First setup of CMake, already has out-of-source build enabled

.gitignore

 junk.py
+stage/

CMakeLists.txt

@@ -2,9 +2,71 @@
 # Author: Stefan Bienert
 #-------------------------------------------------------------------------------
 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(PROMOD)
 
+set(PROMOD3_VERSION_MAJOR 0)
+set(PROMOD3_VERSION_MINOR 0)
+set(PROMOD_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
+
+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}
+     ${LIBEXEC_STAGE_PATH})
+
+setup_compiler_flags()
+setup_boost()
+
+find_package(Python 2.7 REQUIRED)
+find_package(OPENSTRUCTURE 1.4 REQUIRED 
+             COMPONENTS io mol seq seq_alg mol_alg conop)
+
+if (CMAKE_COMPILER_IS_GNUCXX)
+  # do not write back into cache, otherwise the compile command line gets
+  # expanded with multiple -fno-strict-aliasing flags, triggering a complete
+  # rebuild whenever cmake is run
+  set(CMAKE_CXX_FLAGS_RELEASE "${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 ${CMAKE_SOURCE_DIR}/stage)
+set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
+                             "${FILES_TO_BE_REMOVED}")
+
+## sub dirs to be recognised by CMake
+## e.g. add_subdirectory(src), subdirs have thier own CMakeLists.txt
+add_subdirectory(meld)
+
+## 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/FindPython.cmake

@@ -17,8 +17,8 @@
 # Author: Marco Biasini
 #-------------------------------------------------------------------------------
 
-set(PYTHON_VERSIONS 2.7 2.6 2.5 2.4 2.3 2.2)
-set(PYTHON_MIN_VERSION 2.2.1)
+set(PYTHON_VERSIONS 2.7)
+set(PYTHON_MIN_VERSION 2.7)
 
 #-------------------------------------------------------------------------------
 # check for python framework
@@ -42,12 +42,12 @@ endmacro()
 
 
 macro(_find_python PYTHON_ROOT VERSION)
-  string(REPLACE "." "" _VERSION_NO_DOTS ${VERSION})
+  string(REPLACE "." "" _VERSION_NO_DOTS "${VERSION}")
   if(PYTHON_ROOT)
     find_library(PYTHON_LIBRARIES
       NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
       HINTS "${PYTHON_ROOT}"
-      PATH_SUFFIXES lib
+      PATH_SUFFIXES lib libs
       NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
     )
     find_path(PYTHON_INCLUDE_PATH
@@ -69,17 +69,17 @@ macro(_find_python PYTHON_ROOT VERSION)
 endmacro()
 
 macro(_find_python_bin PYTHON_ROOT VERSION)
-  string(REPLACE "." "" _VERSION_NO_DOTS ${VERSION})
+  string(REPLACE "." "" _VERSION_NO_DOTS "${VERSION}")
   if(PYTHON_ROOT)
     find_program(PYTHON_BINARY
-      NAMES "python" "python${_VERSION_NO_DOTS}" "python${VERSION}"
+      NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}" python.exe
       HINTS "${PYTHON_ROOT}"
       PATH_SUFFIXES bin
       NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
     )
   else()
     find_program(PYTHON_BINARY
-      NAMES "python" "python${_VERSION_NO_DOTS}" "python${VERSION}"
+      NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
       HINTS "${CMAKE_PREFIX_PATH}"
       PATH_SUFFIXES bin
     )  
@@ -96,7 +96,8 @@ macro(check_for_python_lib)
     _find_python("${PYTHON_ROOT}" "${PYTHON_VERSION}")
   else()
     foreach(_VERSION ${PYTHON_VERSIONS})
-     if(${PYTHON_MIN_VERSION} VERSION_LESS ${_VERSION})
+     if((${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}")
@@ -105,6 +106,10 @@ macro(check_for_python_lib)
       endif()
     endforeach()
   endif()
+  # fallback to non-versioned naming scheme
+  if (NOT $PYTHON_LIBRARIES)
+    _find_python("${PYTHON_ROOT}" "")
+  endif()
 endmacro()
 
 macro(check_for_python_binary)
@@ -112,15 +117,22 @@ macro(check_for_python_binary)
     _find_python_bin("${PYTHON_ROOT}" "${PYTHON_VERSION}")
   else()
     foreach(_VERSION ${PYTHON_VERSIONS})
-      if(${PYTHON_MIN_VERSION} VERSION_LESS ${_VERSION})
+      if((${PYTHON_MIN_VERSION} VERSION_LESS ${_VERSION}) OR
+         (${PYTHON_MIN_VERSION} VERSION_EQUAL ${_VERSION}))
         _find_python_bin("${PYTHON_ROOT}" "${_VERSION}")
-        if(PYTHON_LIBRARIES)
+        if(PYTHON_BINARY)
           set(PYTHON_VERSION "${_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)
@@ -134,11 +146,13 @@ 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()
 
-check_for_python_binary()
 mark_as_advanced(
   PYTHON_LIBRARIES
   PYTHON_INCLUDE_PATH
@@ -159,6 +173,8 @@ if(PYTHON_LIBRARIES)
 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()