Python support added

autogen.sh

@@ -1,7 +1,7 @@
 #!/bin/sh
 # Run this to generate all the initial makefiles, etc.
 
-ACLOCAL_FLAGS="-I m4 $ACLOCAL_FLAGS"
+ACLOCAL_FLAGS="-I m4 -I . $ACLOCAL_FLAGS"
 LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
 AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
 

ax_pkg_swig.m4

@@ -0,0 +1,135 @@
+# ===========================================================================
+#        http://www.gnu.org/software/autoconf-archive/ax_pkg_swig.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_PKG_SWIG([major.minor.micro], [action-if-found], [action-if-not-found])
+#
+# DESCRIPTION
+#
+#   This macro searches for a SWIG installation on your system. If found,
+#   then SWIG is AC_SUBST'd; if not found, then $SWIG is empty.  If SWIG is
+#   found, then SWIG_LIB is set to the SWIG library path, and AC_SUBST'd.
+#
+#   You can use the optional first argument to check if the version of the
+#   available SWIG is greater than or equal to the value of the argument. It
+#   should have the format: N[.N[.N]] (N is a number between 0 and 999. Only
+#   the first N is mandatory.) If the version argument is given (e.g.
+#   1.3.17), AX_PKG_SWIG checks that the swig package is this version number
+#   or higher.
+#
+#   As usual, action-if-found is executed if SWIG is found, otherwise
+#   action-if-not-found is executed.
+#
+#   In configure.in, use as:
+#
+#     AX_PKG_SWIG(1.3.17, [], [ AC_MSG_ERROR([SWIG is required to build..]) ])
+#     AX_SWIG_ENABLE_CXX
+#     AX_SWIG_MULTI_MODULE_SUPPORT
+#     AX_SWIG_PYTHON
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Sebastian Huber <sebastian-huber@web.de>
+#   Copyright (c) 2008 Alan W. Irwin
+#   Copyright (c) 2008 Rafael Laboissiere <rafael@laboissiere.net>
+#   Copyright (c) 2008 Andrew Collier
+#   Copyright (c) 2011 Murray Cumming <murrayc@openismus.com>
+#
+#   This program is free software; you can redistribute it and/or modify it
+#   under the terms of the GNU General Public License as published by the
+#   Free Software Foundation; either version 2 of the License, or (at your
+#   option) any later version.
+#
+#   This program is distributed in the hope that it will be useful, but
+#   WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+#   Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License along
+#   with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+#   As a special exception, the respective Autoconf Macro's copyright owner
+#   gives unlimited permission to copy, distribute and modify the configure
+#   scripts that are the output of Autoconf when processing the Macro. You
+#   need not follow the terms of the GNU General Public License when using
+#   or distributing such scripts, even though portions of the text of the
+#   Macro appear in them. The GNU General Public License (GPL) does govern
+#   all other use of the material that constitutes the Autoconf Macro.
+#
+#   This special exception to the GPL applies to versions of the Autoconf
+#   Macro released by the Autoconf Archive. When you make and distribute a
+#   modified version of the Autoconf Macro, you may extend this special
+#   exception to the GPL to apply to your modified version as well.
+
+#serial 11
+
+AC_DEFUN([AX_PKG_SWIG],[
+        # Ubuntu has swig 2.0 as /usr/bin/swig2.0
+        AC_PATH_PROGS([SWIG],[swig swig2.0])
+        if test -z "$SWIG" ; then
+                m4_ifval([$3],[$3],[:])
+        elif test -n "$1" ; then
+                AC_MSG_CHECKING([SWIG version])
+                [swig_version=`$SWIG -version 2>&1 | grep 'SWIG Version' | sed 's/.*\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\).*/\1/g'`]
+                AC_MSG_RESULT([$swig_version])
+                if test -n "$swig_version" ; then
+                        # Calculate the required version number components
+                        [required=$1]
+                        [required_major=`echo $required | sed 's/[^0-9].*//'`]
+                        if test -z "$required_major" ; then
+                                [required_major=0]
+                        fi
+                        [required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
+                        [required_minor=`echo $required | sed 's/[^0-9].*//'`]
+                        if test -z "$required_minor" ; then
+                                [required_minor=0]
+                        fi
+                        [required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
+                        [required_patch=`echo $required | sed 's/[^0-9].*//'`]
+                        if test -z "$required_patch" ; then
+                                [required_patch=0]
+                        fi
+                        # Calculate the available version number components
+                        [available=$swig_version]
+                        [available_major=`echo $available | sed 's/[^0-9].*//'`]
+                        if test -z "$available_major" ; then
+                                [available_major=0]
+                        fi
+                        [available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
+                        [available_minor=`echo $available | sed 's/[^0-9].*//'`]
+                        if test -z "$available_minor" ; then
+                                [available_minor=0]
+                        fi
+                        [available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
+                        [available_patch=`echo $available | sed 's/[^0-9].*//'`]
+                        if test -z "$available_patch" ; then
+                                [available_patch=0]
+                        fi
+                        # Convert the version tuple into a single number for easier comparison.
+                        # Using base 100 should be safe since SWIG internally uses BCD values
+                        # to encode its version number.
+                        required_swig_vernum=`expr $required_major \* 10000 \
+                            \+ $required_minor \* 100 \+ $required_patch`
+                        available_swig_vernum=`expr $available_major \* 10000 \
+                            \+ $available_minor \* 100 \+ $available_patch`
+
+                        if test $available_swig_vernum -lt $required_swig_vernum; then
+                                AC_MSG_WARN([SWIG version >= $1 is required.  You have $swig_version.])
+                                SWIG=''
+                                m4_ifval([$3],[$3],[])
+                        else
+                                AC_MSG_CHECKING([for SWIG library])
+                                SWIG_LIB=`$SWIG -swiglib`
+                                AC_MSG_RESULT([$SWIG_LIB])
+                                m4_ifval([$2],[$2],[])
+                        fi
+                else
+                        AC_MSG_WARN([cannot determine SWIG version])
+                        SWIG=''
+                        m4_ifval([$3],[$3],[])
+                fi
+        fi
+        AC_SUBST([SWIG_LIB])
+])

