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dssp
Commit dd8a9c3c by Maarten L. Hekkelman
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refactored into a lib and an executable

parent 833a10f3
Showing with 532 additions and 453 deletions
.gitignore
...@@ -4,3 +4,4 @@ build/ ...@@ -4,3 +4,4 @@ build/
.gdb_history .gdb_history
**/*.dssp **/*.dssp
src/revision.hpp src/revision.hpp
libdssp/src/revision.hpp
CMakeLists.txt
...@@ -108,23 +108,7 @@ if(NOT PDB_REDO_META) ...@@ -108,23 +108,7 @@ if(NOT PDB_REDO_META)
find_package(cifpp 5.1.0 REQUIRED) find_package(cifpp 5.1.0 REQUIRED)
endif() endif()
# The DSSP code is in a separate library, optionally to be used by others add_subdirectory(libdssp)
add_library(dssp
${PROJECT_SOURCE_DIR}/src/dssp.cpp
${PROJECT_SOURCE_DIR}/include/dssp.hpp
${PROJECT_SOURCE_DIR}/src/dssp-io.cpp
${PROJECT_SOURCE_DIR}/src/dssp-io.hpp
)
add_library(dssp::dssp ALIAS dssp)
target_link_libraries(dssp PUBLIC cifpp::cifpp)
target_include_directories(dssp
PUBLIC
"$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
)
add_executable(mkdssp ${PROJECT_SOURCE_DIR}/src/mkdssp.cpp) add_executable(mkdssp ${PROJECT_SOURCE_DIR}/src/mkdssp.cpp)
...@@ -134,87 +118,14 @@ if(USE_RSRC) ...@@ -134,87 +118,14 @@ if(USE_RSRC)
mrc_target_resources(mkdssp mrc_target_resources(mkdssp
${CIFPP_SHARE_DIR}/mmcif_pdbx.dic ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic
${CIFPP_SHARE_DIR}/mmcif_ddl.dic ${CIFPP_SHARE_DIR}/mmcif_ddl.dic
${PROJECT_SOURCE_DIR}/mmcif_pdbx/dssp-extension.dic) ${PROJECT_SOURCE_DIR}/libdssp/mmcif_pdbx/dssp-extension.dic)
endif() endif()
# Install rules # Install rules
install(TARGETS dssp
EXPORT dsspTargets
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
if(MSVC AND BUILD_SHARED_LIBS)
install(
FILES $<TARGET_PDB_FILE:${PROJECT_NAME}>
DESTINATION ${CMAKE_INSTALL_LIBDIR}
OPTIONAL)
endif()
install(EXPORT dsspTargets
FILE "dsspTargets.cmake"
NAMESPACE dssp::
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/dssp
)
install(
FILES include/dssp.hpp
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
COMPONENT Devel
)
set(CONFIG_TEMPLATE_FILE ${PROJECT_SOURCE_DIR}/cmake/dsspConfig.cmake.in)
configure_package_config_file(
${CONFIG_TEMPLATE_FILE}
${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfig.cmake
INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/dssp
)
install(FILES
"${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfig.cmake"
"${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfigVersion.cmake"
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/dssp
COMPONENT Devel
)
set(dssp_MAJOR_VERSION ${CMAKE_PROJECT_VERSION_MAJOR})
set_target_properties(dssp PROPERTIES
VERSION ${PROJECT_VERSION}
SOVERSION ${dssp_MAJOR_VERSION}
INTERFACE_dssp_MAJOR_VERSION ${dssp_MAJOR_VERSION})
set_property(TARGET dssp APPEND PROPERTY
COMPATIBLE_INTERFACE_STRING dssp_MAJOR_VERSION
)
write_basic_package_version_file(
"${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfigVersion.cmake"
VERSION ${PROJECT_VERSION}
COMPATIBILITY AnyNewerVersion
)
# pkgconfig support
set(prefix ${CMAKE_INSTALL_PREFIX})
set(exec_prefix ${CMAKE_INSTALL_PREFIX})
set(libdir ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
set(includedir ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/libdssp.pc.in
${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc.in @ONLY)
file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc
INPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc.in)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(TARGETS ${PROJECT_NAME} install(TARGETS ${PROJECT_NAME}
RUNTIME DESTINATION ${BIN_INSTALL_DIR} RUNTIME DESTINATION ${BIN_INSTALL_DIR}
) )
set(CIFPP_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}/libcifpp")
