diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8fc6f636ef5ccdc81431c7a30e4493913ad73488..39c0db72a9258fde881e2fb72eb26e47d5d63648 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -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)
diff --git a/doc/contributing.rst b/doc/contributing.rst
index 16777995889be1ef15ace977e1f43b2b3da3f940..b9bd37f83a2caf79ad5b82a0da3e5b81bc53da76 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -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