= Physics-Unit PORTVERSION= 0.54 CATEGORIES= science perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Manipulate Physics units and dimensions LICENSE= ART10 GPLv1+ LICENSE_COMB= dual NO_ARCH= YES USES= perl5 USE_PERL5= modbuild OPTIONS_DEFINE= EXAMPLES PORTEXAMPLES= * .include post-install: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/eg/ && ${COPYTREE_SHARE} '*.pl' ${STAGEDIR}${EXAMPLESDIR}) .include diff --git a/science/paje/Makefile b/science/paje/Makefile index 0e0853ce5991..708385df71ea 100644 --- a/science/paje/Makefile +++ b/science/paje/Makefile @@ -1,42 +1,40 @@ -# Created by: gurkan@phys.ethz.ch - PORTNAME= paje PORTVERSION= 1.97 PORTREVISION= 11 CATEGORIES= science gnustep MASTER_SITES= SF/${PORTNAME}/Releases DISTNAME= Paje_${PORTVERSION} EXTRACT_SUFX= .tar.gz.gz MAINTAINER= ports@FreeBSD.org COMMENT= Generic visualization tool for GNUstep (Gantt chart and more) LICENSE= LGPL21 USES= gnustep USE_GNUSTEP= gui base back build WRKSRC= ${WRKDIR}/${DISTNAME} post-patch: ${REINPLACE_CMD} -e 's|^GNUSTEP_INSTALLATION_DOMAIN|#GNUSTEP_INSTALLATION_DOMAIN|' \ ${WRKSRC}/GNUmakefile post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/GNUstep/System/Applications/Paje.app/Paje \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/AggregatingFilter.bundle/AggregatingFilter \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/ContainerFilter.bundle/ContainerFilter \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/EntityTypeFilter.bundle/EntityTypeFilter \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/FieldFilter.bundle/FieldFilter \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/FileReader.bundle/FileReader \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/General.bundle/General \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/ImbricationFilter.bundle/ImbricationFilter \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/OrderFilter.bundle/OrderFilter \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/PajeEventDecoder.bundle/PajeEventDecoder \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/PajeSimulator.bundle/PajeSimulator \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/ReductionFilter.bundle/ReductionFilter \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/SpaceTimeViewer.bundle/SpaceTimeViewer \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/StatViewer.bundle/StatViewer \ ${STAGEDIR}${PREFIX}/GNUstep/System/Library/Bundles/Paje/StorageController.bundle/StorageController .include diff --git a/science/paraview/Makefile b/science/paraview/Makefile index 41e3ad65e3ed..cde6ea58ea7d 100644 --- a/science/paraview/Makefile +++ b/science/paraview/Makefile @@ -1,166 +1,164 @@ -# Created by: anholt@FreeBSD.org - PORTNAME= paraview DISTVERSION= 5.10.1 PORTREVISION= 1 CATEGORIES= science graphics MASTER_SITES= http://www.paraview.org/files/v${VERMAJORMINOR}/ DISTNAME= ParaView-v${PORTVERSION} MAINTAINER= thierry@FreeBSD.org COMMENT= Powerful scientific data visualization application LICENSE= ParaView_License_1.2 LICENSE_NAME= ParaView_License LICENSE_FILE= ${WRKSRC}/License_v1.2.txt LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BROKEN_aarch64= fails to link: undefined reference to `sbrk' BUILD_DEPENDS= ${PYNUMPY} \ cli11>0:devel/cli11 \ utf8cpp>0:devel/utf8cpp \ ${LOCALBASE}/include/exprtk.hpp:math/exprtk \ ${PYTHON_SITELIBDIR}/matplotlib/pyplot.py:math/py-matplotlib@${PY_FLAVOR} LIB_DEPENDS= libhdf5.so:science/hdf5 \ libpng.so:graphics/png \ libtiff.so:graphics/tiff \ libfreetype.so:print/freetype2 \ libexpat.so:textproc/expat2 \ libjbig.so:graphics/jbigkit \ liborc-0.4.so:devel/orc \ libpcre.so:devel/pcre \ libicuuc.so:devel/icu \ libffi.so:devel/libffi \ liblas.so:devel/liblas \ libtbb.so:devel/onetbb \ libogg.so:audio/libogg \ libgl2ps.so:print/gl2ps \ libOT.so:math/openturns \ libgdal.so:graphics/gdal \ libgeos.so:graphics/geos \ libhpdf.so:print/libharu \ libpdal_base.so:math/pdal \ libdrm.so:graphics/libdrm \ libcgns.so:science/cgnslib \ liblz4.so:archivers/liblz4 \ libnetcdf.so:science/netcdf \ libjsoncpp.so:devel/jsoncpp \ libprotobuf.so:devel/protobuf \ libpugixml.so:textproc/pugixml \ libavutil.so:multimedia/ffmpeg \ libcgraph.so:graphics/graphviz \ libtheora.so:multimedia/libtheora \ libgeotiff.so:graphics/libgeotiff \ libboost_thread.so:devel/boost-libs \ libfontconfig.so:x11-fonts/fontconfig \ libdouble-conversion.so:devel/double-conversion RUN_DEPENDS= ${PYNUMPY} \ bash:shells/bash \ vtk9>0:math/vtk9 \ ${PYTHON_SITELIBDIR}/matplotlib/pyplot.py:math/py-matplotlib@${PY_FLAVOR} USES= alias cmake compiler:c11 eigen:3 fortran gl gnome jpeg localbase \ pkgconfig python qt:5 shebangfix tar:xz xorg USE_GL= gl glew glu glut USE_GNOME= libxml2 USE_QT= buildtools_build core gui help network opengl qmake_build sql svg \ widgets x11extras xmlpatterns USE_XORG= ice sm x11 xau xcb xcursor xdamage xdmcp xext xfixes xorgproto xrender \ xxf86vm USE_LDCONFIG= yes CMAKE_ARGS+= -DPARAVIEW_BUILD_SHARED_LIBS=ON \ -DPARAVIEW_BUILD_WITH_EXTERNAL=ON \ -DVTK_HAVE_GETSOCKNAME_WITH_SOCKLEN_T=1 \ -DPARAVIEW_USE_PYTHON:BOOL=ON \ -DPARAVIEW_ENABLE_FFMPEG:BOOL=ON \ -DPARAVIEW_ENABLE_LAS:BOOL=ON \ -DPARAVIEW_ENABLE_WEB:BOOL=ON \ -DPARAVIEW_ENABLE_GDAL:BOOL=ON \ -DPARAVIEW_ENABLE_PDAL:BOOL=ON \ -DPARAVIEW_ENABLE_OPENTURNS:BOOL=ON \ -DPARAVIEW_ENABLE_OPENTURNS:BOOL=ON \ -DPARAVIEW_ENABLE_MOTIONFX:BOOL=ON \ -DPARAVIEW_ENABLE_XDMF2:BOOL=ON \ -DPARAVIEW_ENABLE_XDMF3:BOOL=ON \ -DVTK_MODULE_USE_EXTERNAL_VTK_fmt:BOOL=OFF \ -DVTK_MODULE_USE_EXTERNAL_VTK_ioss:BOOL=OFF \ -DVTK_MODULE_USE_EXTERNAL_VTK_pegtl=OFF \ -DVTK_MODULE_USE_EXTERNAL_ParaView_vtkcatalyst:BOOL=OFF \ -DExternalData_OBJECT_STORES="${WRKDIR}/VTK/ExternalData/MD5" \ -DFREETYPE_INCLUDE_DIRS="${LOCALBASE}/include/freetype2" .if !defined(MAINTAINER_MODE) CMAKE_ARGS+= -DVTK_FORBID_DOWNLOADS:BOOL=ON .endif MAKE_ENV= XDG_CONFIG_HOME=${WRKDIR} SHEBANG_GLOB= *.py SHEBANG_FILES= VTK/Examples/SearchScript.sh \ VTK/Utilities/Maintenance/*.sh \ Clients/CommandLineExecutables/paraview-config.in VERMAJORMINOR= ${PORTVERSION:R} OPTIONS_DEFINE= DOCS EXAMPLES MPI OSMESA OPTIONS_SUB= yes OSMESA_DESC= Use Mesa for off-screen rendering # mpi4py and other programs must be compiled against the same MPI provider MPI_BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mpi4py>0:net/py-mpi4py@${PY_FLAVOR} MPI_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mpi4py>0:net/py-mpi4py@${PY_FLAVOR} MPI_USES= mpi # mpich is set by default, use mpi:openmpi if needed MPI_CMAKE_ON= -DPARAVIEW_USE_MPI:BOOL=ON MPI_CMAKE_OFF= -DPARAVIEW_USE_MPI:BOOL=OFF OSMESA_LIB_DEPENDS= libOSMesa.so:graphics/libosmesa OSMESA_USES_OFF= desktop-file-utils OSMESA_CMAKE_BOOL= VTK_OPENGL_HAS_OSMESA OSMESA_CMAKE_ON= -DVTK_USE_X:BOOL="OFF" \ -DOSMESA_INCLUDE_DIR:PATH=${LOCALBASE}/include/Mesa \ -DOSMESA_LIBRARY:FILEPATH=${LOCALBASE}/lib/libOSMesa.so OSMESA_CMAKE_OFF= -DVTK_USE_X:BOOL="ON" EXAMPLES_CMAKE_BOOL= PARAVIEW_BUILD_EXAMPLES PORTEXAMPLES= * #TEST_CMAKE_ON= -DPARAVIEW_BUILD_TESTING=WANT \ -DPARAVIEW_BUILD_VTK_TESTING=WANT # Error with ADIOS2 #LIB_DEPENDS+= libadios2_c.so:misc/adios2 #CMAKE_ARGS+= -DPARAVIEW_ENABLE_ADIOS2:BOOL=ON # Missing GenericIO for CosmoTools #CMAKE_ARGS+= -DPARAVIEW_ENABLE_COSMOTOOLS:BOOL=ON # Errors with VisItBridge / VisItLib #CMAKE_ARGS+= -DPARAVIEW_ENABLE_VISITBRIDGE:BOOL=ON # MomentInvariants needs to download a module #CMAKE_ARGS+= -DPARAVIEW_ENABLE_MOMENTINVARIANTS:BOOL=ON # No package for graphics/ospray #LIB_DEPENDS+= libospray.so:graphics/ospray #CMAKE_ARGS+= -DPARAVIEW_ENABLE_RAYTRACING PLIST_SUB+= VERMAJORMINOR=${VERMAJORMINOR} VTK9_CONFLICTS= vtk.py vtkmodules/__init__.py vtkmodules/all.py \ vtkmodules/gtk vtkmodules/numpy_interface \ vtkmodules/qt vtkmodules/test vtkmodules/tk \ vtkmodules/util vtkmodules/wx pre-configure: ${REINPLACE_CMD} -e 's|png_set_gray_1_2_4_to_8|png_set_expand_gray_1_2_4_to_8|' \ ${PATCH_WRKSRC}/VTK/IO/Image/vtkPNGReader.cxx ${REINPLACE_CMD} -e 's|/bin/bash|${LOCALBASE}/bin/bash|' \ ${PATCH_WRKSRC}/VTK/Utilities/Maintenance/vtk_site_history.py post-install: # vtk9 is not a real run dependency, but it installs several common files .for py in ${VTK9_CONFLICTS} ${RM} -r ${STAGEDIR}${PYTHON_SITELIBDIR}/${py} .endfor post-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/Examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/pastix/Makefile b/science/pastix/Makefile index 5f7ff4300b0c..a9578c0b0ee9 100644 --- a/science/pastix/Makefile +++ b/science/pastix/Makefile @@ -1,49 +1,47 @@ -# Created by: thierry@pompo.net - PORTNAME= pastix PORTVERSION= 6.2.1 DISTVERSIONPREFIX= v CATEGORIES= science MAINTAINER= thierry@FreeBSD.org COMMENT= PaStiX: a sparse direct solver LICENSE= LGPL3 BUILD_DEPENDS= bash:shells/bash \ ${PYNUMPY} LIB_DEPENDS= libcblas.so:math/cblas \ libmetis.so:math/metis \ libscotch.so:cad/scotch \ liblapacke.so:math/lapacke \ libhwloc.so:devel/hwloc2 RUN_DEPENDS= bash:shells/bash \ ${PYNUMPY} USES= cmake blaslapack:openblas fortran pkgconfig python USE_GITLAB= yes GL_SITE= https://gitlab.inria.fr/ GL_ACCOUNT= solverstack GL_PROJECT= pastix spm:s morse_cmake:m GL_COMMIT= 071d5ae165c744ec3e62f5bdd246b12f8fa90662 \ ebbd88ff3808c50e04119d0b42faf055c6eada2a:s \ 31cd2bbb0d76f2b9fd83011d8f079d97540b0ba8:m GL_SUBDIR= spm:s cmake_modules/morse_cmake:m CMAKE_ARGS= -DBUILD_SHARED_LIBS:BOOL=ON \ -DPASTIX_ORDERING_METIS:BOOL=ON USE_LDCONFIG= yes TEST_TARGET= test OPTIONS_DEFINE= EXAMPLES EX2FIX= example spm/examples spm/wrappers/fortran90 spm/wrappers/python \ wrappers/fortran90 wrappers/python example/old pre-configure: .for ex in ${EX2FIX} ${REINPLACE_CMD} -e 's|DESTINATION examples|DESTINATION ${EXAMPLESDIR}/${ex:C/examples//:C/example//}|' \ ${WRKSRC}/${ex}/CMakeLists.txt .endfor .include diff --git a/science/pnetcdf/Makefile b/science/pnetcdf/Makefile index 6a33ad1a60ce..f9b4cdb14beb 100644 --- a/science/pnetcdf/Makefile +++ b/science/pnetcdf/Makefile @@ -1,42 +1,40 @@ -# Created by: Chao Shin - PORTNAME= pnetcdf PORTVERSION= 1.12.3 CATEGORIES= science parallel MASTER_SITES= https://parallel-netcdf.github.io/Release/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= Library providing high-performance I/O USES= fortran gmake libtool pathfix perl5 USE_PERL5= build CFLAGS+= -fPIC CONFIGURE_ARGS= --with-mpi=${MPI_HOME} ac_cv_fc_compiler_nag=no GNU_CONFIGURE= yes MAKE_JOBS_UNSAFE= yes CONFLICTS_INSTALL= hdf-4.* OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= OPENMPI MPICH OPTIONS_DEFAULT=OPENMPI MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi .include .