Directory restructuring of graph_tool Python module (now a package)

Everything was moved into the graph_tool directory, which should have,
after installation, the following structure:

graph_tool/                          Top-level package
      __init__.py                    Initialize the graph_tool package
      libgraph_tool.so               libgraph_tool submodule
      libgraph_tool.la               libtool file for libgraph_tool
      include/                       C++ include files for dynamically
                                     compiled code

configure.in

 dnl Process this file with autoconf to produce a configure script.
 
-AC_INIT(graph-tool, 1.2.0devel)
+AC_INIT(graph-tool, 1.2.0devel, [http://graph-tool.forked.de])
 AC_CONFIG_SRCDIR(src/graph-tool)
 AM_INIT_AUTOMAKE
 AM_PROG_CC_C_O
@@ -21,13 +21,13 @@ dnl Checks for options
 
 dnl Turn debugging on or off
 AC_MSG_CHECKING(whether to enable debug info...)
-   
+
 AC_ARG_ENABLE([debug], [AC_HELP_STRING([--enable-debug@<:@=full@:>@],
         [compile debug information [default=yes] ])],
         [AC_MSG_RESULT(yes)]
         [AC_DEFINE([DEBUG], 1, [compile debug info])]
         [CXXFLAGS=" $CXXFLAGS -ggdb3 "],
-        [AC_MSG_RESULT(no)] 
+        [AC_MSG_RESULT(no)]
         )
 
 dnl set template depth and hidden visibility
@@ -35,7 +35,7 @@ dnl set template depth and hidden visibility
 [CXXFLAGS="$CXXFLAGS -ftemplate-depth-150 "]
 
 AC_MSG_CHECKING(whether to enable function inlining...)
-                                                                                
+
 AC_ARG_ENABLE([inline], [AC_HELP_STRING([--disable-inline],
         [disable inline functions [default=enabled] ])],
         if test $enableval = no; then
@@ -50,11 +50,11 @@ AC_ARG_ENABLE([inline], [AC_HELP_STRING([--disable-inline],
         [AC_MSG_RESULT(yes)]
         NO_INLINE=no
         )
-         
+
 AM_CONDITIONAL(NO_INLINE, test $NO_INLINE = yes)
 
 AC_MSG_CHECKING(whether to enable optimizations...)
-                                                                                
+
 AC_ARG_ENABLE([optimization], [AC_HELP_STRING([--disable-optimization],
         [disable optimization [default=enabled] ])],
         [AC_MSG_RESULT(no)]
@@ -64,7 +64,7 @@ AC_ARG_ENABLE([optimization], [AC_HELP_STRING([--disable-optimization],
         )
 
 AC_MSG_CHECKING(whether to enable hidden visibility...)
-                                                                                
+
 AC_ARG_ENABLE([visibility], [AC_HELP_STRING([--disable-visibility],
         [disable hidden visibility [default=enabled] ])],
         [AC_MSG_RESULT(no)]
@@ -95,8 +95,8 @@ AC_ARG_ENABLE([openmp], [AC_HELP_STRING([--enable-openmp],
         if test $enableval = yes; then
            [AC_MSG_RESULT(yes)]
            [AC_DEFINE([USING_OPENMP], 1, [using openmp])]
-           USING_OPENMP=yes  
-           [CXXFLAGS="$CXXFLAGS -fopenmp"]  
+           USING_OPENMP=yes
+           [CXXFLAGS="$CXXFLAGS -fopenmp"]
            [OPENMP_LDFLAGS=" -lgomp "]
         fi
         ,
@@ -108,7 +108,7 @@ AC_ARG_ENABLE([openmp], [AC_HELP_STRING([--enable-openmp],
         )
 AC_SUBST(OPENMP_LDFLAGS)
 
-         
+
 dnl Checks for programs.
 
 dnl Checks for libraries.
@@ -164,6 +164,12 @@ AC_SUBST(NO_PREFIX_PACKAGE_DOC_DIR)
 PACKAGE_DOC_DIR="${packageprefix}/${packagedocdir}"
 AC_SUBST(PACKAGE_DOC_DIR)
 
+dnl Subst PYTHON_DIR.
+AC_DEFINE_UNQUOTED([INSTALL_PREFIX],"${prefix}", [python prefix])
+AC_DEFINE_UNQUOTED([PYTHON_DIR], "${pythondir}", [The directory name for the site-packages subdirectory of the standard Python install tree.])
+
+AC_DEFINE_UNQUOTED([CXXFLAGS],"${CXXFLAGS}", [c++ compilation options])
+
 AC_DEFINE_UNQUOTED([PACKAGE_DATA_DIR], "${packageprefix}/${packagedatadir}", [package data dir])
 AC_DEFINE_UNQUOTED([PACKAGE_DOC_DIR], "${packageprefix}/${packagedocdir}", [package doc dir])
 AC_DEFINE_UNQUOTED([PACKAGE_SOURCE_DIR], "${packagesrcdir}", [package source dir])
@@ -181,5 +187,6 @@ AC_OUTPUT([
 Makefile
 src/Makefile
 src/graph/Makefile
+src/graph_tool/Makefile
 ])
 

src/Makefile.am

@@ -2,10 +2,7 @@
 
 AUTOMAKE_OPTIONS = subdir-objects
 
-SUBDIRS = graph .
-
-graph_tool_PYTHON = graph_tool.py
-graph_tooldir = $(pythondir)
+SUBDIRS = graph graph_tool .
 
 bin_SCRIPTS = graph-tool
 

src/graph/Makefile.am

@@ -12,13 +12,11 @@ AM_CXXFLAGS =\
 
 AM_CFLAGS=$(AM_CXXFLAGS)
 
