Merge remote-tracking branch 'origin/develop' into trunk

CMakeLists.txt

@@ -27,11 +27,12 @@ cmake_minimum_required(VERSION 3.23)
 # set the project name
 project(
 	libcifpp
-	VERSION 7.0.4
+	VERSION 7.0.5
 	LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
+include(FindAtomic)
 include(CheckFunctionExists)
 include(CheckIncludeFiles)
 include(CheckLibraryExists)
@@ -41,8 +42,6 @@ include(GenerateExportHeader)
 include(CTest)
 include(FetchContent)
 
-message(STATUS "DESTDIR is '${DESTDIR}'")
-
 # When building with ninja-multiconfig, build both debug and release by default
 if(CMAKE_GENERATOR STREQUAL "Ninja Multi-Config")
 	set(CMAKE_CROSS_CONFIGS "Debug;Release")
@@ -188,10 +187,6 @@ if(GXX_LIBSTDCPP)
 	endif()
 endif()
 
-set(CMAKE_THREAD_PREFER_PTHREAD)
-set(THREADS_PREFER_PTHREAD_FLAG)
-find_package(Threads)
-
 if(MSVC)
 	# Avoid linking the shared library of zlib Search ZLIB_ROOT first if it is
 	# set.
@@ -221,6 +216,7 @@ if(MSVC)
 endif()
 
 find_package(ZLIB QUIET)
+find_package(Threads)
 
 if(NOT ZLIB_FOUND)
 	message(FATAL_ERROR "The zlib development files were not found you this system, please install them and try again (hint: on debian/ubuntu use apt-get install zlib1g-dev)")
@@ -260,6 +256,8 @@ if(CIFPP_RECREATE_SYMOP_DATA)
 	add_executable(symop-map-generator
 		"${CMAKE_CURRENT_SOURCE_DIR}/src/symop-map-generator.cpp")
 
+	target_compile_features(symop-map-generator PUBLIC cxx_std_20)
+
 	add_custom_command(
 		OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/src/symop_table_data.hpp
 		COMMAND
@@ -331,7 +329,7 @@ set(project_headers
 	include/cif++/validate.hpp
 )
 
-add_library(cifpp STATIC)
+add_library(cifpp)
 add_library(cifpp::cifpp ALIAS cifpp)
 
 target_sources(cifpp
@@ -371,7 +369,7 @@ target_include_directories(
 	"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
 	PRIVATE "${BOOST_REGEX_INCLUDE_DIR}" "${EIGEN_INCLUDE_DIR}")
 
-target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB)
+target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB std::atomic)
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 	target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -444,6 +442,10 @@ if(CIFPP_DATA_DIR)
 	target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
 endif()
 
+if(NOT PROJECT_IS_TOP_LEVEL)
+	set(CIFPP_SHARE_DIR ${CIFPP_DATA_DIR} PARENT_SCOPE)
+endif()
+
 if(UNIX AND NOT BUILD_FOR_CCP4)
 	if("${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local")
 		set(CIFPP_CACHE_DIR
@@ -464,75 +466,72 @@ else()
 	unset(CIFPP_CACHE_DIR)
 endif()
 
-# Avoid full installation in case we are not the top level target
-if(PROJECT_IS_TOP_LEVEL OR BUILD_FOR_CCP4)
-	# Install rules
-	install(TARGETS cifpp
-		EXPORT cifpp
-		FILE_SET cifpp_headers DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+# Install rules
+install(TARGETS cifpp
+	EXPORT cifpp
+	FILE_SET cifpp_headers DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 
-	if(MSVC AND BUILD_SHARED_LIBS)
-		install(
-			FILES $<TARGET_PDB_FILE:cifpp>
-			DESTINATION ${CMAKE_INSTALL_LIBDIR}
-			OPTIONAL)
-	endif()
+if(MSVC AND BUILD_SHARED_LIBS)
+	install(
+		FILES $<TARGET_PDB_FILE:cifpp>
+		DESTINATION ${CMAKE_INSTALL_LIBDIR}
+		OPTIONAL)
+endif()
 
-	# Clean up old config files (with old names)
-	file(GLOB OLD_CONFIG_FILES
-		${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppConfig*.cmake
-		${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppTargets*.cmake)
+# Clean up old config files (with old names)
+file(GLOB OLD_CONFIG_FILES
+	${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppConfig*.cmake
+	${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppTargets*.cmake)
 
-	if(OLD_CONFIG_FILES)
-		message(
-			STATUS "Installation will remove old config files: ${OLD_CONFIG_FILES}")
-		install(CODE "file(REMOVE ${OLD_CONFIG_FILES})")
-	endif()
+if(OLD_CONFIG_FILES)
+	message(
+		STATUS "Installation will remove old config files: ${OLD_CONFIG_FILES}")
+	install(CODE "file(REMOVE ${OLD_CONFIG_FILES})")
+endif()
 
