Merge branch 'develop'

.gitignore

 junk.py
+stage/
+\.AppleDouble
+\.DS_Store

CHANGELOG

+Changes in Release 0.1
+--------------------------------------------------------------------------------
+ * initial setup of the CMake build system
+ * first idea of the documentation system
+ * meld included from SMNG as first module (to be modified/ renamed)

CMakeLists.txt

 #-------------------------------------------------------------------------------
-# Author: Stefan Bienert
+# Author: Bienchen
 #-------------------------------------------------------------------------------
+# Options to CMake:
+#    DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx
 cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
 
-project(PROMOD2)
+project(PROMOD3 CXX C)
 
-set (PROMOD2_VERSION_MAJOR 0)
-set (PROMOD2_VERSION_MINOR 0)
+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 ${PYTHON_VERSION} REQUIRED)
+  set(PYTHON_DOC_URL "http://docs.python.org/${PYTHON_VERSION}")
+endif()
+find_package(OPENSTRUCTURE 1.4 REQUIRED 
+             COMPONENTS io mol seq seq_alg mol_alg conop)
+
+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})
+
+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 thier own CMakeLists.txt
+add_subdirectory(config)
+add_subdirectory(core)
+add_subdirectory(meld)
+add_subdirectory(scripts)
+add_subdirectory(doc)
+
+## report setup
+message(STATUS "PROMOD3 will be built with the following options:\n"
+        "   OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"
+        "   Optimized     (-DOPTIMIZE) : ${_OPT}\n"
+        "   Python                     : ${PYTHON_BINARY}\n")

cmake_support/FindOPENSTRUCTURE.cmake

+#-------------------------------------------------------------------------------
+# Check for OpenStructure Libraries
+#
+#    OST_ROOT                 Prefix for OpenStructure libraries
+#    OST_MIN_VERSION          minimal OPenStructure version required
+#  
+# When OpenStructure is found, the result is placed in the following variables:
+# 
+#    OST_LIBRARIES           is set to the library and linker flags used to
+#                            link against python
+#    OST_VERSION             is set to the version of OpenStructure
+#    OST_INCLUDE_DIR         is set to the path that contains base.hh
+#
+# Author: Valerio Mariani, Marco Biasini
+#-------------------------------------------------------------------------------
+
+macro(find_OPENSTRUCTURE OST_ROOT NAMES HEADER_NAMES)
+  if (NOT OPENSTRUCTURE_FIND_COMPONENTS)
+    message(FATAL_ERROR "Please specify which modules of OpenStructure you "
+            "would like to use after the COMPONENTS keyword.")
+  endif()
+  list(APPEND OPENSTRUCTURE_FIND_COMPONENTS base geom)
+  list(REMOVE_DUPLICATES OPENSTRUCTURE_FIND_COMPONENTS)
+  foreach (LIB ${OPENSTRUCTURE_FIND_COMPONENTS})
+    set(FOUND_LIB FOUND_LIB-NOTFOUND)
+    find_library(FOUND_LIB 
+      NAMES ost_${LIB}
+      HINTS "${PYTHON_ROOT}"
+      PATH ${OST_ROOT}
+      PATH_SUFFIXES lib lib64
+      NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
+    )
+    if (NOT FOUND_LIB)
+      if (OPENSTRUCTURE_FIND_REQUIRED)
+        message(FATAL_ERROR "Could not find library ost_${LIB}. Please specify"
+                " the location of your OpenStructure installation with"
+                " OST_ROOT")
+      endif()
+    else()
+       set(OST_LIBRARIES ${OST_LIBRARIES}  ${FOUND_LIB})
+    endif()
+
+  endforeach()
+
+  find_path(OST_INCLUDE_DIR
+    NAMES "${HEADER_NAMES}"
+    HINTS "${OST_ROOT}/include"
+    NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
+  )    
+  set(OPENSTRUCTURE_FOUND 1)
+endmacro()
+
+#-------------------------------------------------------------------------------
+SET(LIBNAMES
+ost_base
+ost_gfx
+ost_info
+ost_qa
+ost_conop
+ost_gui
+ost_io
+ost_seq
+ost_db
+ost_img
+ost_mol
+ost_seq
+ost_seq_alg
+ost_geom
+ost_img_alg	
+ost_mol_alg
+)
+
+find_OPENSTRUCTURE("${OST_ROOT}" "${LIBNAMES}" "ost/config.hh")
+
+mark_as_advanced(
+  OST_LIBRARIES
+  OST_INCLUDE_DIR
+  OST_VERSION
+)
+
+if (OPENSTRUCTURE_FOUND)
+   if (NOT OPENSTRUCTURE_FIND_QUIETLY)
+   endif ()
+else (OPENSTRUCTURE_FOUND)
+   if (OPENSTRUCTURE_FIND_REQUIRED)
+      message(FATAL_ERROR "Could not find OpenStructure")
+   endif () 
+endif ()
\ No newline at end of file

