File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/codemill/bessen/versioned_hdf5_env/lib64/python3.7/site-packages/h5py/_hl/files.py", line 461, in __exit__
    self.close()
  File "/codemill/bessen/versioned_hdf5_env/lib64/python3.7/site-packages/h5py/_hl/files.py", line 431, in close
    id_list = h5f.get_obj_ids(self.id, ~h5f.OBJ_FILE)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 269, in h5py.h5f.get_obj_ids
RuntimeError: Can't increment id ref count (can't locate ID)

import h5py
import numpy as np
from versioned_hdf5 import VersionedHDF5File

ds_names = ['ds{}'.format(i) for i in range(10)]
num_versions = 101


def f1():
    with h5py.File('foo.h5', 'w') as f:
        vf = VersionedHDF5File(f)
        with vf.stage_version('0') as sv:
            data_group = sv.create_group('data')
            for name in ds_names:
                data_group.create_dataset(name, data=np.arange(4))


def f2():
    for i in range(1, num_versions):
        with h5py.File('foo.h5', 'r+') as f:
            vf = VersionedHDF5File(f)
            with vf.stage_version(str(i)) as sv:
                data_group = sv['data']
                for name in ds_names:
                    ds = data_group[name]
                    ds.resize((i + 4,))
                    ds[:] = np.arange(i, 2 * i + 4)


def f3():
    with h5py.File('foo.h5', 'r') as f:
        versions = f['_version_data/versions']
        version_names = list(versions.keys())
        return version_names


def f4(version_names):
    with h5py.File('foo.h5', 'r') as f:
        vf = VersionedHDF5File(f)
        for version_name in version_names:
            if version_name != '__first_version__':
                cv = vf[version_name]
                data_group = cv['data']
                for name in ds_names:
                    ds = data_group[name]
                    _ = ds[:]


if __name__ == '__main__':
    f1()
    f2()
    for _ in range(10):
        version_names = f3()
        f4(version_names)
        version_names = f3()
        f4(version_names)