-	install(EXPORT cifpp
-		NAMESPACE cifpp::
-		FILE "cifpp-targets.cmake"
-		DESTINATION lib/cmake/cifpp)
+install(EXPORT cifpp
+	NAMESPACE cifpp::
+	FILE "cifpp-targets.cmake"
+	DESTINATION lib/cmake/cifpp)
 
-	if(CIFPP_DATA_DIR AND CIFPP_DOWNLOAD_CCD)
-		install(
-			FILES ${CMAKE_CURRENT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
-			${CMAKE_CURRENT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
-			${CMAKE_CURRENT_SOURCE_DIR}/rsrc/mmcif_ma.dic ${COMPONENTS_CIF}
-			DESTINATION ${CMAKE_INSTALL_DATADIR}/libcifpp)
-	endif()
+install(
+	FILES ${CMAKE_CURRENT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
+	${CMAKE_CURRENT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
+	${CMAKE_CURRENT_SOURCE_DIR}/rsrc/mmcif_ma.dic
+	DESTINATION ${CMAKE_INSTALL_DATADIR}/libcifpp)
+
+if(CIFPP_DATA_DIR AND CIFPP_DOWNLOAD_CCD)
+	install(FILES ${COMPONENTS_CIF}
+		DESTINATION ${CMAKE_INSTALL_DATADIR}/libcifpp)
+endif()
 
-	set(CONFIG_TEMPLATE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/cmake/cifpp-config.cmake.in)
+set(CONFIG_TEMPLATE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/cmake/cifpp-config.cmake.in)
 
-	configure_package_config_file(
-		${CONFIG_TEMPLATE_FILE} ${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake
-		INSTALL_DESTINATION lib/cmake/cifpp
-		PATH_VARS CIFPP_DATA_DIR)
+configure_package_config_file(
+	${CONFIG_TEMPLATE_FILE} ${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake
+	INSTALL_DESTINATION lib/cmake/cifpp
+	PATH_VARS CIFPP_DATA_DIR)
 
-	install(
-		FILES "${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake"
-		"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
-		DESTINATION lib/cmake/cifpp)
-
-	set_target_properties(
-		cifpp
-		PROPERTIES VERSION ${PROJECT_VERSION}
-		SOVERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}"
-		INTERFACE_cifpp_MAJOR_VERSION ${PROJECT_VERSION_MAJOR})
-
-	set_property(
-		TARGET cifpp
-		APPEND
-		PROPERTY COMPATIBLE_INTERFACE_STRING cifpp_MAJOR_VERSION)
-
-	write_basic_package_version_file(
-		"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
-		VERSION ${PROJECT_VERSION}
-		COMPATIBILITY AnyNewerVersion)
-else()
-	# Set this variable so that consumers can find the files in rsrc
-	set(CIFPP_SHARE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/rsrc PARENT_SCOPE)
-endif()
+install(
+	FILES "${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake"
+	"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
+	DESTINATION lib/cmake/cifpp)
+
+set_target_properties(
+	cifpp
+	PROPERTIES VERSION ${PROJECT_VERSION}
+	SOVERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}"
+	INTERFACE_cifpp_MAJOR_VERSION ${PROJECT_VERSION_MAJOR})
+
+set_property(
+	TARGET cifpp
+	APPEND
+	PROPERTY COMPATIBLE_INTERFACE_STRING cifpp_MAJOR_VERSION)
+
+write_basic_package_version_file(
+	"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
+	VERSION ${PROJECT_VERSION}
+	COMPATIBILITY AnyNewerVersion)
 
 if(BUILD_TESTING)
 	add_subdirectory(test)

README.md

@@ -52,7 +52,7 @@ int main(int argc, char *argv[])
 
     if (file.empty())
     {
-        std::cerr << "Empty file" << std::endl;
+        std::cerr << "Empty file\n";
         exit(1);
     }
 
@@ -66,8 +66,8 @@ int main(int argc, char *argv[])
     auto n = atom_site.count(cif::key("label_atom_id") == "OXT");
 
     std::cout << "File contains " << atom_site.size() << " atoms of which "
-              << n << (n == 1 ? " is" : " are") << " OXT" << std::endl
-              << "residues with an OXT are:" << std::endl;
+              << n << (n == 1 ? " is" : " are") << " OXT\n"
+              << "residues with an OXT are:\n";
 