cmake_support/FindPython.cmake

+#-------------------------------------------------------------------------------
+# Check for Python Libraries
+#
+#    PYTHON_IGNORE_FRAMEWORKS if set, do not check for python frameworks. 
+#                             has meaning on MacOS X only
+#    PYTHON_ROOT              Prefix for python libraries
+#    PYTHON_MIN_VERSION       minimal python version required
+#  
+# When Python is found, the result is placed in the following variables:
+# 
+#    PYTHON_LIBRARIES         is set to the library and linker flags used to
+#                             link against python
+#    PYTHON_VERSION           is set to the version of python
+#    PYTHON_INCLUDE_PATH      is set to the path that contains Python.h
+#    PYTHON_BINARY            is set to the path to the python executable
+#
+# Author: Marco Biasini
+#-------------------------------------------------------------------------------
+
+set(PYTHON_VERSIONS 2.7)
+set(PYTHON_MIN_VERSION 2.7)
+
+#-------------------------------------------------------------------------------
+# check for python framework
+# this macro honours the values of PYTHON_ROOT
+#-------------------------------------------------------------------------------
+macro(check_for_python_framework)
+  set(_FRAMEWORK_SEARCH_PATHS /Library/Frameworks/ /System/Library/Frameworks)
+  if(PYTHON_ROOT)
+    set(_FRAMEWORK_SEARCH_PATHS ${PYTHON_ROOT}/Library/Frameworks)
+  endif()
+  foreach(_PATH ${_FRAMEWORK_SEARCH_PATHS})
+    set(_FULL_FRAMEWORK_NAME "${_PATH}/Python.framework")
+    if(EXISTS ${_FULL_FRAMEWORK_NAME})
+      set(PYTHON_FRAMEWORK ON)
+      set(PYTHON_INCLUDE_PATH "${_FULL_FRAMEWORK_NAME}/Headers")
+      set(PYTHON_FRAMEWORK_PATH "${_FULL_FRAMEWORK_NAME}/Python")
+    endif()
+  endforeach()
+endmacro()
+
+
+
+macro(_find_python PYTHON_ROOT VERSION)
+  string(REPLACE "." "" _VERSION_NO_DOTS "${VERSION}")
+  if(PYTHON_ROOT)
+    find_library(PYTHON_LIBRARIES
+      NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
+      HINTS "${PYTHON_ROOT}"
+      PATH_SUFFIXES lib libs
+      NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
+    )
+    find_path(PYTHON_INCLUDE_PATH
+      NAMES Python.h
+      HINTS "${PYTHON_ROOT}/include"
+      PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"
+      NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
+    )
+  else()
+    find_library(PYTHON_LIBRARIES
+      NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
+      PATH_SUFFIXES lib
+    )
+    find_path(PYTHON_INCLUDE_PATH
+      NAMES Python.h
+      PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"     
+    )    
+  endif()  
+endmacro()
+
+macro(_find_python_bin PYTHON_ROOT VERSION)
+  string(REPLACE "." "" _VERSION_NO_DOTS "${VERSION}")
+  if(PYTHON_ROOT)
+    find_program(PYTHON_BINARY
+      NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}" python.exe
+      HINTS "${PYTHON_ROOT}"
+      PATH_SUFFIXES bin