configure.ac

@@ -16,6 +16,7 @@ ENABLE_DEBUG='no'
 ENABLE_C='yes'
 ENABLE_FORTRAN='no'
 ENABLE_PARALLEL='no'
+ENABLE_PYTHON='no'
 
 ###############################################################################
 # --enable-xxx and --with-xxx Arguments
@@ -39,6 +40,13 @@ AC_ARG_ENABLE(
 	[ENABLE_FORTRAN=$enableval])
 AM_CONDITIONAL([ENABLE_FORTRAN], [test "$ENABLE_FORTRAN" = "yes"])
 
+AC_ARG_ENABLE(
+    [python],
+    [AS_HELP_STRING([--enable-python],
+    [Compile the Python interface [default=no]])],
+    [ENABLE_PYTHON=$enableval])
+AM_CONDITIONAL([ENABLE_PYTHON], [test "$ENABLE_PYTHON" = "yes"])
+
 AC_ARG_ENABLE(
 	[parallel],
 	[AS_HELP_STRING([--enable-parallel],
@@ -280,6 +288,50 @@ else
 	AC_MSG_RESULT([no])
 fi
 
+# python enabled?
+if test "X$ENABLE_PYTHON" = "Xyes"; then
+
+    AM_PATH_PYTHON([2.5])
+    AX_PKG_SWIG([1.3], [], [ AC_MSG_ERROR([SWIG is required to build..]) ])
+    #SWIG_ENABLE_CXX
+    #SWIG_PYTHON
+
+    PYTHON_PREFIX=`python-config --prefix`
+    PYTHON_EXEC_PREFIX=`python-config --exec-prefix`
+
+    # make sure numpy is available..
+    AC_MSG_CHECKING([for numpy support])
+    NUMPY_INCLUDE=`${PYTHON} -c 'import numpy; print numpy.get_include()'`
+
+    if test "X$?" = "X0" ; then
+        AC_MSG_RESULT([$NUMPY_INCLUDE])
+    else
+        AC_MSG_RESULT([no])
+        exit 1
+    fi
+    AC_SUBST([NUMPY_INCLUDE])
+
+    #check for parallel support
+    if test "X$ENABLE_PARALLEL" = "Xyes"; then
+        AC_MSG_CHECKING([for mpi4py support])
+        MPI4PY_INCLUDE=`${PYTHON} -c 'import mpi4py; print mpi4py.get_include()'`
+
+        if test "X$?" = "X0" ; then
+            AC_MSG_RESULT([$MPI4PY_INCLUDE])
+        else
+            AC_MSG_RESULT([no])
+            exit 1
+        fi
+	AC_SUBST([MPI4PY_INCLUDE])
+    fi
+
+    AC_MSG_RESULT([ok])
+
+else
+    AC_MSG_CHECKING([if python interface is enabled])
+    AC_MSG_RESULT([no])
+fi
+
 ######################## large indices enabled ###########################
 AC_MSG_CHECKING([if large indices are enabled])
 if test "X$USE_LARGE_INDICES" = "Xyes"; then
@@ -403,6 +455,7 @@ AC_CONFIG_FILES([