-libgraph_tool_ladir = ${pythondir}
-libgraph_tool_includedir = $(includedir)/graph_tool
-install-data-hook:		
-	chmod 755 $(includedir)/graph_tool
+libgraph_tooldir = $(pythondir)/graph_tool
 
+libgraph_tool_LTLIBRARIES = libgraph_tool.la
 
-lib_LTLIBRARIES = libgraph_tool.la
+libgraph_tool_la_includedir = $(pythondir)/graph_tool/include
 
 libgraph_tool_la_SOURCES = \
     graph.hh\
@@ -51,7 +49,7 @@ libgraph_tool_la_SOURCES = \
     ../boost-workaround/boost/graph/fruchterman_reingold.hpp\
     ../boost-workaround/boost/graph/graphml.hpp
 
-libgraph_tool_include_HEADERS = \
+libgraph_tool_la_include_HEADERS = \
     graph_adaptor.hh\
     graph.hh\
     graph_filtering.hh\
@@ -73,4 +71,9 @@ libgraph_tool_la_LIBADD = \
 # needed for typeinfo objects to work across DSO boundaries.
 # see http://gcc.gnu.org/faq.html#dso
 libgraph_tool_la_LDFLAGS = \
-    -Wl,-E 
+    -module \
+    -avoid-version \
+    -export-dynamic \
+    -no-undefined \
+    -Wl,-E
+

src/graph/graph_bind.cc

@@ -225,6 +225,9 @@ struct LibInfo
     string GetCopyright() const {return COPYRIGHT;}
     string GetVersion()   const {return VERSION " (commit " GIT_COMMIT ", " GIT_COMMIT_DATE ")";}
     string GetLicense()   const {return "GPL version 3 or above";}
+    string GetCXXFLAGS()  const {return CXXFLAGS;}
+    string GetInstallPrefix() const {return INSTALL_PREFIX;}
+    string GetPythonDir() const {return PYTHON_DIR;}
 };
 
 // overloads
@@ -357,5 +360,8 @@ BOOST_PYTHON_MODULE(libgraph_tool)
         .add_property("author", &LibInfo::GetAuthor)
         .add_property("copyright", &LibInfo::GetCopyright)
         .add_property("version", &LibInfo::GetVersion)
-        .add_property("license", &LibInfo::GetLicense);
+        .add_property("license", &LibInfo::GetLicense)
+        .add_property("cxxflags", &LibInfo::GetCXXFLAGS)
+        .add_property("install_prefix", &LibInfo::GetInstallPrefix)
+        .add_property("python_dir", &LibInfo::GetPythonDir);
 }

src/graph_tool/Makefile.am

+## Process this file with automake to produce Makefile.in
+
+graph_tool_PYTHON = __init__.py
+graph_tooldir = $(pythondir)/graph_tool

src/graph_tool.py → src/graph_tool/__init__.py

@@ -1049,26 +1049,31 @@ class Graph(object):
             raise GraphError(self, "You need to have scipy installed to use" + \
                              " 'run_action'.")
 
+        prefix_dir = libgraph_tool.mod_info().install_prefix
+        python_dir = libgraph_tool.mod_info().python_dir
+        python_dir = string.Template(python_dir).substitute(prefix=prefix_dir)
+        cxxflags = libgraph_tool.mod_info().cxxflags
+        
         # this is the code template which defines the action functor
         support_template = r"""
         #include <map>
         #include <set>
+        #include <list>
         #include <tr1/unordered_set>
         #include <tr1/unordered_map>
         #include <boost/lambda/lambda.hpp>
         #include <boost/lambda/bind.hpp>
         #include <boost/tuple/tuple.hpp>
         #include <boost/type_traits.hpp>
-        #include <graph_tool/graph.hh>
-        #include <graph_tool/graph_filtering.hh>
-        #include <graph_tool/graph_properties.hh>
+        #include "${include_prefix}/graph.hh"
+        #include "${include_prefix}/graph_filtering.hh"
+        #include "${include_prefix}/graph_properties.hh"
 
         using namespace boost;
         using namespace boost::tuples;
         using namespace std;
         using namespace graph_tool;
 
-
         template <class IndexMap>
         struct prop_bind_t
         {
@@ -1155,9 +1160,12 @@ class Graph(object):
         arg_expansion = "\n".join([ exp_term % (i,arg_names[i],i) for i in \
                                     xrange(0, len(arg_names))])
         support_template = string.Template(support_template)
+        inc_prefix = python_dir + "/graph_tool/include"
         support_code = support_template.substitute(code_hash=code_hash,
                                                    arg_expansion=arg_expansion,
-                                                   code=code) + support_code
+                                                   code=code,
+                                                   include_prefix = inc_prefix)\
+                                                   + support_code
 
         # insert a hash value of the support_code into the code below, to force
         # recompilation when support_code (and module version) changes
@@ -1199,12 +1207,12 @@ class Graph(object):
                            support_code=support_code,
                            libraries=["graph_tool"] + libraries,
                            library_dirs=sys.path + library_dirs,
-                           extra_compile_args=["-O3","-ftemplate-depth-150",
-                                               "-Wall", "-Wno-deprecated"] + \
+                           extra_compile_args=[cxxflags] + \
                                             extra_compile_args,
                            runtime_library_dirs=runtime_library_dirs,
                            extra_objects=extra_objects,
-                           extra_link_args=["-Wl,-E"]+extra_link_args)
+                           extra_link_args=["-L" + python_dir + "/graph_tool/",
+                                            "-Wl,-E"] + extra_link_args)
 
         sys.setdlopenflags(_orig_dlopen_flags) # reset dlopen to normal case to
                                                # avoid unnecessary symbol