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(8)/CHARACTER(*)). FCFLAGS+= -fallow-argument-mismatch .endif post-patch: @${REINPLACE_CMD} -e '/$$(INSTALL.*$$(PREFIX)/ s|$$(PREFIX)|$$(DESTDIR)&|' ${WRKSRC}/Makefile.in x-post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/cdfdiff ${STAGEDIR}${PREFIX}/bin/n* ${STAGEDIR}${PREFIX}/bin/pnetcdf_version .include diff --git a/science/pulseview/Makefile b/science/pulseview/Makefile index 2229fb5e79a0..45c1fbb49ab1 100644 --- a/science/pulseview/Makefile +++ b/science/pulseview/Makefile @@ -1,38 +1,36 @@ -# Created by: Uffe Jakobsen - PORTNAME= pulseview PORTVERSION= 0.4.2 PORTREVISION= 2 CATEGORIES= science cad MASTER_SITES= http://sigrok.org/download/source/pulseview/ # Fix build with glib 2.68.3 PATCH_SITES= https://github.com/sigrokproject/pulseview/commit/ PATCHFILES= ed643f0b4ac587204a5243451cda181ee1405d62.diff:-p1 MAINTAINER= ports@FreeBSD.org COMMENT= GUI client that supports various hardware logic analyzers LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libsigrok.so:devel/libsigrok \ libsigrokdecode.so:devel/libsigrokdecode USES= cmake compiler:c++14-lang desktop-file-utils gnome pkgconfig qt:5 USE_GNOME= glibmm glib20 libsigc++20 USE_QT= buildtools_build core gui linguisttools_build qmake_build svg widgets CMAKE_ARGS+= -DCMAKE_INSTALL_MANDIR:PATH=${MANPREFIX}/man \ -DDISABLE_WERROR:BOOL=TRUE PLIST_FILES= bin/pulseview man/man1/pulseview.1.gz \ share/applications/org.sigrok.PulseView.desktop \ share/icons/hicolor/48x48/apps/pulseview.png \ share/icons/hicolor/scalable/apps/pulseview.svg \ share/metainfo/org.sigrok.PulseView.appdata.xml MAKE_JOBS_UNSAFE=yes .include diff --git a/science/py-DendroPy/Makefile b/science/py-DendroPy/Makefile index fc80e1259aa2..db40305dd3e6 100644 --- a/science/py-DendroPy/Makefile +++ b/science/py-DendroPy/Makefile @@ -1,17 +1,15 @@ -# Created by: Wen Heping - PORTNAME= DendroPy PORTVERSION= 4.5.2 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= cs@FreeBSD.org COMMENT= Phylogenetic computing library LICENSE= BSD3CLAUSE USES= python:3.7+ USE_PYTHON= distutils autoplist .include diff --git a/science/py-access/Makefile b/science/py-access/Makefile index cdc378336b57..3612671dae61 100644 --- a/science/py-access/Makefile +++ b/science/py-access/Makefile @@ -1,24 +1,22 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= access PORTVERSION= 1.1.8 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Calculate spatial accessibility metrics LICENSE= BSD3CLAUSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geopandas>=0:graphics/py-geopandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=1.3,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0.23.4,1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2:www/py-requests@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-asdf-standard/Makefile b/science/py-asdf-standard/Makefile index 2ddeb00a9606..d805ef8aa715 100644 --- a/science/py-asdf-standard/Makefile +++ b/science/py-asdf-standard/Makefile @@ -1,29 +1,27 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= asdf-standard PORTVERSION= 1.0.2 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= asdf_standard-${PORTVERSION} MAINTAINER= sunpoet@FreeBSD.org COMMENT= ASDF Standard schemas LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools_scm>=0:devel/py-setuptools_scm@${PY_FLAVOR} USES= python:3.8+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include .if ${PYTHON_REL} < 30800 RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}importlib-resources>=3:devel/py-importlib-resources@${PY_FLAVOR} .endif .include diff --git a/science/py-asdf-transform-schemas/Makefile b/science/py-asdf-transform-schemas/Makefile index d4a8a65bbe9f..a8781b2e1f67 100644 --- a/science/py-asdf-transform-schemas/Makefile +++ b/science/py-asdf-transform-schemas/Makefile @@ -1,24 +1,22 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= asdf-transform-schemas PORTVERSION= 0.2.2 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= asdf_transform_schemas-${PORTVERSION} MAINTAINER= sunpoet@FreeBSD.org COMMENT= ASDF schemas for transforms LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools_scm>=0:devel/py-setuptools_scm@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}asdf-standard>=1.0.1:science/py-asdf-standard@${PY_FLAVOR} USES= python:3.8+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-asdf/Makefile b/science/py-asdf/Makefile index 96862277d8fa..b39d89f2ca6a 100644 --- a/science/py-asdf/Makefile +++ b/science/py-asdf/Makefile @@ -1,37 +1,35 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= asdf PORTVERSION= 2.12.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Python tools to handle ASDF files LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools_scm>=0:devel/py-setuptools_scm@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}asdf-standard>=1.0.1:science/py-asdf-standard@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}asdf-transform-schemas>=0.2.2:science/py-asdf-transform-schemas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}jmespath>=0.6.2:devel/py-jmespath@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}jsonschema>=4.0.1:devel/py-jsonschema@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lz4>=0.10:archivers/py-lz4@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=1.10,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>=16.0:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>=3.10:devel/py-yaml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}semantic-version>=2.8:devel/py-semantic-version@${PY_FLAVOR} USES= python:3.8+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include .if ${PYTHON_REL} < 30900 RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}importlib-resources>=3:devel/py-importlib-resources@${PY_FLAVOR} .endif .include diff --git a/science/py-cdo/Makefile b/science/py-cdo/Makefile index fd763ad36379..6797753984a9 100644 --- a/science/py-cdo/Makefile +++ b/science/py-cdo/Makefile @@ -1,22 +1,20 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= cdo PORTVERSION= 1.5.6 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Python binding to CDO (Climate Data Operators) LICENSE= GPLv2 RUN_DEPENDS= cdo:science/cdo \ ${PYTHON_PKGNAMEPREFIX}six>=0:devel/py-six@${PY_FLAVOR} USES= python:3.6+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-coards/Makefile b/science/py-coards/Makefile index ec935bd1aa04..c3396617b8b2 100644 --- a/science/py-coards/Makefile +++ b/science/py-coards/Makefile @@ -1,20 +1,18 @@ -# Created by: Johannes Meixner - PORTNAME= coards PORTVERSION= 1.0.5 PORTREVISION= 3 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= COARDS compliant time parser LICENSE= MIT USES= python:3.6+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-eccodes/Makefile b/science/py-eccodes/Makefile index 29a7c5458c7b..90ce29083c6a 100644 --- a/science/py-eccodes/Makefile +++ b/science/py-eccodes/Makefile @@ -1,33 +1,31 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= eccodes PORTVERSION= 1.4.2 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Python interface to the ecCodes BUFR and GRIB de/encoder LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libeccodes.so:science/eccodes RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}attrs>=0:devel/py-attrs@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}cffi>=0:devel/py-cffi@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}findlibs>=0:devel/py-findlibs@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>=0:devel/py-pytest@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-cov>=0:devel/py-pytest-cov@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-flakes>=0:devel/py-pytest-flakes@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}typing-extensions>=0:devel/py-typing-extensions@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes do-test: cd ${WRKSRC} && ${SETENV} PYTHONPATH=${STAGEDIR}${PYTHON_SITELIBDIR} ${PYTHON_CMD} -m pytest -rs -v .include diff --git a/science/py-esda/Makefile b/science/py-esda/Makefile index dd703eeeafc1..169162e2a96e 100644 --- a/science/py-esda/Makefile +++ b/science/py-esda/Makefile @@ -1,31 +1,29 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= esda PORTVERSION= 2.4.1 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Exploratory Spatial Data Analysis LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}libpysal>=0:science/py-libpysal@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0,1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.11:science/py-scipy@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes OPTIONS_DEFINE= SHAPE SHAPE_DESC= Shape statistics support SHAPE_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geopandas>=0:graphics/py-geopandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pygeos>=0:graphics/py-pygeos@${PY_FLAVOR} .include diff --git a/science/py-geolinks/Makefile b/science/py-geolinks/Makefile index 4c4203cfac4b..97e9fc678ed6 100644 --- a/science/py-geolinks/Makefile +++ b/science/py-geolinks/Makefile @@ -1,19 +1,17 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= geolinks PORTVERSION= 0.2.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Utilities to deal with geospatial links LICENSE= MIT USES= python:3.6+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-geomet/Makefile b/science/py-geomet/Makefile index 4107687bac35..875a8fb38bb9 100644 --- a/science/py-geomet/Makefile +++ b/science/py-geomet/Makefile @@ -1,22 +1,20 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= geomet PORTVERSION= 0.3.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= GeoJSON <-> WKT/WKB conversion utilities LICENSE= APACHE20 RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>=0:devel/py-six@${PY_FLAVOR} USES= python:3.6+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-geometer/Makefile b/science/py-geometer/Makefile index 7b625ad3abb1..7a857ee074c4 100644 --- a/science/py-geometer/Makefile +++ b/science/py-geometer/Makefile @@ -1,23 +1,21 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= geometer PORTVERSION= 0.3.4 PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Python geometry package based on projective geometry and numpy LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.15,1<1.24,1:math/py-numpy@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-h5py/Makefile b/science/py-h5py/Makefile index edf0d497b87c..3bf98e24c519 100644 --- a/science/py-h5py/Makefile +++ b/science/py-h5py/Makefile @@ -1,38 +1,36 @@ -# Created by: TAOKA Fumiyoshi - PORTNAME= h5py PORTVERSION= 3.7.