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Bug#1108997: unblock: mdanalysis/2.9.0-9

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  Bug#1108997: unblock: mdanalysis/2.9.0-9 Drew Parsons <dparsons@debian.org> - 2025-07-09 11:20 +0200
    Bug#1108997: unblock: mdanalysis/2.9.0-9 Drew Parsons <dparsons@debian.org> - 2025-07-09 14:00 +0200
    Bug#1108997: [Debichem-devel] Bug#1108997: unblock: mdanalysis/2.9.0-9 Graham Inggs <ginggs@debian.org> - 2025-07-09 14:30 +0200
    Bug#1108997: unblock: mdanalysis/2.9.0-9 Drew Parsons <dparsons@debian.org> - 2025-07-09 14:50 +0200
    Bug#1108997: unblock: mdanalysis/2.9.0-9 Drew Parsons <dparsons@debian.org> - 2025-07-09 15:00 +0200
    Bug#1108997: unblock: mdanalysis/2.9.0-9 Drew Parsons <dparsons@debian.org> - 2025-07-10 16:10 +0200
      Bug#1108997: unblock: mdanalysis/2.9.0-12 Graham Inggs <ginggs@debian.org> - 2025-07-14 16:20 +0200
        Bug#1108997: unblock: mdanalysis/2.9.0-12 Santiago Vila <sanvila@debian.org> - 2025-07-14 20:40 +0200
    Bug#1108997: unblock: mdanalysis/2.9.0-12 Drew Parsons <dparsons@debian.org> - 2025-07-14 17:20 +0200

#1252225 — Bug#1108997: unblock: mdanalysis/2.9.0-9

Package: release.debian.org
Severity: normal
X-Debbugs-Cc: mdanalysis@packages.debian.org
Control: affects -1 + src:mdanalysis
User: release.debian.org@packages.debian.org
Usertags: unblock

Please unblock package mdanalysis

[ Reason ]

mdanalysis tests are generally flakey, randomly timing out.
In response to Bug#1108309, mdanalysis/2.9.0-9 adds
Restrictions: flaky to debian/tests and skips a few more tests in
order to reduce the level of nuisance from the flakey tests in
trixie-stable.

Tests are currently halted on riscv64 so 2.9.0-9 will not
automatically migrate. Hence filing this unblock request to consider
if we're happy to provide mdanalysis/2.9.0-9 in trixie.

[ Impact ]

Without this update, random timeouts in debci will be registed as
"Failed" rather than "Flakey", making the state of mdanalysis seem
worse than its actual "known flakey" state.

[ Tests ]
debian/tests runs the upstream test-suite, which is actually the cause
of the problem.  Would it be better to stop running mdanalysis tests
altogether?

[ Risks ]
No risk in 2.9.0-9 compared to 2.9.0-8. It skips more tests so in
principle reduces the risk of test failure.

[ Checklist ]
  [x ] all changes are documented in the d/changelog
  [x ] I reviewed all changes and I approve them
  [x ] attach debdiff against the package in testing

[ Other info ]
This update does not fix the random timeouts, but rather marks them as
flaky in debci to keep them from blocking the package.  Santiago Vila
has requested to keep Bug#1108309 open for communication with upstream
to find a more fundamental fix.  We are suggesting this bug be tagged
not-trixie, to let mdanalysis/2.9.0-9 into trixie.

unblock mdanalysis/2.9.0-9

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#1252237

[Multipart message — attachments visible in raw view] — view raw

Package: release.debian.org
Followup-For: Bug #1108997

Forgot to attach the debdiff

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#1252241 — Bug#1108997: [Debichem-devel] Bug#1108997: unblock: mdanalysis/2.9.0-9

Control: tag -1 + moreinfo

Hi Drew

On Wed, 9 Jul 2025 at 11:17, Drew Parsons <dparsons@debian.org> wrote:
> This update does not fix the random timeouts, but rather marks them as
> flaky in debci to keep them from blocking the package.