+      NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
+    )
+  else()
+    find_program(PYTHON_BINARY
+      NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
+      HINTS "${CMAKE_PREFIX_PATH}"
+      PATH_SUFFIXES bin
+    )  
+  endif()  
+endmacro()
+
+#-------------------------------------------------------------------------------
+# check for python lib
+#
+# this macro honours the values of PYTHON_ROOT and PYTHON_VERSION
+#-------------------------------------------------------------------------------
+macro(check_for_python_lib)
+  if(PYTHON_VERSION)
+    _find_python("${PYTHON_ROOT}" "${PYTHON_VERSION}")
+  else()
+    foreach(_VERSION ${PYTHON_VERSIONS})
+     if((${PYTHON_MIN_VERSION} VERSION_LESS ${_VERSION}) OR
+        (${PYTHON_MIN_VERSION} VERSION_EQUAL ${_VERSION}))
+        _find_python("${PYTHON_ROOT}" "${_VERSION}")
+        if(PYTHON_LIBRARIES)
+          set(PYTHON_VERSION "${_VERSION}")
+          break()
+        endif()
+      endif()
+    endforeach()
+  endif()
+  # fallback to non-versioned naming scheme
+  if (NOT $PYTHON_LIBRARIES)
+    _find_python("${PYTHON_ROOT}" "")
+  endif()
+endmacro()
+
+macro(check_for_python_binary)
+  if(PYTHON_VERSION)
+    _find_python_bin("${PYTHON_ROOT}" "${PYTHON_VERSION}")
+  else()
+    foreach(_VERSION ${PYTHON_VERSIONS})
+      if((${PYTHON_MIN_VERSION} VERSION_LESS ${_VERSION}) OR
+         (${PYTHON_MIN_VERSION} VERSION_EQUAL ${_VERSION}))
+        _find_python_bin("${PYTHON_ROOT}" "${_VERSION}")
+        if(PYTHON_BINARY)
+          set(PYTHON_VERSION "${_VERSION}")
+          # disallow all versions except for the one we just found. This makes
+          # sure we don't mismatch the python binary and the libraries.
+          set(PYTHON_VERSIONS "${_VERSION}")
+          break()
+        endif()
+      endif()
+    endforeach()
+  endif()
+  if (NOT PYTHON_BINARY)
+    _find_python("${PYTHON_ROOT}" "")
+  endif()
+endmacro()
+
+if(NOT PYTHON_ROOT)
+  if(WIN32)
+    set(PYTHON_ROOT "${CMAKE_PREFIX_PATH}")
+  else()
+    set(PYTHON_ROOT "/usr")
+  endif()
+endif()
+if(APPLE AND NOT PYTHON_IGNORE_FRAMEWORKS)
+  check_for_python_framework()
+endif()
+
+# first check for python binary.
+check_for_python_binary()
+
+if(NOT PYTHON_FRAMEWORK_FOUND)
+  check_for_python_lib()
+endif()
+
+mark_as_advanced(
+  PYTHON_LIBRARIES
+  PYTHON_INCLUDE_PATH
+  PYTHON_VERSION
+  PYTHON_BINARY
+)
+
+if(PYTHON_LIBRARIES)
+  if(PYTHON_FRAMEWORK)
+    set(PYTHON_LIBRARIES "${PYTHON_FRAMEWORK_PATH}"
+        CACHE FILEPATH "Python Libraries" FORCE)
+  else()
+    set(PYTHON_LIBRARIES "${PYTHON_LIBRARIES}"
+        CACHE FILEPATH "Python Libraries" FORCE)
+  endif()
+  set(PYTHON_INCLUDE_PATH "${PYTHON_INCLUDE_PATH}"
+      CACHE FILEPATH "Python Include Path" FORCE)
+endif()
+
+if (PYTHON_BINARY)
+  set(PYTHON_VERSION "${PYTHON_VERSION}"
+      CACHE STRING "Python Version" FORCE)
+  set(PYTHON_BINARY "${PYTHON_BINARY}"
+      CACHE FILEPATH "Python Binary" FORCE)
+endif()

