diff --git a/science/rmf/Makefile b/science/rmf/Makefile index 431a4b74a912..c76e625087b2 100644 --- a/science/rmf/Makefile +++ b/science/rmf/Makefile @@ -1,25 +1,32 @@ PORTNAME= rmf -DISTVERSION= 1.1 -PORTREVISION= 8 +DISTVERSION= 1.2 CATEGORIES= science graphics MAINTAINER= yuri@FreeBSD.org COMMENT= Library to support reading and writing of Rich Molecular Format files LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ libsz.so:science/szip USES= compiler:c++11-lang cmake python:build shebangfix +USE_LDCONFIG= yes + USE_GITHUB= yes GH_ACCOUNT= salilab -GH_TAGNAME= f917cf2 + SHEBANG_GLOB= *.py -USE_LDCONFIG= yes BINARY_ALIAS= python=${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} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ + ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test + .include diff --git a/science/rmf/distinfo b/science/rmf/distinfo index b71e79ddbf9f..f595de328afd 100644 --- a/science/rmf/distinfo +++ b/science/rmf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1535650020 -SHA256 (salilab-rmf-1.1-f917cf2_GH0.tar.gz) = 9c877539b8c7a6af38b3d7155522a90b16b3e28596ec27ac941c7f812f1a1c6f -SIZE (salilab-rmf-1.1-f917cf2_GH0.tar.gz) = 15087905 +TIMESTAMP = 1618991588 +SHA256 (salilab-rmf-1.2_GH0.tar.gz) = 72ee7c8083f1c1f089fda239b4e94297252149aafefdd71736ede04e00267420 +SIZE (salilab-rmf-1.2_GH0.tar.gz) = 15090975 diff --git a/science/rmf/files/patch-CMakeLists.txt b/science/rmf/files/patch-CMakeLists.txt index 6df7a51d65e3..71804333cac4 100644 --- a/science/rmf/files/patch-CMakeLists.txt +++ b/science/rmf/files/patch-CMakeLists.txt @@ -1,45 +1,46 @@ ---- CMakeLists.txt.orig 2018-06-15 00:56:51 UTC +--- CMakeLists.txt.orig 2021-04-19 19:25:22 UTC +++ CMakeLists.txt -@@ -4,15 +4,15 @@ project(RMF) - # needs to be in main CMakeLists.txt - enable_testing() +@@ -18,15 +18,15 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_S + include(cmake_modules/IMPFindPython.cmake) + imp_find_python() --execute_process(COMMAND python setup_git.py +-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 setup_git.py ++#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() - set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_modules) - -@@ -140,12 +140,12 @@ else() + # Don't deref quoted variables in if() + if(POLICY CMP0054) +@@ -168,12 +168,14 @@ else() endif() -add_subdirectory(swig) +#add_subdirectory(swig) --add_subdirectory(test) ++if (FREEBSD_BUILS_WITH_TESTS) + add_subdirectory(test) -add_subdirectory(examples) -add_subdirectory(benchmark) -add_subdirectory(doc) -+#add_subdirectory(test) ++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 0b784ecb1081..b923de1888ac 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 2019-10-16 16:05:15 UTC +--- src/hdf5_wrapper.cpp.orig 2021-04-19 19:25:22 UTC +++ src/hdf5_wrapper.cpp -@@ -138,7 +138,7 @@ hid_t get_parameters() { - RMF_HDF5_CALL(H5Pset_cache(plist, 0, 10000, 10000000, 0.0)); - #if defined(H5_VERS_MAJOR) && H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && \ - H5_VERS_RELEASE >= 6 +@@ -150,7 +150,7 @@ 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; } diff --git a/science/rmf/pkg-plist b/science/rmf/pkg-plist index b7db19bfa0ea..e07f57114647 100644 --- a/science/rmf/pkg-plist +++ b/science/rmf/pkg-plist @@ -1,98 +1,100 @@ 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.h 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/decorator/uncertainty.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