science/{,py-}gemmi: update 0.6.3 → 0.6.4
Reported by: portscout
This commit is contained in:
Yuri Victorovich
parent
ba33e2445b
commit
ce82996724
@ -1,6 +1,6 @@
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PORTNAME= gemmi
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DISTVERSIONPREFIX= v
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DISTVERSION= 0.6.3
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DISTVERSION= 0.6.4
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CATEGORIES= science # chemistry
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MAINTAINER= yuri@FreeBSD.org
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@ -16,6 +16,7 @@ USE_GITHUB= yes
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GH_ACCOUNT= project-gemmi
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CMAKE_ON= BUILD_SHARED_LIBS
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CMAKE_ARGS= -DCMAKE_CXX_VISIBILITY_PRESET=default # for the Python extension science/py-gemmi to see all symbols
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CMAKE_TESTING_TARGET= check
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OPTIONS_DEFINE= FORTRAN
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@ -1,3 +1,3 @@
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TIMESTAMP = 1694327240
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SHA256 (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = d7fa5e2a96f2093900a8ceaf835d2761562b5c42403e3f4cc98d32bb94f6a091
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SIZE (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = 1756098
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TIMESTAMP = 1702577537
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SHA256 (project-gemmi-gemmi-v0.6.4_GH0.tar.gz) = 507eea6ea112e2b142cc3dfa7de20c25e9f34c76ef77ef3caabfaf94d3657cb3
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SIZE (project-gemmi-gemmi-v0.6.4_GH0.tar.gz) = 1778062
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@ -77,6 +77,7 @@ include/gemmi/scaling.hpp
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include/gemmi/select.hpp
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include/gemmi/seqalign.hpp
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include/gemmi/seqid.hpp
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include/gemmi/seqtools.hpp
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include/gemmi/sfcalc.hpp
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include/gemmi/small.hpp
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include/gemmi/smcif.hpp
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@ -1,6 +1,6 @@
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PORTNAME= gemmi
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DISTVERSIONPREFIX= v
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DISTVERSION= 0.6.3
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DISTVERSION= 0.6.4
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CATEGORIES= science python
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PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
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@ -16,6 +16,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \
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pybind11>=2.6:devel/pybind11
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LIB_DEPENDS= libgemmi_cpp.so:science/gemmi
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TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR}
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USES= cmake compiler:c++20-lang localbase:ldflags python
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USE_PYTHON= flavors
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@ -32,7 +33,7 @@ TEST_WRKSRC= ${BUILD_WRKSRC}/tests
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PLIST_SUB= VER=${PORTVERSION}
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do-test:
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do-test: # 1 test fails, see https://github.com/project-gemmi/gemmi/issues/291
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@cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -v tests/
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.include <bsd.port.mk>
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@ -1,3 +1,3 @@
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TIMESTAMP = 1694328516
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SHA256 (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = d7fa5e2a96f2093900a8ceaf835d2761562b5c42403e3f4cc98d32bb94f6a091
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SIZE (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = 1756098
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TIMESTAMP = 1702578897
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SHA256 (project-gemmi-gemmi-v0.6.4_GH0.tar.gz) = 507eea6ea112e2b142cc3dfa7de20c25e9f34c76ef77ef3caabfaf94d3657cb3
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SIZE (project-gemmi-gemmi-v0.6.4_GH0.tar.gz) = 1778062
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@ -1,62 +1,107 @@
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--- CMakeLists.txt.orig 2023-09-07 09:12:22 UTC
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--- CMakeLists.txt.orig 2023-12-13 10:39:37 UTC
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+++ CMakeLists.txt
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@@ -187,21 +187,22 @@ if (GEMMI_VERSION_INFO)
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target_compile_definitions(options PRIVATE GEMMI_VERSION_INFO=${GEMMI_VERSION_INFO})
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endif()
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@@ -6,7 +6,7 @@ file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/include/gemm
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string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-dev)?\"" "\\1"
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gemmi_version_str ${gemmi_version_line})
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-project(gemmi LANGUAGES C CXX VERSION ${gemmi_version_str})
