h5py fails to build with pytest 8. =================================== FAILURES =================================== _________________________________ test_default _________________________________ request = <FixtureRequest for <Function test_default>> @pytest.mark.mpi_skip @insubprocess @subproc_env({'HDF5_PLUGIN_PATH': 'h5py_plugin_test'}) def test_default(request): assert h5pl.size() == 1 > assert h5pl.get(0) == b'h5py_plugin_test' E AssertionError: assert b'/usr/lib64/hdf5/plugin' == b'h5py_plugin_test' E E At index 0 diff: b'/' != b'h' E Use -v to get more diff serial/build/lib.linux-x86_64-cpython-312/h5py/tests/test_h5pl.py:21: AssertionError _________________________________ test_append __________________________________ request = <FixtureRequest for <Function test_append>> @pytest.mark.mpi_skip @insubprocess @subproc_env({'HDF5_PLUGIN_PATH': 'h5py_plugin_test'}) def test_append(request): h5pl.append(b'/opt/hdf5/vendor-plugin') assert h5pl.size() == 2 > assert h5pl.get(0) == b'h5py_plugin_test' E AssertionError: assert b'/usr/lib64/hdf5/plugin' == b'h5py_plugin_test' E E At index 0 diff: b'/' != b'h' E Use -v to get more diff serial/build/lib.linux-x86_64-cpython-312/h5py/tests/test_h5pl.py:30: AssertionError _________________________________ test_prepend _________________________________ request = <FixtureRequest for <Function test_prepend>> @pytest.mark.mpi_skip @insubprocess @subproc_env({'HDF5_PLUGIN_PATH': 'h5py_plugin_test'}) def test_prepend(request): h5pl.prepend(b'/opt/hdf5/vendor-plugin') > assert h5pl.size() == 2 E assert 3 == 2 E + where 3 = <cyfunction size at 0x7f78c5303e00>() E + where <cyfunction size at 0x7f78c5303e00> = h5pl.size serial/build/lib.linux-x86_64-cpython-312/h5py/tests/test_h5pl.py:39: AssertionError _________________________________ test_insert __________________________________ request = <FixtureRequest for <Function test_insert>> @pytest.mark.mpi_skip @insubprocess @subproc_env({'HDF5_PLUGIN_PATH': 'h5py_plugin_test'}) def test_insert(request): h5pl.insert(b'/opt/hdf5/vendor-plugin', 0) > assert h5pl.size() == 2 E assert 4 == 2 E + where 4 = <cyfunction size at 0x7f78c5303e00>() E + where <cyfunction size at 0x7f78c5303e00> = h5pl.size serial/build/lib.linux-x86_64-cpython-312/h5py/tests/test_h5pl.py:49: AssertionError _________________________________ test_replace _________________________________ request = <FixtureRequest for <Function test_replace>> @pytest.mark.mpi_skip @insubprocess @subproc_env({'HDF5_PLUGIN_PATH': 'h5py_plugin_test'}) def test_replace(request): h5pl.replace(b'/opt/hdf5/vendor-plugin', 0) > assert h5pl.size() == 1 E assert 4 == 1 E + where 4 = <cyfunction size at 0x7f78c5303e00>() E + where <cyfunction size at 0x7f78c5303e00> = h5pl.size serial/build/lib.linux-x86_64-cpython-312/h5py/tests/test_h5pl.py:59: AssertionError _________________________________ test_remove __________________________________ request = <FixtureRequest for <Function test_remove>> @pytest.mark.mpi_skip @insubprocess def test_remove(request): h5pl.remove(0) > assert h5pl.size() == 0 E assert 3 == 0 E + where 3 = <cyfunction size at 0x7f78c5303e00>() E + where <cyfunction size at 0x7f78c5303e00> = h5pl.size serial/build/lib.linux-x86_64-cpython-312/h5py/tests/test_h5pl.py:67: AssertionError https://docs.pytest.org/en/stable/changelog.html For the build logs, see: https://copr-be.cloud.fedoraproject.org/results/thrnciar/pytest/fedora-rawhide-x86_64/07247580-h5py/ For all our attempts to build h5py with pytest 8, see: https://copr.fedorainfracloud.org/coprs/thrnciar/pytest/package/h5py/ Let us know here if you have any questions. Pytest 8 is planned to be included in Fedora 41. And this bugzilla is a heads up before we merge new pytest into rawhide. For more info see a Fedora Change proposal https://fedoraproject.org/wiki/Changes/Pytest_8 We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.
