Merge branch 'develop' of github.com:PDB-REDO/dssp into develop

CMakeLists.txt

@@ -239,15 +239,20 @@ if(ENABLE_TESTING)
 	add_test(NAME unit-test-dssp COMMAND $<TARGET_FILE:unit-test-dssp> -- ${PROJECT_SOURCE_DIR}/test)
 endif()
 
-option(DSSP_BUILD_INSTALLER "Build an installer" OFF)
-
-if(DSSP_BUILD_INSTALLER)
-	include(InstallRequiredSystemLibraries)
-	set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
-
-	# NSIS options
-	set(CPACK_NSIS_MODIFY_PATH ON)
-
-	# configuration done, include CPack
-	include(CPack)
-endif()
+include(InstallRequiredSystemLibraries)
+set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
+
+# Tarball generation
+set(CPACK_SOURCE_TGZ ON)
+set(CPACK_SOURCE_TBZ2 OFF)
+set(CPACK_SOURCE_TXZ OFF)
+set(CPACK_SOURCE_TZ OFF)
+set(CPACK_SOURCE_IGNORE_FILES "/data/components.cif;/build;/.vscode;/.git")
+set (CPACK_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION}")
+set (CPACK_SOURCE_PACKAGE_FILE_NAME ${CPACK_PACKAGE_FILE_NAME})
+
+# NSIS options
+set(CPACK_NSIS_MODIFY_PATH ON)
+
+# configuration done, include CPack
+include(CPack)

changelog

-Version 4.1.1
-- Better packaging
+Version 4.2
+- Changes for packaging
+- New mmCIF DSSP output, added several categories
 
 Version 4.1.0
 - Based on new libcifpp version 5

libconfig/CMakeLists.txt

+# Copyright Maarten L. Hekkelman, 2022
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+
+cmake_minimum_required(VERSION 3.16)
+
+# set the project name
+project(libconfig VERSION 1.2.0 LANGUAGES CXX)
+
+include(GNUInstallDirs)
+include(CMakePackageConfigHelpers)
+include(Dart)
+
+set(CXX_EXTENSIONS OFF)
+set(CMAKE_CXX_STANDARD 17 CACHE STRING "The minimum version of C++ required for this library")
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+option(ENABLE_TESTING "Build the unit test applications" OFF)
+
+if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers")
+elseif(MSVC)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
+endif()
+
+if(MSVC)
+	# make msvc standards compliant...
+	add_compile_options(/permissive-)
+
+	macro(get_WIN32_WINNT version)
+		if(WIN32 AND CMAKE_SYSTEM_VERSION)
+			set(ver ${CMAKE_SYSTEM_VERSION})
+			string(REPLACE "." "" ver ${ver})
+			string(REGEX REPLACE "([0-9])" "0\\1" ver ${ver})
+
+			set(${version} "0x${ver}")
+		endif()
+	endmacro()
+
+	get_WIN32_WINNT(ver)
+	add_definitions(-D_WIN32_WINNT=${ver})
+endif()
+
+add_library(libconfig INTERFACE)
+add_library(libconfig::libconfig ALIAS libconfig)
+
+target_include_directories(libconfig INTERFACE
+	$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+	$<INSTALL_INTERFACE:include>
+)
+
+# adding header sources just helps IDEs
+target_sources(libconfig INTERFACE
+	$<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/include>$<INSTALL_INTERFACE:include>/cfg.hpp
+)
+
+set_target_properties(libconfig PROPERTIES PUBLIC_HEADER include/cfg.hpp)
+
+# installation
+set(version_config "${CMAKE_CURRENT_BINARY_DIR}/libconfigConfigVersion.cmake")
+
+set(INCLUDE_INSTALL_DIR ${CMAKE_INSTALL_INCLUDEDIR})
+
+write_basic_package_version_file("${version_config}"
+	VERSION ${PROJECT_VERSION}
+	COMPATIBILITY SameMajorVersion)
+
+install(TARGETS libconfig
+	EXPORT libconfigConfig
+	PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+install(
+	DIRECTORY include/cfg
+	DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+	COMPONENT Devel
+)
+
+export(TARGETS libconfig NAMESPACE libconfig:: FILE libconfigTargets.cmake)
+
+if(WIN32 AND NOT CYGWIN)
+	set(CONFIG_LOC CMake)
+else()
+	set(CONFIG_LOC "${CMAKE_INSTALL_LIBDIR}/cmake/libconfig")
+endif()
+
+configure_package_config_file(
+	${PROJECT_SOURCE_DIR}/cmake/libconfigConfig.cmake.in
+	${PROJECT_SOURCE_DIR}/cmake/libconfigConfig.cmake
+	INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/libconfig
+	PATH_VARS INCLUDE_INSTALL_DIR
+)
+
+install(EXPORT libconfigConfig
+	FILE libconfigTargets.cmake
+	NAMESPACE libconfig::
+	DESTINATION ${CONFIG_LOC})
+
+install(
+	FILES cmake/libconfigConfig.cmake "${version_config}"
+	DESTINATION ${CONFIG_LOC})
+
+# if(ENABLE_TESTING)
+# 	enable_testing()
+
+# 	add_executable(libconfig-unit-test ${PROJECT_SOURCE_DIR}/test/unit-test.cpp)
+
+# 	target_link_libraries(libconfig-unit-test libconfig::libconfig)
+
+# 	if(MSVC)
+# 		# Specify unwind semantics so that MSVC knowns how to handle exceptions
+# 		target_compile_options(libconfig-unit-test PRIVATE /EHsc)
+# 	endif()
+
+# 	add_test(NAME libconfig-unit-test
+# 		COMMAND $<TARGET_FILE:libconfig-unit-test> -- ${PROJECT_SOURCE_DIR}/test)
+# endif()

