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.

[orbeckst]

I am seeing the same failure (same two tests) coming up in many of our standard CI runners with development branch, see e.g. https://github.com/MDAnalysis/mdanalysis/actions/runs/29134494537/job/86496075443?pr=5344 . Is it possible that filelock changed behavior?

[orbeckst]

I can also locally reproduce on macOS with Python 3.14 and latest develop

$ pytest  -v -k test_offset_lock_created testsuite/
...
============================================== short test summary info ==============================================
FAILED testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_offset_lock_created - AssertionError: assert not True
FAILED testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_offset_lock_created - AssertionError: assert not True
=========================== 2 failed, 7 skipped, 21667 deselected, 33 warnings in 36.29s ============================

$ mamba list filelock
List of packages in environment: "/Users/oliver/miniforge3/envs/mdadev314"

  Name      Version  Build         Channel
────────────────────────────────────────────────
  filelock  3.29.7   pyhd8ed1ab_0  conda-forge

[orbeckst]

It looks as if filelock 3.29.5 switched to keeping the lock file around as it lead to race conditions, see tox-dev/filelock#577

From what I understand, the new behavior is to always keep the lock file.

I think we just have to change the test.