 	src/include/h5core/Makefile
         src/C/Makefile
         src/Fortran/Makefile
+        src/Python/Makefile
 	test/Makefile
         doc/Makefile
 	tools/Makefile
@@ -434,4 +487,13 @@ AC_MSG_RESULT([AM_LDFLAGS =         $AM_LDFLAGS])
 AC_MSG_RESULT([LIBS =               $LIBS])
 AC_MSG_RESULT([HDF5_PREFIX =        $HDF5_PREFIX])
 AC_MSG_RESULT([LUSTREROOT =         $LUSTREROOT])
+
+if test "x$ENABLE_PYTHON" = "xyes"; then
+    AC_MSG_RESULT([PYTHON =             $PYTHON])
+    AC_MSG_RESULT([SWIG =               $SWIG])
+    AC_MSG_RESULT([NUMPY_INCLUDE =      $NUMPY_INCLUDE])
+    if test "x$ENABLE_PARALLEL" = "xyes"; then
+        AC_MSG_RESULT([MPI4PY_INCLUDE =     $MPI4PY_INCLUDE])
+    fi
+fi
 AC_MSG_RESULT([ ])

src/Python/H5hut.i

@@ -0,0 +1,58 @@
+%module H5hut
+%{
+#define SWIG_FILE_WITH_INIT
+#include <stdint.h>
+#include "h5core/h5_types.h"
+//#include "H5.h"
+#include "H5hut.h"
+%}
+
+%import <stdint.i>
+
+%include numpy.i
+
+%apply unsigned long int { h5_prop_t };
+%apply unsigned long int { h5_file_t };
+
+
+%apply (unsigned long long* IN_ARRAY1) { h5_size_t* };
+%apply (unsigned int* IN_ARRAY1) { h5_uint32_t* }; //uint32_t
+%apply (unsigned long long* IN_ARRAY1) { h5_uint64_t* }; //uint64_t
+%apply (int* IN_ARRAY1) { h5_int32_t* }; //int32_t
+%apply (long long* IN_ARRAY1) { h5_int64_t* }; //int64_t
+%apply (float* IN_ARRAY1) { h5_float32_t* };
+%apply (double* IN_ARRAY1) { h5_float64_t* };
+
+
+%init %{
+import_array();
+%}
+
+
+%ignore h5_report_errorhandler;
+%ignore h5_abort_errorhandler;
+%ignore h5priv_vprintf;
+%ignore h5_verror;
+%ignore H5ReportErrorhandler;
+%ignore H5AbortErrorhandler;
+
+%include "h5core/h5_types.h"
+//%include "H5.h"
+//%include "H5_attribs.h"
+%include "H5_model.h"
+%include "H5hut.h"
+%include "H5Block_attribs.h"
+//%include "H5Block.h"
+%include "H5Block_io.h"
+%include "H5Block_model.h"
+//%include "H5Part.h"
+%include "H5Part_io.h"
+%include "H5Part_model.h"
+//%include "H5Fed_adjacency.h"
+//%include "H5Fed.h"
+//%include "H5Fed_model.h"
+//%include "H5Fed_retrieve.h"
+//%include "H5Fed_store.h"
+//%include "H5Fed_tags.h"
+
+