libconfig/README.md

+# libconfig
+
+A library for parsing command line arguments and making them available throughout a program.
+
+## Synopsis
+
+```c++
+#include <cfg.hpp>
+
+int VERBOSE = 0;
+
+int main(int argc, char * const argv[])
+{
+    // config is a singleton class
+    auto &config = cfg::config::instance();
+
+    // Tell config what options to accept
+    // This can be done more than once, replacing
+    // the current set of options.
+    config.init("usage: test [options] input output",
+        cfg::make_option("verbose,v", "Use verbose output"),
+        cfg::make_option("help,h", "Show this help"),
+        cfg::make_option<std::string>("opt1", "foo", "First option"),
+        cfg::make_option<std::string>("config", "Name of a config file to use"),
+        cfg::make_option<float>("float-value,f", "Another option")
+    );
+
+    // Do the parsing of argv
+    config.parse(argc, argv);
+
+    // Set verbose based on number of times the
+    // -v or --verbose flag was passed
+    VERBOSE = config.count("verbose");
+
+    // Check for the help flag
+    if (config.has("help"))
+    {
+        // print out the options to the screen
+        std::cout << config << std::endl;
+        exit(0);
+    }
+
+    // Optionally read a config file
+    // Config file is by default called myapp.conf
+    // but can be overridden with the --config parameter
+    // Files will be located in current dictory and /etc
+    if (config.has("config"))
+        config.parse_config_file("config", "myapp.conf",
+            { fs::current_path().string(), "/etc/" }
+        );
+
+    // Operands are parameters that are not options
+    // E.g. filenames to process
+    if (config.operands().size() != 2)
+    {
+        std::cerr << config << std::endl;
+        exit(1);
+    }
+
+    std::filesystem::path input = config.operands().front();
+    std::filesystem::path output = config.operands().back();
+    
+    // Get values from options with a value
+    std::option1 = config.get<std::string>("opt1");
+    float option2 = 3.14;
+    if (config.has("float-value"))
+        option2 = config.get<float>("float-value");
+
+    ... etc
+
+}
+```

