Skip to content

D
dssp
Commit adbd3ec0 by Maarten L. Hekkelman
Options

Move to cmake permanently

parent 50255594
Showing with 455 additions and 1200 deletions
.gitignore
.vscode .vscode
node_modules
rsrc/version.txt rsrc/version.txt
version-info*.txt version-info*.txt
docroot/fonts
docroot/scripts
obj
obj.dbg
mini-ibs
make.config
docroot/css/google-font*.css
autom4te.cache/
GNUmakefile
config.status
config.log
aclocal.m4
dssp
*.dssp
src/config.hpp
src/config.hpp.in~
src/revision.hpp
mkdssp mkdssp
msvc/x64/
.vscode/
.vs/ .vs/
build build
CMakeLists.txt
cmake_minimum_required(VERSION 3.10) cmake_minimum_required(VERSION 3.15)
# set the project name # set the project name
project(mkdssp VERSION 4.0.0) project(mkdssp VERSION 4.0.0 LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
enable_testing()
include(GNUInstallDirs)
include(CheckFunctionExists)
include(CheckIncludeFiles)
include(CheckLibraryExists)
include(CMakePackageConfigHelpers)
include(Dart)
include(GenerateExportHeader)
set(CXX_EXTENSIONS OFF)
set(CMAKE_CXX_STANDARD 17) set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Set bindir, if not use -DBIN_INSTALL_DIR if(CMAKE_COMPILER_IS_GNUCC)
if(NOT BIN_INSTALL_DIR) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter")
if(CMAKE_INSTALL_BINDIR) endif()
set(BIN_INSTALL_DIR ${CMAKE_INSTALL_BINDIR}) if(MSVC)
else(CMAKE_INSTALL_BINDIR) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
set(BIN_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/bin") endif()
endif(CMAKE_INSTALL_BINDIR)
endif(NOT BIN_INSTALL_DIR)
# Set libdir, if not use -DLIB_INSTALL_DIR
if(NOT LIB_INSTALL_DIR)
if(CMAKE_INSTALL_LIBDIR)
set(LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR})
else(CMAKE_INSTALL_LIBDIR)
set(LIB_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}")
endif(CMAKE_INSTALL_LIBDIR)
endif(NOT LIB_INSTALL_DIR)
# Set includedir, if not use -DINCLUDE_INSTALL_DIR
if(NOT INCLUDE_INSTALL_DIR)
if(CMAKE_INSTALL_INCLUDEDIR)
set(INCLUDE_INSTALL_DIR ${CMAKE_INSTALL_INCLUDEDIR})
else(CMAKE_INSTALL_INCLUDEDIR)
set(INCLUDE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/include")
endif(CMAKE_INSTALL_INCLUDEDIR)
endif(NOT INCLUDE_INSTALL_DIR)
# Set sharedir, if not use -DSHARE_INSTALL_DIR
if(NOT SHARE_INSTALL_DIR)
if(CMAKE_INSTALL_DATADIR)
set(SHARE_INSTALL_DIR "${CMAKE_INSTALL_DATADIR}")
else(CMAKE_INSTALL_DATADIR)
set(SHARE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/share")
endif(CMAKE_INSTALL_DATADIR)
endif(NOT SHARE_INSTALL_DIR)
set (Boost_DETAILED_FAILURE_MSG ON) if(MSVC)
# set (BOOST_ROOT ${PROJECT_SOURCE_DIR}/../boost_1_75_0) # make msvc standards compliant...
# set (Boost_COMPILER "-vc") add_compile_options(/permissive-)
# set (Boost_USE_STATIC_RUNTIME ON)
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})
# On Windows, do not install in the system location by default
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
message(WARNING "The library and auxiliary files will be installed in $ENV{LOCALAPPDATA}/${PROJECT_NAME}")
set(CMAKE_INSTALL_PREFIX "$ENV{LOCALAPPDATA}/${PROJECT_NAME}" CACHE PATH "..." FORCE)
endif()
# Find out the processor type for the target
if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "AMD64")
set(COFF_TYPE "x64")
elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "i386")
set(COFF_TYPE "x86")
elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "ARM64")
set(COFF_TYPE "arm64")
else()
message(FATAL_ERROR "Unsupported or unknown processor type ${CMAKE_SYSTEM_PROCESSOR}")
endif()
set(COFF_SPEC "--coff=${COFF_TYPE}")
endif()
find_package(Boost 1.73.0 REQUIRED COMPONENTS system iostreams regex date_time program_options) # Create a revision file, containing the current git version info
find_package(cifpp 1.0 REQUIRED) find_package(Git)
if(GIT_FOUND AND EXISTS "${CMAKE_SOURCE_DIR}/.git")
include(GetGitRevisionDescription)
get_git_head_revision(REFSPEC COMMITHASH)
# Generate our own version string
git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty)
else()
message(WARNING "Git not found, cannot set version info")
SET(BUILD_VERSION_STRING "unknown")
endif()
# generate version.h
include_directories(${CMAKE_BINARY_DIR} PRIVATE)
string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%d" UTC)
configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
# Optionally use mrc to create resources
find_program(MRC mrc HINTS "$ENV{LOCALAPPDATA}/mrc" "${CMAKE_INSTALL_PREFIX}/../mrc" "/usr/local/bin")
if(MRC)
option(USE_RSRC "Use mrc to create resources" ON)
else()
message(WARNING "Not using resources since mrc was not found")
endif()
if(USE_RSRC STREQUAL "ON")
set(USE_RSRC 1)
message("Using resources compiled with ${MRC}")
add_compile_definitions(USE_RSRC)
endif()
set(CMAKE_THREAD_PREFER_PTHREAD) set(CMAKE_THREAD_PREFER_PTHREAD)
set(THREADS_PREFER_PTHREAD_FLAG) set(THREADS_PREFER_PTHREAD_FLAG)
find_package(Threads) find_package(Threads REQUIRED)
set (Boost_DETAILED_FAILURE_MSG ON)
find_package(Boost 1.71.0 REQUIRED COMPONENTS program_options system iostreams regex date_time)
# extra diagnostic -- helpful for problem with FindBoost.cmake
message(STATUS "Boost headers in: ${Boost_INCLUDE_DIR}")
message(STATUS "Boost libraries in: ${Boost_LIBRARY_DIRS}")
find_package(ZLIB)
find_package(BZip2)
find_package(cifpp 1.0 REQUIRED)
if(USE_RSRC)
add_compile_definitions("DATA_DIR=\"${CIFPP_SHARE_DIR}\"")
endif()
include_directories(${Boost_INCLUDE_DIR} cifpp::cifpp ${CMAKE_SOURCE_DIR}/include)
link_libraries(${Boost_LIBRARIES} cifpp::cifpp ${CMAKE_THREAD_LIBS_INIT})
if (ZLIB_FOUND)
link_libraries(ZLIB::ZLIB)
endif()
if (BZIP2_FOUND)
link_libraries(BZip2::BZip2)
endif()
include_directories( include_directories(
${PROJECT_SOURCE_DIR}/src ${PROJECT_SOURCE_DIR}/src
PUBLIC ${cifpp_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS} PUBLIC ${cifpp_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS}
) )
add_executable(mkdssp ${PROJECT_SOURCE_DIR}/src/mkdssp.cpp) add_executable(mkdssp
${PROJECT_SOURCE_DIR}/src/mkdssp.cpp)
install(TARGETS ${PROJECT_NAME} install(TARGETS ${PROJECT_NAME}
RUNTIME DESTINATION ${BIN_INSTALL_DIR} RUNTIME DESTINATION ${BIN_INSTALL_DIR}
) )
target_link_libraries(${PROJECT_NAME} CifPP::cifpp ${Boost_LIBRARIES} Threads::Threads)
if(MSVC)