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+project(gemmi_python LANGUAGES C CXX VERSION ${gemmi_version_str})
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message(STATUS "Gemmi version ${PROJECT_VERSION}")
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include(GNUInstallDirs) # for CMAKE_INSTALL_LIBDIR, etc
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@@ -176,37 +176,39 @@ endif()
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# target_link_libraries(fgemmi PRIVATE cgemmi)
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#endif()
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-add_library(gemmi_headers INTERFACE)
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-add_library(gemmi::headers ALIAS gemmi_headers)
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-target_include_directories(gemmi_headers INTERFACE
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- "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
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- "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>")
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-target_compile_features(gemmi_headers INTERFACE cxx_std_11)
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-set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers)
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+#add_library(gemmi_headers INTERFACE)
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+#add_library(gemmi::headers ALIAS gemmi_headers)
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+#target_include_directories(gemmi_headers INTERFACE
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+# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
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+# "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>")
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+#target_compile_features(gemmi_headers INTERFACE cxx_std_11)
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+#set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers)
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-add_library(gemmi_cpp
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- src/assembly.cpp src/calculate.cpp src/crd.cpp
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- src/align.cpp src/assembly.cpp src/calculate.cpp src/crd.cpp
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- src/ddl.cpp src/eig3.cpp
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- src/mmcif.cpp src/mmread_gz.cpp src/mtz.cpp src/mtz2cif.cpp
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- src/polyheur.cpp src/read_cif.cpp src/resinfo.cpp
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- src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp
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- src/to_pdb.cpp src/monlib.cpp src/topo.cpp src/xds_ascii.cpp)
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-add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp)
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-set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON)
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+#add_library(gemmi_cpp
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+# src/assembly.cpp src/calculate.cpp src/crd.cpp
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+# src/align.cpp src/assembly.cpp src/calculate.cpp src/crd.cpp
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+# src/ddl.cpp src/eig3.cpp
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+# src/mmcif.cpp src/mmread_gz.cpp src/mtz.cpp src/mtz2cif.cpp
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+# src/polyheur.cpp src/read_cif.cpp src/resinfo.cpp
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+# src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp
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+# src/to_pdb.cpp src/monlib.cpp src/topo.cpp src/xds_ascii.cpp)
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+#add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp)
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+#set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON)
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#set_property(TARGET gemmi_cpp PROPERTY CXX_VISIBILITY_PRESET hidden)
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-target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD)
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-target_include_directories(gemmi_cpp PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party")
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+#target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD)
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+#target_include_directories(gemmi_cpp PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party")
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-if (BUILD_SHARED_LIBS)
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- target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED)
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-endif()
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-target_link_libraries(gemmi_cpp PUBLIC gemmi_headers)
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-support_gz(gemmi_cpp)
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+#target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD)
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+#if (BUILD_SHARED_LIBS)
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+# target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED)
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+#endif()
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+#target_link_libraries(gemmi_cpp PUBLIC gemmi_headers)
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+#support_gz(gemmi_cpp)
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+find_package(gemmi REQUIRED)
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+
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### programs from prog/ ###
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# Gemmi subcommands compiled as individual binaries.
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# Not built by default and used mostly for testing.