Marking them 'flaky' is really bad for the infrastructure, as when the
tests fail, they run for the full time before timing out anyway.

Also, this upload does not address the FTBFS in bug #1108997, which
according to past buildd logs, seems to occur on all release
architectures (except ppc64el and s390x).

We won't unblock this upload.  Please remove the 'moreinfo' tag when
there is an upload fixing these issues.

Regards
Graham

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#1252242

Package: release.debian.org
Followup-For: Bug #1108997
X-Debbugs-Cc: 1108309@bugs.debian.org

It sounds like the only thing we can do is to just deactivate all
tests altogether (build and runtime), until upstream gets back to us
on Issue#5078 (Bug#1108309).

Drew

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#1252247

Package: release.debian.org
Followup-For: Bug #1108997

But before entirely deactivating all tests,
I'll first try Santiago's patch which conditionally deactivates them
depending on the number of cpus at hand.

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#1252325

[Multipart message — attachments visible in raw view] — view raw

Package: release.debian.org
Followup-For: Bug #1108997
Control: retitle 1108997 unblock: mdanalysis/2.9.0-12
Control: tags 1108997 - moreinfo

Santiago clarified that skipping tests on 1 or 2 cpu won't actually
help.  Tests still randomly timeout on more than 2 cpu.

mdanalysis/2.9.0-12 deactivates all tests altogether, both build-time
and run-time.  Can this one be unblocked?  debdiff attached.

unblock mdanalysis/2.9.0-12

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#1252740 — Bug#1108997: unblock: mdanalysis/2.9.0-12

On Thu, 10 Jul 2025 at 16:09, Drew Parsons <dparsons@debian.org> wrote:
> Santiago clarified that skipping tests on 1 or 2 cpu won't actually
> help.  Tests still randomly timeout on more than 2 cpu.
>
> mdanalysis/2.9.0-12 deactivates all tests altogether, both build-time
> and run-time.  Can this one be unblocked?  debdiff attached.
>
> unblock mdanalysis/2.9.0-12

Please confirm that the package no longer randomly FTBFS and downgrade
the severity of #1108309 if this is the case.

I've added a skiptest hint for now.  This will be  fine for trixie.
Please let elbrus know when the autopkgtests are properly fixed and
can be enabled again.

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#1252766 — Bug#1108997: unblock: mdanalysis/2.9.0-12

severity 1108309 normal
thanks

On Mon, Jul 14, 2025 at 04:16:55PM +0200, Graham Inggs wrote:
> Please confirm that the package no longer randomly FTBFS and downgrade
> the severity of #1108309 if this is the case.

I confirm that the package builds ok now without random failures.

> I've added a skiptest hint for now.  This will be  fine for trixie.
> Please let elbrus know when the autopkgtests are properly fixed and
> can be enabled again.

Ok, I hope Drew can take care of that (whenever the time come).

Thanks.

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#1252746 — Bug#1108997: unblock: mdanalysis/2.9.0-12

Package: release.debian.org
Followup-For: Bug #1108997
Control: severity 1108309 important

Graham Inggs wrote:
> Please confirm that the package no longer randomly FTBFS and downgrade
> the severity of #1108309 if this is the case.

That's right, mdanalysis/2.9.0-12 skips tests altogether so by
construction they will not randomly fail during build.

For autopkgtest I implemented the change with Restrictions: flaky
in mind.  So the skip is applied via "exit 2" in debian/tests/test-mdanalysis.
I did it this way so that debci tests can continue to be undertaken in
experimental, without locking up the test machines in unstable,
testing and trixie.

Downgrading #1108309 bug severity accordingly.


> I've added a skiptest hint for now.  This will be  fine for trixie.
> Please let elbrus know when the autopkgtests are properly fixed and
> can be enabled again.

Thanks. It will be safe to restart autopkgtest once 2.9.0-12 is in
trixie.

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