cmake_support/FindSphinx.cmake

+#-------------------------------------------------------------------------------
+# Check for Sphinx binary
+#
+#    SPHINX_BINARY            is set to the path to the sphinx-build executable,
+#                             preferably sphinx-build-${Sphinx_FIND_VERSION} if
+#                             provided. Also admires PYTHON_ROOT if available.
+#
+# Author: Bienchen
+#-------------------------------------------------------------------------------
+
+if(Sphinx_FIND_VERSION)
+  set(ADD_SPHINX_NAMES "sphinx-build-${Sphinx_FIND_VERSION}")
+endif()
+
+if(PYTHON_ROOT)
+  find_program(SPHINX_BINARY NAMES sphinx-build ${ADD_SPHINX_NAMES}
+    HINTS ${PYTHON_ROOT}
+    PATH_SUFFIXES bin
+    DOC "Sphinx documentation generator"
+  )
+else()
+  find_program(SPHINX_BINARY NAMES sphinx-build ${ADD_SPHINX_NAMES}
+    PATH_SUFFIXES bin
+    DOC "Sphinx documentation generator"
+  )
+endif()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(Sphinx DEFAULT_MSG
+  SPHINX_BINARY
+)
+
+mark_as_advanced(
+  SPHINX_BINARY
+)

cmake_support/substitute.cmake

+configure_file(${INPUT_FILE} ${OUT_FILE} @ONLY)
\ No newline at end of file

conf-scripts/bc2-conf

+#!/bin/sh
+
+# This script is aware of out-of-source builds. Just call it from within the
+# build directory.
+
+function usage
+{
+  echo 'usage:'  
+  echo '  fedora-19-conf <OST_ROOT> [OPTIONS]'
+  echo '  OST_ROOT is the staging directory of OST.'
+  echo '  Valid options are anything that CMake accepts.'
+  exit
+}
+
+NUM_PARAMS=$#
+if [[ "$NUM_PARAMS" -lt "1" ]] ; then
+  echo 'You must specify the location of promod3 and OST (in that order).';
+  usage
+fi
+
+OST_ROOT=$(cd $1; pwd)
+shift
+PROMOD3_SRC=$(cd `dirname $0`; pwd)
+PROMOD3_SRC=${PROMOD3_SRC}/..
+
+cmake $PROMOD3_SRC -DOST_ROOT=$OST_ROOT                                  \
+                   -DBOOST_ROOT=/import/bc2/soft/app/boost/1.47.0/Linux/ \
+                   -DPYTHON_ROOT=/import/bc2/soft/app/Python/2.7.5/Linux \
+                   $@
+
+
+## Emacs magic
+# Local Variables:
+# mode: shell-script
+# End:
+
+#  LocalWords:  OSX MacPorts uname SRC OST promod CMake NUM PARAMS lt fi cd
+#  LocalWords:  pwd dirname cmake DPYTHON DBOOST conf