src/Python/H5hut_mpi.i

@@ -0,0 +1,71 @@
+%module H5hut_mpi
+%{
+#define SWIG_FILE_WITH_INIT
+#define PARALLEL_IO 1
+#include <mpi.h>
+#include <stdint.h>
+#include "h5core/h5_types.h"
+//#include "H5.h"
+#include "H5hut.h"
+%}
+
+%import <stdint.i>
+
+%include numpy.i
+
+%apply unsigned long int { h5_prop_t };
+%apply unsigned long int { h5_file_t };
+
+
+%apply (unsigned long long* IN_ARRAY1) { h5_size_t* };
+%apply (unsigned int* IN_ARRAY1) { h5_uint32_t* }; //uint32_t
+%apply (unsigned long long* IN_ARRAY1) { h5_uint64_t* }; //uint64_t
+%apply (int* IN_ARRAY1) { h5_int32_t* }; //int32_t
+%apply (long long* IN_ARRAY1) { h5_int64_t* }; //int64_t
+%apply (float* IN_ARRAY1) { h5_float32_t* };
+%apply (double* IN_ARRAY1) { h5_float64_t* };
+
+
+%init %{
+import_array();
+%}
+
+%include mpi4py/mpi4py.i
+%mpi4py_typemap(Comm, MPI_Comm);
+%typemap(in) MPI_Comm* {
+    MPI_Comm *ptr = (MPI_Comm *)0;
+    int res = SWIG_AsPtr_MPI_Comm($input, &ptr);
+    if (!SWIG_IsOK(res) || !ptr) {
+      SWIG_exception_fail(SWIG_ArgError((ptr ? res : SWIG_TypeError)), "in method '" "$symname" "', argument " "$argnum"" of type '" "MPI_Comm""'");
+    }
+    $1 = ptr;
+    if (SWIG_IsNewObj(res)) free((char*)ptr);
+}
+
+%ignore h5_report_errorhandler;
+%ignore h5_abort_errorhandler;
+%ignore h5priv_vprintf;
+%ignore h5_verror;
+%ignore H5ReportErrorhandler;
+%ignore H5AbortErrorhandler;
+
+%include "h5core/h5_types.h"
+//%include "H5.h"
+//%include "H5_attribs.h"
+%include "H5_model.h"
+%include "H5hut.h"
+%include "H5Block_attribs.h"
+//%include "H5Block.h"
+%include "H5Block_io.h"
+%include "H5Block_model.h"
+//%include "H5Part.h"
+%include "H5Part_io.h"
+%include "H5Part_model.h"
+//%include "H5Fed_adjacency.h"
+//%include "H5Fed.h"
+//%include "H5Fed_model.h"
+//%include "H5Fed_retrieve.h"
+//%include "H5Fed_store.h"
+//%include "H5Fed_tags.h"
+
+