libconfig/changelog

+Version 1.1.1
+- Better support for older GCC compilers
+Version 1.2.0
+- New, tuples base implementation
+- Add 'usage' parameter to init
+
+Version 1.1.0
+- Parse config files
+
+Version 1.0.2
+- Fix get_terminal_width. Should be inline of course.
+
+Version 1.0.1
+- printing options, word-wrapped
+
+Version 1.0.0
+- initial release
\ No newline at end of file

libconfig/cmake/libconfigConfig.cmake

+
+####### Expanded from @PACKAGE_INIT@ by configure_package_config_file() #######
+####### Any changes to this file will be overwritten by the next CMake run ####
+####### The input file was libconfigConfig.cmake.in                            ########
+
+get_filename_component(PACKAGE_PREFIX_DIR "${CMAKE_CURRENT_LIST_DIR}/../../../" ABSOLUTE)
+
+macro(set_and_check _var _file)
+  set(${_var} "${_file}")
+  if(NOT EXISTS "${_file}")
+    message(FATAL_ERROR "File or directory ${_file} referenced by variable ${_var} does not exist !")
+  endif()
+endmacro()
+
+macro(check_required_components _NAME)
+  foreach(comp ${${_NAME}_FIND_COMPONENTS})
+    if(NOT ${_NAME}_${comp}_FOUND)
+      if(${_NAME}_FIND_REQUIRED_${comp})
+        set(${_NAME}_FOUND FALSE)
+      endif()
+    endif()
+  endforeach()
+endmacro()
+
+####################################################################################
+
+INCLUDE("${CMAKE_CURRENT_LIST_DIR}/libconfigTargets.cmake")
+
+check_required_components(libconfig)

libconfig/cmake/libconfigConfig.cmake.in

+@PACKAGE_INIT@
+
+INCLUDE("${CMAKE_CURRENT_LIST_DIR}/libconfigTargets.cmake")
+
+check_required_components(libconfig)

libconfig/include/cfg/utilities.hpp

+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ *
+ * Copyright (c) 2022 Maarten L. Hekkelman
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#pragma once
+
+#include <climits>
+#include <cstdint>
+
+#if __has_include(<sys/ioctl.h>)
+#include <sys/ioctl.h>
+#include <fcntl.h>
+#include <unistd.h>
+#elif defined(_MSC_VER)
+#include <windows.h>
+#endif
+
+namespace cfg
+{
+
+#if defined(_MSC_VER)
+/// @brief Get the width in columns of the current terminal
+/// @return number of columns of the terminal
+inline uint32_t get_terminal_width()
+{
+    CONSOLE_SCREEN_BUFFER_INFO csbi;
+    ::GetConsoleScreenBufferInfo(::GetStdHandle(STD_OUTPUT_HANDLE), &csbi);
+    return csbi.srWindow.Right - csbi.srWindow.Left + 1;
+}
+
+#elif __has_include(<sys/ioctl.h>)
+/// @brief Get the width in columns of the current terminal
+/// @return number of columns of the terminal
+inline uint32_t get_terminal_width()
+{
+	uint32_t result = 80;
+
+	if (::isatty(STDOUT_FILENO))
+	{
+		struct winsize w;
+		::ioctl(0, TIOCGWINSZ, &w);
+		result = w.ws_col;
+	}
+	return result;
+}
+#else
+#warning "Could not find the terminal width, falling back to default"
+inline uint32_t get_terminal_width()
+{
+	return 80;
+}
+#endif
+
+} // namespace cfg
\ No newline at end of file

libconfig/test/unit-test.conf

+# A simple test config file
+aap = 2
+noot = 3
\ No newline at end of file

src/mkdssp.cpp

@@ -112,8 +112,6 @@ int d_main(int argc, const char *argv[])
 	}
 
 	cif::VERBOSE = config.count("verbose");
-	if (config.has("debug"))
-		cif::VERBOSE = config.get<int>("debug");
 
 	// --------------------------------------------------------------------