update changelog

* Use `find_package` for FastFloat prior to `FetchContent_Declare`

* Convert space to tab

CMakeLists.txt

@@ -32,7 +32,7 @@ endif()
 # set the project name
 project(
 	libcifpp
-	VERSION 9.0.5
+	VERSION 9.0.6
 	LANGUAGES CXX C)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
@@ -43,6 +43,7 @@ include(GenerateExportHeader)
 include(CTest)
 include(ExternalProject)
 include(FetchContent)
+include(VersionString)
 
 # When building with ninja-multiconfig, build both debug and release by default
 if(CMAKE_GENERATOR STREQUAL "Ninja Multi-Config")
@@ -129,13 +130,6 @@ if(MSVC)
 	# make msvc standards compliant...
 	add_compile_options(/permissive- /bigobj)
 	add_link_options(/NODEFAULTLIB:library)
-
-	# This is dubious...
-	if(BUILD_SHARED_LIBS)
-		set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>DLL")
-	else()
-		set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
-	endif()
 endif()
 
 # Libraries
@@ -170,14 +164,21 @@ endif()
 
 # Using fast_float for float parsing, but only if needed
 try_compile(STD_CHARCONV_COMPILING
-	SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/cmake/test-charconv.cpp)
+	SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/cmake/test-charconv.cpp
+	CXX_STANDARD 20
+	CXX_STANDARD_REQUIRED ON)
 
 if(NOT STD_CHARCONV_COMPILING)
 	message(NOTICE "libcifpp: Using fast_float for std::from_chars")
-	FetchContent_Declare(fastfloat
-		GIT_REPOSITORY "https://github.com/fastfloat/fast_float"
-		GIT_TAG v8.0.2)
-	FetchContent_MakeAvailable(fastfloat)
+	find_package(FastFloat 8.0 QUIET CONFIG)
+	if(NOT FastFloat_FOUND)
+		message(STATUS "FastFloat not found in system, fetching from GitHub")
+		FetchContent_Declare(fastfloat
+			GIT_REPOSITORY "https://github.com/fastfloat/fast_float"
+			GIT_TAG v8.0.2
+			EXCLUDE_FROM_ALL)
+		FetchContent_MakeAvailable(fastfloat)
+	endif()
 endif()
 
 find_package(Threads)
@@ -239,6 +240,9 @@ if(CIFPP_RECREATE_SYMOP_DATA)
 		"$ENV{CLIBD}/symop.lib")
 endif()
 
+# Create a revision file, containing the current git version info
+write_version_header("${CMAKE_CURRENT_SOURCE_DIR}/src/" LIB_NAME "LibCIFPP")
+
 # Sources
 set(project_sources
 	${CMAKE_CURRENT_SOURCE_DIR}/src/category.cpp
@@ -300,10 +304,6 @@ set(project_headers
 add_library(cifpp)
 add_library(cifpp::cifpp ALIAS cifpp)
 
-# Create a revision file, containing the current git version info
-include(VersionString)
-add_version_header(cifpp "${CMAKE_CURRENT_SOURCE_DIR}/src/revision.hpp" LIB_NAME "LibCIFPP")
-
 if(TARGET my-eigen3)
 	add_dependencies(cifpp my-eigen3)
 endif()
@@ -346,7 +346,7 @@ else()
 endif()
 
 if(NOT STD_CHARCONV_COMPILING)
-	target_link_libraries(cifpp PUBLIC FastFloat::fast_float)
+	target_link_libraries(cifpp PRIVATE FastFloat::fast_float)
 endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")

changelog

@@ -1,3 +1,6 @@
+Version 9.0.6
+- Various small fixes
+
 Version 9.0.5
 - Added exists to compound_factory
 - Added sub_matrix, fix and extend determinant calculation

cmake/VersionString.cmake

@@ -199,13 +199,24 @@ endif()
 endfunction()
 
 # Create a revision file, containing the current git version info, if any
-function(add_version_header _target _header_file)
+function(write_version_header dir)
 
 	set(flags )
-	set(options LIB_NAME)
+	set(options LIB_NAME FILE_NAME)
 	set(sources )
 	cmake_parse_arguments(VERSION_STRING_OPTION "${flags}" "${options}" "${sources}" ${ARGN})
 