conf-scripts/fedora-19-conf

+#!/bin/sh
+
+# To find out your version of Fedora, run 'cat /etc/issue'.
+# This script is aware of out-of-source builds. Just call it from within the
+# build directory.
+
+function usage
+{
+  echo 'usage:'  
+  echo '  fedora-19-conf <OST_ROOT> [OPTIONS]'
+  echo '  OST_ROOT is the staging directory of OST.'
+  echo '  Valid options are anything that CMake accepts.'
+  exit
+}
+
+NUM_PARAMS=$#
+if [[ "$NUM_PARAMS" -lt "1" ]] ; then
+  echo 'You must specify the location of promod3 and OST (in that order).';
+  usage
+fi
+
+OST_ROOT=$(cd $1; pwd)
+shift
+PROMOD3_SRC=$(cd `dirname $0`; pwd)
+PROMOD3_SRC=${PROMOD3_SRC}/..
+
+cmake $PROMOD3_SRC -DOST_ROOT=$OST_ROOT \
+                   -DPYTHON_ROOT=/usr   \
+                   $@
+
+## Emacs magic
+# Local Variables:
+# mode: shell-script
+# End:
+
+#  LocalWords:  OSX MacPorts uname SRC OST promod CMake NUM PARAMS lt fi cd
+#  LocalWords:  pwd dirname cmake DPYTHON DBOOST conf

conf-scripts/osx-11.4.2-conf

+#!/bin/sh
+
+# For OSX we assume that all missing dependencies are built with MacPorts
+# and are located in '/opt/local'.
+# To find out your version of OSX, run 'uname -r'.
+# This script is aware of out-of-source builds. Just call it from within the
+# build directory.
+
+function usage
+{
+  echo 'usage:'  
+  echo '  osx-11.4.2-conf <OST_ROOT> [OPTIONS]'
+  echo '  OST_ROOT is the staging directory of OST.'
+  echo '  Valid options are anything that CMake accepts.'
+  exit
+}
+
+NUM_PARAMS=$#
+if [[ "$NUM_PARAMS" -lt "1" ]] ; then
+  echo 'You must specify the location of promod3 and OST (in that order).';
+  usage
+fi
+
+OST_ROOT=$(cd $1; pwd)
+shift
+PROMOD3_SRC=$(cd `dirname $0`; pwd)
+PROMOD3_SRC=${PROMOD3_SRC}/..
+
+cmake $PROMOD3_SRC -DOST_ROOT=$OST_ROOT     \
+                   -DPYTHON_ROOT=/opt/local \
+                   -DBOOST_ROOT=/opt/local  \
+                   -DPYTHON_INCLUDE_PATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/ \
+                   -DPYTHON_LIBRARIES=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib \
+                   $@
+
+## Emacs magic
+# Local Variables:
+# mode: shell-script
+# End:
+
+#  LocalWords:  OSX MacPorts uname SRC OST promod CMake NUM PARAMS lt fi cd
+#  LocalWords:  pwd dirname cmake DPYTHON DBOOST

config/CMakeLists.txt

+add_subdirectory(src)

config/src/CMakeLists.txt

+# if we need more than one configurational header, add path in front of every
+# file via loop!
+set(CONFIG_HH_FILE "config.hh")
+
+configure_file(config.hh.in ${CONFIG_HH_FILE})
+
+add_custom_target(config_header ALL)
+copy_if_different("${CMAKE_CURRENT_BINARY_DIR}" "${HEADER_STAGE_PATH}/promod3"
+                  "${CONFIG_HH_FILE}" "config_headers" config_header)
+
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${CONFIG_HH_FILE} DESTINATION "include/promod3/")

config/src/config.hh.in

+#ifndef PROMOD3_CONFIG_HH
+#define PROMOD3_CONFIG_HH
+
+/*
+  DO NOT EDIT the '.hh' file, it is processed from a template '.hh.in' by CMake.
+*/
+
+/* fetch version from top level CMakeLists.txt */
+#define PROMOD3_VERSION_MAJOR @PROMOD3_VERSION_MAJOR@
+#define PROMOD3_VERSION_MINOR @PROMOD3_VERSION_MINOR@
+#define PROMOD3_VERSION_STRING "@PROMOD3_VERSION_STRING@"
+
+#endif

core/CMakeLists.txt

+add_subdirectory(pymod)

core/pymod/CMakeLists.txt

+set(PROMOD3_CORE_FILES __init__.py)
+
+pymod(NAME core PY ${PROMOD3_CORE_FILES} OUTPUT_DIR "promod3")