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= General-purpose Python interface to the HDF5 library LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/licenses/license.txt BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cython>=0.29.15:lang/cython@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pkgconfig>=0,1:devel/py-pkgconfig@${PY_FLAVOR} \ ${RUN_DEPENDS} LIB_DEPENDS= libhdf5.so:science/hdf5 RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.14.5,1:math/py-numpy@${PY_FLAVOR} USES= localbase pkgconfig python:3.7+ USE_PYTHON= autoplist concurrent cython distutils pytest OPTIONS_DEFINE= DOCS EXAMPLES post-install: ${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR} -name '*.so' -exec ${STRIP_CMD} {} + post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/README.rst ${STAGEDIR}${DOCSDIR} cd ${WRKSRC}/docs/ && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/examples/*.py ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/py-inequality/Makefile b/science/py-inequality/Makefile index 1995389ccb1f..460af4d0a3a6 100644 --- a/science/py-inequality/Makefile +++ b/science/py-inequality/Makefile @@ -1,22 +1,20 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= inequality PORTVERSION= 1.0.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Spatial inequality analysis for PySAL LICENSE= BSD3CLAUSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.3,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.11:science/py-scipy@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-jupyter_jsmol/Makefile b/science/py-jupyter_jsmol/Makefile index fb106695b4f8..806fd28c03b2 100644 --- a/science/py-jupyter_jsmol/Makefile +++ b/science/py-jupyter_jsmol/Makefile @@ -1,41 +1,39 @@ -# Created by: thierry@pompo.net - PORTNAME= jupyter-jsmol PORTVERSION= 2021.3.0 DISTVERSIONPREFIX= v CATEGORIES= science devel python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= thierry@FreeBSD.org COMMENT= JSmol viewer widget for Jupyter Notebooks and JupyterLab LICENSE= BSD3CLAUSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pygments>=0:textproc/py-pygments@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}widgetsnbextension>0:devel/py-widgetsnbextension@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipykernel5>=5.0.0:devel/py-ipykernel5@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipywidgets>0:devel/py-ipywidgets@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipython>=7.0.0:devel/ipython@${PY_FLAVOR} USE_GITHUB= yes GH_ACCOUNT= fekad USES= python:3.7+ pytest USE_PYTHON= distutils PYDISTUTILS_CONFIGUREARGS= --skip-npm PYDISTUTILS_BUILDARGS= --skip-npm OPTIONS_DEFINE= EXAMPLES EXAMPLES_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plotly>0:graphics/py-plotly@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} PORTEXAMPLES= * PLIST_SUB+= VER=${PORTVERSION} NO_ARCH= yes post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/py-kinematics/Makefile b/science/py-kinematics/Makefile index 7247522474fa..82d5c463dcb0 100644 --- a/science/py-kinematics/Makefile +++ b/science/py-kinematics/Makefile @@ -1,24 +1,22 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= kinematics PORTVERSION= 0.1.7 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Python module to do attitude kinematics LICENSE= GPLv3 RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}coverage>=0:devel/py-coverage@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest>=0:devel/py-pytest@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-cov>=0:devel/py-pytest-cov@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-liac-arff/Makefile b/science/py-liac-arff/Makefile index 939fb7e4653f..72c1807fc2ff 100644 --- a/science/py-liac-arff/Makefile +++ b/science/py-liac-arff/Makefile @@ -1,21 +1,19 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= liac-arff PORTVERSION= 2.5.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Read and write ARFF files in Python LICENSE= MIT TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mock>=0:devel/py-mock@${PY_FLAVOR} USES= python:3.6+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-libpysal/Makefile b/science/py-libpysal/Makefile index 2e785244f826..084db98ebb90 100644 --- a/science/py-libpysal/Makefile +++ b/science/py-libpysal/Makefile @@ -1,29 +1,27 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= libpysal PORTVERSION= 4.6.2 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Core components of PySAL A library of spatial analysis functions LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}appdirs>=0:devel/py-appdirs@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}beautifulsoup>=0:www/py-beautifulsoup@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=0:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=1.3,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>=0:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0,1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.11:science/py-scipy@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-mdp/Makefile b/science/py-mdp/Makefile index 6a4ff472a08e..c1ddaad21c7e 100644 --- a/science/py-mdp/Makefile +++ b/science/py-mdp/Makefile @@ -1,30 +1,28 @@ -# Created by: Li-Lun Wang - PORTNAME= mdp PORTVERSION= 3.5 PORTREVISION= 3 CATEGORIES= science python MASTER_SITES= SF/${PORTNAME}-toolkit/${PORTNAME}-toolkit/${PORTVERSION} PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:tu}-${PORTVERSION} MAINTAINER= bofh@FreeBSD.org COMMENT= Modular toolkit for Data Processing LICENSE= BSD3CLAUSE RUN_DEPENDS= ${PYNUMPY} USES= python:3.6+ USE_PYTHON= distutils autoplist OPTIONS_DEFINE= LIBSVM SCIPY LIBSVM_DESC= Provide the LibSVMClassifier node SCIPY_DESC= Instal SciPy versions of eigensolver, FFT and convolution LIBSVM_RUN_DEPENDS= libsvm>2.91:science/libsvm \ libsvm-python>2.91:science/libsvm-python SCIPY_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}scipy>=0.5.2:science/py-scipy@${PY_FLAVOR} .include diff --git a/science/py-netCDF4/Makefile b/science/py-netCDF4/Makefile index b6dd4bc9e40f..f2422030ea2d 100644 --- a/science/py-netCDF4/Makefile +++ b/science/py-netCDF4/Makefile @@ -1,55 +1,53 @@ -# Created by: Wen Heping - PORTNAME= netCDF4 PORTVERSION= 1.5.8 PORTREVISION= 1 DISTVERSIONPREFIX= v DISTVERSIONSUFFIX= rel CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= bofh@FreeBSD.org COMMENT= Python Interface to the NetCDF Library (versions 3 and 4) LICENSE= MIT BUILD_DEPENDS= ${PYNUMPY} LIB_DEPENDS= libhdf5.so:science/hdf5 \ libnetcdf.so:science/netcdf RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}cftime>=0:devel/py-cftime@${PY_FLAVOR} USES= python:3.6+ USE_GITHUB= yes GH_ACCOUNT= Unidata GH_PROJECT= netcdf4-python USE_PYTHON= autoplist concurrent cython cython_run distutils DOCSDIR= ${PREFIX}/share/doc/py-${PORTNAME} EXAMPLESDIR= ${PREFIX}/share/examples/py-${PORTNAME} PORTDOCS= * PORTEXAMPLES= * OPTIONS_DEFINE= DOCS EXAMPLES post-patch: @${ECHO_CMD} -n > ${WRKSRC}/setup.cfg @${ECHO_CMD} "[options]" >> ${WRKSRC}/setup.cfg @${ECHO_CMD} "use_ncconfig=True" >> ${WRKSRC}/setup.cfg @${ECHO_CMD} "ncconfig=${LOCALBASE}/bin/nc-config" >> ${WRKSRC}/setup.cfg @${ECHO_CMD} "[directories]" >> ${WRKSRC}/setup.cfg @${ECHO_CMD} "HDF5_libdir=${LOCALBASE}/lib" >> ${WRKSRC}/setup.cfg @${ECHO_CMD} "HDF5_incdir=${LOCALBASE}/include" >> ${WRKSRC}/setup.cfg post-install: ${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/netCDF4/_netCDF4*.so post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} (cd ${WRKSRC}/docs && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}) post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/examples && ${INSTALL_DATA} * ${STAGEDIR}${EXAMPLESDIR}) .include diff --git a/science/py-netcdf-flattener/Makefile b/science/py-netcdf-flattener/Makefile index 4cad44dde866..aa9fa07c8167 100644 --- a/science/py-netcdf-flattener/Makefile +++ b/science/py-netcdf-flattener/Makefile @@ -1,26 +1,24 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= netcdf-flattener PORTVERSION= 1.2.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Flatten NetCDF files while preserving references LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}netCDF4>=0:science/py-netCDF4@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>=0:devel/py-pytest@${PY_FLAVOR} USES= python:3.6+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes do-test: cd ${WRKSRC} && ${PYTHON_CMD} -m pytest -rs -v .include diff --git a/science/py-obspy/Makefile b/science/py-obspy/Makefile index 4cd3e7d10a55..7bfaf3f7a589 100644 --- a/science/py-obspy/Makefile +++ b/science/py-obspy/Makefile @@ -1,38 +1,36 @@ -# Created by: Wen Heping - PORTNAME= obspy PORTVERSION= 1.3.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Python framework for seismological observatories LICENSE= LGPL3 BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.0.