zlib, again (use the zlib from boost in Windows)

.gitignore

@@ -9,4 +9,6 @@ test/rename-compound-test
 tools/update-dictionary-script
 tools/update-dictionary-script
 data/
 data/
 CMakeSettings.json
 CMakeSettings.json
-msvc/
+msvc/
\ No newline at end of file
+Testing/
+

CMakeLists.txt

@@ -182,7 +182,9 @@ if(NOT BUILD_SHARED_LIBS)
 endif()
 endif()
 find_package(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex date_time program_options)
 find_package(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex date_time program_options)
 
 
-find_package(ZLIB REQUIRED)
+if(NOT MSVC AND Boost_USE_STATIC_LIBS)
+	find_package(ZLIB REQUIRED)
+endif()
 
 
 # Create a revision file, containing the current git version info
 # Create a revision file, containing the current git version info
 
 
@@ -209,7 +211,7 @@ if(RECREATE_SYMOP_DATA)
 
 
 	add_executable(symop-map-generator "${CMAKE_SOURCE_DIR}/tools/symop-map-generator.cpp")
 	add_executable(symop-map-generator "${CMAKE_SOURCE_DIR}/tools/symop-map-generator.cpp")
 
 
-	target_link_libraries(symop-map-generator Threads::Threads ${Boost_LIBRARIES} std::filesystem ZLIB::ZLIB)
+	target_link_libraries(symop-map-generator Threads::Threads ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES})
 	if(Boost_INCLUDE_DIR)
 	if(Boost_INCLUDE_DIR)
 		target_include_directories(symop-map-generator PUBLIC ${Boost_INCLUDE_DIR})
 		target_include_directories(symop-map-generator PUBLIC ${Boost_INCLUDE_DIR})
 	endif()
 	endif()
@@ -282,7 +284,7 @@ target_include_directories(cifpp
 	${CMAKE_BINARY_DIR}
 	${CMAKE_BINARY_DIR}
 )
 )
 
 
-target_link_libraries(cifpp Threads::Threads ${Boost_LIBRARIES} std::filesystem ZLIB::ZLIB)
+target_link_libraries(cifpp Threads::Threads ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES})
 
 
 if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
     target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
     target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -446,7 +448,7 @@ if(CIFPP_BUILD_TESTS)
 			${CMAKE_CURRENT_BINARY_DIR}  # for config.h
 			${CMAKE_CURRENT_BINARY_DIR}  # for config.h
 		)
 		)
 
 
-		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp ${Boost_LIBRARIES} std::filesystem ZLIB::ZLIB)
+		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES})
 	
 	
 		if(MSVC)
 		if(MSVC)
 			# Specify unwind semantics so that MSVC knowns how to handle exceptions
 			# Specify unwind semantics so that MSVC knowns how to handle exceptions

include/cif++/Cif++.hpp

@@ -2141,15 +2141,15 @@ class File
 
 
 	File();
 	File();
 	File(std::istream &is, bool validate = false);
 	File(std::istream &is, bool validate = false);
-	File(const std::string &path, bool validate = false);
+	File(const std::filesystem::path &path, bool validate = false);
 	File(File &&rhs);
 	File(File &&rhs);
 	File(const File &rhs) = delete;
 	File(const File &rhs) = delete;
 	File &operator=(const File &rhs) = delete;
 	File &operator=(const File &rhs) = delete;
 
 
 	~File();
 	~File();
 
 
-	void load(const std::string &p);
-	void save(const std::string &p);
+	void load(const std::filesystem::path &p);
+	void save(const std::filesystem::path &p);
 
 
 	void load(std::istream &is);
 	void load(std::istream &is);
 	void save(std::ostream &os);
 	void save(std::ostream &os);

include/cif++/Compound.hpp

@@ -162,8 +162,8 @@ class CompoundFactory
 	static CompoundFactory &instance();
 	static CompoundFactory &instance();
 	static void clear();
 	static void clear();
 
