Changed boost::regex dependency to git submodule, in case it is needed

.gitmodules

+[submodule "regex"]
+	path = regex
+	url = https://github.com/boostorg/regex

CMakeLists.txt

@@ -156,17 +156,14 @@ try_run(STD_REGEX_RUNNING STD_REGEX_COMPILING
 if(STD_REGEX_RUNNING STREQUAL FAILED_TO_RUN)
 	message(WARNING "You are probably trying to compile using the g++ standard library which contains a crashing std::regex implementation. Will try to use boost::regex instead")
 
-	set(NEED_BOOST_REGEX ON)
+	set(BOOST_REGEX_STANDALONE ON)
+	add_subdirectory(regex)
 endif()
 
 set(CMAKE_THREAD_PREFER_PTHREAD)
 set(THREADS_PREFER_PTHREAD_FLAG)
 find_package(Threads)
 
-if(NEED_BOOST_REGEX)
-	find_package(Boost 1.70.0 REQUIRED COMPONENTS system regex)
-endif()
-
 find_package(gxrio REQUIRED)
 
 include(FindFilesystem)
@@ -215,15 +212,16 @@ set(project_sources
 	# ${PROJECT_SOURCE_DIR}/src/pdb/PDB2Cif.cpp
 	# ${PROJECT_SOURCE_DIR}/src/pdb/PDB2CifRemark3.cpp
 
-	${PROJECT_SOURCE_DIR}/src/structure/AtomType.cpp
-	${PROJECT_SOURCE_DIR}/src/structure/BondMap.cpp
+	# ${PROJECT_SOURCE_DIR}/src/structure/AtomType.cpp
+	# ${PROJECT_SOURCE_DIR}/src/structure/BondMap.cpp
 	# ${PROJECT_SOURCE_DIR}/src/structure/Compound.cpp
 	# ${PROJECT_SOURCE_DIR}/src/structure/Secondary.cpp
 	# ${PROJECT_SOURCE_DIR}/src/structure/Structure.cpp
 	# ${PROJECT_SOURCE_DIR}/src/structure/Symmetry.cpp
 	# ${PROJECT_SOURCE_DIR}/src/structure/TlsParser.cpp
 	${PROJECT_SOURCE_DIR}/src/utilities.cpp
-	${PROJECT_SOURCE_DIR}/src/point.cpp
+
+	# ${PROJECT_SOURCE_DIR}/src/point.cpp
 )
 
 set(project_headers
@@ -258,24 +256,21 @@ set(project_headers
 )
 
 add_library(cifpp ${project_sources} ${project_headers} ${CMAKE_SOURCE_DIR}/src/structure/SymOpTable_data.hpp)
+add_library(cifpp::cifpp ALIAS cifpp)
+
 set_target_properties(cifpp PROPERTIES POSITION_INDEPENDENT_CODE ON)
 
-if(NEED_BOOST_REGEX)
-	target_compile_definitions(cifpp PUBLIC USE_BOOST_REGEX=1 BOOST_REGEX_STANDALONE=1)
-endif()
+# if(NEED_BOOST_REGEX)
+target_compile_definitions(cifpp PUBLIC USE_BOOST_REGEX=1 BOOST_REGEX_STANDALONE=1)
 
+# endif()
 target_include_directories(cifpp
 	PUBLIC
 	"$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
 	"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
 )
 
-target_include_directories(cifpp
-	PRIVATE
-	${CMAKE_BINARY_DIR}
-)
-
-target_link_libraries(cifpp PUBLIC Threads::Threads Boost::regex gxrio::gxrio ${CIFPP_REQUIRED_LIBRARIES})
+target_link_libraries(cifpp PUBLIC Threads::Threads gxrio::gxrio ${CIFPP_REQUIRED_LIBRARIES} PRIVATE Boost::regex)
 
 # target_link_libraries(cifpp PRIVATE)
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
@@ -416,7 +411,7 @@ if(CIFPP_BUILD_TESTS)
 
 	list(APPEND CIFPP_tests
 
-		pdb2cif
+		# pdb2cif
 		# rename-compound
 		# structure
 		# sugar
@@ -429,12 +424,7 @@ if(CIFPP_BUILD_TESTS)
 
 		add_executable(${CIFPP_TEST} ${CIFPP_TEST_SOURCE})
 
