Dear Maintainer,

The autopkgtest tets for mdtraj attempts to download a pdb file and then use
that in calculations. This is failing (either all the time or intermittently)
with a timeout:

https://ci.debian.net/data/autopkgtest/unstable/arm64/m/mdtraj/20581005/log.gz

           except Empty:
E               traj = md.load_pdb('http://www.rcsb.org/pdb/files/2MI7.pdb')
E
E               # just for example, use the first frame as the 'native' conformation
E               q = best_hummer_q(traj, traj[0])"

rscb.org is not fast to serve up the pdb files, but I'm not sure if that is
the cause, whether the download is failing entirely, or whether the computation
that follows is just slow.

If this is an isolated use of a single pdb file in the tests, perhaps the
Debian package could carry that pdb file as some test data and patch the test
to use the local file instead.

An internest using test should also be marked as "needs-internet".

regards
Stuart

Hi,

I looked at the results of the autopkgtest of you package because it was
showing up as a regression for the upload of gcc-12.

Because the unstable-to-testing migration software now blocks on
regressions in testing, flaky tests, i.e. tests that flip between
passing and failing without changes to the list of installed packages,
are causing people unrelated to your package to spend time on these
tests.

Don't hesitate to reach out if you need help and some more information
from our infrastructure. Our arm64 workers are located in China, I
wouldn't be surprised if the required connection isn't optimal, so I
suspect increasing the timeout sufficiently is going to solve the issue,
although making it more robust against connection issues would be smart
too (e.g. retrying a small number of times in case of failure).

Also, as the autopkgtest spec says [1], please mark your test with the
"needs-internet" restriction.

Paul

[1]
https://salsa.debian.org/ci-team/autopkgtest/-/blob/master/doc/README.package-tests.rst

Dear maintainer,

I've prepared an NMU for mdtraj (versioned as 1.9.7-3.1) and
uploaded it to DELAYED/14. Please feel free to tell me if I
should cancel it.

cu
Adrian

We believe that the bug you reported is fixed in the latest version of
mdtraj, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1009079@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Adrian Bunk <bunk@debian.org> (supplier of updated mdtraj package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 11 May 2022 23:49:37 +0300
Source: mdtraj
Architecture: source
Version: 1.9.7-3.1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Adrian Bunk <bunk@debian.org>
Closes: 1009079
Changes:
 mdtraj (1.9.7-3.1) unstable; urgency=medium
 .
   * Non-maintainer upload.
   * debian/tests/control: Add Restrictions: needs-internet
     (Closes: #1009079)
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We believe that the bug you reported is fixed in the latest version of
mdtraj, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1009079@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Drew Parsons <dparsons@debian.org> (supplier of updated mdtraj package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 01 Jun 2022 18:02:27 +0200
Source: mdtraj
Architecture: source
Version: 1.9.7-4
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Drew Parsons <dparsons@debian.org>
Closes: 1009079
Changes:
 mdtraj (1.9.7-4) unstable; urgency=medium
 .
   * debian/tests: add Restrictions: needs-internet
     (test_examples.py pulls a random PDB sample file from www.rcsb.org)
   * debian patch test_increase_timeout.patch increases TIMEOUT to
     180 sec in test_examples.py to allow for poor internet connections.
     Closes: #1009079.
   * Standards-Version: 4.6.1
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