# make msvc standards compliant...
target_compile_options(${PROJECT_NAME} PRIVATE /permissive-)
else()
find_library(Z z)
find_library(BZ2 bz2)
target_link_libraries(${PROJECT_NAME} ${Z} ${BZ2})
endif()
GNUmakefile.in deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# 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.
firstTarget: all
empty =
space = $(empty) $(empty)
CXX = @CXX@
CXXFLAGS = @BOOST_CPPFLAGS@ \
@CXXFLAGS@ \
@CPPFLAGS@ \
@PTHREAD_CFLAGS@ \
@CIFPP_CFLAGS@
LDFLAGS = @BOOST_LDFLAGS@ \
@LDFLAGS@ \
@PTHREAD_CFLAGS@
LIBS = @PTHREAD_LIBS@ \
@CIFPP_LIBS@ \
@BOOST_PROGRAM_OPTIONS_LIB@ \
@BOOST_IOSTREAMS_LIB@ \
@BOOST_DATE_TIME_LIB@ \
@BOOST_REGEX_LIB@ \
@LIBS@
prefix = $(DESTDIR)@prefix@
exec_prefix = @exec_prefix@
bindir = @bindir@
datarootdir = @datarootdir@
datadir = @datadir@
mandir = @mandir@
GNUmakefile: config.status GNUmakefile.in
$(SHELL) ./config.status
# main build variables
PROGRAM = @PACKAGE_NAME@
VERSION = @PACKAGE_VERSION@
SEARCH_PATHS = src test @LIBCIFPP_DATA_DIR@
OBJECTS = $(PROGRAM).o
RESOURCES = mmcif_pdbx_v50.dic
# Use the DEBUG flag to build debug versions of the code
DEBUG = @DEBUG@
ifeq "$(DEBUG)" "1"
DEFINES += DEBUG
CXXFLAGS += -g -O0
LDFLAGS += -g
else
CXXFLAGS += -O2
DEFINES += NDEBUG
endif
MRC = @MRC@
USE_RSRC = @USE_RSRC@
VPATH += $(subst $(space),:,$(SEARCH_PATHS))
CXXFLAGS += -Wall -Wno-multichar
CXXFLAGS += $(DEFINES:%=-D%)
OBJDIR = obj
ifeq "$(DEBUG)" "1"
OBJDIR := $(OBJDIR).dbg
endif
$(OBJDIR):
mkdir -p $(OBJDIR)
$(OBJDIR)/%.o: %.cpp | $(OBJDIR)
@ echo ">>" $<
@ $(CXX) -MD -c -o $@ $< $(CFLAGS) $(CXXFLAGS)
# We have development releases and official releases, for each we
# maintain different versioning schemes.
ifneq "x@UPDATE_REVISION@" "x"
REVISION = $(shell git log --pretty=format:%h --max-count=1)
REVISION_FILE = version-info-$(REVISION).txt
$(REVISION_FILE):
rm -f version-info-*.txt
@ echo $(PROGRAM)-version: $(VERSION) > $@
@ git describe --match=build --dirty >> $@
@ git log --pretty=medium --date=iso8601 -1 >> $@
src/revision.hpp: $(REVISION_FILE)
@ echo 'const char kRevision[] = R"(' > $@
@ cat $? >> $@
@ echo ')";' >> $@
else
src/revision.hpp:
@ echo 'const char kRevision[] = R"(' > $@
@ echo $(PROGRAM)-version: $(VERSION) >> $@
@ echo Date: $$(TZ=GMT date +"%Y-%m-%d") >> $@
@ echo ')";' >> $@
endif
# The program rules
ifneq "$(USE_RSRC)" "0"
OBJECTS += $(PROGRAM)_rsrc.o
# dictionaries may be found compressed
%.dic: %.dic.gz
gunzip -c $^ > $@
$(OBJDIR)/$(PROGRAM)_rsrc.o: $(RESOURCES)
$(MRC) -o $@ $^
endif
$(OBJDIR)/$(PROGRAM).o: src/revision.hpp
$(PROGRAM): $(OBJECTS:%.o=$(OBJDIR)/%.o)
@ echo '->' $@
@ $(CXX) -o $@ $^ $(CXXFLAGS) $(LDFLAGS) $(LIBS)
$(OBJDIR)/%.d: $(OBJDIR)/%.o
-include $(OBJECTS:%.o=$(OBJDIR)/%.d)
.PHONY: clean all
clean:
rm -rf $(PROGRAM) $(OBJDIR)/* src/revision.hpp
all: $(PROGRAM)
.PHONY: install
install: $(PROGRAM)
install -d $(bindir)
install $(PROGRAM) $(bindir)/$(PROGRAM)
install -d $(mandir)/man1
install -m 644 doc/$(PROGRAM).1 $(mandir)/man1/$(PROGRAM).1;
gzip $(mandir)/man1/$(PROGRAM).1;
.PHONY: FORCE
FORCE:
.PHONY: test
test:
@ echo $(OBJECTS)
