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Commit d20b8fcc authored by Bienchen's avatar Bienchen Committed by BIOPZ-Johner Niklaus
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Update CMakeLists.txt in docu

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CMakeLists.txt
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− 3
View file @ d20b8fcc
......@@ -18,9 +18,9 @@ set(PROMOD3_VERSION_MINOR 1)
set(PROMOD3_VERSION_PATCH 0)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR}.${PROMOD3_VERSION_PATCH})
option(DISABLE_DOCUMENTATION "whether to compile with shader support" OFF)
option(DISABLE_DISABLE_DOCTEST "whether to compile with shader support" OFF)
option(DISABLE_DISABLE_LINKCHECK "whether to compile with shader support" OFF)
option(DISABLE_DOCUMENTATION "Do not build documentation" OFF)
option(DISABLE_DISABLE_DOCTEST "Do not check examples in documentation" OFF)
option(DISABLE_DISABLE_LINKCHECK "Do not check links in the documentation" OFF)
if (CMAKE_COMPILER_IS_GNUCXX)
exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
......
doc/contributing.rst
+ 123
− 101
View file @ d20b8fcc
......@@ -189,7 +189,7 @@ the Internet. Nevertheless, here is a short list of most important advices:
:file:`tests/data`
* If 'exotic' |python| modules are used, consider making the test aware of the
possibility that the module is not available
* Test do not fail on purpose
* Tests do not fail on purpose
* No failing tests, that are considered 'this does not affect anything'
To run the whole test suite, ``make check`` is enough. This will also trigger
......@@ -359,108 +359,130 @@ top level :file:`CMakeLists.txt`:
.. code-block:: cmake
:linenos:
:emphasize-lines: 83
#-------------------------------------------------------------------------------
# Author: Bienchen
#-------------------------------------------------------------------------------
# Options to CMake:
# DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx
# DISABLE_DOCTEST: Don't run example code from documentation on 'make check'
# DISABLE_LINKCHECK: Don't test links from documentation on 'make check'
# (if documentation is disabled, there is no doctest, linkcheck at all)
cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
project(PROMOD3 CXX C)
include(PROMOD3)
set(PROMOD3_VERSION_MAJOR 0)
set(PROMOD3_VERSION_MINOR 1)
set(PROMOD3_VERSION_PATCH 0)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR}.${PROMOD3_VERSION_PATCH})
if (CMAKE_COMPILER_IS_GNUCXX)
exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
if(CMAKE_C_COMPILER_VERSION MATCHES ".*4\\.[5-9].*")
set(PROMOD_GCC_45 true)
else()
set(PROMOD_GCC_45 false)
endif()
endif()
if (OPTIMIZE)
set(CMAKE_BUILD_TYPE Release)
set(_OPT ON)
else()
set(CMAKE_BUILD_TYPE Debug)
set(_OPT OFF)
endif()
setup_stage()
file(MAKE_DIRECTORY ${STAGE_DIR}
${EXECUTABLE_OUTPUT_PATH}
${HEADER_STAGE_PATH}
${LIB_STAGE_PATH}
${LIBEXEC_STAGE_PATH})
setup_compiler_flags()
setup_boost()
find_package(Python 2.7 REQUIRED)
if(NOT DISABLE_DOCUMENTATION)
find_package(Sphinx ${PYTHON_VERSION} REQUIRED)
set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
# set this to the URL corresponding to the version of OST you are using
set(OST_DOC_URL "http://www.openstructure.org/docs/1.3")
endif()
find_package(OPENSTRUCTURE 1.4 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop)
find_package(QMEAN 1.0 REQUIRED)
if (CMAKE_COMPILER_IS_GNUCXX)
# do not write back into cache, otherwise the compile command line gets
# expanded with multiple -fno-strict-aliasing flags, triggering a complete
# rebuild whenever cmake is run
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing")
if("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-attributes")
endif("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
endif()
# basic environment
include_directories(${Boost_INCLUDE_DIRS}
${OST_INCLUDE_DIR}
${QMEAN_INCLUDE_DIR})
set(FILES_TO_BE_REMOVED ${PROJECT_BINARY_DIR}/stage)
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
"${FILES_TO_BE_REMOVED}")
## sub dirs to be recognised by CMake
## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
add_subdirectory(config)
add_subdirectory(core)
add_subdirectory(meld)
add_subdirectory(sidechains)
add_subdirectory(scripts)
add_subdirectory(actions)
add_subdirectory(extras)
if(NOT DISABLE_DOCUMENTATION)
add_changelog_to_doc(FILE "${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG")
add_subdirectory(doc)
endif()
