1   2008-04-07 boost python documentation

main doc: http://www.boost.org/doc/libs/release/libs/python/doc/

code repositary: https://svn.boost.org/svn/boost/

on wiki.python.org: http://wiki.python.org/moin/boost.python/

a package called "HippoDraw" from http://www.slac.stanford.edu/grp/ek/hippodraw/ heavily used boost.python (such as http://www.slac.stanford.edu/grp/ek/hippodraw/lib/num__util_8h.html). but i haven't got overall picture.

2   2006-01-10 build and install Boost Graph Library - Python Bindings

Starting from 1.33.1, it's separated from boost. http://www.osl.iu.edu/~dgregor/bgl-python/

source

download development version: 'svn co https://svn.osl.iu.edu/svn/projects/viz/bgl-python'

get info

README

boost source directory

export BOOST_ROOT=/home/rcf-14/yuhuang/lib/boost/boost_1_33_1

python version

export PYTHON_VERSION=2.2

build

bjam

install boost python library

mv python/libboost_python.so* to somewhere in LD_LIBRARY_PATH

install bgl python package

mv python/boost to somewhere in PYTHONPATH

(python2.2 only)

enumerate is not available in 2.2. add following to boost/graph/docstring.py:

def enumerate(ls):
     ls_to_return = []
     for i in range(len(ls)):
             ls_to_return.append((i,ls[i]))
     return ls_to_return

3   2006-01-10 boost::noncopyable

it's a useful operative.

When there's 'fstream'-related variables in the source file, usual boost.python fails. The error message looks like:

PostFim.cc:105:   instantiated from here
/usr/include/c++/3.3/bits/ios_base.h:668: error: `std::ios_base::ios_base(const std::ios_base&)' is private
/usr/include/boost/python/object/value_holder.hpp:133: error: within this context
/usr/include/c++/3.3/streambuf: In copy constructor  `std::basic_filebuf<char, std::char_traits<char> >::basic_filebuf(const std::basic_filebuf<char, std::char_traits<char> >&)':
/usr/include/c++/3.3/streambuf:921: error:  `std::basic_streambuf<_CharT, _Traits>::basic_streambuf(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char, _Traits = std::char_traits<char>]' is private
/usr/include/boost/python/object/value_holder.hpp:133: error: within this context

Have to put boost::noncopyable into module declaration such as _class<PostFime, boost::noncopyable>....

4   2006-01-10 compile a inherited class into python module

The two parent-child classes have to be put into one file because when loading python module, the other(parent) module won't be loaded into memory.

Another way to solve this is to separate the parent-child relationship (copy).

5   2008-04-07 make boost python module standalone

Usually, flag such as -fPIC -shared -lboost_python in g++ transforms the .o file into .so file (dynamic library). Removing -shared used to be enough to make the .o become binary executable.

But now i found out, -lpython2.5 has to be added to make .o become binary executable. Final linking flag is -fPIC -lpython2.5 -lboost_python.

6   2009-11-23 select numpy/numeric array

One example in annot/bin/graph/biclustering.cc:

BOOST_PYTHON_MODULE(biclustering)
{
      boost::python::class_<biclustering>("biclustering", init<double, int, int, int>())
              .def("data_read_in", &biclustering::data_read_in)
              .def("scoring", &biclustering::scoring)
              .def("getbicluster", &biclustering::getbicluster)
              .def("return_matrix_data", &biclustering::return_matrix_data)
              .def_readonly("maxScore", &biclustering::maxScore)
              .def_readonly("minHeight", &biclustering::minHeight)
              .def_readonly("minWidth", &biclustering::minWidth)
              .def_readonly("batchThreshold", &biclustering::batchThreshold)
      ;
      boost::python::class_<bicluster>("bicluster")
              .def_readonly("row_index_list", &bicluster::row_index_list)
              .def_readonly("column_index_list", &bicluster::column_index_list)
              .def_readonly("consensus_list", &bicluster::consensus_list)
              .def_readonly("score", &bicluster::score)
      ;
      def("set_module_and_type", &numeric::array::set_module_and_type);
}