install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/mmcif_pdbx/dssp-extension.dic"
DESTINATION ${CIFPP_DATA_DIR})
if(GENERATE_DOCUMENTATION) if(GENERATE_DOCUMENTATION)
# manual # manual
find_program(PANDOC pandoc) find_program(PANDOC pandoc)
...@@ -268,12 +179,12 @@ if(ENABLE_TESTING) ...@@ -268,12 +179,12 @@ if(ENABLE_TESTING)
# We still depend on boost for the testing headers-only library # We still depend on boost for the testing headers-only library
find_package(Boost REQUIRED) find_package(Boost REQUIRED)
add_executable(unit-test-dssp ${PROJECT_SOURCE_DIR}/test/unit-test-dssp.cpp ${PROJECT_SOURCE_DIR}/src/dssp-io.cpp) add_executable(unit-test-dssp ${PROJECT_SOURCE_DIR}/test/unit-test-dssp.cpp ${PROJECT_SOURCE_DIR}/libdssp/src/dssp-io.cpp)
if(USE_RSRC) if(USE_RSRC)
mrc_target_resources(unit-test-dssp mrc_target_resources(unit-test-dssp
${CIFPP_SHARE_DIR}/mmcif_pdbx.dic ${CIFPP_SHARE_DIR}/mmcif_ddl.dic ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic ${CIFPP_SHARE_DIR}/mmcif_ddl.dic
${CMAKE_CURRENT_SOURCE_DIR}/mmcif_pdbx/dssp-extension.dic) ${CMAKE_CURRENT_SOURCE_DIR}/libdssp/mmcif_pdbx/dssp-extension.dic)
endif() endif()
target_include_directories(unit-test-dssp PRIVATE target_include_directories(unit-test-dssp PRIVATE
......
cmake/GetGitRevisionDescription.cmake deleted 100644 → 0
# - 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(${_var}
"DIRTY"
PARENT_SCOPE)
endif()
endfunction()
cmake/GetGitRevisionDescription.cmake.in deleted 100644 → 0
#
# Internal file for GetGitRevisionDescription.cmake
#
# Requires CMake 2.6 or newer (uses the 'function' command)
#
# Original Author:
# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
# http://academic.cleardefinition.com
# Iowa State University HCI Graduate Program/VRAC
#
# Copyright 2009-2012, Iowa State University
# Copyright 2011-2015, Contributors
# Distributed under the Boost Software License, Version 1.0.
# (See accompanying file LICENSE_1_0.txt or copy at
# http://www.boost.org/LICENSE_1_0.txt)
# SPDX-License-Identifier: BSL-1.0
set(HEAD_HASH)
file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
string(STRIP "${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()
cmake/VersionString.cmake
# SPDX-License-Identifier: BSD-2-Clause # SPDX-License-Identifier: BSD-2-Clause
# Copyright (c) 2021 NKI/AVL, Netherlands Cancer Institute # Copyright (c) 2021-2023 NKI/AVL, Netherlands Cancer Institute
# Redistribution and use in source and binary forms, with or without # Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met: # modification, are permitted provided that the following conditions are met:
...@@ -22,60 +22,359 @@ ...@@ -22,60 +22,359 @@
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# This cmake extension writes out a revision.hpp file in a specified directory.
# The file will contain a C++ inline function that can be used to write out
# version information.
cmake_minimum_required(VERSION 3.15) cmake_minimum_required(VERSION 3.15)
# We want the revision.hpp file to be updated whenever the status of the
# git repository changes. Use the same technique as in GetGitRevisionDescription.cmake
#[=======================================================================[.rst:
.. command:: write_version_header
Write a file named revision.hpp containing version info::
write_version_header(<destdir>
[FILE_NAME <file-name>]
[LIB_NAME <library-name>]
)
This command will generate the code to write a file name
revision.hpp in the directory ``<destdir>``.
``FILE_NAME``
Specify the name of the file to create, default is ``revision.hpp``.
``LIB_NAME``
Specify the library name which will be used as a prefix part for the
variables contained in the revision file.