cmake/GetGitRevisionDescription.cmake 0 → 100644
# - Returns a version string from Git
#
# These functions force a re-configure on each git commit so that you can
# trust the values of the variables in your build system.
#
# get_git_head_revision(<refspecvar> <hashvar> [ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR])
#
# Returns the refspec and sha hash of the current head revision
#
# git_describe(<var> [<additional arguments to git describe> ...])
#
# Returns the results of git describe on the source tree, and adjusting
# the output so that it tests false if an error occurs.
#
# git_describe_working_tree(<var> [<additional arguments to git describe> ...])
#
# Returns the results of git describe on the working tree (--dirty option),
# and adjusting the output so that it tests false if an error occurs.
#
# git_get_exact_tag(<var> [<additional arguments to git describe> ...])
#
# Returns the results of git describe --exact-match on the source tree,
# and adjusting the output so that it tests false if there was no exact
# matching tag.
#
# git_local_changes(<var>)
#
# Returns either "CLEAN" or "DIRTY" with respect to uncommitted changes.
# Uses the return code of "git diff-index --quiet HEAD --".
# Does not regard untracked files.
#
# Requires CMake 2.6 or newer (uses the 'function' command)
#
# Original Author:
# 2009-2020 Ryan Pavlik <ryan.pavlik@gmail.com> <abiryan@ryand.net>
# http://academic.cleardefinition.com
#
# Copyright 2009-2013, Iowa State University.
# Copyright 2013-2020, Ryan Pavlik
# Copyright 2013-2020, Contributors
# SPDX-License-Identifier: BSL-1.0
# 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)
if(__get_git_revision_description)
return()
endif()
set(__get_git_revision_description YES)
# We must run the following at "include" time, not at function call time,
# to find the path to this module rather than the path to a calling list file
get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
# Function _git_find_closest_git_dir finds the next closest .git directory
# that is part of any directory in the path defined by _start_dir.
# The result is returned in the parent scope variable whose name is passed
# as variable _git_dir_var. If no .git directory can be found, the
# function returns an empty string via _git_dir_var.
#
# Example: Given a path C:/bla/foo/bar and assuming C:/bla/.git exists and
# neither foo nor bar contain a file/directory .git. This wil return
# C:/bla/.git
#
function(_git_find_closest_git_dir _start_dir _git_dir_var)
set(cur_dir "${_start_dir}")
set(git_dir "${_start_dir}/.git")
while(NOT EXISTS "${git_dir}")
# .git dir not found, search parent directories
set(git_previous_parent "${cur_dir}")
get_filename_component(cur_dir "${cur_dir}" DIRECTORY)
if(cur_dir STREQUAL git_previous_parent)
# We have reached the root directory, we are not in git
set(${_git_dir_var}
""
PARENT_SCOPE)
return()
endif()
set(git_dir "${cur_dir}/.git")
endwhile()
set(${_git_dir_var}
"${git_dir}"
PARENT_SCOPE)
endfunction()
function(get_git_head_revision _refspecvar _hashvar)
_git_find_closest_git_dir("${CMAKE_CURRENT_SOURCE_DIR}" GIT_DIR)
if("${ARGN}" STREQUAL "ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR")
set(ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR TRUE)
else()
set(ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR FALSE)
endif()
if(NOT "${GIT_DIR}" STREQUAL "")
file(RELATIVE_PATH _relative_to_source_dir "${CMAKE_SOURCE_DIR}"
"${GIT_DIR}")
if("${_relative_to_source_dir}" MATCHES "[.][.]" AND NOT ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR)
# We've gone above the CMake root dir.
set(GIT_DIR "")
endif()
endif()
if("${GIT_DIR}" STREQUAL "")
set(${_refspecvar}
"GITDIR-NOTFOUND"
PARENT_SCOPE)
set(${_hashvar}
"GITDIR-NOTFOUND"
PARENT_SCOPE)
return()
endif()
# Check if the current source dir is a git submodule or a worktree.
# In both cases .git is a file instead of a directory.
#
if(NOT IS_DIRECTORY ${GIT_DIR})
# The following git command will return a non empty string that
# points to the super project working tree if the current
# source dir is inside a git submodule.
# Otherwise the command will return an empty string.
#
execute_process(
COMMAND "${GIT_EXECUTABLE}" rev-parse
--show-superproject-working-tree
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
OUTPUT_VARIABLE out
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT "${out}" STREQUAL "")
# If out is empty, GIT_DIR/CMAKE_CURRENT_SOURCE_DIR is in a submodule
file(READ ${GIT_DIR} submodule)
string(REGEX REPLACE "gitdir: (.*)$" "\\1" GIT_DIR_RELATIVE
${submodule})
string(STRIP ${GIT_DIR_RELATIVE} GIT_DIR_RELATIVE)
get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH)
get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE}
ABSOLUTE)
set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD")
else()
# GIT_DIR/CMAKE_CURRENT_SOURCE_DIR is in a worktree
file(READ ${GIT_DIR} worktree_ref)
# The .git directory contains a path to the worktree information directory
# inside the parent git repo of the worktree.
#
string(REGEX REPLACE "gitdir: (.*)$" "\\1" git_worktree_dir
${worktree_ref})
string(STRIP ${git_worktree_dir} git_worktree_dir)
_git_find_closest_git_dir("${git_worktree_dir}" GIT_DIR)
set(HEAD_SOURCE_FILE "${git_worktree_dir}/HEAD")
endif()
else()
set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD")
endif()
set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
if(NOT EXISTS "${GIT_DATA}")
file(MAKE_DIRECTORY "${GIT_DATA}")
endif()
if(NOT EXISTS "${HEAD_SOURCE_FILE}")
return()
endif()
set(HEAD_FILE "${GIT_DATA}/HEAD")
configure_file("${HEAD_SOURCE_FILE}" "${HEAD_FILE}" COPYONLY)
configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
"${GIT_DATA}/grabRef.cmake" @ONLY)
include("${GIT_DATA}/grabRef.cmake")
set(${_refspecvar}
"${HEAD_REF}"
PARENT_SCOPE)
set(${_hashvar}
"${HEAD_HASH}"
PARENT_SCOPE)
endfunction()
function(git_describe _var)
if(NOT GIT_FOUND)
find_package(Git QUIET)
endif()
get_git_head_revision(refspec hash)
if(NOT GIT_FOUND)
set(${_var}
"GIT-NOTFOUND"
PARENT_SCOPE)
return()
endif()
if(NOT hash)
set(${_var}
"HEAD-HASH-NOTFOUND"
PARENT_SCOPE)
return()
endif()