+	# parameter check
+	if(NOT IS_DIRECTORY ${dir})
+		message(FATAL_ERROR "First parameter to write_version_header should be a directory where the final revision.hpp file will be placed")
+	endif()
+
+	if(VERSION_STRING_OPTION_FILE_NAME)
+		set(file_name "${VERSION_STRING_OPTION_FILE_NAME}")
+	else()
+		set(file_name "revision.hpp")
+	endif()
+
 	# Where to store intermediate files
 	set(VERSION_STRING_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/VersionString")
 	if(NOT EXISTS "${VERSION_STRING_DATA}")
@@ -259,27 +270,6 @@ function(add_version_header _target _header_file)
 		set(BOOL_IS_MAIN "true")
 	endif()
 
-	set(HEADER_IN_FILE "${_current_cmake_module_dir}/revision.hpp.in")
-	set(HEADER_OUT_FILE "${_header_file}")
-
-	file(WRITE "${VERSION_STRING_DATA}/generate-header.cmake.in" [[
-set(REVISION_GIT_TAGREF "@REVISION_GIT_TAGREF@")
-set(BUILD_NUMBER "@BUILD_NUMBER@")
-set(REVISION_DATE_TIME	 "@REVISION_DATE_TIME@")
-set(VAR_PREFIX "@VAR_PREFIX@")
-set(IDENT_PREFIX "@IDENT_PREFIX@")
-set(BOOL_IS_MAIN "@BOOL_IS_MAIN@")
-configure_file("@HEADER_IN_FILE@" "@HEADER_OUT_FILE@" @ONLY)
-]])
-
-	configure_file("${VERSION_STRING_DATA}/generate-header.cmake.in" "${VERSION_STRING_DATA}/generate-header.cmake" @ONLY)
-
-	add_custom_command(
-		OUTPUT "${_header_file}"
-		COMMAND "${CMAKE_COMMAND}" -P "${VERSION_STRING_DATA}/generate-header.cmake"
-	)
-
-	target_sources("${_target}" PRIVATE "${_header_file}")
-	set_target_properties("${_target}" PROPERTIES ADDITIONAL_CLEAN_FILES "${_header_file}")
+	configure_file("${_current_cmake_module_dir}/revision.hpp.in" "${dir}/${file_name}" @ONLY)
 endfunction()
 

include/cif++/pdb.hpp

@@ -64,7 +64,7 @@ file read(std::istream &is);
  * @brief Read a file in legacy PDB format from std::istream @a is and
  * put the data into @a cifFile
  */
-file read_pdb_file(std::istream &pdbFile);
+void read_pdb_file(std::istream &pdbFile, cif::file &cifFile);
 
 // mmCIF to PDB
 

src/validate.cpp

@@ -27,12 +27,11 @@
 #include "cif++/validate.hpp"
 #include "cif++/category.hpp"
 #include "cif++/dictionary_parser.hpp"
-#include "cif++/gzio.hpp"
 #include "cif++/utilities.hpp"
 
 #include <cassert>
-#include <fstream>
 #include <iostream>
+#include <mutex>
 
 // The validator depends on regular expressions. Unfortunately,
 // the implementation of std::regex in g++ is buggy and crashes
@@ -75,6 +74,7 @@ struct regex_impl
   private:
 	pcre2_code *m_rx = nullptr;
 	pcre2_match_data *m_data = nullptr;
+	mutable std::mutex m_mutex;
 };
 
 regex_impl::regex_impl(std::string_view rx)
@@ -95,6 +95,8 @@ regex_impl::regex_impl(std::string_view rx)
 
 regex_impl::~regex_impl()
 {
+	std::unique_lock lock(m_mutex);
+
 	if (m_data)
 		pcre2_match_data_free(m_data);
 
@@ -104,6 +106,8 @@ regex_impl::~regex_impl()
 
 bool regex_impl::match(std::string_view v) const
 {
+	std::unique_lock lock(m_mutex);
+
 	bool result = false;
 
 	if (int rc = pcre2_match(m_rx, (PCRE2_SPTR)v.data(), v.length(), 0, 0, m_data, nullptr); rc >= 0)