 
-	void setDefaultDictionary(const std::string &inDictFile);
-	void pushDictionary(const std::string &inDictFile);
+	void setDefaultDictionary(const std::filesystem::path &inDictFile);
+	void pushDictionary(const std::filesystem::path &inDictFile);
 	void popDictionary();
 	void popDictionary();
 
 
 	bool isKnownPeptide(const std::string &res_name) const;
 	bool isKnownPeptide(const std::string &res_name) const;

include/cif++/Structure.hpp

@@ -397,7 +397,7 @@ class File : public std::enable_shared_from_this<File>
 {
 {
   public:
   public:
 	File();
 	File();
-	File(const std::string &path);
+	File(const std::filesystem::path &path);
 	File(const char *data, size_t length); // good luck trying to find out what it is...
 	File(const char *data, size_t length); // good luck trying to find out what it is...
 	~File();
 	~File();
 
 
@@ -406,8 +406,8 @@ class File : public std::enable_shared_from_this<File>
 
 
 	cif::Datablock& createDatablock(const std::string &name);
 	cif::Datablock& createDatablock(const std::string &name);
 
 
-	void load(const std::string &path);
-	void save(const std::string &path);
+	void load(const std::filesystem::path &path);
+	void save(const std::filesystem::path &path);
 
 
 	Structure *model(size_t nr = 1);
 	Structure *model(size_t nr = 1);
 
 

src/Cif++.cpp

@@ -3399,7 +3399,7 @@ File::File(std::istream &is, bool validate)
 	load(is);
 	load(is);
 }
 }
 
 
-File::File(const std::string &path, bool validate)
+File::File(const std::filesystem::path &path, bool validate)
 	: File()
 	: File()
 {
 {
 	try
 	try
@@ -3452,7 +3452,7 @@ void File::append(Datablock *e)
 	}
 	}
 }
 }
 
 
-void File::load(const std::string &p)
+void File::load(const std::filesystem::path &p)
 {
 {
 	fs::path path(p);
 	fs::path path(p);
 
 
@@ -3482,7 +3482,7 @@ void File::load(const std::string &p)
 	}
 	}
 }
 }
 
 
-void File::save(const std::string &p)
+void File::save(const std::filesystem::path &p)
 {
 {
 	fs::path path(p);
 	fs::path path(p);
 
 

src/Compound.cpp

@@ -268,7 +268,7 @@ class CompoundFactoryImpl : public std::enable_shared_from_this<CompoundFactoryI
   public:
   public:
 	CompoundFactoryImpl(std::shared_ptr<CompoundFactoryImpl> next);
 	CompoundFactoryImpl(std::shared_ptr<CompoundFactoryImpl> next);
 
 
-	CompoundFactoryImpl(const std::string &file, std::shared_ptr<CompoundFactoryImpl> next);
+	CompoundFactoryImpl(const std::filesystem::path &file, std::shared_ptr<CompoundFactoryImpl> next);
 
 
 	virtual ~CompoundFactoryImpl()
 	virtual ~CompoundFactoryImpl()
 	{
 	{
@@ -362,7 +362,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(std::shared_ptr<CompoundFactoryImpl> ne
 		mKnownBases.insert(key);
 		mKnownBases.insert(key);
 }
 }
 
 
-CompoundFactoryImpl::CompoundFactoryImpl(const std::string &file, std::shared_ptr<CompoundFactoryImpl> next)
+CompoundFactoryImpl::CompoundFactoryImpl(const std::filesystem::path &file, std::shared_ptr<CompoundFactoryImpl> next)
 	: mNext(next)
 	: mNext(next)
 {
 {
 	cif::File cifFile(file);
 	cif::File cifFile(file);
@@ -677,10 +677,10 @@ void CompoundFactory::clear()
 		sInstance.reset();
 		sInstance.reset();
 }
 }
 
 
-void CompoundFactory::setDefaultDictionary(const std::string &inDictFile)
+void CompoundFactory::setDefaultDictionary(const std::filesystem::path &inDictFile)
 {
 {
 	if (not fs::exists(inDictFile))
 	if (not fs::exists(inDictFile))
-		throw std::runtime_error("file not found: " + inDictFile);
+		throw std::runtime_error("file not found: " + inDictFile.string());
 
 
 	try
 	try
 	{
 	{
@@ -693,10 +693,10 @@ void CompoundFactory::setDefaultDictionary(const std::string &inDictFile)
 	}
 	}
 }
 }
 