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}future>=0.12.4:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.2.0:math/py-matplotlib@${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} RUN_DEPENDS:= ${BUILD_DEPENDS} USES= fortran python:3.7+ shebangfix SHEBANG_FILES= obspy/taup/tests/data/TauP_test_data/gendata.sh USE_LDCONFIG= yes LDFLAGS+= -shared USE_PYTHON= autoplist distutils LDFLAGS+= -shared post-patch: ${REINPLACE_CMD} -e "s#FC#${FC}#g" ${WRKSRC}/setup.py post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/obspy/lib/*.so .include diff --git a/science/py-paida/Makefile b/science/py-paida/Makefile index c1c3a1ed2af4..0ce44c7d18c4 100644 --- a/science/py-paida/Makefile +++ b/science/py-paida/Makefile @@ -1,19 +1,17 @@ -# Created by: Vsevolod Stakhov - PORTNAME= paida PORTVERSION= 3.2.1.2.10 PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= SF/${PORTNAME}/${PORTNAME}/${PORTNAME}-3.2.1_2.10.1 PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME}-3.2.1_2.10.1 BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}tkinter>0:x11-toolkits/py-tkinter@${PY_FLAVOR} MAINTAINER= ports@FreeBSD.org COMMENT= Pure Python scientific analysis package USES= dos2unix python:3.6+ USE_PYTHON= distutils autoplist .include diff --git a/science/py-pupynere/Makefile b/science/py-pupynere/Makefile index 35677fef15af..664948a503b7 100644 --- a/science/py-pupynere/Makefile +++ b/science/py-pupynere/Makefile @@ -1,22 +1,20 @@ -# Created by: Johannes Meixner - PORTNAME= pupynere PORTVERSION= 1.0.15 PORTREVISION= 8 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= NetCDF file reader and writer LICENSE= MIT RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-pyaixi/Makefile b/science/py-pyaixi/Makefile index ce31379ea63c..aa531113138c 100644 --- a/science/py-pyaixi/Makefile +++ b/science/py-pyaixi/Makefile @@ -1,35 +1,33 @@ -# Created by: Johannes Meixner - PORTNAME= pyaixi PORTVERSION= 1.0.4 DISTVERSIONSUFFIX= .post1 PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Implementation of the MC-AIXI-CTW AI algorithm LICENSE= CC-BY-SA-3.0 LICENSE_FILE= ${WRKSRC}/LICENSE.txt USES= dos2unix python:3.6+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes PORTDOCS= changelog.txt todo.txt PORTEXAMPLES= * OPTIONS_DEFINE= DOCS EXAMPLES post-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${WRKSRC}/doc/ && ${INSTALL_DATA} ${PORTDOCS} ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/conf/ && ${INSTALL_DATA} ${PORTEXAMPLES} ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/py-pycsw/Makefile b/science/py-pycsw/Makefile index 73d56dbbf460..1c0ba72498ad 100644 --- a/science/py-pycsw/Makefile +++ b/science/py-pycsw/Makefile @@ -1,27 +1,25 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= pycsw PORTVERSION= 2.6.1 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= OGC CSW server implementation LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geolinks>=0:science/py-geolinks@${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} \ ${PYTHON_PKGNAMEPREFIX}xmltodict>=0:devel/py-xmltodict@${PY_FLAVOR} USES= cpe python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-pydicom/Makefile b/science/py-pydicom/Makefile index 6a10c0f13624..ccaa04410237 100644 --- a/science/py-pydicom/Makefile +++ b/science/py-pydicom/Makefile @@ -1,19 +1,17 @@ -# Created by: Wen Heping - PORTNAME= pydicom PORTVERSION= 2.3.0 DISTVERSIONPREFIX=v CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Read, modify, and write DICOM files with Python code LICENSE= MIT USES= python:3.7+ shebangfix USE_GITHUB= yes USE_PYTHON= distutils autoplist NO_ARCH= yes .include diff --git a/science/py-pygeodesy/Makefile b/science/py-pygeodesy/Makefile index 6efaf58ea9b1..d6f72271503c 100644 --- a/science/py-pygeodesy/Makefile +++ b/science/py-pygeodesy/Makefile @@ -1,21 +1,19 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= pygeodesy PORTVERSION= 22.7.7 CATEGORIES= science python MASTER_SITES= CHEESESHOP \ https://github.com/mrJean1/PyGeodesy/raw/master/dist/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= PyGeodesy-${PORTVERSION} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Pure Python geodesy tools LICENSE= MIT USES= python:3.8+ zip USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-pygeometa/Makefile b/science/py-pygeometa/Makefile index 5fcf0a12d532..852b6393f056 100644 --- a/science/py-pygeometa/Makefile +++ b/science/py-pygeometa/Makefile @@ -1,27 +1,25 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= pygeometa PORTVERSION= 0.11.1 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Generate metadata for geospatial datasets LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.md RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=0:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}jsonschema>=0:devel/py-jsonschema@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>=0:devel/py-yaml@${PY_FLAVOR} USES= python:3.6+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-pymol/Makefile b/science/py-pymol/Makefile index ad97e32bf541..8550d013d755 100644 --- a/science/py-pymol/Makefile +++ b/science/py-pymol/Makefile @@ -1,58 +1,56 @@ -# Created by: Nakata Maho - PORTNAME= pymol DISTVERSIONPREFIX= v DISTVERSION= 2.4.0 PORTREVISION= 6 CATEGORIES= science biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= OpenGL-based molecular visualization system LICENSE= PyMOL LICENSE_NAME= Open-Source PyMOL Copyright LICENSE_FILE= ${WRKSRC}/LICENSE LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BUILD_DEPENDS= ${PYNUMPY} \ ${LOCALBASE}/include/glm/glm.hpp:math/glm \ ${LOCALBASE}/include/mmtf.hpp:science/mmtf-cpp LIB_DEPENDS= libfreetype.so:print/freetype2 \ libpng.so:graphics/png \ libmsgpackc.so:devel/msgpack \ libnetcdf.so:science/netcdf RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}msgpack>0:devel/py-msgpack@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Pmw>0:x11-toolkits/py-Pmw@${PY_FLAVOR} \ ${PYNUMPY} USES= compiler:c++11-lang gl gnome python:3.5+ shebangfix tar:bz2 USE_GITHUB= yes GH_ACCOUNT= schrodinger GH_PROJECT= ${PORTNAME}-open-source USE_GL= gl glew glu glut USE_GNOME= libxml2 USE_PYTHON= distutils concurrent # autoplist is broken: https://github.com/schrodinger/pymol-open-source/issues/99 SHEBANG_FILES= test/show test/run test/cyg CONFLICTS_INSTALL= ${PYTHON_PKGNAMEPREFIX}chempy # https://github.com/schrodinger/pymol-open-source/issues/100 OPTIONS_SINGLE= GUI OPTIONS_SINGLE_GUI= QT5 TK OPTIONS_DEFAULT= QT5 QT5_USES= pyqt:5 QT5_USE= PYQT=pyqt5_run post-patch-TK-on: @${REINPLACE_CMD} -e ' \ 23s|if not PYQT_NAME:|if False:| ; \ s|from PyQt5 import|from X import|' \ ${WRKSRC}/modules/${PORTNAME}/Qt/__init__.py post-install: @${REINPLACE_CMD} -i '' -e 's|#!/bin/bash|#!/bin/sh|' ${STAGEDIR}${PREFIX}/bin/${PORTNAME} @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/${PORTNAME}/_cmd*.so @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/chempy/champ/_champ*.so .include diff --git a/science/py-pysal/Makefile b/science/py-pysal/Makefile index 494c5846a27c..1dc8dff00b7e 100644 --- a/science/py-pysal/Makefile +++ b/science/py-pysal/Makefile @@ -1,39 +1,37 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= pysal PORTVERSION= 2.6.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Cross-platform library of spatial analysis functions LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}access>=1.1.3:science/py-access@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}esda>=2.4.1:science/py-esda@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}giddy>=2.3.3:graphics/py-giddy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}inequality>=1.0.0:science/py-inequality@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}libpysal>=4.6.0:science/py-libpysal@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mapclassify>=2.4.3:graphics/py-mapclassify@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mgwr>=2.1.2:graphics/py-mgwr@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}momepy>=0.5.2:graphics/py-momepy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pointpats>=2.2.0:graphics/py-pointpats@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}segregation>=2.1.0:science/py-segregation@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spaghetti>=1.6.5:science/py-spaghetti@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spglm>=1.0.8:math/py-spglm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spint>=1.0.7:math/py-spint@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}splot>=1.1.4:math/py-splot@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spopt>=0.2.1:math/py-spopt@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spreg>=1.2.4:math/py-spreg@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spvcm>=0.3.0:math/py-spvcm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tobler>=0.8.2:science/py-tobler@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-scikit-fuzzy/Makefile b/science/py-scikit-fuzzy/Makefile index b5866157c120..07718cb10df0 100644 --- a/science/py-scikit-fuzzy/Makefile +++ b/science/py-scikit-fuzzy/Makefile @@ -1,25 +1,23 @@ -# Created by: Yuri Victorovich - PORTNAME= scikit-fuzzy DISTVERSION= 0.4.2 PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Fuzzy logic toolkit for SciPy LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}networkx>=1.9.0:math/py-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.9.0:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${RUN_DEPENDS} USES= python:3.6+ USE_PYTHON= autoplist distutils NO_ARCH= yes .include diff --git a/science/py-scikit-learn/Makefile b/science/py-scikit-learn/Makefile index 2885ea589dcb..a10a853d9035 100644 --- a/science/py-scikit-learn/Makefile +++ b/science/py-scikit-learn/Makefile @@ -1,33 +1,31 @@ -# Created by: Dmitry Sivachenko - PORTNAME= scikit-learn DISTVERSION= 1.1.1 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Machine learning algorithms for python LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.1.0:science/py-scipy@${PY_FLAVOR} RUN_DEPENDS:= ${BUILD_DEPENDS} USES= fortran python:3.7+ localbase USE_PYTHON= distutils autoplist cython POST_PLIST= fix-plist fix-plist: # https://github.com/scikit-learn/scikit-learn/issues/12681 @${REINPLACE_CMD} -e "s|lib/python.*/sklearn/datasets/tests/data/openml$$||" ${TMPPLIST} post-install: # strip binaries @${STRIP_CMD} \ ${STAGEDIR}${PYTHON_SITELIBDIR}/sklearn/*.cpython*.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/sklearn/*/*.cpython*.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/sklearn/*/*/*.cpython*.so .include diff --git a/science/py-scikit-optimize/Makefile b/science/py-scikit-optimize/Makefile index 49a072385376..76ad9f759479 100644 --- a/science/py-scikit-optimize/Makefile +++ b/science/py-scikit-optimize/Makefile @@ -1,31 +1,29 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= scikit-optimize PORTVERSION= 0.9.