h5merge.py

import h5py
import click


@click.command()
@click.argument('sources', nargs=-1, type=click.Path(exists=True, dir_okay=False))
@click.argument('destination', type=click.Path(dir_okay=False, writable=True))
def main(sources, destination):
    outfd = h5py.File(destination, 'a')

    for src in sources:
        with h5py.File(src, 'r') as srcfd:
            for key in list(srcfd):
                h5py.h5o.copy(srcfd.id, key.encode('ascii'), outfd.id, key.encode('ascii'))

    outfd.close()


if __name__ == '__main__':
    main()