 
-void CompoundFactory::pushDictionary(const std::string &inDictFile)
+void CompoundFactory::pushDictionary(const std::filesystem::path &inDictFile)
 {
 {
 	if (not fs::exists(inDictFile))
 	if (not fs::exists(inDictFile))
-		throw std::runtime_error("file not found: " + inDictFile);
+		throw std::runtime_error("file not found: " + inDictFile.string());
 
 
 	//	ifstream file(inDictFile);
 	//	ifstream file(inDictFile);
 	//	if (not file.is_open())
 	//	if (not file.is_open())

src/Structure.cpp

@@ -59,8 +59,8 @@ struct FileImpl
 
 
 	void load_data(const char *data, size_t length);
 	void load_data(const char *data, size_t length);
 
 
-	void load(const std::string &p);
-	void save(const std::string &p);
+	void load(const std::filesystem::path &path);
+	void save(const std::filesystem::path &path);
 };
 };
 
 
 void FileImpl::load_data(const char *data, size_t length)
 void FileImpl::load_data(const char *data, size_t length)
@@ -112,10 +112,8 @@ void FileImpl::load_data(const char *data, size_t length)
 		std::cerr << "Invalid mmCIF file" << (cif::VERBOSE ? "." : " use --verbose option to see errors") << std::endl;
 		std::cerr << "Invalid mmCIF file" << (cif::VERBOSE ? "." : " use --verbose option to see errors") << std::endl;
 }
 }
 
 
-void FileImpl::load(const std::string &p)
+void FileImpl::load(const std::filesystem::path &path)
 {
 {
-	fs::path path(p);
-
 	std::ifstream inFile(path, std::ios_base::in | std::ios_base::binary);
 	std::ifstream inFile(path, std::ios_base::in | std::ios_base::binary);
 	if (not inFile.is_open())
 	if (not inFile.is_open())
 		throw std::runtime_error("No such file: " + path.string());
 		throw std::runtime_error("No such file: " + path.string());
@@ -185,18 +183,13 @@ void FileImpl::load(const std::string &p)
 		std::cerr << "Invalid mmCIF file" << (cif::VERBOSE ? "." : " use --verbose option to see errors") << std::endl;
 		std::cerr << "Invalid mmCIF file" << (cif::VERBOSE ? "." : " use --verbose option to see errors") << std::endl;
 }
 }
 
 
-void FileImpl::save(const std::string &p)
+void FileImpl::save(const std::filesystem::path &path)
 {
 {
-	fs::path path(p);
-
-	std::ofstream outFile(p, std::ios_base::out | std::ios_base::binary);
+	std::ofstream outFile(path, std::ios_base::out | std::ios_base::binary);
 	io::filtering_stream<io::output> out;
 	io::filtering_stream<io::output> out;
 
 
 	if (path.extension() == ".gz")
 	if (path.extension() == ".gz")
-	{
 		out.push(io::gzip_compressor());
 		out.push(io::gzip_compressor());
-		path = path.stem();
-	}
 
 
 	out.push(outFile);
 	out.push(outFile);
 
 
@@ -1732,7 +1725,7 @@ File::File(const char *data, size_t length)
 	mImpl->load_data(data, length);
 	mImpl->load_data(data, length);
 }
 }
 
 
-File::File(const std::string &File)
+File::File(const std::filesystem::path &File)
 	: mImpl(new FileImpl)
 	: mImpl(new FileImpl)
 {
 {
 	load(File);
 	load(File);
@@ -1753,12 +1746,12 @@ cif::Datablock& File::createDatablock(const std::string &name)
 	return *mImpl->mDb;
 	return *mImpl->mDb;
 }
 }
 
 
-void File::load(const std::string &p)
+void File::load(const std::filesystem::path &p)
 {
 {
 	mImpl->load(p);
 	mImpl->load(p);
 }
 }
 
 
-void File::save(const std::string &file)
+void File::save(const std::filesystem::path &file)
 {
 {
 	mImpl->save(file);
 	mImpl->save(file);
 }
 }