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Sequential model-based optimization toolbox LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}joblib>=0.11:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=1.13.3,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyaml>=16.9:textproc/py-pyaml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.20.0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.19.1:science/py-scipy@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes OPTIONS_DEFINE= PLOTS PLOTS_DESC= Plotting support PLOTS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.0.0:math/py-matplotlib@${PY_FLAVOR} .include diff --git a/science/py-scikit-sparse/Makefile b/science/py-scikit-sparse/Makefile index bfabc673de05..a2867c8b745c 100644 --- a/science/py-scikit-sparse/Makefile +++ b/science/py-scikit-sparse/Makefile @@ -1,29 +1,27 @@ -# Created by: Yuri Victorovich - PORTNAME= scikit-sparse DISTVERSION= 0.4.6 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Sparse matrix package LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${RUN_DEPENDS} LIB_DEPENDS= libumfpack.so:math/suitesparse-umfpack RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} USES= fortran python:3.6+ USE_PYTHON= distutils cython autoplist CFLAGS+= -I${LOCALBASE}/include/suitesparse LDFLAGS+= -shared post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/sksparse/cholmod*.so .include diff --git a/science/py-scimath/Makefile b/science/py-scimath/Makefile index 325aa0b4cbea..6327acdf0407 100644 --- a/science/py-scimath/Makefile +++ b/science/py-scimath/Makefile @@ -1,22 +1,20 @@ -# Created by: Wen Heping - PORTNAME= scimath PORTVERSION= 4.2.0 CATEGORIES= science math python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Scientific and Mathematical calculations LICENSE= BSD3CLAUSE LGPL3 LICENSE_COMB= dual BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}traits>=0:devel/py-traits@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0:math/py-numpy@${PY_FLAVOR} RUN_DEPENDS:= ${BUILD_DEPENDS} USES= python:3.6+ USE_PYTHON= distutils autoplist .include diff --git a/science/py-scipy/Makefile b/science/py-scipy/Makefile index 41e7e4a3a3ab..50c782729017 100644 --- a/science/py-scipy/Makefile +++ b/science/py-scipy/Makefile @@ -1,50 +1,48 @@ -# Created by: ijliao - PORTNAME= scipy DISTVERSION= 1.8.1 CATEGORIES= science python MASTER_SITES= https://docs.scipy.org/doc/scipy-${PORTVERSION}/:doc \ CHEESESHOP:source \ SF:source PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTFILES= ${DISTNAME}${EXTRACT_SUFX}:source \ scipy-ref-${PORTVERSION}.pdf:doc EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= python@FreeBSD.org COMMENT= Scientific tools for Python LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pybind11>0:devel/py-pybind11@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pythran>=0:devel/py-pythran@${PY_FLAVOR} LIB_DEPENDS= libblas.so:math/blas \ libopenblas.so:math/openblas RUN_DEPENDS= ${PYNUMPY} USES= compiler:c++14-lang cpe fortran python:3.8-3.10 shebangfix USE_PYTHON= autoplist concurrent cython distutils FFLAGS+= -std=legacy LDFLAGS+= -shared PYDISTUTILS_BUILDARGS= --fcompiler=gnu95 PYDISTUTILS_CONFIGUREARGS= --fcompiler=gnu95 PORTDOCS= scipy-ref-${PORTVERSION}.pdf OPTIONS_DEFINE= DOCS post-install: ${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR}/scipy/ -name '*.so' | ${XARGS} ${STRIP_CMD} post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${PORTDOCS} ${STAGEDIR}${DOCSDIR} do-test: @cd ${WRKSRC} && ${PYTHON_CMD} runtests.py .include diff --git a/science/py-segregation/Makefile b/science/py-segregation/Makefile index e712527bb738..2adcf6cfe2c8 100644 --- a/science/py-segregation/Makefile +++ b/science/py-segregation/Makefile @@ -1,39 +1,37 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= segregation PORTVERSION= 2.3.1 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Analytics for spatial and non-spatial segregation in Python LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}deprecation>=0:devel/py-deprecation@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}geopandas>=0.9:graphics/py-geopandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}joblib>=0:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}libpysal>=0:science/py-libpysal@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mapclassify>=0:graphics/py-mapclassify@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numba>=0:devel/py-numba@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0,1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pip>=0:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pygeos>=0:graphics/py-pygeos@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyproj>=3:graphics/py-pyproj@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}quilt3>=0:www/py-quilt3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}rvlib>=0.0.5:math/py-rvlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.21.3:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}seaborn>=0:math/py-seaborn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tqdm>=0:misc/py-tqdm@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-sklearn-pandas/Makefile b/science/py-sklearn-pandas/Makefile index 0ef910ff4119..98409e225c1d 100644 --- a/science/py-sklearn-pandas/Makefile +++ b/science/py-sklearn-pandas/Makefile @@ -1,26 +1,24 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= sklearn-pandas PORTVERSION= 2.2.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Pandas integration with sklearn LICENSE= BSD2CLAUSE ZLIB LICENSE_COMB= multi LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.18.1,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=1.1.4,1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.23.0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.5.1:science/py-scipy@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-skrebate/Makefile b/science/py-skrebate/Makefile index 35757970deaa..807ede87d842 100644 --- a/science/py-skrebate/Makefile +++ b/science/py-skrebate/Makefile @@ -1,24 +1,22 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= skrebate PORTVERSION= 0.62 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Relief-based feature selection algorithms LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0:science/py-scipy@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-spaghetti/Makefile b/science/py-spaghetti/Makefile index a193193a2f66..ba985bf93e59 100644 --- a/science/py-spaghetti/Makefile +++ b/science/py-spaghetti/Makefile @@ -1,27 +1,25 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= spaghetti PORTVERSION= 1.6.5 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Analysis of Network-constrained Spatial Data LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}esda>=0:science/py-esda@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}libpysal>=0:science/py-libpysal@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=1.3,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=1.0,1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}rtree>=0:devel/py-rtree@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.0:science/py-scipy@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-tobler/Makefile b/science/py-tobler/Makefile index 81d38158ed79..fe5972253bd2 100644 --- a/science/py-tobler/Makefile +++ b/science/py-tobler/Makefile @@ -1,30 +1,28 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= tobler PORTVERSION= 0.9.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Areal Interpolation LICENSE= BSD3CLAUSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geopandas>=0:graphics/py-geopandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}joblib>=0:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}libpysal>=0:science/py-libpysal@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0,1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}rasterio>=0:graphics/py-rasterio@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}rasterstats>=0:graphics/py-rasterstats@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}statsmodels>=0:math/py-statsmodels@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tqdm>=0:misc/py-tqdm@${PY_FLAVOR} USES= python:3.8+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes .include diff --git a/science/py-veusz/Makefile b/science/py-veusz/Makefile index ebabe5cc3e06..038ca736b658 100644 --- a/science/py-veusz/Makefile +++ b/science/py-veusz/Makefile @@ -1,30 +1,28 @@ -# Created by: Stas Timokhin - PORTNAME= veusz DISTVERSIONPREFIX= ${PORTNAME}- DISTVERSION= 3.4 PORTREVISION= 1 CATEGORIES= science PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Scientific plotting package LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} USES= compiler:c++11-lang python:3.5+ pyqt:5 qt:5 shebangfix USE_GITHUB= yes USE_PYQT= pyqt5 sip USE_PYTHON= distutils concurrent autoplist USE_QT= core gui xml widgets qmake_build SHEBANG_FILES= examples/embedexample.py post-install: # strip ${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/veusz/helpers/*.so .include diff --git a/science/pybrain/Makefile b/science/pybrain/Makefile index 3c9e02b4ffe3..9427fad0484a 100644 --- a/science/pybrain/Makefile +++ b/science/pybrain/Makefile @@ -1,20 +1,18 @@ -# Created by: Wen Heping - PORTNAME= pybrain PORTVERSION= 0.3.3 PORTREVISION= 4 CATEGORIES= science python MAINTAINER= wen@FreeBSD.org COMMENT= Swiss Army knife for neural networking LICENSE= BSD3CLAUSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}scipy>=0.7.1:science/py-scipy@${PY_FLAVOR} USE_GITHUB= yes USES= python:3.6+ USE_PYTHON= autoplist distutils concurrent optsuffix .include diff --git a/science/pynn/Makefile b/science/pynn/Makefile index 3f36d7512b65..4a7146a81167 100644 --- a/science/pynn/Makefile +++ b/science/pynn/Makefile @@ -1,27 +1,25 @@ -# Created by: Ju Pengfei - PORTNAME= pynn PORTVERSION= 0.10.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= PyNN-${PORTVERSION} MAINTAINER= wen@FreeBSD.org COMMENT= Simulator-independent language for building neuronal network models LICENSE= CeCILL LICENSE_NAME= CeCILL Free Software License Version 2.0 LICENSE_FILE= ${WRKSRC}/LICENSE LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} NO_ARCH= yes USES= python:3.6+ USE_PYTHON= autoplist distutils PYDISTUTILS_PKGNAME= PyNN .include diff --git a/science/qcl/Makefile b/science/qcl/Makefile index a0bb59fc14ec..698623882f8d 100644 --- a/science/qcl/Makefile +++ b/science/qcl/Makefile @@ -1,45 +1,43 @@ -# Created by: Brad Huntting - PORTNAME= qcl PORTVERSION= 0.6.4 PORTREVISION= 2 CATEGORIES= science math MASTER_SITES= http://tph.tuwien.ac.at/~oemer/tgz/ MAINTAINER= ports@FreeBSD.org COMMENT= Quantum computer simulator LICENSE= GPLv2+ USES= bison gmake readline tar:tgz PLIST_FILES= bin/qcl PORTDATA= * OPTIONS_DEFINE= PLOTUTILS PLOTUTILS_DESC= Plotting support via plotutils PLOTUTILS_LIB_DEPENDS= libplotter.so:graphics/plotutils PLOTUTILS_CXXFLAGS= -I${LOCALBASE}/include -DQCL_PLOT PLOTUTILS_LDFLAGS= -L${LOCALBASE}/lib -lplotter post-patch: @${REINPLACE_CMD} -e \ 's|/usr/local|${PREFIX}| ; \ s|lib/qcl|share/qcl| ; \ s|-O2 -g|| ; \ s|^PLOPT|#PLOPT| ; \ s|^PLLIB|#PLLIB| ; \ /^CXXFLAGS/s| =| +=| ; \ /^LDFLAGS/s| =| +=|' ${WRKSRC}/Makefile @${REINPLACE_CMD} -e \ 's|-g -O2|| ; \ /^CXXFLAGS/s| =| +=| ; \ /^LDFLAGS/s| =| +=|' ${WRKSRC}/qc/Makefile do-install: (cd ${WRKSRC} && ${INSTALL_PROGRAM} qcl ${STAGEDIR}${PREFIX}/bin) @${MKDIR} ${STAGEDIR}${DATADIR} (cd ${WRKSRC}/lib && ${INSTALL_DATA} *.qcl ${STAGEDIR}${DATADIR}) .include diff --git a/science/rubygem-ai4r/Makefile b/science/rubygem-ai4r/Makefile index 8fa7c5b31ff1..3053e1477787 100644 --- a/science/rubygem-ai4r/Makefile +++ b/science/rubygem-ai4r/Makefile @@ -1,17 +1,15 @@ -# Created by: Eric Freeman - PORTNAME= ai4r PORTVERSION= 1.13 CATEGORIES= science rubygems MASTER_SITES= RG MAINTAINER= ruby@FreeBSD.org COMMENT= Various Ruby artificial intelligence algorithm implementations LICENSE= MPL11 NO_ARCH= yes USE_RUBY= yes USES= gem .include diff --git a/science/rubygem-cdo/Makefile b/science/rubygem-cdo/Makefile index 18efe88b4b97..81a15d63bbb1 100644 --- a/science/rubygem-cdo/Makefile +++ b/science/rubygem-cdo/Makefile @@ -1,20 +1,18 @@ -# Created by: Sunpoet Po-Chuan Hsieh - PORTNAME= cdo PORTVERSION= 1.5.1 CATEGORIES= science rubygems MASTER_SITES= RG MAINTAINER= sunpoet@FreeBSD.org COMMENT= Ruby binding to CDO (Climate Data Operators) LICENSE= BSD3CLAUSE RUN_DEPENDS= cdo:science/cdo USES= gem USE_RUBY= yes NO_ARCH= yes .include diff --git a/science/rubygem-rgeo-geojson/Makefile b/science/rubygem-rgeo-geojson/Makefile index c91c022dc21a..42447f43bb86 100644 --- a/science/rubygem-rgeo-geojson/Makefile +++ b/science/rubygem-rgeo-geojson/Makefile @@ -1,21 +1,19 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= rgeo-geojson PORTVERSION= 2.1.1 CATEGORIES= science rubygems MASTER_SITES= RG MAINTAINER= sunpoet@FreeBSD.org COMMENT= GeoJSON formatting and parsing in Ruby LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= rubygem-rgeo>=1.0.0:science/rubygem-rgeo USES= gem USE_RUBY= yes NO_ARCH= yes .include diff --git a/science/rubygem-rgeo-proj4/Makefile b/science/rubygem-rgeo-proj4/Makefile index a60c6a01e4d3..80938a1e8e45 100644 --- a/science/rubygem-rgeo-proj4/Makefile +++ b/science/rubygem-rgeo-proj4/Makefile @@ -1,22 +1,20 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= rgeo-proj4 PORTVERSION= 3.1.1 CATEGORIES= science rubygems MASTER_SITES= RG MAINTAINER= sunpoet@FreeBSD.org COMMENT= Proj.4 extension for RGeo LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libproj.so:graphics/proj RUN_DEPENDS= rubygem-rgeo>=2.0<3:science/rubygem-rgeo USES= gem USE_RUBY= yes CONFIGURE_ARGS= --with-proj-dir=${LOCALBASE} .include diff --git a/science/rubygem-rgeo-shapefile/Makefile b/science/rubygem-rgeo-shapefile/Makefile index 948683e9b1e0..3b1d64a6e425 100644 --- a/science/rubygem-rgeo-shapefile/Makefile +++ b/science/rubygem-rgeo-shapefile/Makefile @@ -1,22 +1,20 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= rgeo-shapefile PORTVERSION= 3.0.0 CATEGORIES= science rubygems MASTER_SITES= RG MAINTAINER= sunpoet@FreeBSD.org COMMENT= RGeo module for reading the ESRI shapefile format LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= rubygem-dbf>=4.0<5:databases/rubygem-dbf \ rubygem-rgeo>=1.0:science/rubygem-rgeo USES= gem USE_RUBY= yes NO_ARCH= yes .include diff --git a/science/rubygem-rgeo/Makefile b/science/rubygem-rgeo/Makefile index 1daea82c1287..566290f7880a 100644 --- a/science/rubygem-rgeo/Makefile +++ b/science/rubygem-rgeo/Makefile @@ -1,19 +1,17 @@ -# Created by: Po-Chuan Hsieh - PORTNAME= rgeo PORTVERSION= 2.4.0 CATEGORIES= science rubygems MASTER_SITES= RG MAINTAINER= sunpoet@FreeBSD.org COMMENT= Geospatial data library for Ruby (RGeo) LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libgeos.so:graphics/geos USES= gem USE_RUBY= yes .include diff --git a/science/rubygem-ruby-dcl/Makefile b/science/rubygem-ruby-dcl/Makefile index 98541633a336..3dd51480c965 100644 --- a/science/rubygem-ruby-dcl/Makefile +++ b/science/rubygem-ruby-dcl/Makefile @@ -1,26 +1,24 @@ -# Created by: Shin-ya MURAKAMI - PORTNAME= ruby-dcl PORTVERSION= 1.8.1 CATEGORIES= science rubygems MASTER_SITES= RG MAINTAINER= murashin@gfd-dennou.org COMMENT= Ruby interface to the scientific graphic library DCL LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= rubygem-narray>=0.5.5:math/rubygem-narray LIB_DEPENDS= libcdcl.so:science/cdcl \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 RUN_DEPENDS= rubygem-narray>=0.5.5:math/rubygem-narray \ rubygem-narray_miss>0:math/rubygem-narray_miss USES= gem gettext-runtime gnome xorg USE_GNOME= atk cairo gdkpixbuf2 glib20 gtk20 pango USE_XORG= ice sm x11 USE_RUBY= yes .include diff --git a/science/rubygem-ruby-netcdf/Makefile b/science/rubygem-ruby-netcdf/Makefile index 1f8ac9dbb629..f43fed0667c7 100644 --- a/science/rubygem-ruby-netcdf/Makefile +++ b/science/rubygem-ruby-netcdf/Makefile @@ -1,21 +1,19 @@ -# Created by: Shin-ya Murakami - PORTNAME= ruby-netcdf PORTVERSION= 0.8.0 CATEGORIES= science rubygems MASTER_SITES= RG MAINTAINER= ruby@FreeBSD.org COMMENT= Ruby interface to the NetCDF scientific IO library LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libnetcdf.so:science/netcdf RUN_DEPENDS= rubygem-narray>=0:math/rubygem-narray \ rubygem-narray_miss>=0:math/rubygem-narray_miss USES= gem USE_RUBY= yes .include diff --git a/science/sigrok-cli/Makefile b/science/sigrok-cli/Makefile index d986374262ad..ef9d56e240fb 100644 --- a/science/sigrok-cli/Makefile +++ b/science/sigrok-cli/Makefile @@ -1,29 +1,27 @@ -# Created by: Uffe Jakobsen - PORTNAME= sigrok-cli PORTVERSION= 0.7.2 CATEGORIES= science cad MASTER_SITES= http://sigrok.org/download/source/sigrok-cli/ MAINTAINER= bofh@FreeBSD.org COMMENT= Framework for hardware logic analyzers, CLI client LICENSE= GPLv3 LIB_DEPENDS= libserialport.so:devel/libserialport \ libsigrok.so:devel/libsigrok \ libsigrokdecode.so:devel/libsigrokdecode USES= desktop-file-utils gettext-runtime gmake gnome libtool pathfix \ pkgconfig GNU_CONFIGURE= yes MAKE_JOBS_UNSAFE= yes PLIST_FILES= bin/sigrok-cli \ man/man1/sigrok-cli.1.gz \ share/applications/org.sigrok.sigrok-cli.desktop \ share/icons/hicolor/scalable/apps/sigrok-cli.svg .include diff --git a/science/sigrok-firmware-fx2lafw/Makefile b/science/sigrok-firmware-fx2lafw/Makefile index f1e90e25b69f..1c108fc31dd0 100644 --- a/science/sigrok-firmware-fx2lafw/Makefile +++ b/science/sigrok-firmware-fx2lafw/Makefile @@ -1,47 +1,45 @@ -# Created by: Uffe Jakobsen - PORTNAME= firmware PORTVERSION= 0.1.7 CATEGORIES= science MASTER_SITES= http://sigrok.org/download/binary/${PKGNAMEPREFIX}${PORTNAME}${PKGNAMESUFFIX}/ PKGNAMEPREFIX= sigrok- PKGNAMESUFFIX= -fx2lafw DISTNAME= ${PKGNAMEPREFIX}${PORTNAME}${PKGNAMESUFFIX}-bin-${PORTVERSION} MAINTAINER= bofh@FreeBSD.org COMMENT= Cypress FX2 firmware for hardware logic analyzers LICENSE= GPLv2 NO_BUILD= yes FW_FILES= fx2lafw-braintechnology-usb-lps.fw \ fx2lafw-cwav-usbeeax.fw \ fx2lafw-cwav-usbeedx.fw \ fx2lafw-cwav-usbeesx.fw \ fx2lafw-cwav-usbeezx.fw \ fx2lafw-cypress-fx2.fw \ fx2lafw-hantek-6022be.fw \ fx2lafw-hantek-6022bl.fw \ fx2lafw-sainsmart-dds120.fw \ fx2lafw-saleae-logic.fw \ fx2lafw-sigrok-fx2-16ch.fw \ fx2lafw-sigrok-fx2-8ch.fw PORTDOCS= README NEWS PLIST_FILES= ${FW_FILES:S,^,share/sigrok-firmware/,} OPTIONS_DEFINE= DOCS do-install: @${MKDIR} ${STAGEDIR}${DOCSDIR} .for docfile in README NEWS ${INSTALL_DATA} ${WRKSRC}/${docfile} ${STAGEDIR}${DOCSDIR} .endfor @${MKDIR} ${STAGEDIR}${PREFIX}/share/sigrok-firmware .for fwfile in ${FW_FILES} ${INSTALL_DATA} ${WRKSRC}/${fwfile} \ ${STAGEDIR}${PREFIX}/share/sigrok-firmware/ .endfor .include diff --git a/science/sigrok-firmware-utils/Makefile b/science/sigrok-firmware-utils/Makefile index c5dee6608213..9a4f72892bd8 100644 --- a/science/sigrok-firmware-utils/Makefile +++ b/science/sigrok-firmware-utils/Makefile @@ -1,51 +1,49 @@ -# Created by: Uffe Jakobsen - PORTNAME= firmware PORTVERSION= 20140418 PORTREVISION= 2 CATEGORIES= science MASTER_SITES= #none PKGNAMEPREFIX= sigrok- PKGNAMESUFFIX= -utils DISTFILES= #none MAINTAINER= bofh@FreeBSD.org COMMENT= Sigrok firmware extraction utilities LICENSE= GPLv3+ USES= python:3.4+ shebangfix SHEBANG_FILES= ${PY_FILES} ${EX_FILES} NO_BUILD= yes NO_ARCH= yes PORTDOCS= README.parsepe PY_FILES= parsepe.py parseelf.py EX_FILES= sigrok-fwextract-hantek-dso \ sigrok-fwextract-saleae-logic16 \ sigrok-fwextract-sysclk-lwla PLIST_FILES= ${PY_FILES:S,^,bin/,} \ ${EX_FILES:S,^,bin/,} \ ${EX_FILES:S,^,man/man1/,:S,$,.1.gz,} OPTIONS_DEFINE= DOCS do-extract: @${MKDIR} ${WRKSRC} @${CP} ${FILESDIR}/* ${WRKSRC} do-install: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/README.parsepe ${STAGEDIR}${DOCSDIR} .for fil in ${PY_FILES} ${INSTALL_SCRIPT} ${WRKSRC}/${fil} ${STAGEDIR}${PREFIX}/bin .endfor .for fil in ${EX_FILES} ${INSTALL_SCRIPT} ${WRKSRC}/${fil} ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/${fil}.1 ${STAGEDIR}${MAN1PREFIX}/man/man1 .endfor .include diff --git a/science/sigrok-firmware/Makefile b/science/sigrok-firmware/Makefile index dce7e80401d2..a0193b1126a5 100644 --- a/science/sigrok-firmware/Makefile +++ b/science/sigrok-firmware/Makefile @@ -1,34 +1,32 @@ -# Created by: Uffe Jakobsen - PORTNAME= firmware PORTVERSION= 20150123 CATEGORIES= science PKGNAMEPREFIX= sigrok- MAINTAINER= bofh@FreeBSD.org COMMENT= Sigrok firmware RUN_DEPENDS= parseelf.py:science/sigrok-firmware-utils \ ${LOCALBASE}/share/sigrok-firmware/fx2lafw-cypress-fx2.fw:science/sigrok-firmware-fx2lafw USE_GITHUB= yes GH_ACCOUNT= uffejakobsen GH_PROJECT= ${PKGNAMEPREFIX}${PORTNAME} GH_TAGNAME= 2632d74 GNU_CONFIGURE=yes USES= autoreconf gmake FW_FILES= \ LICENSE.Sigma asix-sigma-100.fw asix-sigma-200.fw asix-sigma-50.fw asix-sigma-50sync.fw \ LICENSE.LWLA sysclk-lwla1034-extneg.rbf sysclk-lwla1034-extpos.rbf sysclk-lwla1034-int.rbf sysclk-lwla1034-off.rbf PLIST_FILES= \ ${FW_FILES:S,^,share/sigrok-firmware/,} \ post-install: ${INSTALL_DATA} ${WRKSRC}/asix-sigma/LICENSE.Sigma ${STAGEDIR}${PREFIX}/share/sigrok-firmware ${INSTALL_DATA} ${WRKSRC}/sysclk-lwla/LICENSE.LWLA ${STAGEDIR}${PREFIX}/share/sigrok-firmware .include diff --git a/science/silo/Makefile b/science/silo/Makefile index 4fb942697d17..2d575f359636 100644 --- a/science/silo/Makefile +++ b/science/silo/Makefile @@ -1,64 +1,62 @@ -# Created by: Pedro F. Giffuni - PORTNAME= silo PORTVERSION= 4.10.2 DISTVERSIONSUFFIX= -bsd PORTREVISION= 14 CATEGORIES= science MASTER_SITES= http://wci.llnl.gov/content/assets/docs/simulation/computer-codes/${PORTNAME}/silo-${PORTVERSION}/ MAINTAINER= dbaio@FreeBSD.org COMMENT= Mesh and field I/O library and scientific database LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYRIGHT USES= gmake libtool readline USE_LDCONFIG= yes GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared --disable-static INSTALL_TARGET= install-strip CONFLICTS_INSTALL= deforaos-browser # bin/browser OPTIONS_DEFINE= FORTRAN HDF5 PYTHON OPTIONS_DEFAULT= HDF5 OPTIONS_SUB= yes FORTRAN_CONFIGURE_ENABLE= fortran FORTRAN_USES= fortran HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_CFLAGS= -DH5_USE_110_API=1 HDF5_CONFIGURE_ON= --with-hdf5=${LOCALBASE}/include,${LOCALBASE}/lib HDF5_PLIST_SUB= SUFX_HDF5="h5" HDF5_PLIST_SUB_OFF= SUFX_HDF5="" PYTHON_CONFIGURE_ENABLE= pythonmodule PYTHON_USES= python post-patch: @${REINPLACE_CMD} -e \ 's|\(_Qt_dir/include\)"|\1/qt4"| ; \ s|\(_Qt_dir/lib\)"|\1/qt4"| ; \ s|\(/uic\)"|\1-qt4"| ; \ s|\(/moc\)"|\1-qt4"| ; \ s|\(/lrelease\)"|\1-qt4"| ; \ s|\(/lupdate\)"|\1-qt4"|' ${WRKSRC}/configure @${REINPLACE_CMD} -e \ '/-avoid-version/s|^|#| ; \ /^install-data-am/s|:.