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@@ -210,7 +211,7 @@ function(add_single_prog target)
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add_library(options OBJECT prog/options.cpp)
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-target_link_libraries(options PUBLIC gemmi_headers)
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+#target_link_libraries(options PUBLIC gemmi_headers)
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target_include_directories(options PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/third_party")
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if (GEMMI_VERSION_INFO)
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target_compile_definitions(options PRIVATE GEMMI_VERSION_INFO=${GEMMI_VERSION_INFO})
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@@ -218,11 +220,11 @@ function(add_single_prog target)
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cmake_parse_arguments(arg "NOLIB;GZ" "ADD_SRC" "" ${ARGN})
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add_executable(gemmi-${target} EXCLUDE_FROM_ALL prog/${target}.cpp ${arg_ADD_SRC}
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$<TARGET_OBJECTS:options>)
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if (NOT arg_NOLIB)
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- if (arg_NOLIB)
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- target_link_libraries(gemmi-${target} PRIVATE gemmi_headers)
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- else()
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- target_link_libraries(gemmi-${target} PRIVATE gemmi_cpp)
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+ #target_link_libraries(gemmi-${target} PRIVATE gemmi_cpp)
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endif()
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- endif()
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+ #if (arg_NOLIB)
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+ # target_link_libraries(gemmi-${target} PRIVATE gemmi_headers)
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+ #else()
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+ # target_link_libraries(gemmi-${target} PRIVATE gemmi_cpp)
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+ #endif()
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target_include_directories(gemmi-${target} PRIVATE
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"${CMAKE_CURRENT_SOURCE_DIR}/third_party")
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if (arg_GZ)
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support_gz(gemmi-${target})
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@@ -264,7 +265,7 @@ add_executable(gemmi_prog
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prog/validate.cpp prog/validate_mon.cpp prog/wcn.cpp
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@@ -279,7 +281,7 @@ add_executable(gemmi_prog
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prog/xds2mtz.cpp
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$<TARGET_OBJECTS:options>)
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add_executable(gemmi::prog ALIAS gemmi_prog)
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-target_link_libraries(gemmi_prog PRIVATE gemmi_cpp)
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+#target_link_libraries(gemmi_prog PRIVATE gemmi_cpp)
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+target_link_libraries(gemmi_prog PRIVATE gemmi)
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support_gz(gemmi_prog)
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target_include_directories(gemmi_prog PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party")
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target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1)
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set_property(TARGET gemmi_prog PROPERTY OUTPUT_NAME gemmi)
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@@ -304,10 +305,10 @@ add_executable(doc_example EXCLUDE_FROM_ALL
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docs/code/cell.cpp src/resinfo.cpp)
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@@ -324,10 +326,10 @@ target_link_libraries(doc_example PRIVATE gemmi_header
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add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp)
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target_link_libraries(doc_example2 PRIVATE gemmi_headers)
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add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/maybegz.cpp docs/code/mutate.cpp)
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-target_link_libraries(doc_maybegz PRIVATE gemmi_cpp)
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+target_link_libraries(doc_maybegz PRIVATE gemmi)
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@ -67,7 +112,7 @@
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support_gz(doc_newmtz)
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# always compile these tests with assertions enabled
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@@ -316,7 +317,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel")
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@@ -336,7 +338,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel")
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endif()
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add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp)
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@ -76,7 +121,7 @@
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support_gz(test_disulf)
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# auth_label requires <experimental/filesystem> and -lstdc++fs
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@@ -327,7 +328,7 @@ endif()
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@@ -348,7 +350,7 @@ endif()
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support_gz(auth_label)
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add_executable(check_conn EXCLUDE_FROM_ALL examples/check_conn.cpp)
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@ -85,66 +130,56 @@
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enable_testing()
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@@ -364,7 +365,7 @@ if (benchmark_FOUND)
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foreach(b stoi elem mod niggli pdb resinfo round sym)
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@@ -385,7 +387,7 @@ if (benchmark_FOUND)
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foreach(b stoi elem mod niggli pdb resinfo round sym writecif)
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add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp)
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if (b MATCHES "resinfo|pdb")
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if (b MATCHES "resinfo|pdb|writecif")
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- target_link_libraries(${b}-bm PRIVATE gemmi_cpp)
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+ target_link_libraries(${b}-bm PRIVATE gemmi)
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endif()
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target_link_libraries(${b}-bm PRIVATE benchmark::benchmark)
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target_link_libraries(${b}-bm PRIVATE gemmi_headers benchmark::benchmark)
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set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY
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@@ -392,8 +393,8 @@ if (USE_PYTHON)
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@@ -421,9 +423,8 @@ if (USE_PYTHON)
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python/mtz.cpp python/read.cpp python/recgrid.cpp
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python/scaling.cpp python/search.cpp
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python/sf.cpp python/sym.cpp python/topo.cpp
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- python/unitcell.cpp python/write.cpp
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- $<TARGET_OBJECTS:gemmi_cpp>)
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- target_link_libraries(gemmi_py PRIVATE gemmi_headers)
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+ python/unitcell.cpp python/write.cpp)
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+ target_link_libraries(gemmi_py PRIVATE gemmi::gemmi_cpp)
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set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi)
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if(CMAKE_CXX_FLAGS MATCHES "-Wshadow")
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target_compile_options(gemmi_py PRIVATE "-Wno-shadow")
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@@ -416,21 +417,21 @@ write_basic_package_version_file(gemmi-config-version.