doc/CMakeLists.txt

+# preparing sphinx build
+# - setup directories: sources go to BUILD/doc/source
+# - every module gets its own directory
+# - rst files are copied to this spot
+# - compiled documentation goes to STAGE/share/promod3
+
+# set up commands for the rst source files
+# take care of Sphinx config, conf.py; will be created from conf.py.in since
+# some values from CMake have to be substituted
+set(_RST_DEPS)
+set(_RST_SOURCE_DIR "${CMAKE_CURRENT_BINARY_DIR}/source")
+file(MAKE_DIRECTORY ${_RST_SOURCE_DIR})
+set(_SPHINX_CONF_PY "${_RST_SOURCE_DIR}/conf.py")
+set(_SPHINX_CONF_SUBST_DICT PROMOD3_VERSION_MAJOR="${PROMOD3_VERSION_MAJOR}"
+                            PROMOD3_VERSION_MINOR="${PROMOD3_VERSION_MINOR}"
+                            PROMOD3_VERSION_PATCH="${PROMOD3_VERSION_PATCH}"
+                            PYTHON_DOC_URL="${PYTHON_DOC_URL}")
+set(_CONF_SUBST_DICT -DINPUT_FILE=${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in -DOUT_FILE=${_SPHINX_CONF_PY})
+foreach(_subst ${_SPHINX_CONF_SUBST_DICT})
+  list(APPEND _CONF_SUBST_DICT -D${_subst})
+endforeach()
+message(STATUS "FOO ${CMAKE_COMMAND} ${_CONF_SUBST_DICT} -P ${CMAKE_SOURCE_DIR}/cmake_support/substitute.cmake")
+add_custom_command(OUTPUT ${_SPHINX_CONF_PY}
+                   MAIN_DEPENDENCY "${CMAKE_SOURCE_DIR}/CMakeLists.txt"
+                   DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in"
+                   COMMAND ${CMAKE_COMMAND} ${_CONF_SUBST_DICT}
+                   -P ${CMAKE_SOURCE_DIR}/cmake_support/substitute.cmake)
+# we need to copy index.rst from the doc dir, to have everything together in
+# the build dir as 'source'; conf.py may stay where it is, may be pulled by '-c'
+set(_SPHINX_INDEX_RST "${_RST_SOURCE_DIR}/index.rst")
+add_custom_command(OUTPUT "${_SPHINX_INDEX_RST}"
+                   MAIN_DEPENDENCY "${CMAKE_CURRENT_SOURCE_DIR}/index.rst"
+                   COMMAND ${CMAKE_COMMAND} -E copy "${CMAKE_CURRENT_SOURCE_DIR}/index.rst" ${_SPHINX_INDEX_RST})
+set(_RST_DEPS ${_RST_DEPS} ${_SPHINX_INDEX_RST})
+# iterate list of ALL modules registered by pymod()/ add_doc_source()
+foreach(mod ${PM3_MODULES})
+  # only modules with dedicated rst files are considered for documentation, so
+  # we check if a list PM3_RST_{module name} exists (filled by add_doc_source()
+  if(DEFINED PM3_RST_${mod})
+    # this is a list of rst files, of which everyone becomes a Make target
+    foreach(rst ${PM3_RST_${mod}})
+      # the list come swith full path, the targets point towards the build dir
+      # so we need to extract the filename
+      get_filename_component(rst_name ${rst} NAME)
+      set(_RST_SOURCE_MOD_DIR "${_RST_SOURCE_DIR}/${mod}")
+      # create directory, since it does not come with any CMake file, it will   
+      # not be created by CMake
+      file(MAKE_DIRECTORY ${_RST_SOURCE_MOD_DIR})
+      set(_RST_OUTPUT "${_RST_SOURCE_MOD_DIR}/${rst_name}")
+      add_custom_command(OUTPUT "${_RST_OUTPUT}"
+                         MAIN_DEPENDENCY "${rst}"
+                         DEPENDS ${PM3_DOC_DEPS_${mod}}
+                         COMMAND ${CMAKE_COMMAND} -E copy ${rst} ${_RST_OUTPUT})
+      # we need a list of dependencies to create the effective targets, since