#]=======================================================================]
# First locate a .git file or directory.
function(_get_git_dir _start_dir _variable)
set(cur_dir "${_start_dir}")
set(git_dir "${_start_dir}/.git")
while(NOT EXISTS "${git_dir}")
# .git dir not found, search parent directories
set(prev_dir "${cur_dir}")
get_filename_component(cur_dir "${cur_dir}" DIRECTORY)
if(cur_dir STREQUAL prev_dir OR cur_dir STREQUAL ${_start_dir})
# we are not in git since we either hit root or
# the CMAKE_SOURCE_DIR which should be the top
set(${_variable}
""
PARENT_SCOPE)
return()
endif()
set(git_dir "${cur_dir}/.git")
endwhile()
set(${_variable} "${git_dir}" PARENT_SCOPE)
endfunction()
# Locate the git refspec hash and load the hash
# This code locates the file containing the git refspec/hash
# and loads it. Doing it this way assures that each time the git
# repository changes the revision.hpp file gets out of date.
function(_get_git_hash _data_dir _variable)
# Be pessimistic
set(_variable "" PARENT_SCOPE)
# Load git package if needed
if(NOT GIT_FOUND)
find_package(Git QUIET)
endif()
# And fail if not found
if(NOT GIT_FOUND)
return()
endif()
# Locate the nearest .git file or directory
_get_git_dir(${CMAKE_CURRENT_SOURCE_DIR} GIT_DIR)
# And fail if not found
if("${GIT_DIR}" STREQUAL "")
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(IS_DIRECTORY ${GIT_DIR})
set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD")
else()
# 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 not 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 ${git_worktree_dir} git_worktree_dir)
_get_git_dir("${git_worktree_dir}" GIT_DIR)
set(HEAD_SOURCE_FILE "${git_worktree_dir}/HEAD")
endif()
endif()
# Fail if the 'head' file was not found
if(NOT EXISTS "${HEAD_SOURCE_FILE}")
return()
endif()
# Make a copy of the head file
set(HEAD_FILE "${_data_dir}/HEAD")
configure_file("${HEAD_SOURCE_FILE}" "${HEAD_FILE}" COPYONLY)
# Now we create a cmake file that will read the contents of this
# head file in the appropriate way
file(WRITE "${_data_dir}/grab-ref.cmake.in" [[
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}" "@VERSION_STRING_DATA@/head-ref" COPYONLY)
else()
configure_file("@GIT_DIR@/packed-refs" "@VERSION_STRING_DATA@/packed-refs" COPYONLY)
file(READ "@VERSION_STRING_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" "@VERSION_STRING_DATA@/head-ref" COPYONLY)
endif()
if(NOT HEAD_HASH)
file(READ "@VERSION_STRING_DATA@/head-ref" HEAD_HASH LIMIT 1024)
string(STRIP "${HEAD_HASH}" HEAD_HASH)
endif()
]])
configure_file("${VERSION_STRING_DATA}/grab-ref.cmake.in"
"${VERSION_STRING_DATA}/grab-ref.cmake" @ONLY)
# Include the aforementioned file, this will define
# the HEAD_HASH variable we're looking for
include("${VERSION_STRING_DATA}/grab-ref.cmake")
set(${_variable} "${HEAD_HASH}" PARENT_SCOPE)
endfunction()
# Create a revision file, containing the current git version info, if any # Create a revision file, containing the current git version info, if any
function(write_version_header dir) function(write_version_header dir)
set(flags )
set(options LIB_NAME FILE_NAME)
set(sources )
cmake_parse_arguments(VERSION_STRING_OPTION "${flags}" "${options}" "${sources}" ${ARGN})
# parameter check # parameter check
if(NOT IS_DIRECTORY ${dir}) if(NOT IS_DIRECTORY ${dir})
message(FATAL_ERROR "First parameter to write_version_header should be a directory where the final revision.hpp file will be placed") message(FATAL_ERROR "First parameter to write_version_header should be a directory where the final revision.hpp file will be placed")
endif() endif()
include(GetGitRevisionDescription) if(VERSION_STRING_OPTION_FILE_NAME)
if(NOT(GIT-NOTFOUND OR HEAD-HASH-NOTFOUND)) set(file_name "${VERSION_STRING_OPTION_FILE_NAME}")
git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty)
if(BUILD_VERSION_STRING MATCHES "build-([0-9]+)-g([0-9a-f]+)(-dirty)?")