*|:|' ${WRKSRC}/src/Makefile.in @${REINPLACE_CMD} -e \ '/-ldl/s|^|#|' ${WRKSRC}/tests/Makefile.in @${REINPLACE_CMD} -e \ 's|@libdir@|@pythondir@|' ${WRKSRC}/tools/python/Makefile.in @${REINPLACE_CMD} -e \ 's|\(INBUILD\));|\1, me);|' ${WRKSRC}/src/hdf5_drv/silo_hdf5.c .if defined(MAINTAINER_MODE) regression-test: build @cd ${WRKSRC}/tests && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} check .endif .include diff --git a/science/simlib/Makefile b/science/simlib/Makefile index ab03a78e8e6d..3ae6c5f69faa 100644 --- a/science/simlib/Makefile +++ b/science/simlib/Makefile @@ -1,49 +1,47 @@ -# Created by: Pav Lucistnik - PORTNAME= simlib DISTVERSION= 3.06 DISTVERSIONSUFFIX= -20181003 CATEGORIES= science MASTER_SITES= http://www.fit.vutbr.cz/~peringer/SIMLIB/source/ MAINTAINER= ports@FreeBSD.org COMMENT= SIMulation LIBrary for C++ programming language LICENSE= LGPL20 USES= gmake USE_LDCONFIG= yes WRKSRC= ${WRKDIR}/${PORTNAME} CXXFLAGS+= -fPIC BROKEN_riscv64= fails to compile: process.cc:53:3: module process.cc is not ported to this processor architecture NOT_FOR_ARCHS= aarch64 armv6 armv7 mips mips64 powerpc powerpc64 sparc64 NOT_FOR_ARCHS_REASON= contains not working ${ARCH}-dependent assembly code .include .if ${OPSYS} == FreeBSD # nm crashes during the build: # Assertion failed: (ddata->output.size > 0), function cpp_demangle_read_sname, file /usr/src/contrib/elftoolchain/libelftc/libelftc_dem_gnu3.c, line 2137. USE_BINUTILS= yes BINARY_ALIAS= nm=${NM} .endif post-patch: @${REINPLACE_CMD} -e 's|make|gmake|g' ${WRKSRC}/Makefile @${REINPLACE_CMD} -e 's#%%PREFIX%%#${PREFIX}#g' \ ${WRKSRC}/src/Makefile.generic @${REINPLACE_CMD} -e 's#g++#${CXX}#g' \ ${WRKSRC}/src/Makefile.FreeBSD-i386 \ ${WRKSRC}/examples/Makefile.FreeBSD-i386 \ ${WRKSRC}/tests/Makefile.FreeBSD-i386 @${MV} ${WRKSRC}/src/Makefile.FreeBSD-i386 ${WRKSRC}/src/Makefile @${MV} ${WRKSRC}/examples/Makefile.FreeBSD-i386 ${WRKSRC}/examples/Makefile @${MV} ${WRKSRC}/tests/Makefile.FreeBSD-i386 ${WRKSRC}/tests/Makefile post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libsimlib.so .include diff --git a/science/simsmith/Makefile b/science/simsmith/Makefile index 074303636f13..34ce3cd965ac 100644 --- a/science/simsmith/Makefile +++ b/science/simsmith/Makefile @@ -1,29 +1,27 @@ -# Created by: shurd@FreeBSD.org - PORTNAME= simsmith PORTVERSION= 9.9 PORTREVISION= 1 CATEGORIES= science hamradio MASTER_SITES= http://ae6ty.com/Smith_Charts_files/ \ LOCAL/shurd DISTNAME= SimSmith9p9 EXTRACT_SUFX= .jar EXTRACT_ONLY= MAINTAINER= hamradio@FreeBSD.org COMMENT= Java-based Smith Chart program USE_JAVA= yes JAVA_RUN= yes PLIST_FILES= %%JAVAJARDIR%%/${DISTNAME}${EXTRACT_SUFX} \ bin/${PORTNAME} SUB_FILES= simsmith SUB_LIST+= DISTNAME=${DISTNAME} NO_BUILD= yes do-install: @${INSTALL_DATA} ${DISTDIR}/${DISTNAME}${EXTRACT_SUFX} ${STAGEDIR}${JAVAJARDIR} @${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin .include diff --git a/science/svmlight/Makefile b/science/svmlight/Makefile index 80dea0bfebf3..f8b0f44f57de 100644 --- a/science/svmlight/Makefile +++ b/science/svmlight/Makefile @@ -1,40 +1,38 @@ -# Created by: Gea-Suan Lin - PORTNAME= svmlight PORTVERSION= 6.02 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= http://osmot.cs.cornell.edu/svm_light/v${PORTVERSION}/ DISTNAME= svm_light PATCH_SITES= http://cpansearch.perl.org/src/KWILLIAMS/Algorithm-SVMLight-0.09/ PATCHFILES= SVMLight.patch PATCH_DIST_STRIP=-p1 LICENSE= SVM-Light LICENSE_NAME= SVM-Light license LICENSE_FILE= ${WRKSRC}/LICENSE.txt LICENSE_PERMS= # none MAINTAINER= ports@FreeBSD.org COMMENT= Implementation of Support Vector Machines (SVMs) in C CFLAGS+= -fPIC -fcommon MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}" LD="${CC}" LFLAGS="${CFLAGS}" NO_WRKSUBDIR= yes USES= gmake USE_LDCONFIG= yes OPTIONS_DEFINE= DOCS do-install: @${MKDIR} ${STAGEDIR}${PREFIX}/include/svmlight ${INSTALL_DATA} ${WRKSRC}/*.h ${STAGEDIR}${PREFIX}/include/svmlight .for file in svm_classify svm_learn ${INSTALL_PROGRAM} ${WRKSRC}/${file} ${STAGEDIR}${PREFIX}/bin .endfor ${INSTALL_DATA} ${WRKSRC}/libsvmlight.a ${STAGEDIR}${PREFIX}/lib/ ${INSTALL_LIB} ${WRKSRC}/libsvmlight.so ${STAGEDIR}${PREFIX}/lib/libsvmlight.so.1 ${LN} -s libsvmlight.so.1 ${STAGEDIR}${PREFIX}/lib/libsvmlight.so .include diff --git a/science/tfel-edf/Makefile b/science/tfel-edf/Makefile index e20f5fceb26f..4a0261842b6a 100644 --- a/science/tfel-edf/Makefile +++ b/science/tfel-edf/Makefile @@ -1,54 +1,52 @@ -# Created by: Pedro F. Giffuni - PORTNAME= tfel DISTVERSION= 3.2.1-1 PORTREVISION= 2 CATEGORIES= science PKGNAMESUFFIX= -mfront-edf MAINTAINER= thierry@FreeBSD.org COMMENT= Code generation tool dedicated to material knowledge LICENSE= GPLv3 BUILD_DEPENDS= gnuplot:math/gnuplot \ ${PYNUMPY} LIB_DEPENDS= ${PY_BOOST} \ libboost_thread.so:devel/boost-libs RUN_DEPENDS= gnuplot:math/gnuplot \ ${PYNUMPY} USES= cmake compiler:c++0x fortran localbase python CONFLICTS= tfel-mfront-3.* OPTIONS_DEFINE= DOCS OPTIONS_DEFAULT=DOCS OPTIONS_SUB= yes WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION:R} CMAKE_ON= enable-aster enable-calculix enable-fortran \ enable-python enable-python-bindings CMAKE_ARGS+= -DCOMPILER_CXXFLAGS="${CXXFLAGS}" -DCOMPILER_FLAGS="${CFLAGS}" USE_LDCONFIG= yes .ifdef PACKAGE_BUILDING CMAKE_ON+= enable-portable-build .endif TEST_TARGET= check .include .include "${.CURDIR}/../../french/aster/bsd.aster.mk" .if ${FORTRAN_DEFAULT} == gfortran && ${GCC_DEFAULT} >= 10 FCFLAGS+= -fallow-argument-mismatch .endif post-install: (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) .include diff --git a/science/tfel/Makefile b/science/tfel/Makefile index fc2b9f6b036a..271c0da6f65b 100644 --- a/science/tfel/Makefile +++ b/science/tfel/Makefile @@ -1,51 +1,49 @@ -# Created by: Pedro F. Giffuni - PORTNAME= tfel PORTVERSION= 4.0.0 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= SF/${PORTNAME}/ PKGNAMESUFFIX= -mfront MAINTAINER= ports@FreeBSD.org COMMENT= Code generation tool dedicated to material knowledge LICENSE= GPLv3 BUILD_DEPENDS= gnuplot:math/gnuplot RUN_DEPENDS= gnuplot:math/gnuplot USES= cmake compiler:c++0x fortran CONFLICTS_INSTALL= tfel-mfront-edf-3.* OPTIONS_DEFINE= DOCS PYTHON OPTIONS_DEFAULT= DOCS PYTHON OPTIONS_SUB= yes PYTHON_USES= localbase python PYTHON_BUILD_DEPENDS= ${PYNUMPY} PYTHON_LIB_DEPENDS= ${PY_BOOST} \ libboost_thread.so:devel/boost-libs PYTHON_RUN_DEPENDS= ${PYNUMPY} PYTHON_CMAKE_BOOL= enable-python enable-python-bindings CMAKE_ON= enable-aster enable-calculix enable-fortran CMAKE_ARGS+= -DCOMPILER_CXXFLAGS="${CXXFLAGS}" -DCOMPILER_FLAGS="${CFLAGS}" PLIST_SUB= VER=${PORTVERSION} USE_LDCONFIG= yes .ifdef PACKAGE_BUILDING CMAKE_ON+= enable-portable-build .endif TEST_TARGET= check post-install: (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) .include diff --git a/science/tinker/Makefile b/science/tinker/Makefile index e460802bcbe7..25c11cd6a6e6 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,88 +1,86 @@ -# Created by: Glenn Johnson - PORTNAME= tinker DISTVERSION= 8.10.2 PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ MAINTAINER= yuri@FreeBSD.org COMMENT= General purpose molecular modelling package LICENSE= TINKER LICENSE_NAME= TINKER license agreement LICENSE_FILE= ${WRKSRC}/doc/license.pdf LICENSE_PERMS= auto-accept # internal academic purposes only, no commercial use LIB_DEPENDS= libfftw3.so:math/fftw3 USES= fortran gmake WRKSRC= ${WRKDIR}/${PORTNAME} BUILD_WRKSRC= ${WRKSRC}/source INSTALL_WRKSRC= ${WRKSRC}/source MAKE_ENV= HAVE_G2C=yes MAKE_ARGS= RANLIB=ranlib BINDIR=${STAGEDIR}${PREFIX}/bin MAKEFILE= ${WRKSRC}/make/Makefile EXTRACT_AFTER_ARGS=--exclude fftw --exclude windows --exclude macosx SUB_FILES= pkg-message BINARY_ALIAS= gfortran=gfortran${GCC_DEFAULT} OPTIONS_DEFINE= OPTIMIZED_FFLAGS DOCS EXAMPLES OPTIONS_DEFINE_amd64= SSE OPTIONS_DEFINE_i386= SSE OPTIONS_DEFAULT_amd64= SSE OPTIONS_DEFAULT_i386= SSE SSE_MAKE_ARGS= PORT_SIMD_FLAGS="-msse -msse2 -mfpmath=sse" OPTIMIZED_FFLAGS_DESC= compilation optimizations PORTDOCS= * PORTEXAMPLES= * .include .if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS} FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations .if (${ARCH} == "i386") FFLAGS+= -mfancy-math-387 -malign-double .endif # i386 .endif post-extract: @${RM} ${BUILD_WRKSRC}/*.c @${RM} ${WRKSRC}/other/eopbend.orig # remove bundled linux libraries @${RM} ${WRKSRC}/lib/linux/* post-patch: @${REINPLACE_CMD} -i '' 's|\.