# TODO sanitize
#if((${ARGN}" MATCHES "&&") OR
# (ARGN MATCHES "||") OR
# (ARGN MATCHES "\\;"))
# message("Please report the following error to the project!")
# message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
#endif()
#message(STATUS "Arguments to execute_process: ${ARGN}")
execute_process(
COMMAND "${GIT_EXECUTABLE}" describe --tags --always ${hash} ${ARGN}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
RESULT_VARIABLE res
OUTPUT_VARIABLE out
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT res EQUAL 0)
set(out "${out}-${res}-NOTFOUND")
endif()
set(${_var}
"${out}"
PARENT_SCOPE)
endfunction()
function(git_describe_working_tree _var)
if(NOT GIT_FOUND)
find_package(Git QUIET)
endif()
if(NOT GIT_FOUND)
set(${_var}
"GIT-NOTFOUND"
PARENT_SCOPE)
return()
endif()
execute_process(
COMMAND "${GIT_EXECUTABLE}" describe --dirty ${ARGN}
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
RESULT_VARIABLE res
OUTPUT_VARIABLE out
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT res EQUAL 0)
set(out "${out}-${res}-NOTFOUND")
endif()
set(${_var}
"${out}"
PARENT_SCOPE)
endfunction()
function(git_get_exact_tag _var)
git_describe(out --exact-match ${ARGN})
set(${_var}
"${out}"
PARENT_SCOPE)
endfunction()
function(git_local_changes _var)
if(NOT GIT_FOUND)
find_package(Git QUIET)
endif()
get_git_head_revision(refspec hash)
if(NOT GIT_FOUND)
set(${_var}
"GIT-NOTFOUND"
PARENT_SCOPE)
return()
endif()
if(NOT hash)
set(${_var}
"HEAD-HASH-NOTFOUND"
PARENT_SCOPE)
return()
endif()
execute_process(
COMMAND "${GIT_EXECUTABLE}" diff-index --quiet HEAD --
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
RESULT_VARIABLE res
OUTPUT_VARIABLE out
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(res EQUAL 0)
set(${_var}
"CLEAN"
PARENT_SCOPE)
else()
set(${_var}
"DIRTY"
PARENT_SCOPE)
endif()
endfunction()
cmake/GetGitRevisionDescription.cmake.in 0 → 100644
#
# Internal file for GetGitRevisionDescription.cmake
#
# Requires CMake 2.6 or newer (uses the 'function' command)
#
# Original Author:
# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
# http://academic.cleardefinition.com
# Iowa State University HCI Graduate Program/VRAC
#
# Copyright 2009-2012, Iowa State University
# Copyright 2011-2015, Contributors
# Distributed under the Boost Software License, Version 1.0.
# (See accompanying file LICENSE_1_0.txt or copy at
# http://www.boost.org/LICENSE_1_0.txt)
# SPDX-License-Identifier: BSL-1.0
set(HEAD_HASH)
file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS)
if(HEAD_CONTENTS MATCHES "ref")
# named branch
string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}")
if(EXISTS "@GIT_DIR@/${HEAD_REF}")
configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
else()
configure_file("@GIT_DIR@/packed-refs" "@GIT_DATA@/packed-refs" COPYONLY)
file(READ "@GIT_DATA@/packed-refs" PACKED_REFS)
if(${PACKED_REFS} MATCHES "([0-9a-z]*) ${HEAD_REF}")
set(HEAD_HASH "${CMAKE_MATCH_1}")
endif()
endif()
else()
# detached HEAD
configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY)
endif()
if(NOT HEAD_HASH)
file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024)
string(STRIP "${HEAD_HASH}" HEAD_HASH)
endif()
config/m4/ax_filesystem.m4 deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Description: m4 macro to detect std::filesystem and optionally the linker flags to use it
AC_DEFUN([AX_FILESYSTEM],
[
AC_CHECK_HEADER([filesystem], [], [AC_MSG_ERROR([The file <filesystem> is missing, perhaps you should install a more recent libstdc++ implementation.])])
dnl check if we need stdc++fs as library
AC_TRY_LINK(
[#include <filesystem>],
[(void)std::filesystem::current_path();],
[],
[
LIBS="$LIBS -lstdc++fs"
AC_TRY_LINK(
[#include <filesystem>],
[(void)std::filesystem::current_path();],
[],
[
AC_MSG_ERROR([Could not link filesystem])
]
)
]
)
])
config/m4/ax_libcifpp.m4 deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# 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.
#
# Description: m4 macro to detect std::filesystem and optionally the linker flags to use it
#
# Description: Check for libcifpp
AC_DEFUN([AX_LIBCIFPP],
[
AC_ARG_WITH([cif++],
AS_HELP_STRING([--with-cif++=@<:@location@:>@],
[Use the cif++ library as specified.]),
[
AS_IF([test -d ${withval}/include], [], [
AC_MSG_ERROR(['${withval}'' is not a valid directory for --with-cif++])
])
CIFPP_CFLAGS="-I ${withval}/include"
CIFPP_LIBS="-L${withval}/.libs -lcifpp"
LIBCIFPP_DATA_DIR="${withval}/rsrc"
AC_SUBST([CIFPP_CFLAGS], [$CIFPP_CFLAGS])
AC_SUBST([CIFPP_LIBS], [$CIFPP_LIBS])
])
AS_IF([test "x$CIFPP_LIBS" = "x"], [
if test -x "$PKG_CONFIG"
then
AX_PKG_CHECK_MODULES([CIFPP], [libcifpp], [], [], [AC_MSG_ERROR([the required package libcif++ is not installed])])
LIBCIFPP_DATA_DIR=$(pkg-config --variable=datalibdir libcifpp)
else
AC_CHECK_HEADER(
[cif++/Cif++.hpp],
[
dnl CIFPP_CFLAGS="-I ${withval}/include"
],
[AC_MSG_ERROR([
Can't find the libcif++ header, Config.hpp. Make sure that it
is installed, and either use the --with-cif++ option or install
pkg-config.])])
