Merge branch 'pomo_mpi_nonrev' into liemarkov

.gitignore

@@ -8,5 +8,12 @@ pll/Makefile
 pll/cmake_install.cmake
 pll/libpll.a
 pll_test/
+test_scripts/iqtree_release
+test_scripts/iqtree_test
+tags
+test_scripts/iqtree_test_cmds.txt
+pllrepo/
 build/
 /Default-clang
+.idea/
+.idea/codeStyleSettings.xml

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "pllrepo"]
-	path = pllrepo
-	url = git@git.assembla.com:phylogenetic-likelihood-library.git

.ycm_extra_conf.py

@@ -0,0 +1,144 @@
+# Generated by YCM Generator at 2015-06-04 16:56:30.936482
+
+# This file is NOT licensed under the GPLv3, which is the license for the rest
+# of YouCompleteMe.
+#
+# Here's the license text for this file:
+#
+# This is free and unencumbered software released into the public domain.
+#
+# Anyone is free to copy, modify, publish, use, compile, sell, or
+# distribute this software, either in source code form or as a compiled
+# binary, for any purpose, commercial or non-commercial, and by any
+# means.
+#
+# In jurisdictions that recognize copyright laws, the author or authors
+# of this software dedicate any and all copyright interest in the
+# software to the public domain. We make this dedication for the benefit
+# of the public at large and to the detriment of our heirs and
+# successors. We intend this dedication to be an overt act of
+# relinquishment in perpetuity of all present and future rights to this
+# software under copyright law.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+# IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+# OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+# OTHER DEALINGS IN THE SOFTWARE.
+#
+# For more information, please refer to <http://unlicense.org/>
+
+import os
+import ycm_core
+
+flags = [
+    '-x',
+    'c++',
+    '-DIQ_TREE',
+    '-D_IQTREE_MPI',
+    '-D__AVX',
+    '-D__SSE3',
+    '-I/home/CIBIV/tung/Dropbox/CODE_GIT_REPO/iqtree',
+    '-I/tmp/tmp6htKo0',
+    '-I/tmp/tmp6htKo0/zlib-1.2.7',
+]
+
+
+# Set this to the absolute path to the folder (NOT the file!) containing the
+# compile_commands.json file to use that instead of 'flags'. See here for
+# more details: http://clang.llvm.org/docs/JSONCompilationDatabase.html
+#
+# You can get CMake to generate this file for you by adding:
+#   set( CMAKE_EXPORT_COMPILE_COMMANDS 1 )
+# to your CMakeLists.txt file.
+#
+# Most projects will NOT need to set this to anything; you can just change the
+# 'flags' list of compilation flags. Notice that YCM itself uses that approach.
+compilation_database_folder = ''
+
+if os.path.exists( compilation_database_folder ):
+  database = ycm_core.CompilationDatabase( compilation_database_folder )
+else:
+  database = None
+
+SOURCE_EXTENSIONS = [ '.cpp', '.cxx', '.cc', '.c', '.m', '.mm' ]
+
+def DirectoryOfThisScript():
+  return os.path.dirname( os.path.abspath( __file__ ) )
+
+
+def MakeRelativePathsInFlagsAbsolute( flags, working_directory ):
+  if not working_directory:
+    return list( flags )
+  new_flags = []
+  make_next_absolute = False
+  path_flags = [ '-isystem', '-I', '-iquote', '--sysroot=' ]
+  for flag in flags:
+    new_flag = flag
+
+    if make_next_absolute:
+      make_next_absolute = False
+      if not flag.startswith( '/' ):
+        new_flag = os.path.join( working_directory, flag )
+
+    for path_flag in path_flags:
+      if flag == path_flag:
+        make_next_absolute = True
+        break
+
+      if flag.startswith( path_flag ):
+        path = flag[ len( path_flag ): ]
+        new_flag = path_flag + os.path.join( working_directory, path )
+        break
+
+    if new_flag:
+      new_flags.append( new_flag )
+  return new_flags
+
+
+def IsHeaderFile( filename ):
+  extension = os.path.splitext( filename )[ 1 ]
+  return extension in [ '.h', '.hxx', '.hpp', '.hh' ]
+
+
+def GetCompilationInfoForFile( filename ):
+  # The compilation_commands.json file generated by CMake does not have entries
+  # for header files. So we do our best by asking the db for flags for a
+  # corresponding source file, if any. If one exists, the flags for that file
+  # should be good enough.
+  if IsHeaderFile( filename ):
+    basename = os.path.splitext( filename )[ 0 ]
+    for extension in SOURCE_EXTENSIONS:
+      replacement_file = basename + extension
+      if os.path.exists( replacement_file ):
+        compilation_info = database.GetCompilationInfoForFile(
+          replacement_file )
+        if compilation_info.compiler_flags_:
+          return compilation_info
+    return None
+  return database.GetCompilationInfoForFile( filename )
+
+
+def FlagsForFile( filename, **kwargs ):
+  if database:
+    # Bear in mind that compilation_info.compiler_flags_ does NOT return a
+    # python list, but a "list-like" StringVec object
+    compilation_info = GetCompilationInfoForFile( filename )
+    if not compilation_info:
+      return None
+
+    final_flags = MakeRelativePathsInFlagsAbsolute(
+      compilation_info.compiler_flags_,
+      compilation_info.compiler_working_dir_ )
+
+  else:
+    relative_to = DirectoryOfThisScript()
+    final_flags = MakeRelativePathsInFlagsAbsolute( flags, relative_to )
+
+  return {
+    'flags': final_flags,
+    'do_cache': True
+  }
+