This package has changed maintainer in Fedora. Reassigning to the new maintainer of this component.
Tomáš, any idea what changes in pyteest 8 causes the errors? The pytest 8 changelog i massive.
I did some investigation and ran tests locally, where all of them passed. Thus, I think it's not an upstream problem and we should be able to fix it on Fedora's side. ==================================== test session starts ===================================== platform linux -- Python 3.13.0rc2, pytest-8.3.3, pluggy-1.5.0 cachedir: .tox/py313-test-deps/.pytest_cache rootdir: /home/thrnciar/python-maint/upstream/h5py configfile: pytest.ini plugins: mpi-0.6, cov-5.0.0 collected 768 items ... py313-test-deps/lib64/python3.13/site-packages/h5py/tests/test_h5pl.py ...... [ 88%] ... ============================== 744 passed, 24 skipped in 11.14s ============================== py313-test-mindeps: OK ✔ in 2 minutes 38.7 seconds
I was looking into the first failing test (test_default), but I am afraid I don't understand how HDF5 plugins work and how to debug a Cython file. h5pl.get(0) is here: https://github.com/h5py/h5py/blob/3.12.1/h5py/h5pl.pyx#L57 Could you please help me out? Why is "h5py_plugin_test" expected from h5pl.get(0) and how is it related to the environment variable defined in the test decorator? _________________________________ test_default _________________________________ request = <FixtureRequest for <Function test_default>> @pytest.mark.mpi_skip @insubprocess @subproc_env({'HDF5_PLUGIN_PATH': 'h5py_plugin_test'}) def test_default(request): assert h5pl.size() == 1 > assert h5pl.get(0) == b'h5py_plugin_test' E AssertionError: assert b'/usr/lib64/hdf5/plugin' == b'h5py_plugin_test' E E At index 0 diff: b'/' != b'h' E Use -v to get more diff serial/build/lib.linux-x86_64-cpython-312/h5py/tests/test_h5pl.py:21: AssertionError
I was debugging this to see what is happening with the custom @insubprocess + @subproc_env decorator combo. Anyway, while doing it, I realized that removing --pyargs makes it work: https://src.fedoraproject.org/rpms/h5py/pull-request/11
These tests are rather because they seems to start a new pytest process inside the test[1]: with closed_tempfile() as stdout: with open(stdout, 'w+t') as fh: rtn = subprocess.call([sys.executable, '-m', 'pytest', curr_test], stdout=fh, stderr=fh, env=env) with open(stdout, 'rt') as fh: out = fh.read() [1]: https://github.com/h5py/h5py/blob/master/h5py/tests/common.py#L223 The point of this is set the environmental variable $HDF5_PLUGIN_PATH to a special custom value. @subproc_env({'HDF5_PLUGIN_PATH': 'h5py_plugin_test'}) https://github.com/h5py/h5py/blob/master/h5py/tests/test_h5pl.py#L18 Variable $HDF5_PLUGIN_PATH is read and respected by underlying hdf5 library and should in theory propagate to h5py too. The value of '/usr/lib64/hdf5/plugin' the default value if $HDF5_PLUGIN_PATH is not found in environment. I am not sure how this is related to --pyargs, maybe --pyargs h5py causes h5py lib to loaded twice in some way, I wonder this is the case as h5pl.size() seems to return too high values.
FEDORA-2024-4be1012558 (h5py-3.12.1-2.fc42) has been submitted as an update to Fedora 42. https://bodhi.fedoraproject.org/updates/FEDORA-2024-4be1012558
FEDORA-2024-4be1012558 (h5py-3.12.1-2.fc42) has been pushed to the Fedora 42 stable repository. If problem still persists, please make note of it in this bug report.