Date: Fri, 29 Jun 2018 09:04:22 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r473535 - in head/science: . rmf rmf/files Message-ID: <201806290904.w5T94M3o023157@repo.freebsd.org>
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Author: yuri Date: Fri Jun 29 09:04:22 2018 New Revision: 473535 URL: https://svnweb.freebsd.org/changeset/ports/473535 Log: New port: science/rmf: Library to support reading and writing of Rich Molecular Format files Added: head/science/rmf/ head/science/rmf/Makefile (contents, props changed) head/science/rmf/distinfo (contents, props changed) head/science/rmf/files/ head/science/rmf/files/patch-CMakeLists.txt (contents, props changed) head/science/rmf/pkg-descr (contents, props changed) head/science/rmf/pkg-plist (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Fri Jun 29 08:37:21 2018 (r473534) +++ head/science/Makefile Fri Jun 29 09:04:22 2018 (r473535) @@ -212,6 +212,7 @@ SUBDIR += qcl SUBDIR += qtresistors SUBDIR += rdkit + SUBDIR += rmf SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-rgeo Added: head/science/rmf/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rmf/Makefile Fri Jun 29 09:04:22 2018 (r473535) @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= rmf +DISTVERSION= g20180614 +CATEGORIES= science graphics + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Library to support reading and writing of Rich Molecular Format files + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/COPYING + +LIB_DEPENDS= libboost_system.so:devel/boost-libs \ + libhdf5.so:science/hdf5 \ + libsz.so:science/szip + +USES= cmake:outsource python:build shebangfix +USE_GITHUB= yes +GH_ACCOUNT= salilab +GH_TAGNAME= f917cf2 +SHEBANG_GLOB= *.py +USE_LDCONFIG= yes + +BINARY_ALIAS= python=${PYTHON_CMD} + +.include <bsd.port.mk> Added: head/science/rmf/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rmf/distinfo Fri Jun 29 09:04:22 2018 (r473535) @@ -0,0 +1,9 @@ +TIMESTAMP = 1530254926 +SHA256 (salilab-rmf-g20180614-f917cf2_GH0.tar.gz) = 9c877539b8c7a6af38b3d7155522a90b16b3e28596ec27ac941c7f812f1a1c6f +SIZE (salilab-rmf-g20180614-f917cf2_GH0.tar.gz) = 15087905 +SHA256 (salilab-cmake_modules-412ee17_GH0.tar.gz) = ea4867f9239f68c235183e5397804091a528af94a28de93e93bca4a3d5bc1202 +SIZE (salilab-cmake_modules-412ee17_GH0.tar.gz) = 25035 +SHA256 (salilab-developer_tools-91e94c7_GH0.tar.gz) = 6e512ca15c89803828daaa6dfc44aa836fbf4f7f72aa5240f0b3709c17d85521 +SIZE (salilab-developer_tools-91e94c7_GH0.tar.gz) = 34682 +SHA256 (salilab-avrocpp-10f7084_GH0.tar.gz) = 0d8501103ddd22c06b1f973fd48d2bbd616b4c01a1214c06412cc5d0d371361c +SIZE (salilab-avrocpp-10f7084_GH0.tar.gz) = 123182 Added: head/science/rmf/files/patch-CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rmf/files/patch-CMakeLists.txt Fri Jun 29 09:04:22 2018 (r473535) @@ -0,0 +1,45 @@ +--- CMakeLists.txt.orig 2018-06-15 00:56:51 UTC ++++ CMakeLists.txt +@@ -4,15 +4,15 @@ project(RMF) + # needs to be in main CMakeLists.txt + enable_testing() + +-execute_process(COMMAND python setup_git.py +- RESULT_VARIABLE setup +- OUTPUT_VARIABLE toutput +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} +- OUTPUT_STRIP_TRAILING_WHITESPACE) +-if(NOT ${setup} EQUAL 0) +- message(FATAL_ERROR " Failed to run setup_git.py: ${setup}; ${error}") +-endif() ++#execute_process(COMMAND python setup_git.py ++# RESULT_VARIABLE setup ++# OUTPUT_VARIABLE toutput ++# ERROR_VARIABLE error ++# WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} ++# OUTPUT_STRIP_TRAILING_WHITESPACE) ++#if(NOT ${setup} EQUAL 0) ++# message(FATAL_ERROR " Failed to run setup_git.py: ${setup}; ${error}") ++#endif() + + set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_modules) + +@@ -140,12 +140,12 @@ else() + endif() + + +-add_subdirectory(swig) ++#add_subdirectory(swig) + +-add_subdirectory(test) +-add_subdirectory(examples) +-add_subdirectory(benchmark) +-add_subdirectory(doc) ++#add_subdirectory(test) ++#add_subdirectory(examples) ++#add_subdirectory(benchmark) ++#add_subdirectory(doc) + + add_custom_target(RMF DEPENDS ${RMF_BINS} ${RMF_SWIG} ${RMF_TESTS} ${RMF_VMD} RMF-decorators) + set_property(TARGET "RMF" PROPERTY FOLDER "RMF") Added: head/science/rmf/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rmf/pkg-descr Fri Jun 29 09:04:22 2018 (r473535) @@ -0,0 +1,6 @@ +The library provides support for the Rich Molecular Format (RMF) file format for +storing hierarchical molecular data (such as atomic or coarse grained +representations of proteins), along with markup, including geometry and score +data. + +WWW: https://integrativemodeling.org/rmf/ Added: head/science/rmf/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rmf/pkg-plist Fri Jun 29 09:04:22 2018 (r473535) @@ -0,0 +1,98 @@ +bin/rmf3_dump +bin/rmf_cat +bin/rmf_frames +bin/rmf_info +bin/rmf_interpolate +bin/rmf_pdb +bin/rmf_show +bin/rmf_signature +bin/rmf_slice +bin/rmf_transform +bin/rmf_update +bin/rmf_validate +bin/rmf_xml +include/RMF/BufferConstHandle.h +include/RMF/BufferHandle.h +include/RMF/CoordinateTransformer.h +include/RMF/Decorator.h +include/RMF/Enum.h +include/RMF/FileConstHandle.h +include/RMF/FileHandle.h +include/RMF/HDF5.h +include/RMF/HDF5/ConstAttributes.h +include/RMF/HDF5/ConstDataSetD.h +include/RMF/HDF5/ConstFile.h +include/RMF/HDF5/ConstGroup.h +include/RMF/HDF5/DataSetAccessPropertiesD.h +include/RMF/HDF5/DataSetCreationPropertiesD.h +include/RMF/HDF5/DataSetD.h +include/RMF/HDF5/DataSetIndexD.h +include/RMF/HDF5/File.h +include/RMF/HDF5/Group.h +include/RMF/HDF5/MutableAttributes.h +include/RMF/HDF5/Object.h +include/RMF/HDF5/handle.h +include/RMF/HDF5/infrastructure_macros.h +include/RMF/HDF5/internal/types.h +include/RMF/HDF5/types.h +include/RMF/ID.h +include/RMF/Label.h +include/RMF/NodeConstHandle.h +include/RMF/NodeHandle.h +include/RMF/Nullable.h +include/RMF/RestoreCurrentFrame.h +include/RMF/SetCurrentFrame.h +include/RMF/TraverseHelper.h +include/RMF/Vector.h +include/RMF/compiler_macros.h +include/RMF/config.h +include/RMF/constants.h +include/RMF/decorator/alias.h +include/RMF/decorator/alternatives.h +include/RMF/decorator/bond.h +include/RMF/decorator/external.h +include/RMF/decorator/feature.h +include/RMF/decorator/labels.h +include/RMF/decorator/physics.h +include/RMF/decorator/provenance.h +include/RMF/decorator/publication.h +include/RMF/decorator/reference.h +include/RMF/decorator/representation.h +include/RMF/decorator/sequence.h +include/RMF/decorator/shape.h +include/RMF/decorators.h +include/RMF/enums.h +include/RMF/exceptions.h +include/RMF/info.h +include/RMF/infrastructure_macros.h +include/RMF/internal/SharedData.h +include/RMF/internal/SharedDataCategory.h +include/RMF/internal/SharedDataData.h +include/RMF/internal/SharedDataData_impl.h +include/RMF/internal/SharedDataFile.h +include/RMF/internal/SharedDataFrames.h +include/RMF/internal/SharedDataHierarchy.h +include/RMF/internal/SharedDataKeys.h +include/RMF/internal/SharedDataUserData.h +include/RMF/internal/SharedData_impl.h +include/RMF/internal/Transform.h +include/RMF/internal/errors.h +include/RMF/internal/hash.h +include/RMF/internal/irange.h +include/RMF/internal/large_set_map.h +include/RMF/internal/paths.h +include/RMF/internal/shared_data_factories.h +include/RMF/internal/shared_data_ranges.h +include/RMF/internal/small_set_map.h +include/RMF/internal/swig_helpers.h +include/RMF/internal/use.h +include/RMF/keys.h +include/RMF/log.h +include/RMF/names.h +include/RMF/show_hierarchy.h +include/RMF/signature.h +include/RMF/traits.h +include/RMF/types.h +include/RMF/utility.h +include/RMF/validate.h +lib/libRMF.so
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