AX_CHECK_LIBRARY([CIFPP], [cif++/Cif++.hpp], [cifpp],
[
LIBS="-lcifpp $LIBS"
],
[AC_MSG_ERROR([libcif++ not found])])
AS_IF([ test -f /usr/local/share/libcifpp/mmcif_pdbx_v50.dic.gz ], [LIBCIFPP_DATA_DIR=/usr/local/share/libcifpp/ ])
AS_IF([ test -f /var/cache/libcifpp/mmcif_pdbx_v50.dic.gz ], [LIBCIFPP_DATA_DIR=/var/cache/libcifpp ])
fi
])
AC_ARG_VAR([LIBCIFPP_DATA_DIR], [Directory containing mmcif_pdbx_v50.dic file])
AC_SUBST([LIBCIFPP_DATA_DIR], [$LIBCIFPP_DATA_DIR])
])
\ No newline at end of file
config/m4/ax_mrc.m4 deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# 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.
#
# Description: m4 macro to detect mrc, the resource compiler
AC_DEFUN([AX_MRC],
[
AC_ARG_VAR([MRC], [Specify a location for the mrc executable])
dnl using resources?
USE_RSRC=0
if test "x$MRC" = "x"; then
AC_PATH_PROG([MRC], [mrc])
fi
if test "x$MRC" = "x"; then
AC_MSG_WARN([The mrc application was not found, not using resources.])
else
AC_ARG_ENABLE(
resources,
[AS_HELP_STRING([--disable-resources], [Do not use mrc to store data in resources])])
AS_IF([test "x$enable_resources" != "xno" ], [
USE_RSRC=1
])
fi
AC_SUBST([USE_RSRC], [$USE_RSRC])
AC_DEFINE_UNQUOTED([USE_RSRC], [$USE_RSRC], [Use mrc to store resources])
])
\ No newline at end of file
config/m4/ax_z_bz2.m4 deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# 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.
#
# Description: m4 macro to detect whether the z and bz2 libraries needs to be linked
# when using boost::iostreams
AC_DEFUN([read_test], [
AC_LANG_SOURCE(esyscmd(config/tools/m4esc.sh config/test/$1))])
AC_DEFUN([AX_IOSTREAMS_Z],
[
AC_MSG_CHECKING([need to link zlib])
save_CPPFLAGS="$CPPFLAGS"
CPPFLAGS="$BOOST_CPPFLAGS $CPPFLAGS "
save_LDFLAGS="$LDFLAGS"
LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
save_LIBS="$LIBS"
LIBS="$LIBS $BOOST $BOOST_IOSTREAMS_LIB"
NEED_ZLIB=0
AC_LINK_IFELSE(
[read_test(iostreams-zlib-test.cpp)],
[AC_MSG_RESULT([no])],
[
LIBS="$LIBS -lz"
AC_LINK_IFELSE(
[read_test(iostreams-zlib-test.cpp)],
[
AC_MSG_RESULT([yes])
NEED_ZLIB=1
],
[AC_MSG_ERROR([Could not link iostreams, even with zlib])])
])
CPPFLAGS="$save_CPPFLAGS"
LDFLAGS="$save_LDFLAGS"
LIBS="$save_LIBS"
if [ test "x$NEED_ZLIB" != "x" ]; then
LIBS="$LIBS -lz"
fi
])
AC_DEFUN([AX_IOSTREAMS_BZ2],
[
AC_MSG_CHECKING([need to link bzip2])
save_CPPFLAGS="$CPPFLAGS"
CPPFLAGS="$BOOST_CPPFLAGS $CPPFLAGS "
save_LDFLAGS="$LDFLAGS"
LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
save_LIBS="$LIBS"
LIBS="$LIBS $BOOST $BOOST_IOSTREAMS_LIB"
NEED_BZLIB=0
AC_LINK_IFELSE(
[read_test(iostreams-bzip2-test.cpp)],
[AC_MSG_RESULT([no])],
[
LIBS="$LIBS -lbz2"
AC_LINK_IFELSE(
[read_test(iostreams-bzip2-test.cpp)],
[
AC_MSG_RESULT([yes])
NEED_BZLIB=1
],
[AC_MSG_ERROR([Could not link iostreams, even with bzip2])])
])
CPPFLAGS="$save_CPPFLAGS"
LDFLAGS="$save_LDFLAGS"
LIBS="$save_LIBS"
if [ test "x$NEED_BZLIB" != "x" ]; then
LIBS="$LIBS -lbz2"
fi
])
\ No newline at end of file
config/test/iostreams-bzip2-test.cpp deleted 100644 → 0
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/bzip2.hpp>
namespace io = boost::iostreams;
int main()
{
io::filtering_stream<io::input> in;
in.push(io::bzip2_decompressor());
return 0;
}
config/test/iostreams-zlib-test.cpp deleted 100644 → 0
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
namespace io = boost::iostreams;
int main()
{
io::filtering_stream<io::input> in;
in.push(io::gzip_decompressor());
return 0;
}
config/tools/m4esc.sh deleted 100755 → 0
#!/bin/bash
set -e
file="$1"
echo -n "[["
while IFS= read -r line; do
echo $line | sed -e 's/\[/@<:@/g' -e 's/\]/@:>@/g' -e 's/#/@%:@/g' -e 's/\$/@S|@/g'
echo
done < "$file"
echo -n "]]"
configure deleted 100755 → 0
This source diff could not be displayed because it is too large. You can view the blob instead.
configure.ac deleted 100644 → 0
AC_PREREQ([2.69])
m4_define([dssp_version_major],[4])
m4_define([dssp_version_minor],[0])
m4_define([dssp_version_micro],[0])
m4_define([dssp_version_extra],[])
m4_define([dssp_version],[dssp_version_major().dssp_version_minor().dssp_version_micro()dssp_version_extra])
AC_INIT([mkdssp], [dssp_version], [m.hekkelman@nki.nl])
dnl Switch to a decent C++ compiler, and check if it works.
