TestXTCReader_offsets.test_offset_lock_created and TestTRRReader_offsets.test_offset_lock_created always fail

[sanvila]

Hello. When building (the Debian package of) mdanalysis, version 2.10.0 on a Debian unstable system, modified so that all the tests are enabled again, I get the following two failures:

=================================== FAILURES ===================================
________________ TestXTCReader_offsets.test_offset_lock_created ________________

self = <MDAnalysisTests.coordinates.test_xdr.TestXTCReader_offsets object at 0x7fde5ad05c50>
traj = '/tmp/pytest-of-buildd/pytest-0/xtc0/adk_oplsaa.xtc'

    @pytest.mark.skipif(
        sys.platform.startswith("win"),
        reason="The lock file only exists when it's locked in windows",
    )
    def test_offset_lock_created(self, traj):
>       assert os.path.exists(XDR.offsets_filename(traj, ending="lock"))
E       AssertionError: assert False
E        +  where False = <function exists at 0x7fde706321f0>('/tmp/pytest-of-buildd/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.lock')
E        +    where <function exists at 0x7fde706321f0> = <module 'posixpath' (frozen)>.exists
E        +      where <module 'posixpath' (frozen)> = os.path
E        +    and   '/tmp/pytest-of-buildd/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.lock' = <function offsets_filename at 0x7fde69f333d0>('/tmp/pytest-of-buildd/pytest-0/xtc0/adk_oplsaa.xtc', ending='lock')
E        +      where <function offsets_filename at 0x7fde69f333d0> = XDR.offsets_filename

/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/coordinates/test_xdr.py:1059: AssertionError
________________ TestTRRReader_offsets.test_offset_lock_created ________________

self = <MDAnalysisTests.coordinates.test_xdr.TestTRRReader_offsets object at 0x7fde5accc3d0>
traj = '/tmp/pytest-of-buildd/pytest-0/xtc1/adk_oplsaa.trr'

    @pytest.mark.skipif(
        sys.platform.startswith("win"),
        reason="The lock file only exists when it's locked in windows",
    )
    def test_offset_lock_created(self, traj):
>       assert os.path.exists(XDR.offsets_filename(traj, ending="lock"))
E       AssertionError: assert False
E        +  where False = <function exists at 0x7fde706321f0>('/tmp/pytest-of-buildd/pytest-0/xtc1/.adk_oplsaa.trr_offsets.lock')
E        +    where <function exists at 0x7fde706321f0> = <module 'posixpath' (frozen)>.exists
E        +      where <module 'posixpath' (frozen)> = os.path
E        +    and   '/tmp/pytest-of-buildd/pytest-0/xtc1/.adk_oplsaa.trr_offsets.lock' = <function offsets_filename at 0x7fde69f333d0>('/tmp/pytest-of-buildd/pytest-0/xtc1/adk_oplsaa.trr', ending='lock')
E        +      where <function offsets_filename at 0x7fde69f333d0> = XDR.offsets_filename

/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/coordinates/test_xdr.py:1059: AssertionError

Note: Sorry, I have not tried to create a minimal case. Full build logs will be available here in short, as I've marked those tests as XFAIL in the Debian package version 2.10.0-2:

https://buildd.debian.org/status/package.php?p=mdanalysis

Thanks.

[IAlibay]

Thanks for reporting this @sanvila - could you give us more information about the install environment? By any chance, are you installing GSD as an optional dependency?

[sanvila]

Yes, python3-gsd is in the Build-Depends field for the Debian package. This may also be seen here in the build log:

https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=amd64&ver=2.10.0-2&stamp=1779627819&raw=0

Should we try without GSD?

[IAlibay]

I'm seeing this as a consistent failure with the currently released version of MDAnalysis but not on the development builds. I think the answer here might be that we have to do a release.

It's not immediately clear to me that avoiding GSD will fix the issue, although I do remember it playing a part in the problem.