set(BUILD_GIT_TAGREF "${CMAKE_MATCH_2}")
if(CMAKE_MATCH_3)
set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}*")
else() else()
set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}") set(file_name "revision.hpp")
endif()
# Where to store intermediate files
set(VERSION_STRING_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/VersionString")
if(NOT EXISTS "${VERSION_STRING_DATA}")
file(MAKE_DIRECTORY "${VERSION_STRING_DATA}")
endif()
# Load the git hash using the wizzard-like code above.
_get_git_hash("${VERSION_STRING_DATA}" GIT_HASH)
# If git was found, fetch the git description string
if(GIT_HASH)
execute_process(
COMMAND "${GIT_EXECUTABLE}" describe --dirty --match=build
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
RESULT_VARIABLE res
OUTPUT_VARIABLE out
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(res EQUAL 0)
set(REVISION_STRING "${out}")
endif() endif()
endif() endif()
# Check the revision string, if it matches we fill in the required info
if(REVISION_STRING MATCHES "build-([0-9]+)-g([0-9a-f]+)(-dirty)?")
set(BUILD_NUMBER ${CMAKE_MATCH_1})
if(CMAKE_MATCH_3)
set(REVISION_GIT_TAGREF "${CMAKE_MATCH_2}*")
else() else()
message(WARNING "no git info available, cannot update version string") set(REVISION_GIT_TAGREF "${CMAKE_MATCH_2}")
endif() endif()
string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC) string(TIMESTAMP REVISION_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC)
else()
message(STATUS "no git info available, cannot update version string")
if(ARGC GREATER 1) set(REVISION_GIT_TAGREF "")
set(VAR_PREFIX "${ARGV1}") set(BUILD_NUMBER 0)
set(REVISION_DATE_TIME "")
endif() endif()
file(WRITE "${PROJECT_BINARY_DIR}/revision.hpp.in" [[// Generated revision file if(VERSION_STRING_OPTION_LIB_NAME)
set(VAR_PREFIX "${VERSION_STRING_OPTION_LIB_NAME}")
set(IDENT_PREFIX "${VERSION_STRING_OPTION_LIB_NAME}_")
else()
set(VAR_PREFIX "")
set(IDENT_PREFIX "")
endif()
file(WRITE "${VERSION_STRING_DATA}/${file_name}.in" [[// This file was generated by VersionString.cmake
#pragma once #pragma once
#include <ostream> #include <ostream>
const char k@VAR_PREFIX@ProjectName[] = "@PROJECT_NAME@"; constexpr const char k@VAR_PREFIX@ProjectName[] = "@PROJECT_NAME@";
const char k@VAR_PREFIX@VersionNumber[] = "@PROJECT_VERSION@"; constexpr const char k@VAR_PREFIX@VersionNumber[] = "@PROJECT_VERSION@";
const char k@VAR_PREFIX@VersionGitTag[] = "@BUILD_GIT_TAGREF@"; constexpr int k@VAR_PREFIX@BuildNumber = @BUILD_NUMBER@;
const char k@VAR_PREFIX@BuildInfo[] = "@BUILD_VERSION_STRING@"; constexpr const char k@VAR_PREFIX@RevisionGitTag[] = "@REVISION_GIT_TAGREF@";
const char k@VAR_PREFIX@BuildDate[] = "@BUILD_DATE_TIME@"; constexpr const char k@VAR_PREFIX@RevisionDate[] = "@REVISION_DATE_TIME@";
inline void write_version_string(std::ostream &os, bool verbose) #ifndef VERSION_INFO_DEFINED
#define VERSION_INFO_DEFINED 1
class version_info_base
{ {
os << k@VAR_PREFIX@ProjectName << " version " << k@VAR_PREFIX@VersionNumber << std::endl; public:
virtual ~version_info_base() = default;
static void write(std::ostream &os, bool verbose)
{
auto s_head = head();
if (s_head != nullptr)
write(s_head, os, verbose);
}
protected:
struct instance
{
const char *m_name;
const char *m_version;
int m_build;
const char *m_git_tag;
const char *m_revision_date;
instance *m_next = nullptr;
};
static void write(const instance *inst, std::ostream &os, bool verbose)
{
if (inst->m_next != nullptr)
{
write(inst->m_next, os, verbose);
if (not verbose)
return;
os << '-' << std::endl;
}
os << inst->m_name << " version " << inst->m_version << std::endl;
if (verbose) if (verbose)
{ {
os << "build: " << k@VAR_PREFIX@BuildInfo << ' ' << k@VAR_PREFIX@BuildDate << std::endl; if (inst->m_build != 0)
if (k@VAR_PREFIX@VersionGitTag[0] != 0) {
os << "git tag: " << k@VAR_PREFIX@VersionGitTag << std::endl; os << "build: " << inst->m_build << ' ' << inst->m_revision_date << std::endl;