## report setup
message(STATUS "PROMOD3 will be built with the following options:\n"
" OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"
" QMEAN (-DQMEAN_ROOT) : ${QMEAN_ROOT}\n"
" Optimized (-DOPTIMIZE) : ${_OPT}\n"
" Python : ${PYTHON_BINARY}\n")
:emphasize-lines: 103
#-------------------------------------------------------------------------------
# Author: Bienchen
#-------------------------------------------------------------------------------
# Options to CMake:
# DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx
# DISABLE_DOCTEST: Don't run example code from documentation on 'make check'
# DISABLE_LINKCHECK: Don't test links from documentation on 'make check'
# (if documentation is disabled, there is no doctest, linkcheck at all)
cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
project(ProMod3 CXX C)
include(PROMOD3)
set(PROMOD3_VERSION_MAJOR 0)
set(PROMOD3_VERSION_MINOR 1)
set(PROMOD3_VERSION_PATCH 0)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR}.${PROMOD3_VERSION_PATCH})
option(DISABLE_DOCUMENTATION "Do not build documentation" OFF)
option(DISABLE_DISABLE_DOCTEST "Do not check examples in documentation" OFF)
option(DISABLE_DISABLE_LINKCHECK "Do not check links in the documentation" OFF)
if (CMAKE_COMPILER_IS_GNUCXX)
exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
if(CMAKE_C_COMPILER_VERSION MATCHES ".*4\\.[5-9].*")
set(PROMOD_GCC_45 true)
else()
set(PROMOD_GCC_45 false)
endif()
endif()
if (OPTIMIZE)
set(CMAKE_BUILD_TYPE Release)
set(_OPT ON)
else()
set(CMAKE_BUILD_TYPE Debug)
set(_OPT OFF)
endif()
setup_stage()
file(MAKE_DIRECTORY ${STAGE_DIR}
${EXECUTABLE_OUTPUT_PATH}
${HEADER_STAGE_PATH}
${LIB_STAGE_PATH}
${LIBEXEC_STAGE_PATH})
setup_compiler_flags()
setup_boost()
find_package(Python 2.7 REQUIRED)
if(NOT DISABLE_DOCUMENTATION)
find_package(Sphinx ${PYTHON_VERSION} REQUIRED)
set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
# set this to the URL corresponding to the version of OST you are using
set(OST_DOC_URL "http://www.openstructure.org/docs/1.3")
endif()
find_package(OPENSTRUCTURE 1.4 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop)
find_package(QMEAN 1.0 REQUIRED)
#The KIC loop closing algorithm requires a solver for a generalized eigen
#problem. Eigen3 would provide such a solver, but only allows to extract
#the resulting eigenvalues and not the eigenvectors.
#As soon as there is an Eigen3 release with the required functionality,
#The Lapack dependency can be dropped.
find_package(LAPACK)
if (CMAKE_COMPILER_IS_GNUCXX)
# do not write back into cache, otherwise the compile command line gets
# expanded with multiple -fno-strict-aliasing flags, triggering a complete
# rebuild whenever cmake is run
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing")
if("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-attributes")
endif("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
endif()
# additional packages/ headers/ etc.
# Eigen3 is mandatory right now but may vanish once OST switches to the same
# version.
find_package(Eigen3 3.2.1 REQUIRED)
if(NOT EIGEN3_FOUND)
message(FATAL_ERROR "Eigen3 is essential for building ${PROJECT_NAME}.")
endif()
# basic environment
include_directories(${Boost_INCLUDE_DIRS}
${OST_INCLUDE_DIR}
${QMEAN_INCLUDE_DIR}
${EIGEN3_INCLUDE_DIR})
set(FILES_TO_BE_REMOVED ${PROJECT_BINARY_DIR}/stage)
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
"${FILES_TO_BE_REMOVED}")
## sub dirs to be recognised by CMake
## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
add_subdirectory(config)
add_subdirectory(core)
add_subdirectory(meld)
add_subdirectory(sidechains)
add_subdirectory(loop)
add_subdirectory(scripts)
add_subdirectory(actions)
add_subdirectory(extras)
if(NOT DISABLE_DOCUMENTATION)
add_changelog_to_doc(FILE "${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG")
add_subdirectory(doc)
endif()
## report setup
message(STATUS "${PROJECT_NAME} will be built with the following options:\n"
" OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"
" QMEAN (-DQMEAN_ROOT) : ${QMEAN_ROOT}\n"
" Optimized (-DOPTIMIZE) : ${_OPT}\n"
" Python : ${PYTHON_BINARY}\n"
" Eigen3 : ${EIGEN3_INCLUDE_DIR}\n")
All that needs to be done for |cmake| to recognise your module is adding its
directory as shown in line 83.
directory as shown in line 103.
This was the final step to set up the build system. Running |cmake| at this
point would create the build environment in place. But building software in
......
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