     // Loop over all atoms with atom-id "OXT" and print out some info.
     // That info is extracted using structured binding in C++
@@ -76,7 +76,7 @@ int main(int argc, char *argv[])
                 cif::key("label_atom_id") == "OXT",
                 "label_asym_id", "label_comp_id", "label_seq_id"))
     {
-        std::cout << asym << ' ' << comp << ' ' << seqnr << std::endl;
+        std::cout << asym << ' ' << comp << ' ' << seqnr << '\n';
     }
 
     return 0;

changelog

@@ -1,3 +1,6 @@
+Version 7.0.5
+- Fix case where category index was not updated for updated value
+
 Version 7.0.4
 - Do not install headers and library in case we're not the top project
 

cmake/FindAtomic.cmake

@@ -0,0 +1,63 @@
+# Simple check to see if we need a library for std::atomic
+
+if(TARGET std::atomic)
+	return()
+endif()
+
+cmake_minimum_required(VERSION 3.10)
+
+include(CMakePushCheckState)
+include(CheckIncludeFileCXX)
+include(CheckCXXSourceRuns)
+
+cmake_push_check_state()
+
+check_include_file_cxx("atomic" _CXX_ATOMIC_HAVE_HEADER)
+mark_as_advanced(_CXX_ATOMIC_HAVE_HEADER)
+
+set(code [[
+#include <atomic>
+int main(int argc, char** argv) {
+  std::atomic<long long> s;
+  ++s;
+  return 0;
+}
+]])
+
+check_cxx_source_runs("${code}" _CXX_ATOMIC_BUILTIN)
+
+if(_CXX_ATOMIC_BUILTIN)
+	set(_found 1)
+else()
+  list(APPEND CMAKE_REQUIRED_LIBRARIES atomic)
+  list(APPEND FOLLY_LINK_LIBRARIES atomic)
+
+  check_cxx_source_runs("${code}" _CXX_ATOMIC_LIB_NEEDED)
+  if (NOT _CXX_ATOMIC_LIB_NEEDED)
+    message(FATAL_ERROR "unable to link C++ std::atomic code: you may need \
+      to install GNU libatomic")
+  else()
+	set(_found 1)
+  endif()
+endif()
+
+if(_found)
+	add_library(std::atomic INTERFACE IMPORTED)
+	set_property(TARGET std::atomic APPEND PROPERTY INTERFACE_COMPILE_FEATURES cxx_std_14)
+
+	if(_CXX_ATOMIC_BUILTIN)
+		# Nothing to add...
+	elseif(_CXX_ATOMIC_LIB_NEEDED)
+		set_target_properties(std::atomic PROPERTIES IMPORTED_LIBNAME atomic)
+		set(STDCPPATOMIC_LIBRARY atomic)
+	endif()
+endif()
+
+cmake_pop_check_state()
+
+set(Atomic_FOUND ${_found} CACHE BOOL "TRUE if we can run a program using std::atomic" FORCE)
+mark_as_advanced(Atomic_FOUND)
+
+if(Atomic_FIND_REQUIRED AND NOT Atomic_FOUND)
+    message(FATAL_ERROR "Cannot run simple program using std::atomic")
+endif()

examples/example.cpp

@@ -13,7 +13,7 @@ int main(int argc, char *argv[])
 		exit(1);
 	}
 
-	cif::file file = cif::pdb::read(argv[1]);
+	cif::file file(argv[1]);
 
 	if (file.empty())
 	{

include/cif++/compound.hpp

@@ -138,7 +138,7 @@ struct compound_bond
 /// This information is derived from the CDD by default.
 ///
 /// To create compounds, you use the factory method. You can add your own
-/// compound definitions by calling the addExtraComponents function and
+/// compound definitions by calling the push_dictionary function and
 /// pass it a valid CCD formatted file.
 
 class compound

include/cif++/condition.hpp

@@ -1284,6 +1284,19 @@ condition operator==(const key &key, const std::optional<T> &v)
 		return condition(new detail::key_is_empty_condition_impl(key.m_item_name));
 }
 
+/**
+ * @brief Create a condition to search any item for a value @a v if @a v contains a value
+ * compare to null if not.
+ */
+template <typename T>
+condition operator!=(const key &key, const std::optional<T> &v)
+{
+	if (v.has_value())
+		return condition(new detail::not_condition_impl(condition(new detail::key_equals_condition_impl({ key.m_item_name, *v }))));
+	else
+		return condition(new detail::not_condition_impl(condition(new detail::key_is_empty_condition_impl(key.m_item_name))));
+}
+
 /**
  * @brief Operator to create a boolean opposite of the condition in @a rhs
  */

include/cif++/item.hpp

@@ -378,7 +378,7 @@ struct item_handle
 	template <typename T>
 	item_handle &operator=(T &&value)
 	{
-		assign_value(item{ "", std::move(value) }.value());
+		assign_value(item{ "", std::forward<T>(value) }.value());
 		return *this;
 	}