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)
@@ -218,10 +219,6 @@ else()
 	set(EIGEN_INCLUDE_DIR ${SOURCE_DIR})
 endif()
 
-# Create a revision file, containing the current git version info
-include(VersionString)
-write_version_header(${CMAKE_CURRENT_SOURCE_DIR}/src/ LIB_NAME "LibCIFPP")
-
 # SymOp data table
 if(CIFPP_RECREATE_SYMOP_DATA)
 	# The tool to create the table
@@ -243,6 +240,9 @@ if(CIFPP_RECREATE_SYMOP_DATA)
 		"$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
@@ -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

@@ -1,7 +1,11 @@
+Version 9.0.6
+- Various small fixes
+
 Version 9.0.5
 - Added exists to compound_factory
 - Added sub_matrix, fix and extend determinant calculation
 - Added yet another structure::create_non_poly
+- Remove revision.hpp file in make clean (new VersionString.cmake)
 
 Version 9.0.4
 - Fix various stopping and reconstruction errors

cmake/VersionString.cmake

@@ -238,7 +238,7 @@ function(write_version_header dir)
 		if(res EQUAL 0)
 			set(REVISION_STRING "${out}")
 		else()
-			message(STATUS "Git hash not found, does this project has a 'build' tag?")
+			message(STATUS "Git hash not found, does this project have a 'build' tag?")
 		endif()
 	else()
 		message(STATUS "Git hash not found")

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/model.cpp

@@ -26,6 +26,7 @@
 
 #include "cif++/model.hpp"
 #include "cif++.hpp"
+#include "cif++/point.hpp"
 
 #include <filesystem>
 #include <fstream>
@@ -351,17 +352,7 @@ std::tuple<point, float> residue::center_and_radius() const
 	for (auto &a : m_atoms)
 		pts.push_back(a.get_location());
 
-	auto center = centroid(pts);
-	float radius = 0;
-
-	for (auto &pt : pts)
-	{
-		float d = static_cast<float>(distance(pt, center));
-		if (radius < d)
-			radius = d;
-	}
-
-	return std::make_tuple(center, radius);
+	return smallest_sphere_around_points(pts);
 }
 
 bool residue::has_alternate_atoms() const

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)

test/query-test.cpp

@@ -49,6 +49,4 @@ TEST_CASE("q-1")
 
 		CHECK(pdbx_poly_seq_scheme.count("asym_id"_key == "A" and "entity_id"_key == 1 and "seq_id"_key == 1 and "mon_id"_key == "PRO" and "hetero"_key == false) == 1);
 	}
-	
-
 }