src/Python/Makefile.am

@@ -0,0 +1,48 @@
+
+if ENABLE_PYTHON
+
+if ENABLE_PARALLEL
+
+BUILT_SOURCES = H5hut_mpi_wrap.c
+SWIG_SOURCES = H5hut_mpi.i $(MPI4PY_INCLUDE)/mpi4py/mpi4py.i numpy.i
+
+pkgpython_PYTHON = H5hut_mpi.py __init__.py
+pkgpyexec_LTLIBRARIES = _H5hut_mpi.la
+
+_H5hut_mpi_la_SOURCES = H5hut_mpi_wrap.c $(SWIG_SOURCES)
+_H5hut_mpi_la_CPPFLAGS = -DPARALLEL_IO $(SWIG_PYTHON_CPPFLAGS) -I$(top_srcdir)/src/include -I$(PYTHON_PREFIX)/include/python$(PYTHON_VERSION)/ -I$(MPI4PY_INCLUDE) -I$(NUMPY_INCLUDE)
+_H5hut_mpi_la_LDFLAGS = -module
+_H5hut_mpi_la_LIBADD = $(top_builddir)/src/h5core/libH5hut.la 
+
+H5hut_mpi_wrap.c : $(SWIG_SOURCES)
+	$(SWIG) $(SWIG_PYTHON_OPT) -python -DPARALLEL_IO -I$(top_srcdir)/src/include -I$(MPI4PY_INCLUDE) -o $@ $<
+
+else
+
+BUILT_SOURCES = H5hut_wrap.c
+SWIG_SOURCES = H5hut.i numpy.i
+
+pkgpython_PYTHON = H5hut.py __init__.py
+pkgpyexec_LTLIBRARIES = _H5hut.la
+
+_H5hut_la_SOURCES = H5hut_wrap.c $(SWIG_SOURCES)
+_H5hut_la_CPPFLAGS = $(SWIG_PYTHON_CPPFLAGS) -I$(top_srcdir)/src/include -I$(PYTHON_PREFIX)/include/python$(PYTHON_VERSION)/ -I$(NUMPY_INCLUDE)
+_H5hut_la_LDFLAGS = -module 
+_H5hut_la_LIBADD = $(top_builddir)/src/h5core/libH5hut.la
+
+H5hut_wrap.c : $(SWIG_SOURCES)
+	$(SWIG) $(SWIG_PYTHON_OPT) -python -I$(top_srcdir)/src/include -o $@ $<
+
+
+endif
+
+#all-local: 
+#	$(INSTALL) -d  $(DESTDIR)/site-packages/h5hut
+#	$(INSTALL) -m644 H5hut.py $(DESTDIR)/site-packages/h5hut/
+#	$(INSTALL) -m644 .libs/_H5hut.so $(DESTDIR)/site-packages/h5hut/
+endif
+
+clean: clean-am
+
+clean-local:
+	$(RM) -f *~ H5hut_wrap.c H5hut.py H5hut.pyc H5hut_mpi_wrap.c H5hut_mpi.py H5hut_mpi.pyc

src/Python/__init__.py

@@ -0,0 +1,73 @@
+#TODO: use the rewrite to swap depending whether mpi is there are not..
+
+import numpy
+
+try:
+   import H5hut_mpi as H5hut_rewrite
+   from H5hut_mpi import *
+except:
+   import H5hut as H5hut_rewrite
+   from H5hut import *
+
+
+__h5hut_table__ = {}
+
+# for now assume last parameter is the data field..
+funcx = """
+def {0}(*args, **kwargs): 
+    import numpy 
+    if type(args[-1]) is numpy.ndarray:
+        #print "writing type", args[-1].dtype
+        __h5hut_table__['{0}'][args[-1].dtype](*args, **kwargs)
+    elif ((type(args[-1]) is list or type(args[-1]) is tuple) and len(args[-1]) > 0):
+        #print "writing type", type(args[-1][0]).dtype
+        __h5hut_table__['{0}'][numpy.dtype(type(args[-1][0]))](*args, **kwargs)
+    else:
+        print 'last argument is not a numpy data array'
+"""
+
+def __update_types__():
+    import numpy
+    import sys
+    import inspect
+
+    __h5hut_api__ = dir(H5hut_rewrite)
+
+    __h5hut_types__ = [ "Int32", "Int64", "Float32", "Float64" ]
+    __numpy_types__ = [ numpy.dtype(numpy.int32), 
+                        numpy.dtype(numpy.int64), 
+                        numpy.dtype(numpy.float32), 
+                        numpy.dtype(numpy.float64) ]
+
+    for __i__ in __h5hut_api__:
+        for __j__ in __h5hut_types__:
+            if __j__ in __i__:
+                key = __i__[:-len(__j__)]
+
+                numpy_key = __numpy_types__[__h5hut_types__.index(__j__)]
+                func = H5hut_rewrite.__dict__[__i__]
+
+                if key not in __h5hut_table__:
+                    __h5hut_table__[key] = {}
+
+                __h5hut_table__[key][numpy_key] = func
+
+                del H5hut_rewrite.__dict__[__i__]
+                del sys.modules["H5hut"].__dict__[__i__]
+
+    for __new_func__ in __h5hut_table__.keys():
+        types = __h5hut_table__[__new_func__]
+        #args = inspect.getargspec(types[0])
+        #print __new_func__
+        result = funcx.format(__new_func__) 
+        exec(result)
+
+        #H5hut_rewrite.__dict__[__new_func__] = globals()[__new_func__]
+        sys.modules["H5hut"].__dict__[__new_func__] = locals()[__new_func__]
+
+__update_types__()
+        
+
+
+
+