AC_LANG(C++)
AX_CXX_COMPILE_STDCXX_17([noext])
AX_CHECK_COMPILE_FLAG([-fstandalone-debug],
[
CXXFLAGS="$CXXFLAGS -fstandalone-debug"
] , , [-Werror])
AC_CONFIG_SRCDIR([src/mkdssp.cpp])
AC_CONFIG_AUX_DIR(config)
AC_CONFIG_MACRO_DIR([config/m4])
AC_CONFIG_HEADERS([src/config.hpp])
AC_PREFIX_DEFAULT(/usr/local)
AC_PROG_INSTALL
PKG_PROG_PKG_CONFIG
AX_PTHREAD
AC_ARG_VAR([DEBUG], [Build a debug version of the application])
AX_MRC
dnl revision numbering is something used internally at the NKI
AC_ARG_ENABLE(
revision,
[AS_HELP_STRING([--disable-revision], [Create a build number as revision])])
AS_IF([test "x$enable_revision" != "xno" ], [
UPDATE_REVISION=1
])
AC_SUBST([UPDATE_REVISION], [$UPDATE_REVISION])
AX_FILESYSTEM
AX_BOOST_BASE([1.65.1], [], [AC_MSG_ERROR([Could not find a recent version of boost])])
AX_BOOST_IOSTREAMS
AX_BOOST_PROGRAM_OPTIONS
AX_BOOST_DATE_TIME
AX_BOOST_REGEX
AX_IOSTREAMS_Z
AX_IOSTREAMS_BZ2
AX_LIBCIFPP
dnl These are still needed outside the Debian environment
AX_CHECK_LIBRARY([LIBZ], [zlib.h], [z],
[ LIBS="$LIBS -lz" ],
[AC_MSG_ERROR([libz not found - compressed files not supported])])
AX_CHECK_LIBRARY([LIBBZ2], [bzlib.h], [bz2],
[ LIBS="$LIBS -lbz2"],
[AC_MSG_ERROR([libbz2 not found - compressed files not supported])])
AC_SUBST([LIBS], [$LIBS])
dnl Process Makefile.in to create Makefile
AC_OUTPUT([GNUmakefile])
msvc/mkdssp.sln deleted 100644 → 0

Microsoft Visual Studio Solution File, Format Version 12.00
# Visual Studio Version 16
VisualStudioVersion = 16.0.31025.194
MinimumVisualStudioVersion = 10.0.40219.1
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "mkdssp", "mkdssp.vcxproj", "{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
Debug|x64 = Debug|x64
Release|x64 = Release|x64
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}.Debug|x64.ActiveCfg = Debug|x64
{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}.Debug|x64.Build.0 = Debug|x64
{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}.Release|x64.ActiveCfg = Release|x64
{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}.Release|x64.Build.0 = Release|x64
EndGlobalSection
GlobalSection(SolutionProperties) = preSolution
HideSolutionNode = FALSE
EndGlobalSection
GlobalSection(ExtensibilityGlobals) = postSolution
SolutionGuid = {15535352-DFF9-46BB-A6F8-9E3E2B54024F}
EndGlobalSection
EndGlobal
msvc/mkdssp.vcxproj deleted 100644 → 0
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup Label="ProjectConfigurations">
<ProjectConfiguration Include="Debug|Win32">
<Configuration>Debug</Configuration>
<Platform>Win32</Platform>
</ProjectConfiguration>
<ProjectConfiguration Include="Release|Win32">
<Configuration>Release</Configuration>
<Platform>Win32</Platform>
</ProjectConfiguration>
<ProjectConfiguration Include="Debug|x64">
<Configuration>Debug</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
<ProjectConfiguration Include="Release|x64">
<Configuration>Release</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
</ItemGroup>
<PropertyGroup Label="Globals">
<VCProjectVersion>16.0</VCProjectVersion>
<ProjectGuid>{AA05C8D5-829B-4F96-A3E6-E734FB3A1B1E}</ProjectGuid>
<Keyword>Win32Proj</Keyword>
<WindowsTargetPlatformVersion>10.0</WindowsTargetPlatformVersion>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
<ConfigurationType>Application</ConfigurationType>
<UseDebugLibraries>true</UseDebugLibraries>
<PlatformToolset>v142</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
<ConfigurationType>Application</ConfigurationType>
<UseDebugLibraries>false</UseDebugLibraries>
<PlatformToolset>v142</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
<ConfigurationType>Application</ConfigurationType>
<UseDebugLibraries>true</UseDebugLibraries>
<PlatformToolset>v142</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
<ConfigurationType>Application</ConfigurationType>
<UseDebugLibraries>false</UseDebugLibraries>
<PlatformToolset>v142</PlatformToolset>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
<ImportGroup Label="ExtensionSettings">
</ImportGroup>
<ImportGroup Label="Shared">
</ImportGroup>
<ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
<ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
<ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
<ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
<PropertyGroup Label="UserMacros" />
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
<LinkIncremental>true</LinkIncremental>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
<LinkIncremental>true</LinkIncremental>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<IncludePath>$(VC_IncludePath);$(WindowsSDK_IncludePath);$(SolutionDir)\..\..\boost_1_75_0;$(SolutionDir)\..\..\libcifpp\include</IncludePath>
<LibraryPath>$(VC_LibraryPath_x64);$(WindowsSDK_LibraryPath_x64);$(SolutionDir)\..\..\boost_1_75_0\stage\lib;$(SolutionDir)\..\..\libcifpp\msvc\$(Platform)\$(Configuration)</LibraryPath>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
<IncludePath>$(VC_IncludePath);$(WindowsSDK_IncludePath);$(SolutionDir)\..\..\boost_1_75_0;$(SolutionDir)\..\..\libcifpp\include</IncludePath>
<LibraryPath>$(VC_LibraryPath_x64);$(WindowsSDK_LibraryPath_x64);$(SolutionDir)\..\..\boost_1_75_0\stage\lib;$(SolutionDir)\..\..\libcifpp\msvc\$(Platform)\$(Configuration)</LibraryPath>
</PropertyGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
<ClCompile>
<PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
<RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
<WarningLevel>Level3</WarningLevel>
<DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
<Optimization>Disabled</Optimization>
</ClCompile>
<Link>
<TargetMachine>MachineX86</TargetMachine>
<GenerateDebugInformation>true</GenerateDebugInformation>
<SubSystem>Windows</SubSystem>
</Link>
</ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
<ClCompile>
<PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
<RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
<WarningLevel>Level3</WarningLevel>
<DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
</ClCompile>
<Link>
<TargetMachine>MachineX86</TargetMachine>
<GenerateDebugInformation>true</GenerateDebugInformation>
<SubSystem>Windows</SubSystem>