\./bin/|${STAGEDIR}${PREFIX}/bin/|' ${BUILD_WRKSRC}/../bench/bench*.run post-install: @${MKDIR} ${STAGEDIR}${DATADIR} @${MKDIR} ${STAGEDIR}${DATADIR}/params cd ${WRKSRC}/params && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/params @${MKDIR} ${STAGEDIR}${DATADIR}/test cd ${WRKSRC}/test && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/test post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${WRKSRC}/doc && ${INSTALL_DATA} 0README *.pdf ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/example && ${INSTALL_DATA} \ 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz \ ${STAGEDIR}${EXAMPLESDIR} benchmarks: stage .for n in 1 2 3 4 5 6 7 8 9 @cd ${BUILD_WRKSRC}/../bench && ./bench${n}.run .endfor .include diff --git a/science/udunits/Makefile b/science/udunits/Makefile index b9b239921bc4..6a4d75533e66 100644 --- a/science/udunits/Makefile +++ b/science/udunits/Makefile @@ -1,38 +1,36 @@ -# Created by: Greg Lewis - PORTNAME= udunits PORTVERSION= 2.2.28 CATEGORIES= science math MASTER_SITES= ftp://ftp.unidata.ucar.edu/pub/udunits/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= Library for manipulating units of physical quantities LICENSE= UCAR_UNIDATA LICENSE_FILE= ${WRKSRC}/COPYRIGHT LICENSE_NAME= University Corporation for Atmospheric Research/Unidata LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept LIB_DEPENDS= libexpat.so:textproc/expat2 USES= libtool localbase CFLAGS+= -D__BSD_VISIBLE CONFIGURE_ENV= ac_cv_header_CUnit_CUnit_h=no GNU_CONFIGURE= yes INSTALL_TARGET= install-strip TEST_TARGET= check USE_LDCONFIG= yes INFO= udunits2 udunits2lib udunits2prog OPTIONS_DEFINE= DOCS post-patch: @${REINPLACE_CMD} -e '/install-data-hook$$/d' ${WRKSRC}/lib/Makefile.in post-patch-DOCS-on: @${REINPLACE_CMD} -e '/^dist_doc_DATA = / s| COPYRIGHT||' ${WRKSRC}/Makefile.in .include diff --git a/science/v_sim/Makefile b/science/v_sim/Makefile index 5f811443cfcd..854dd32dfb67 100644 --- a/science/v_sim/Makefile +++ b/science/v_sim/Makefile @@ -1,96 +1,94 @@ -# Created by: Thierry Thomas - PORTNAME= v_sim PORTVERSION= 3.8.0 PORTREVISION= 3 CATEGORIES= science MASTER_SITES= https://gitlab.com/l_sim/${PORTNAME}/-/archive/${PORTVERSION}/ MAINTAINER= thierry@FreeBSD.org COMMENT= Visualization of atomic structures LICENSE= CeCILL LICENSE_NAME= CeCILL LICENSE_FILE= ${WRKSRC}/COPYING LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BUILD_DEPENDS= p5-XML-LibXML>0:textproc/p5-XML-LibXML \ libarchive>0:archivers/libarchive \ xcrysden:science/xcrysden \ bash:shells/bash LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ libopenbabel.so:science/openbabel \ libfreetype.so:print/freetype2 \ libyaml.so:textproc/libyaml \ libnetcdf.so:science/netcdf \ libmsym.so:science/libmsym \ libftgl.so:graphics/ftgl \ libxc.so:science/libxc RUN_DEPENDS= ${PYNUMPY} \ xcrysden:science/xcrysden \ libarchive>0:archivers/libarchive \ ${PYTHON_PKGNAMEPREFIX}gobject3>0:devel/py-gobject3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} USES= autoreconf blaslapack compiler:c11 fortran gl gmake gnome \ libtool:keepla localbase:ldflags pkgconfig python:3.7+ \ shebangfix tar:bzip2 xorg SHEBANG_GLOB= *.py USE_XORG= x11 USE_GNOME= cairo gtk30 intltool introspection USE_GL= gl glu GNU_CONFIGURE= yes CONFIGURE_SHELL=${LOCALBASE}/bin/bash CONFIGURE_ARGS= --htmldir=${PREFIX}/share/doc --with-openbabel \ --with-netcdf=${LOCALBASE} --with-etsf-file-format \ --with-xsf --with-cube --with-msym=${LOCALBASE} \ --with-msym-inc=-I${LOCALBASE}/include/libmsym \ --with-libxc=${LOCALBASE} --enable-python-module CPPFLAGS+= ${CFLAGS} USE_LDCONFIG= yes OPTIONS_DEFINE= DOCS NLS EXAMPLES .if defined(WITH_DEBUG) CONFIGURE_ARGS+=--enable-debug-messages .endif .include .if ${ARCH:Mamd64*} || ${ARCH:Mpowerpc64*} BUILD_DEPENDS+= abinit:science/abinit RUN_DEPENDS+= abinit:science/abinit CONFIGURE_ARGS+=--with-abinit PLIST_SUB+= AB="" .else PLIST_SUB+= AB="@comment " .endif .if ${PORT_OPTIONS:MNLS} USES+= gettext PLIST_SUB+= NLS="" .else USES+= gettext-tools PLIST_SUB+= NLS="@comment " .endif pre-configure: ${REINPLACE_CMD} -e 's|$${docdir}/examples|${EXAMPLESDIR}|' \ ${WRKSRC}/configure.ac ${REINPLACE_CMD} -e 's|print sys.prefix|print (sys.prefix)|' \ -e 's|print sys.exec_prefix|print (sys.exec_prefix)|' \ ${WRKSRC}/m4/python.m4 pre-configure-NLS-off: ${REINPLACE_CMD} -e '/^ po /d' ${WRKSRC}/Makefile.am pre-configure-DOCS-off: ${REINPLACE_CMD} -e '/^ Documentation/d' ${WRKSRC}/Makefile.am pre-configure-EXAMPLES-off: ${REINPLACE_CMD} -e '/^ examples/d' \ ${WRKSRC}/Makefile.am ${REINPLACE_CMD} -e 's|: install-v_simexamplesDATA|:|' \ ${WRKSRC}/lib/python/Makefile.am .include diff --git a/science/vmd/Makefile b/science/vmd/Makefile index c352e142ec87..bc0de1d04b46 100644 --- a/science/vmd/Makefile +++ b/science/vmd/Makefile @@ -1,167 +1,165 @@ -# Created by: Stephen Montgomery-Smith - PORTNAME= vmd DISTVERSION= 1.9.3 PORTREVISION= 11 CATEGORIES= science graphics python tcl tk MASTER_SITES= http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/:tachyon \ http://www.photonlimited.com/~johns/tachyon/files/0.99b6/:tachyon \ http://webclu.bio.wzw.tum.de/stride/:stride \ ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/:stride DISTFILES= ${VMD_DIST} \ ${TACHYON_DIST}:tachyon \ ${STRIDE_DIST}:stride MAINTAINER= ports@FreeBSD.org COMMENT= Molecular visualization program LICENSE= VMD BSD3CLAUSE STRIDE LICENSE_COMB= multi BUILD_DEPENDS= makedepend:devel/makedepend \ ${PYNUMPY} LIB_DEPENDS= libexpat.so:textproc/expat2 \ libfltk.so:x11-toolkits/fltk \ libnetcdf.so:science/netcdf RUN_DEPENDS= ${PYNUMPY} LICENSE_FILE_VMD= ${WRKSRC}/LICENSE LICENSE_PERMS_VMD= no-auto-accept LICENSE_NAME_VMD= Visual Molecular Dynamics Software License Agreement LICENSE_DISTFILES_VMD= ${VMD_DIST} LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/lib/tachyon/Copyright LICENSE_DISTFILES_BSD3CLAUSE= ${TACHYON_DIST} LICENSE_TEXT_STRIDE= ${FILESDIR}/stride.txt LICENSE_PERMS_STRIDE= dist-mirror pkg-mirror auto-accept LICENSE_NAME_STRIDE= Stride Copyright Notice LICENSE_DISTFILES_STRIDE=${STRIDE_DIST} USES= gl gmake perl5 python shebangfix sqlite tcl tk xorg SHEBANG_FILES= ${WRKDIR}/plugins/topotools/*.tcl USE_PERL5= build USE_GL= gl glu USE_XORG= x11 ONLY_FOR_ARCHS= amd64 i386 CONFIGURE_ENV= PYTHON_INCLUDE_DIR=${PYTHON_INCLUDEDIR} \ PYTHON_LIBRARY_DIR=${PYTHON_LIBDIR} \ NUMPY_INCLUDE_DIR=${PYTHON_SITELIBDIR}/numpy/core/include \ NUMPY_LIBRARY_DIR=${PYTHON_SITELIBDIR} \ TCL_INCLUDE_DIR=${TCL_INCLUDEDIR} \ TCL_LIBRARY_DIR=${LOCALBASE}/lib \ TK_INCLUDE_DIR=${TK_INCLUDEDIR} \ TK_LIBRARY_DIR=${LOCALBASE}/lib CONFIGURE_ARGS= ${VMD_ARCH} OPENGL FLTK TK IMD TCL PTHREADS LIBTACHYON NETCDF NUMPY PYTHON INSTALL_WRKSRC= ${WRKSRC}/src MAKE_ENV= EXPATINC=-I${LOCALBASE}/include \ EXPATLIB=-L${LOCALBASE}/lib \ EXPATLDFLAGS=-lexpat \ EXPATDYNAMIC=1 \ NETCDFINC=-I${LOCALBASE}/include \ NETCDFLIB=-L${LOCALBASE}/lib \ NETCDFLDFLAGS=-lnetcdf \ SQLITEINC=-I${LOCALBASE}/include \ SQLITELIB=-L${LOCALBASE}/lib \ SQLITELDFLAGS=-lsqlite3 \ SQLITEDYNAMIC=1 \ TCLLIB=-L${LOCALBASE}/lib \ TCLINC=-I${TCL_INCLUDEDIR} \ TCLLDFLAGS=-ltcl${TCL_VER:S/.//} \ TKLDFLAGS="-ltk${TK_VER:S/.//} -lX11" VMD_DIST= ${PORTNAME}-${DISTVERSION}.src.tar.gz TACHYON_DIST= tachyon-0.99b6.tar.gz STRIDE_DIST= stride.tar.gz STRIDE_DOC= stride.doc .include .if ${ARCH} == "amd64" VMD_ARCH= FREEBSDAMD64 .else VMD_ARCH= FREEBSD .endif PLIST_SUB+= VMD_ARCH=${VMD_ARCH} # Check for VMD sources .if !exists(${DISTDIR}/${VMD_DIST}) IGNORE= license restrictions require manual fetching of the distribution\ source. Please visit http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD\ with a browser. You will be required to register, log in, and accept\ the University of Illinois agreement before you can download the\ ${VMD_DIST} source file. Place this file in ${DISTDIR} and try again. .endif do-extract: ${MKDIR} ${WRKDIR} ${WRKSRC}/lib/stride ${TAR} -xzf ${DISTDIR}/${VMD_DIST} -C ${WRKDIR} ${TAR} -xzf ${WRKSRC}/lib/surf/surf.tar.Z -C ${WRKSRC}/lib/surf ${TAR} -xzf ${DISTDIR}/${TACHYON_DIST} -C ${WRKSRC}/lib ${TAR} -xzf ${DISTDIR}/${STRIDE_DIST} -C ${WRKSRC}/lib/stride post-patch: ${REINPLACE_CMD} \ -e "s|-lpython2.5|-l${PYTHON_VERSION}${PYTHON_ABIVER}|" \ -e "s|/usr/local|${LOCALBASE}|g" \ -e "s|-fno-for-scope||g" \ -e "s/\"gcc\"/\"${CC}\"/;s/\"g++\"/\"${CXX}\"/" \ ${WRKSRC}/configure ${REINPLACE_CMD} -e "s/.SILENT:/#.SILENT:/" ${WRKDIR}/plugins/Makefile ${REINPLACE_CMD} "s/.SILENT:/#.SILENT:/" ${WRKDIR}/plugins/*/Makefile ${REINPLACE_CMD} "s%log2f(\([^ ,]*\))%logf(\1)/(float)M_LN2%g" \ ${WRKSRC}/src/Orbital.C ${REINPLACE_CMD} -E "s/(SHLD[[:space:]]*=[[:space:]]*)gcc/\1${CC}/" \ ${WRKDIR}/plugins/Make-arch ${REINPLACE_CMD} -E "s/(CC[[:space:]]*=[[:space:]]*)(gcc|cc)/\1${CC}/" \ ${WRKSRC}/lib/stride/Makefile \ ${WRKSRC}/lib/surf/Makefile \ ${WRKSRC}/lib/tachyon/unix/Make-arch \ ${WRKDIR}/plugins/cionize/Makefile.specialbuilds \ ${WRKDIR}/plugins/cionize/Makefile.mine \ ${WRKDIR}/plugins/cionize/Makefile.testing \ ${WRKDIR}/plugins/Make-arch \ ${WRKDIR}/plugins/molfile_plugin/f77/Makefile ${REINPLACE_CMD} -E "s/(CXX[[:space:]]*=[[:space:]]*)g\+\+/\1${CXX}/" \ ${WRKDIR}/plugins/fmtool/Makefile.specialbuilds \ ${WRKDIR}/plugins/hesstrans/src/foo/Makefile \ ${WRKDIR}/plugins/hesstrans/src/foo/nm_gnu.mak \ ${WRKDIR}/plugins/Make-arch ${REINPLACE_CMD} -e "s/return *;/return 0;/g" \ ${WRKSRC}/lib/surf/*.c do-build: ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${_MAKE_JOBS} bsd -C ${WRKSRC}/lib/tachyon/unix ${MV} ${WRKSRC}/lib/tachyon/compile/bsd/tachyon ${WRKSRC}/lib/tachyon/tachyon_${VMD_ARCH} ${SETENV} ${MAKE_ENV} PLUGINDIR=${WRKSRC}/plugins ${MAKE_CMD} ${VMD_ARCH} distrib -C ${WRKDIR}/plugins cd ${WRKSRC} && ${SETENV} ${CONFIGURE_ENV} ${CONFIGURE_CMD} ${CONFIGURE_ARGS} ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${_MAKE_JOBS} all -C ${WRKSRC}/src ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${_MAKE_JOBS} depend -C ${WRKSRC}/lib/surf ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${_MAKE_JOBS} surf -C ${WRKSRC}/lib/surf ${MV} ${WRKSRC}/lib/surf/surf ${WRKSRC}/lib/surf/surf_${VMD_ARCH} ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${_MAKE_JOBS} -C ${WRKSRC}/lib/stride ${MV} ${WRKSRC}/lib/stride/stride ${WRKSRC}/lib/stride/stride_${VMD_ARCH} post-install: ${REINPLACE_CMD} -i '' -e 's|${STAGEDIR}||g' ${STAGEDIR}${PREFIX}/bin/vmd ${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/*${VMD_ARCH} \ ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/molfile/*.so .for f in tcl/autopsf1.6/psfcheck.so tcl/hesstrans1.0/hesstrans.so \ tcl/mutator1.5/libalchemify.so tcl/pmepot1.0/libpmepot.so \ tcl/psfgen1.6/libpsfgen.so tcl/rnaview1.1/rnaview \ tcl/signalproc1.1/specden.so tcl/signalproc1.1/fftcmds.so \ tcl/signalproc1.1/sgsmooth.so tcl/volutil1.3/volutil \ tcl/clustalw1.1/clustalw tcl/libbiokit1.1/tcl_libbiokit.so \ tcl/libbiokit1.1/q tcl/libbiokit1.1/seqqr \ tcl/libbiokit1.1/structqr tcl/libbiokit1.1/qpair \ tcl/libbiokit1.1/rmsd tcl/libbiokit1.1/percid \ tcl/phylotree1.2/upgmaclu tcl/stamp1.2/stamp \ tcl/bossconvert1.0/Topology \ bin/catdcd5.1/catdcd bin/cionize1.0/cionize ${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/${f} .endfor .include diff --git a/science/xtb/Makefile b/science/xtb/Makefile index 84b637458c40..567c13a675bc 100644 --- a/science/xtb/Makefile +++ b/science/xtb/Makefile @@ -1,22 +1,20 @@ -# Created by: Johannes M Dieterich - PORTNAME= xtb PORTVERSION= 6.4.1 DISTVERSIONPREFIX= v CATEGORIES= science MAINTAINER= jmd@FreeBSD.org COMMENT= Semiempirical Extended Tight-Binding Program Package LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING USES= fortran cmake blaslapack:openblas USE_GITHUB= yes GH_ACCOUNT= grimme-lab USE_LDCONFIG= yes FFLAGS+= -std=legacy .include