Create a copy of HDF5 with compressed everything that could be compressed.

recompress_hdf5.py

import h5py
import os

def _report(operation, key, obj):
    type_str = type(obj).__name__.split(".")[-1].lower()
    print "%s %s: %s." % (operation, type_str, key)

def h5py_compatible_attributes(in_object):
    '''Are all attributes of an object readable in h5py?'''
    try:
        # Force obtaining the attributes so that error may appear
        [ 0 for at in in_object.attrs.iteritems() ]
        return True
    except:
        return False

def copy_attributes(in_object, out_object):
    '''Copy attributes between 2 HDF5 objects.'''
    for key, value in in_object.attrs.iteritems():
        out_object.attrs[key] = value

def walk(in_object, out_object, log=False, compression='gzip'):    
    '''Recursively copy&compress the tree.
    
    If attributes cannot be transferred, a copy is created.
    Otherwise, dataset are compressed.
    '''
    for key, in_obj in in_object.iteritems():
        if not isinstance(in_obj, h5py.Datatype) and h5py_compatible_attributes(in_obj):
            if isinstance(in_obj, h5py.Group):
                out_obj = out_object.create_group(key)
                walk(in_obj, out_obj, log, compression)
                if log:
                    _report("Copied", key, in_obj)
            elif isinstance(in_obj, h5py.Dataset):
                out_obj = out_object.create_dataset(key, data=in_obj, compression=compression)
                if log:
                    _report("Compressed", key, in_obj)
            else:
                raise "Invalid object type %s" % type(in_obj)
            copy_attributes(in_obj, out_obj)
        else:
            # We copy datatypes and objects with non-understandable attributes
            # identically.
            if log:
                _report("Copied", key, in_obj)
            in_object.copy(key, out_object)        
     
def recompress(path1, path2, log=False, compression='gzip'):
    '''Compress a HDF5 file.
    
    :param path1: Input path
    :param path2: Output path
    :param log: Whether to print results of operations'
    :returns: A tuple(original_size, new_size)
    '''
    with h5py.File(path1, "r") as in_file, h5py.File(path2, "w") as out_file:
        walk(in_file, out_file, log=log, compression=compression)
    return os.stat(path1).st_size, os.stat(path2).st_size

There is a utility for that named h5repack :-(