<EnableCOMDATFolding>true</EnableCOMDATFolding>
<OptimizeReferences>true</OptimizeReferences>
</Link>
</ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
<ClCompile>
<LanguageStandard>stdcpp17</LanguageStandard>
<RuntimeLibrary>MultiThreaded</RuntimeLibrary>
<ConformanceMode>true</ConformanceMode>
<EnableModules>true</EnableModules>
<AdditionalIncludeDirectories>$(SolutionDir)\..\src</AdditionalIncludeDirectories>
</ClCompile>
<Link>
<AdditionalDependencies>kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;libcifpp.lib;%(AdditionalDependencies)</AdditionalDependencies>
</Link>
</ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<ClCompile>
<RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
<LanguageStandard>stdcpp17</LanguageStandard>
<ConformanceMode>true</ConformanceMode>
<EnableModules>true</EnableModules>
<AdditionalIncludeDirectories>$(SolutionDir)\..\src</AdditionalIncludeDirectories>
</ClCompile>
<Link>
<AdditionalDependencies>kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;libcifpp.lib;%(AdditionalDependencies)</AdditionalDependencies>
</Link>
</ItemDefinitionGroup>
<ItemGroup>
<ClCompile Include="..\src\mkdssp.cpp" />
</ItemGroup>
<ItemGroup>
<Object Include="..\mkdssp_rsrc.obj" />
</ItemGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
<ImportGroup Label="ExtensionTargets">
</ImportGroup>
</Project>
\ No newline at end of file
msvc/mkdssp.vcxproj.filters deleted 100644 → 0
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup>
<Filter Include="Source Files">
<UniqueIdentifier>{4FC737F1-C7A5-4376-A066-2A32D752A2FF}</UniqueIdentifier>
<Extensions>cpp;c;cc;cxx;def;odl;idl;hpj;bat;asm;asmx</Extensions>
</Filter>
<Filter Include="Header Files">
<UniqueIdentifier>{93995380-89BD-4b04-88EB-625FBE52EBFB}</UniqueIdentifier>
<Extensions>h;hh;hpp;hxx;hm;inl;inc;xsd</Extensions>
</Filter>
<Filter Include="Resource Files">
<UniqueIdentifier>{67DA6AB6-F800-4c08-8B7A-83BB121AAD01}</UniqueIdentifier>
<Extensions>rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav</Extensions>
</Filter>
</ItemGroup>
<ItemGroup>
<ClCompile Include="..\src\mkdssp.cpp">
<Filter>Source Files</Filter>
</ClCompile>
</ItemGroup>
<ItemGroup>
<Object Include="..\mkdssp_rsrc.obj">
<Filter>Source Files</Filter>
</Object>
</ItemGroup>
</Project>
\ No newline at end of file
msvc/mkdssp.vcxproj.user deleted 100644 → 0
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="Current" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<LocalDebuggerCommandArguments>../libcifpp/examples/1cbs.cif.gz</LocalDebuggerCommandArguments>
<LocalDebuggerWorkingDirectory>$(SolutionDir)\..\</LocalDebuggerWorkingDirectory>
<DebuggerFlavor>WindowsLocalDebugger</DebuggerFlavor>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
<LocalDebuggerCommandArguments>../libcifpp/examples/1cbs.cif.gz</LocalDebuggerCommandArguments>
<LocalDebuggerWorkingDirectory>$(SolutionDir)\..\</LocalDebuggerWorkingDirectory>
<DebuggerFlavor>WindowsLocalDebugger</DebuggerFlavor>
</PropertyGroup>
</Project>
\ No newline at end of file
src/config.hpp.in deleted 100644 → 0
/* src/config.hpp.in. Generated from configure.ac by autoheader. */
/* define if the Boost library is available */
#undef HAVE_BOOST
/* define if the Boost::Date_Time library is available */
#undef HAVE_BOOST_DATE_TIME
/* define if the Boost::IOStreams library is available */
#undef HAVE_BOOST_IOSTREAMS
/* define if the Boost::PROGRAM_OPTIONS library is available */
#undef HAVE_BOOST_PROGRAM_OPTIONS
/* define if the Boost::Regex library is available */
#undef HAVE_BOOST_REGEX
/* Define to 1 if CIFPP is found */
#undef HAVE_CIFPP
/* define if the compiler supports basic C++17 syntax */
#undef HAVE_CXX17
/* Define to 1 if you have the <inttypes.h> header file. */
#undef HAVE_INTTYPES_H
/* Define to 1 if LIBBZ2 is found */
#undef HAVE_LIBBZ2
/* Define to 1 if LIBZ is found */
#undef HAVE_LIBZ
/* Define to 1 if you have the <memory.h> header file. */
#undef HAVE_MEMORY_H
/* Define if you have POSIX threads libraries and header files. */
#undef HAVE_PTHREAD
/* Have PTHREAD_PRIO_INHERIT. */
#undef HAVE_PTHREAD_PRIO_INHERIT
/* Define to 1 if you have the <stdint.h> header file. */
#undef HAVE_STDINT_H
/* Define to 1 if you have the <stdlib.h> header file. */
#undef HAVE_STDLIB_H
/* Define to 1 if you have the <strings.h> header file. */
#undef HAVE_STRINGS_H
/* Define to 1 if you have the <string.h> header file. */
#undef HAVE_STRING_H
/* Define to 1 if you have the <sys/stat.h> header file. */
#undef HAVE_SYS_STAT_H
/* Define to 1 if you have the <sys/types.h> header file. */
#undef HAVE_SYS_TYPES_H
/* Define to 1 if you have the <unistd.h> header file. */
#undef HAVE_UNISTD_H
/* Define to the address where bug reports for this package should be sent. */
#undef PACKAGE_BUGREPORT
/* Define to the full name of this package. */
#undef PACKAGE_NAME
/* Define to the full name and version of this package. */
#undef PACKAGE_STRING
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
/* Define to the home page for this package. */
#undef PACKAGE_URL
/* Define to the version of this package. */
#undef PACKAGE_VERSION
/* Define to necessary symbol if this constant uses a non-standard name on
your system. */
#undef PTHREAD_CREATE_JOINABLE
/* Define to 1 if you have the ANSI C header files. */
#undef STDC_HEADERS
/* Use mrc to store resources */
#undef USE_RSRC
src/mkdssp.cpp
...@@ -80,11 +80,7 @@ void load_version_info() ...@@ -80,11 +80,7 @@ void load_version_info()
rxVersionDate(R"(Date: +(\d{4}-\d{2}-\d{2}).*)"), rxVersionDate(R"(Date: +(\d{4}-\d{2}-\d{2}).*)"),
rxVersionNr2(R"(mkdssp-version: (\d+(?:\.\d+)+))"); rxVersionNr2(R"(mkdssp-version: (\d+(?:\.\d+)+))");
#if __has_include("revision.hpp")
#include "revision.hpp" #include "revision.hpp"
#else
const char* kRevision = "";
#endif
struct membuf : public std::streambuf struct membuf : public std::streambuf
{ {
...@@ -624,6 +620,10 @@ int main(int argc, const char* argv[]) ...@@ -624,6 +620,10 @@ int main(int argc, const char* argv[])
try try
{ {
#if defined(DATA_DIR)
cif::addDataDirectory(DATA_DIR);
#endif
load_version_info(); load_version_info();
result = d_main(argc, argv); result = d_main(argc, argv);
......
