Date: Sun, 1 Jul 2018 05:22:27 +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: r473652 - in head/science: . py-rmf py-rmf/files Message-ID: <201807010522.w615MRUx037578@repo.freebsd.org>
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Author: yuri Date: Sun Jul 1 05:22:27 2018 New Revision: 473652 URL: https://svnweb.freebsd.org/changeset/ports/473652 Log: New port: science/py-rmf: Library to support reading and writing of Rich Molecular Format files Added: head/science/py-rmf/ head/science/py-rmf/Makefile (contents, props changed) head/science/py-rmf/distinfo (contents, props changed) head/science/py-rmf/files/ head/science/py-rmf/files/patch-CMakeLists.txt (contents, props changed) head/science/py-rmf/files/patch-include_CMakeLists.txt (contents, props changed) head/science/py-rmf/files/patch-swig_CMakeLists.txt (contents, props changed) head/science/py-rmf/pkg-descr (contents, props changed) head/science/py-rmf/pkg-plist (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Sun Jul 1 03:25:51 2018 (r473651) +++ head/science/Makefile Sun Jul 1 05:22:27 2018 (r473652) @@ -196,6 +196,7 @@ SUBDIR += py-pyteomics.biolccc SUBDIR += py-qspin SUBDIR += py-quantities + SUBDIR += py-rmf SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-sparse Added: head/science/py-rmf/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-rmf/Makefile Sun Jul 1 05:22:27 2018 (r473652) @@ -0,0 +1,28 @@ +# $FreeBSD$ + +PORTNAME= rmf +DISTVERSION= g20180614 +CATEGORIES= science graphics +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Library to support reading and writing of Rich Molecular Format files + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/COPYING + +BUILD_DEPENDS= swig3.0:devel/swig30 +LIB_DEPENDS= libRMF.so:science/rmf + +USES= cmake:outsource python shebangfix +USE_GITHUB= yes +GH_ACCOUNT= salilab +GH_TAGNAME= f917cf2 +SHEBANG_GLOB= *.py +USE_PYTHON= flavors + +CMAKE_ARGS= -DCMAKE_INSTALL_PYTHONDIR:STRING=${PYTHON_SITELIBDIR} +BINARY_ALIAS= python=${PYTHON_CMD} +LDFLAGS+= -lRMF + +.include <bsd.port.mk> Added: head/science/py-rmf/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-rmf/distinfo Sun Jul 1 05:22:27 2018 (r473652) @@ -0,0 +1,3 @@ +TIMESTAMP = 1530396872 +SHA256 (salilab-rmf-g20180614-f917cf2_GH0.tar.gz) = 9c877539b8c7a6af38b3d7155522a90b16b3e28596ec27ac941c7f812f1a1c6f +SIZE (salilab-rmf-g20180614-f917cf2_GH0.tar.gz) = 15087905 Added: head/science/py-rmf/files/patch-CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-rmf/files/patch-CMakeLists.txt Sun Jul 1 05:22:27 2018 (r473652) @@ -0,0 +1,62 @@ +--- 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} ${PROJECT_SOURCE_DIR}/cmake_modules) + +@@ -116,14 +116,14 @@ configure_file ( + "${PROJECT_BINARY_DIR}/include/RMF/config.h" + ) + +-add_subdirectory(data) ++#add_subdirectory(data) + add_subdirectory(include) + +-add_subdirectory(src) +-add_subdirectory(bin) ++#add_subdirectory(src) ++#add_subdirectory(bin) + +-add_subdirectory(plugins/vmd/) +-add_subdirectory(plugins/pymol/) ++#add_subdirectory(plugins/vmd/) ++#add_subdirectory(plugins/pymol/) + + # swig support is a little broken + +@@ -142,10 +142,10 @@ endif() + + 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} ${RMF_VMD} RMF-decorators) + set_property(TARGET "RMF" PROPERTY FOLDER "RMF") Added: head/science/py-rmf/files/patch-include_CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-rmf/files/patch-include_CMakeLists.txt Sun Jul 1 05:22:27 2018 (r473652) @@ -0,0 +1,10 @@ +--- include/CMakeLists.txt.orig 2018-06-30 22:26:02 UTC ++++ include/CMakeLists.txt +@@ -16,5 +16,5 @@ add_custom_target(RMF-decorators ALL DEP + "${PROJECT_SOURCE_DIR}/tools/build/make_decorators.py") + set_property(TARGET "RMF-decorators" PROPERTY FOLDER "RMF") + +-INSTALL(DIRECTORY ${PROJECT_SOURCE_DIR}/include/RMF DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) +-INSTALL(DIRECTORY ${PROJECT_BINARY_DIR}/include/RMF DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) ++#INSTALL(DIRECTORY ${PROJECT_SOURCE_DIR}/include/RMF DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) ++#INSTALL(DIRECTORY ${PROJECT_BINARY_DIR}/include/RMF DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) Added: head/science/py-rmf/files/patch-swig_CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-rmf/files/patch-swig_CMakeLists.txt Sun Jul 1 05:22:27 2018 (r473652) @@ -0,0 +1,37 @@ +--- swig/CMakeLists.txt.orig 2018-06-15 00:56:51 UTC ++++ swig/CMakeLists.txt +@@ -59,7 +59,7 @@ set_target_properties("${SWIG_MODULE_RMF + IF(WIN32) + SWIG_LINK_LIBRARIES(RMF ${PYTHON_LIBRARIES} RMF-lib) + ELSE(WIN32) +- SWIG_LINK_LIBRARIES(RMF RMF-lib) ++ #SWIG_LINK_LIBRARIES(RMF RMF-lib) + ENDIF(WIN32) + + INSTALL(TARGETS ${SWIG_MODULE_RMF_REAL_NAME} DESTINATION ${CMAKE_INSTALL_PYTHONDIR}) +@@ -95,7 +95,7 @@ set_target_properties("${SWIG_MODULE_RMF + set(RMF_SWIG _RMF CACHE INTERNAL "" FORCE) + + +-INSTALL(FILES "RMF.i" ${SWIG_INCLUDES} DESTINATION "${CMAKE_INSTALL_SWIGDIR}") ++#INSTALL(FILES "RMF.i" ${SWIG_INCLUDES} DESTINATION "${CMAKE_INSTALL_SWIGDIR}") + + + # Don't link in libpython (that prevents the extension from being used in +@@ -104,7 +104,7 @@ INSTALL(FILES "RMF.i" ${SWIG_INCLUDES} D + IF(WIN32) + SWIG_LINK_LIBRARIES(RMF_HDF5 ${PYTHON_LIBRARIES} RMF-lib) + ELSE(WIN32) +- SWIG_LINK_LIBRARIES(RMF_HDF5 RMF-lib) ++ #SWIG_LINK_LIBRARIES(RMF_HDF5 RMF-lib) + ENDIF(WIN32) + # Apple linkers complain by default if there are undefined symbols + IF(APPLE) +@@ -116,6 +116,6 @@ INSTALL(TARGETS ${SWIG_MODULE_RMF_HDF5_R + INSTALL(FILES "${CMAKE_BINARY_DIR}/lib/RMF_HDF5.py" DESTINATION ${CMAKE_INSTALL_PYTHONDIR}) + + set(RMF_SWIG _RMF _RMF_HDF5 CACHE INTERNAL "" FORCE) +-INSTALL(FILES "RMF_HDF5.i" DESTINATION "${CMAKE_INSTALL_SWIGDIR}") ++#INSTALL(FILES "RMF_HDF5.i" DESTINATION "${CMAKE_INSTALL_SWIGDIR}") + + endif() Added: head/science/py-rmf/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-rmf/pkg-descr Sun Jul 1 05:22:27 2018 (r473652) @@ -0,0 +1,6 @@ +The Python binding for Rich Molecular Format (RMF) file format library +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/py-rmf/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-rmf/pkg-plist Sun Jul 1 05:22:27 2018 (r473652) @@ -0,0 +1,4 @@ +%%PYTHON_SITELIBDIR%%/RMF.py +%%PYTHON_SITELIBDIR%%/RMF_HDF5.py +%%PYTHON_SITELIBDIR%%/_RMF.so +%%PYTHON_SITELIBDIR%%/_RMF_HDF5.so
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