if (inst->m_git_tag[0] != 0)
os << "git tag: " << inst->m_git_tag << std::endl;
}
else
os << "No revision information available" << std::endl;
}
}
using instance_ptr = instance *;
static instance_ptr &head()
{
static instance_ptr s_head = nullptr;
return s_head;
} }
};
template<typename T>
class version_info : public version_info_base
{
public:
using implementation_type = T;
protected:
version_info()
{
auto &s_head = head();
static instance s_next{
implementation_type::name(),
implementation_type::version(),
implementation_type::build_number(),
implementation_type::git_tag(),
implementation_type::revision_date(),
s_head };
s_head = &s_next;
}
};
inline void write_version_string(std::ostream &os, bool verbose)
{
version_info_base::write(os, verbose);
} }
#endif
class version_info_@IDENT_PREFIX@impl : public version_info<version_info_@IDENT_PREFIX@impl>
{
public:
static constexpr const char *name() { return k@VAR_PREFIX@ProjectName; }
static constexpr const char *version() { return k@VAR_PREFIX@VersionNumber; }
static constexpr int build_number() { return k@VAR_PREFIX@BuildNumber; }
static constexpr const char *git_tag() { return k@VAR_PREFIX@RevisionGitTag; }
static constexpr const char *revision_date() { return k@VAR_PREFIX@RevisionDate; }
} s_@IDENT_PREFIX@instance;
]]) ]])
configure_file("${PROJECT_BINARY_DIR}/revision.hpp.in" "${dir}/revision.hpp" @ONLY) configure_file("${VERSION_STRING_DATA}/${file_name}.in" "${dir}/${file_name}" @ONLY)
endfunction() endfunction()
libdssp/CMakeLists.txt 0 → 100644
# SPDX-License-Identifier: BSD-2-Clause
# Copyright (c) 2021 NKI/AVL, Netherlands Cancer Institute
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
cmake_minimum_required(VERSION 3.15)
# set the project name
project(libdssp VERSION 4.4.2 LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
include(GNUInstallDirs)
include(CheckFunctionExists)
include(CheckIncludeFiles)
include(CheckLibraryExists)
include(CMakePackageConfigHelpers)
include(Dart)
include(FindFilesystem)
include(GenerateExportHeader)
set(CXX_EXTENSIONS OFF)
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
find_package(Filesystem REQUIRED)
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 "${CMAKE_CXX_FLAGS} /W4")
endif()
# Optionally build a version to be installed inside CCP4
option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4" OFF)
option(GENERATE_DOCUMENTATION "Generate the documentation files using pandoc" OFF)
if(BUILD_FOR_CCP4)
if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
message(FATAL_ERROR "A CCP4 built was requested but CCP4 was not sourced")
else()
list(APPEND CMAKE_MODULE_PATH "$ENV{CCP4}")
list(APPEND CMAKE_PREFIX_PATH "$ENV{CCP4}")
set(CMAKE_INSTALL_PREFIX "$ENV{CCP4}")
if(WIN32)
set(BUILD_SHARED_LIBS ON)
endif()
endif()
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()
# Create a revision file, containing the current git version info
include(VersionString)
write_version_header("${PROJECT_SOURCE_DIR}/src" LIB_NAME "libdssp")
# Optionally use mrc to create resources
find_package(Mrc QUIET)
set(CMAKE_THREAD_PREFER_PTHREAD)
set(THREADS_PREFER_PTHREAD_FLAG)
find_package(Threads)
if(NOT PDB_REDO_META)
find_package(cifpp 5.1.0 REQUIRED)
endif()
# The DSSP code is in a separate library, optionally to be used by others
add_library(dssp
${PROJECT_SOURCE_DIR}/src/dssp.cpp
${PROJECT_SOURCE_DIR}/include/dssp.hpp
${PROJECT_SOURCE_DIR}/src/dssp-io.cpp
${PROJECT_SOURCE_DIR}/src/dssp-io.hpp
)
add_library(dssp::dssp ALIAS dssp)
target_link_libraries(dssp PUBLIC cifpp::cifpp)
target_include_directories(dssp
PUBLIC
"$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
)
# Install rules
install(TARGETS dssp
EXPORT dsspTargets
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
if(MSVC AND BUILD_SHARED_LIBS)
install(
FILES $<TARGET_PDB_FILE:${PROJECT_NAME}>
DESTINATION ${CMAKE_INSTALL_LIBDIR}
OPTIONAL)
endif()
install(EXPORT dsspTargets
FILE "dsspTargets.cmake"