+      # in our custom_commands we are dealing with file targets
+      set(_RST_DEPS ${_RST_DEPS} ${_RST_OUTPUT})
+    endforeach()
+  endif()
+endforeach()
+
+# create targets for sphinx
+# for the html target, we make everything depend on index.html
+set(_SPHINX_HTML_DIR "${SHARED_DATA_PATH}/html")
+file(MAKE_DIRECTORY ${_SPHINX_HTML_DIR})
+set(_SPHINX_INDEX_HTML "${_SPHINX_HTML_DIR}/index.html")
+add_custom_command(OUTPUT ${_SPHINX_INDEX_HTML}
+                   MAIN_DEPENDENCY "${_SPHINX_CONF_PY}"
+                   DEPENDS ${_RST_DEPS}
+                   COMMAND ${SPHINX_BINARY} -b html -c "${_RST_SOURCE_DIR}" "${_RST_SOURCE_DIR}" "${_SPHINX_HTML_DIR}")
+add_custom_target(html DEPENDS ${_SPHINX_INDEX_HTML})
+
+# man target
+set(_SPHINX_MAN_DIR "${SHARED_DATA_PATH}/man")
+file(MAKE_DIRECTORY ${_SPHINX_MAN_DIR})
+set(_SPHINX_MAN "${_SPHINX_MAN_DIR}/promod3.1")
+add_custom_command(OUTPUT ${_SPHINX_MAN}
+                   MAIN_DEPENDENCY  "${_SPHINX_CONF_PY}"
+                   DEPENDS ${_RST_DEPS}
+                   COMMAND ${SPHINX_BINARY} -b man -c "${_RST_SOURCE_DIR}" "${_RST_SOURCE_DIR}" "${_SPHINX_MAN_DIR}")
+add_custom_target(man DEPENDS ${_SPHINX_MAN})
+
+# doc target, registered with all
+add_custom_target(doc ALL)
+add_dependencies(doc html)
+add_dependencies(doc man)
+
+# installing: Since shared data goes to our own sub directory, it is assumed
+#             save to just copy over whole directories. This saves us from
+#             keeping track of all output files of a html doc tree
+#             We install FROM the stage dir tree, since Sphinx will build the
+#             documentation right there.
+# install html documentation
+install(DIRECTORY ${_SPHINX_HTML_DIR} DESTINATION "share/promod3")
+# install man pages
+install(DIRECTORY ${_SPHINX_MAN_DIR} DESTINATION "share/promod3")
+
+# doctest & linkcheck goes into check, once its created
+# what about extratcting stuff from code?

doc/conf.py.in

+# -*- coding: utf-8 -*-
+#
+# DO NOT EDIT conf.py! GO FOR conf.py.in, THERE IS VARIABLE SUBSTITUTION
+# INVOLVED
+#
+# ProMod3 documentation build configuration file, originally created by
+# sphinx-quickstart on Thu Oct 10 23:17:00 2013, then modified.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'ProMod3'
+copyright = u'2013, Bienchen'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '@PROMOD3_VERSION_MAJOR@.@PROMOD3_VERSION_MINOR@'
+# The full version, including alpha/beta/rc tags.
+release = '@PROMOD3_VERSION_PATCH@'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+today_fmt = '%B %d %H:%M, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = list()
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+html_last_updated_fmt = '%b %d %H:%M, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'ProMod3doc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'ProMod3.tex', u'ProMod3 Documentation',
+   u'Bienchen', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'promod3', u'ProMod3 Documentation',
+     [u'Bienchen'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'ProMod3', u'ProMod3 Documentation',
+   u'Bienchen', 'ProMod3', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'python': ('@PYTHON_DOC_URL@', None)}