Two build time test errors in connection with hdf5

[tillea]

Bug when building under Debian

There was a bug which essentially boils down to

======================================================================
FAIL: test_link_h5py_dataset_h5dataio_input (tests.unit.test_io_hdf5_h5tools.H5IOTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_hdmf/build/tests/unit/test_io_hdf5_h5tools.py", line 688, in test_link_h5py_dataset_h5dataio_input
    self.assertTrue(isinstance(self.f.get('test_softlink', getlink=True), SoftLink))
AssertionError: False is not true

======================================================================
FAIL: test_link_h5py_dataset_input (tests.unit.test_io_hdf5_h5tools.H5IOTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_hdmf/build/tests/unit/test_io_hdf5_h5tools.py", line 671, in test_link_h5py_dataset_input
    self.assertTrue(isinstance(self.f.get('test_softlink', getlink=True), SoftLink))
AssertionError: False is not true

----------------------------------------------------------------------
Ran 748 tests in 3.146s

FAILED (failures=2, skipped=3, expected failures=1)

Steps to Reproduce

I was able to reproduce this under Debian sid.

Environment

Python Executable: Python
Python Version: Python 39
Operating System: Debian GNU Linux
HDMF Version: 2.2.0

Kind regards, Andreas.

[rly]

Thanks for the bug report. I am finally able to reproduce the bug.

Oddly, running the test stochastically results in either zero, two, or three errors related to hdf5 links. I'll see if I can track down the source of the errors.

[tillea]

On Tue, Dec 08, 2020 at 10:08:47AM -0800, Ryan Ly wrote: Thanks for the bug report. I am finally able to reproduce the bug.

Good to know - thanks for the quick response.

Oddly, running the test stochastically results in either zero, two, or three errors related to hdf5 links. I'll see if I can track down the source of the errors.

I've tried two times but got reproducible results. Kind regards, Andreas.

[rly]

This should be handled now with #496. Thanks for the issue ticket!

[tillea]

On Tue, Dec 08, 2020 at 12:53:31PM -0800, Ryan Ly wrote: This should be handled now with #496. Thanks for the issue ticket!

Thanks, I've uploaded hdmf version 2.3.0 to unstable now.