-		target_include_directories(${CIFPP_TEST} PRIVATE
-			${CMAKE_CURRENT_SOURCE_DIR}/include
-			${CMAKE_CURRENT_BINARY_DIR} # for config.h
-		)
-
-		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp)
+		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp)
 
 		if(CIFPP_USE_RSRC)
 			mrc_target_resources(${CIFPP_TEST} ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic)

Config.cmake.in

@@ -2,8 +2,7 @@
 
 include(CMakeFindDependencyMacro)
 find_dependency(Threads)
-find_dependency(Boost 1.70.0 REQUIRED COMPONENTS system regex)
-find_dependency(gzstream)
+find_dependency(gxrio)
 
 INCLUDE("${CMAKE_CURRENT_LIST_DIR}/cifppTargets.cmake")
 

libcifpp.pc.in

@@ -8,5 +8,5 @@ Name: libcifpp
 Description: C++ library for the manipulation of mmCIF files.
 Version: @PACKAGE_VERSION@
 
-Libs: -L${libdir} -lcifpp -lboost_regex -lz
+Libs: -L${libdir} -lcifpp -lz
 Cflags: -I${includedir} -pthread

regex @ e5979ae1

+Subproject commit e5979ae1af2e5e03a46509048269294bfe9a32c7

src/Cif++.cpp

@@ -38,7 +38,7 @@
 
 #include <filesystem>
 
-#include <zstream/zstream.hpp>
+#include <gxrio.hpp>
 
 #include <boost/logic/tribool.hpp>
 
@@ -3448,7 +3448,7 @@ void File::load(const std::filesystem::path &p)
 {
 	fs::path path(p);
 
-	zstream::ifstream in(p);
+	gxrio::ifstream in(p);
 
 	try
 	{
@@ -3464,7 +3464,7 @@ void File::load(const std::filesystem::path &p)
 
 void File::save(const std::filesystem::path &p)
 {
-	zstream::ofstream outFile(p);
+	gxrio::ofstream outFile(p);
 	save(outFile);
 }
 
@@ -3505,7 +3505,7 @@ void File::load(const char *data, std::size_t length)
 		membuf(char *data, size_t length) { this->setg(data, data, data + length); }
 	} buffer(const_cast<char *>(data), length);
 
-	zstream::istream is(&buffer);
+	gxrio::istream is(&buffer);
 	load(is);
 }
 

src/cif/file.cpp

@@ -24,7 +24,7 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-#include <zstream/zstream.hpp>
+#include <gxrio.hpp>
 
 #include <cif++/cif/file.hpp>
 
@@ -132,16 +132,8 @@ std::tuple<file::iterator, bool> file::emplace(std::string_view name)
 
 void file::load(const std::filesystem::path &p)
 {
-	if (p.extension() == ".gz")
-	{
-		gzstream::ifstream in(p);
-		load(in);
-	}
-	else
-	{
-		std::ifstream in(p, std::ios::binary);
-		load(in);
-	}
+	gxrio::ifstream in(p);
+	load(in);
 }
 
 void file::load(std::istream &is)
@@ -161,7 +153,7 @@ void file::load(std::istream &is)
 
 void file::save(const std::filesystem::path &p) const
 {
-	zstream::ofstream outFile(p);
+	gxrio::ofstream outFile(p);
 	save(outFile);
 }
 

src/cif/validate.cpp

@@ -435,7 +435,7 @@ const validator &validator_factory::operator[](std::string_view dictionary_name)
 
 		if (std::filesystem::exists(p, ec) and not ec)
 		{
-			gzstream::ifstream in(p);
+			gxrio::ifstream in(p);
 
 			if (not in.is_open())
 				throw std::runtime_error("Could not open dictionary (" + p.string() + ")");

src/structure/Structure.cpp

@@ -31,7 +31,7 @@
 #include <iomanip>
 #include <numeric>
 
-#include <zstream/zstream.hpp>
+#include <gxrio.hpp>
 
 #if __cpp_lib_format
 #include <format>
@@ -1285,7 +1285,7 @@ float Branch::weight() const
 
 void File::load(const std::filesystem::path &path)
 {
-	zstream::ifstream in(path);
+	gxrio::ifstream in(path);
 
 	auto ext = path.extension().string();
 	if (ext == ".gz" or ext = ".xz")
@@ -1304,7 +1304,7 @@ void File::load(const std::filesystem::path &path)
 
 void File::save(const std::filesystem::path &path)
 {
-	zstream::ostream outFile(path);
+	gxrio::ostream outFile(path);
 
 	auto ext = path.extension().string();
 	if (ext == ".gz" or ext = ".xz")