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COMPATIBILITY AnyNewerVersion)
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# In CMake 3.23 we'll be able to use FILE_SET to install the headers
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-install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
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+#install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
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if (BUILD_GEMMI_PROGRAM)
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@@ -450,19 +451,19 @@ if (BUILD_GEMMI_PROGRAM)
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install(TARGETS gemmi_prog EXPORT GemmiTargets)
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endif()
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-install(TARGETS gemmi_cpp
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- EXPORT GemmiTargets
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- INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
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+#install(TARGETS gemmi_cpp
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+# EXPORT GemmiTargets
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+# INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
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-install(EXPORT GemmiTargets FILE gemmi-targets.cmake NAMESPACE gemmi::
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-if (INSTALL_DEV_FILES)
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+#if (INSTALL_DEV_FILES)
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# In CMake 3.23 we'll be able to use FILE_SET to install the headers
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- install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
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- install(TARGETS gemmi_headers gemmi_cpp EXPORT GemmiTargets)
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- install(EXPORT GemmiTargets FILE gemmi-targets.cmake NAMESPACE gemmi::
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- DESTINATION "${GEMMI_INSTALL_CMAKEDIR}")
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-install(FILES
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- install(FILES
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- "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config.cmake"
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- "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config-version.cmake"
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- DESTINATION "${GEMMI_INSTALL_CMAKEDIR}")
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+#install(EXPORT GemmiTargets FILE gemmi-targets.cmake NAMESPACE gemmi::
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+# DESTINATION "${GEMMI_INSTALL_CMAKEDIR}")
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+#install(FILES
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+# "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config.cmake"
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+# "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config-version.cmake"
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+# DESTINATION "${GEMMI_INSTALL_CMAKEDIR}")
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-elseif (BUILD_SHARED_LIBS AND BUILD_GEMMI_PROGRAM)
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- install(TARGETS gemmi_cpp)
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-endif()
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+ #install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
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+ #install(TARGETS gemmi_headers gemmi_cpp EXPORT GemmiTargets)
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+ #install(EXPORT GemmiTargets FILE gemmi-targets.cmake NAMESPACE gemmi::
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+ # DESTINATION "${GEMMI_INSTALL_CMAKEDIR}")
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+ #install(FILES
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+ # "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config.cmake"
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+ # "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config-version.cmake"
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+ # DESTINATION "${GEMMI_INSTALL_CMAKEDIR}")
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+#elseif (BUILD_SHARED_LIBS AND BUILD_GEMMI_PROGRAM)
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+# install(TARGETS gemmi_cpp)
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+#endif()
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if (USE_PYTHON)
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if (DEFINED PYTHON_INSTALL_DIR)
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@@ -444,8 +445,8 @@ if (USE_PYTHON)
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# and don't respect CMAKE_INSTALL_PREFIX.
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# https://discourse.cmake.org/t/findpython3-how-to-specify-local-installation-directory-for-python-module/3580/5
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install(TARGETS gemmi_py DESTINATION "${Python_SITEARCH}")
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- install(DIRECTORY examples/ DESTINATION "${Python_SITELIB}/gemmi-examples"
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- FILES_MATCHING PATTERN "*.py")
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+ #install(DIRECTORY examples/ DESTINATION "${Python_SITELIB}/gemmi-examples"
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+ # FILES_MATCHING PATTERN "*.py")
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if (INSTALL_EGG_INFO)
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install(CODE
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"execute_process(COMMAND \"${Python_EXECUTABLE}\" setup.py install_egg_info --install-dir \"\$ENV{DESTDIR}${Python_SITELIB}\"
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@ -1,6 +1 @@
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%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/PKG-INFO
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%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/SOURCES.txt
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%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/dependency_links.txt
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%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/not-zip-safe
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%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/top_level.txt
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%%PYTHON_SITELIBDIR%%/gemmi%%PYTHON_EXT_SUFFIX%%.so
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