src/pr-main.cpp deleted 100644 → 0
/* include/cif++/Config.hpp. Generated from Config.hpp.in by configure. */
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
*
* 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.
*/
#if _MSC_VER
#include <time.h>
#include <winsock.h>
#else
#include <sys/time.h>
#include <sys/resource.h>
#endif
#include <stdexcept>
#include <iostream>
#include <iomanip>
#include <chrono>
#include <cmath>
#include <regex>
#include "cif++/Cif++.hpp"
#include "cif++/CifUtils.hpp"
std::string VERSION_STRING;
int pr_main(int argc, char* argv[]);
// --------------------------------------------------------------------
std::ostream& operator<<(std::ostream& os, const struct timeval& t)
{
uint64_t s = t.tv_sec;
if (s > 24 * 60 * 60)
{
uint32_t days = s / (24 * 60 * 60);
os << days << "d ";
s %= 24 * 60 * 60;
}
if (s > 60 * 60)
{
uint32_t hours = s / (60 * 60);
os << hours << "h ";
s %= 60 * 60;
}
if (s > 60)
{
uint32_t minutes = s / 60;
os << minutes << "m ";
s %= 60;
}
double ss = s + 1e-6 * t.tv_usec;
os << std::fixed << std::setprecision(1) << ss << 's';
return os;
}
std::ostream& operator<<(std::ostream& os, const std::chrono::duration<double>& t)
{
uint64_t s = static_cast<uint64_t>(std::trunc(t.count()));
if (s > 24 * 60 * 60)
{
uint32_t days = s / (24 * 60 * 60);
os << days << "d ";
s %= 24 * 60 * 60;
}
if (s > 60 * 60)
{
uint32_t hours = s / (60 * 60);
os << hours << "h ";
s %= 60 * 60;
}
if (s > 60)
{
uint32_t minutes = s / 60;
os << minutes << "m ";
s %= 60;
}
double ss = s + 1e-6 * (t.count() - s);
os << std::fixed << std::setprecision(1) << ss << 's';
return os;
}
class RUsage
{
public:
~RUsage()
{
#if not _MSC_VER
if (cif::VERBOSE)
{
struct rusage u;
auto end = std::chrono::system_clock::now();
std::chrono::duration<double> diff = end - start;
if (getrusage(RUSAGE_SELF, &u) == 0)
std::cerr << "CPU usage: "
<< u.ru_utime << " user, "
<< u.ru_stime << " system, "
<< diff << " wall" << std::endl;
else
perror("Failed to get rusage");
}
#endif
}
std::chrono::time_point<std::chrono::system_clock> start = std::chrono::system_clock::now();
};
// --------------------------------------------------------------------
namespace {
std::string gVersionNr, gVersionDate;
}
void load_version_info()
{
const std::regex
rxVersionNr(R"(build-(\d+)-g[0-9a-f]{7}(-dirty)?)"),
rxVersionDate(R"(Date: +(\d{4}-\d{2}-\d{2}).*)");
#if __has_include("revision.hpp")
#include "revision.hpp"
#else
const char* kRevision = "";
#endif
struct membuf : public std::streambuf
{
membuf(char* data, size_t length) { this->setg(data, data, data + length); }
} buffer(const_cast<char*>(kRevision), sizeof(kRevision));
std::istream is(&buffer);
std::string line;
while (getline(is, line))
{
std::smatch m;
if (std::regex_match(line, m, rxVersionNr))
{
gVersionNr = m[1];
if (m[2].matched)
gVersionNr += '*';
continue;
}
if (std::regex_match(line, m, rxVersionDate))
{
gVersionDate = m[1];
continue;
}
}
if (not VERSION_STRING.empty())
VERSION_STRING += "\n";
VERSION_STRING += gVersionNr + '.' + cif::get_version_nr() + " " + gVersionDate;
}
std::string get_version_nr()
{
return gVersionNr + '/' + cif::get_version_nr();
}
std::string get_version_date()
{
return gVersionDate;
}
// --------------------------------------------------------------------
// recursively print exception whats:
void print_what (const std::exception& e)
{
std::cerr << e.what() << std::endl;
try
{
std::rethrow_if_nested(e);
}
catch (const std::exception& nested)
{
std::cerr << " >> ";
print_what(nested);
}
}
int main(int argc, char* argv[])
{
int result = -1;
RUsage r;
try
{
#if not _MSC_VER
cif::rsrc_loader::init({
{ cif::rsrc_loader_type::file, "." },
#if defined DATADIR
{ cif::rsrc_loader_type::file, DATADIR },
#endif
#if USE_RSRC
{ cif::rsrc_loader_type::mrsrc, "", { gResourceIndex, gResourceData, gResourceName } }
#endif
});
#endif
load_version_info();
result = pr_main(argc, argv);
}
catch (std::exception& ex)
{
print_what(ex);
exit(1);
}
return result;
}
src/revision.hpp.in 0 → 100644
const char kRevision[] = R"(
mkdssp-version: @PROJECT_VERSION@
@BUILD_VERSION_STRING@
Date: @BUILD_DATE_TIME@
)";
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment