diff --git a/science/py-rmf/Makefile b/science/py-rmf/Makefile index dbe6e2950396..42945910e558 100644 --- a/science/py-rmf/Makefile +++ b/science/py-rmf/Makefile @@ -1,39 +1,40 @@ PORTNAME= rmf -DISTVERSION= 1.7.0 +DISTVERSION= 1.7.1 CATEGORIES= science graphics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library to support reading and writing of Rich Molecular Format files WWW= https://integrativemodeling.org/rmf/ \ https://github.com/salilab/rmf LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= swig:devel/swig LIB_DEPENDS= libRMF.so:science/rmf USES= cmake compiler:c++11-lang localbase:ldflags python shebangfix USE_PYTHON= flavors USE_GITHUB= yes GH_ACCOUNT= salilab SHEBANG_GLOB= *.py CMAKE_ARGS= -DCMAKE_INSTALL_PYTHONDIR:STRING=${PYTHON_SITELIBDIR} LDFLAGS+= -lRMF BINARY_ALIAS= python=${PYTHON_CMD} do-test: # the IMP_MEDIUM_TIMEOUT setting below is to prevent RMF-medium_test_backwards.py from timeing out, see https://github.com/salilab/rmf/issues/126#issuecomment-825145818 @${RM} ${WRKSRC}/test/*.cpp @cd ${BUILD_WRKSRC} && \ - ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DFREEBSD_BUILS_WITH_TESTS:BOOL=ON -DIMP_MEDIUM_TIMEOUT=1000000 ${CMAKE_SOURCE_PATH} && \ + ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DFREEBSD_BUILD_WITH_TESTS:BOOL=ON -DIMP_MEDIUM_TIMEOUT=1000000 ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test +# tests as of 1.7.1: all 49 tests passed .include diff --git a/science/py-rmf/distinfo b/science/py-rmf/distinfo index 12befb80dc94..bfafb42a1d6d 100644 --- a/science/py-rmf/distinfo +++ b/science/py-rmf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1733424482 -SHA256 (salilab-rmf-1.7.0_GH0.tar.gz) = 37997f189702b4705f69b2db5f64cef31cfa9ab9eb151dfc0457c72dba422345 -SIZE (salilab-rmf-1.7.0_GH0.tar.gz) = 15100498 +TIMESTAMP = 1779745644 +SHA256 (salilab-rmf-1.7.1_GH0.tar.gz) = 7f1b7babf687513966a9b3366b9c95dbcce14e1fe9fc22d8ff146f0c5681747f +SIZE (salilab-rmf-1.7.1_GH0.tar.gz) = 16476595 diff --git a/science/py-rmf/files/patch-CMakeLists.txt b/science/py-rmf/files/patch-CMakeLists.txt index 75845b666b0d..248ffabd885e 100644 --- a/science/py-rmf/files/patch-CMakeLists.txt +++ b/science/py-rmf/files/patch-CMakeLists.txt @@ -1,63 +1,63 @@ ---- CMakeLists.txt.orig 2021-04-19 19:25:22 UTC +--- CMakeLists.txt.orig 2026-04-29 23:05:31 UTC +++ CMakeLists.txt -@@ -18,15 +18,15 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_S +@@ -18,15 +18,15 @@ imp_find_python() include(cmake_modules/IMPFindPython.cmake) imp_find_python() -execute_process(COMMAND ${PYTHON_EXECUTABLE} 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_EXECUTABLE} 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}; ${error}") +#endif() # Don't deref quoted variables in if() if(POLICY CMP0054) -@@ -144,14 +144,14 @@ configure_file ( +@@ -159,14 +159,14 @@ configure_file ( "${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 -@@ -170,10 +170,12 @@ endif() +@@ -185,10 +185,12 @@ add_subdirectory(swig) add_subdirectory(swig) -+if (FREEBSD_BUILS_WITH_TESTS) ++if (FREEBSD_BUILD_WITH_TESTS) add_subdirectory(test) -add_subdirectory(examples) -add_subdirectory(benchmark) -add_subdirectory(doc) +endif() +#add_subdirectory(examples) +#add_subdirectory(benchmark) +#add_subdirectory(doc) add_custom_target(RMF DEPENDS ${RMF_BINS} ${RMF_SWIG} ${RMF_TESTS} ${RMF_VMD} RMF-decorators) set_property(TARGET "RMF" PROPERTY FOLDER "RMF") diff --git a/science/py-rmf/files/patch-swig_CMakeLists.txt b/science/py-rmf/files/patch-swig_CMakeLists.txt index 6a815d654e70..ae4a18bc7f19 100644 --- a/science/py-rmf/files/patch-swig_CMakeLists.txt +++ b/science/py-rmf/files/patch-swig_CMakeLists.txt @@ -1,37 +1,37 @@ ---- swig/CMakeLists.txt.orig 2021-04-19 19:25:22 UTC +--- swig/CMakeLists.txt.orig 2026-04-29 23:05:31 UTC +++ swig/CMakeLists.txt -@@ -43,7 +43,7 @@ set_target_properties("${SWIG_MODULE_RMF_REAL_NAME}" P +@@ -47,7 +47,7 @@ ELSE(WIN32) 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 ${CMAKE_INSTALL_PYTHONDIR}) -@@ -79,7 +79,7 @@ set_target_properties("${SWIG_MODULE_RMF_HDF5_REAL_NAM +@@ -83,7 +83,7 @@ set(RMF_SWIG _RMF CACHE INTERNAL "" FORCE) 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 -@@ -88,7 +88,7 @@ INSTALL(FILES "RMF.i" ${SWIG_INCLUDES} DESTINATION "${ +@@ -92,7 +92,7 @@ ELSE(WIN32) 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) -@@ -100,6 +100,6 @@ INSTALL(TARGETS ${SWIG_MODULE_RMF_HDF5_REAL_NAME} DEST +@@ -104,6 +104,6 @@ set(RMF_SWIG _RMF _RMF_HDF5 CACHE INTERNAL "" FORCE) INSTALL(FILES "${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() diff --git a/science/rmf/Makefile b/science/rmf/Makefile index c8519329efa7..e570872c0d19 100644 --- a/science/rmf/Makefile +++ b/science/rmf/Makefile @@ -1,36 +1,36 @@ PORTNAME= rmf -DISTVERSION= 1.7.0 -PORTREVISION= 3 +DISTVERSION= 1.7.1 CATEGORIES= science graphics MAINTAINER= yuri@FreeBSD.org COMMENT= Library to support reading and writing of Rich Molecular Format files WWW= https://integrativemodeling.org/rmf/ \ https://github.com/salilab/rmf LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libhdf5.so:science/hdf5 USES= compiler:c++17-lang cmake:testing localbase:ldflags python:build shebangfix USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= salilab SHEBANG_GLOB= *.py LDFLAGS+= -lhdf5 BINARY_ALIAS= python=${PYTHON_CMD} do-test: @${RM} ${WRKSRC}/test/*.py @cd ${BUILD_WRKSRC} && \ - ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DFREEBSD_BUILS_WITH_TESTS:BOOL=ON ${CMAKE_SOURCE_PATH} && \ + ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DFREEBSD_BUILD_WITH_TESTS:BOOL=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test +# tests as of 1.7.1: all 7 tests passed .include diff --git a/science/rmf/distinfo b/science/rmf/distinfo index 099386120e97..20f470768bb7 100644 --- a/science/rmf/distinfo +++ b/science/rmf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1733424309 -SHA256 (salilab-rmf-1.7.0_GH0.tar.gz) = 37997f189702b4705f69b2db5f64cef31cfa9ab9eb151dfc0457c72dba422345 -SIZE (salilab-rmf-1.7.0_GH0.tar.gz) = 15100498 +TIMESTAMP = 1779745618 +SHA256 (salilab-rmf-1.7.1_GH0.tar.gz) = 7f1b7babf687513966a9b3366b9c95dbcce14e1fe9fc22d8ff146f0c5681747f +SIZE (salilab-rmf-1.7.1_GH0.tar.gz) = 16476595 diff --git a/science/rmf/files/patch-CMakeLists.txt b/science/rmf/files/patch-CMakeLists.txt index 71804333cac4..129d31de527c 100644 --- a/science/rmf/files/patch-CMakeLists.txt +++ b/science/rmf/files/patch-CMakeLists.txt @@ -1,46 +1,46 @@ ---- CMakeLists.txt.orig 2021-04-19 19:25:22 UTC +--- CMakeLists.txt.orig 2026-04-29 23:05:31 UTC +++ CMakeLists.txt -@@ -18,15 +18,15 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_S +@@ -18,15 +18,15 @@ imp_find_python() include(cmake_modules/IMPFindPython.cmake) imp_find_python() -execute_process(COMMAND ${PYTHON_EXECUTABLE} 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_EXECUTABLE} 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() # Don't deref quoted variables in if() if(POLICY CMP0054) -@@ -168,12 +168,14 @@ else() +@@ -183,12 +183,14 @@ endif() endif() -add_subdirectory(swig) +#add_subdirectory(swig) -+if (FREEBSD_BUILS_WITH_TESTS) ++if (FREEBSD_BUILD_WITH_TESTS) add_subdirectory(test) -add_subdirectory(examples) -add_subdirectory(benchmark) -add_subdirectory(doc) +endif() +#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") diff --git a/science/rmf/files/patch-src-hdf5_wrapper.cpp b/science/rmf/files/patch-src-hdf5_wrapper.cpp index b923de1888ac..61df25760a02 100644 --- a/science/rmf/files/patch-src-hdf5_wrapper.cpp +++ b/science/rmf/files/patch-src-hdf5_wrapper.cpp @@ -1,11 +1,11 @@ ---- src/hdf5_wrapper.cpp.orig 2021-04-19 19:25:22 UTC +--- src/hdf5_wrapper.cpp.orig 2026-04-29 23:05:31 UTC +++ src/hdf5_wrapper.cpp -@@ -150,7 +150,7 @@ hid_t get_parameters() { +@@ -149,7 +149,7 @@ hid_t get_parameters() { RMF_HDF5_CALL(H5Pset_libver_bounds(plist, H5F_LIBVER_V18, H5F_LIBVER_LATEST)); #elif defined(H5_VERS_MAJOR) && \ H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8 && H5_VERS_RELEASE >= 6 - RMF_HDF5_CALL(H5Pset_libver_bounds(plist, H5F_LIBVER_18, H5F_LIBVER_LATEST)); + RMF_HDF5_CALL(H5Pset_libver_bounds(plist, H5F_LIBVER_V18, H5F_LIBVER_LATEST)); #endif return plist; }