NAMESPACE dssp::
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/dssp
)
install(
FILES include/dssp.hpp
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
COMPONENT Devel
)
set(CONFIG_TEMPLATE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/cmake/dsspConfig.cmake.in)
configure_package_config_file(
${CONFIG_TEMPLATE_FILE}
${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfig.cmake
INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/dssp
)
install(FILES
"${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfig.cmake"
"${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfigVersion.cmake"
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/dssp
COMPONENT Devel
)
set(dssp_MAJOR_VERSION ${CMAKE_PROJECT_VERSION_MAJOR})
set_target_properties(dssp PROPERTIES
VERSION ${PROJECT_VERSION}
SOVERSION ${dssp_MAJOR_VERSION}
INTERFACE_dssp_MAJOR_VERSION ${dssp_MAJOR_VERSION})
set_property(TARGET dssp APPEND PROPERTY
COMPATIBLE_INTERFACE_STRING dssp_MAJOR_VERSION
)
write_basic_package_version_file(
"${CMAKE_CURRENT_BINARY_DIR}/dssp/dsspConfigVersion.cmake"
VERSION ${PROJECT_VERSION}
COMPATIBILITY AnyNewerVersion
)
# pkgconfig support
set(prefix ${CMAKE_INSTALL_PREFIX})
set(exec_prefix ${CMAKE_INSTALL_PREFIX})
set(libdir ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
set(includedir ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/libdssp.pc.in
${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc.in @ONLY)
file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc
INPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc.in)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
set(CIFPP_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}/libcifpp")
install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/mmcif_pdbx/dssp-extension.dic"
DESTINATION ${CIFPP_DATA_DIR})
src/dssp-io.cpp → libdssp/src/dssp-io.cpp
...@@ -35,7 +35,6 @@ ...@@ -35,7 +35,6 @@
#include <fstream> #include <fstream>
#include <iostream> #include <iostream>
// -------------------------------------------------------------------- // --------------------------------------------------------------------
std::string ResidueToDSSPLine(const dssp::residue_info &info) std::string ResidueToDSSPLine(const dssp::residue_info &info)
...@@ -158,7 +157,7 @@ void writeDSSP(const dssp &dssp, std::ostream &os) ...@@ -158,7 +157,7 @@ void writeDSSP(const dssp &dssp, std::ostream &os)
std::time_t today = system_clock::to_time_t(system_clock::now()); std::time_t today = system_clock::to_time_t(system_clock::now());
std::tm *tm = std::gmtime(&today); std::tm *tm = std::gmtime(&today);
std::string version = kVersionNumber; std::string version = klibdsspVersionNumber;
if (version.length() < 10) if (version.length() < 10)
version.insert(version.end(), 10 - version.length(), ' '); version.insert(version.end(), 10 - version.length(), ' ');
...@@ -875,9 +874,11 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool wr ...@@ -875,9 +874,11 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool wr
} }
auto &software = db["software"]; auto &software = db["software"];
software.emplace({ { "pdbx_ordinal", software.get_unique_id("") }, software.emplace({
{ "pdbx_ordinal", software.get_unique_id("") },
{ "name", "dssp" }, { "name", "dssp" },
{ "version", kVersionNumber }, { "version", klibdsspVersionNumber },
{ "date", kBuildDate }, { "date", klibdsspRevisionDate },
{ "classification", "model annotation" } }); { "classification", "model annotation" }
});
} }
test/unit-test-dssp.cpp
...@@ -30,7 +30,7 @@ ...@@ -30,7 +30,7 @@
#include <boost/test/included/unit_test.hpp> #include <boost/test/included/unit_test.hpp>
#include "dssp.hpp" #include "dssp.hpp"
#include "dssp-io.hpp" #include "../libdssp/src/dssp-io.hpp"
#include "revision.hpp" #include "revision.hpp"
#include <cif++/dictionary_parser.hpp> #include <cif++/dictionary_parser.hpp>
......
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