Your message dated Tue, 03 Mar 2026 20:38:13 +0000
with message-id <[email protected]>
and subject line Bug#1129346: fixed in mdtraj 1.11.1.post1-3
has caused the Debian Bug report #1129346,
regarding mdtraj: FTBFS netcdf test failure test_iterload[nc] IndexError: index
exceeds dimension bounds
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1129346: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1129346
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: mdtraj
Version: 1.11.1.post1-1
Severity: normal
Tags: ftbfs
Control: forwarded -1 https://github.com/mdtraj/mdtraj/issues/2142
mdtraj is FTBFS due to failure of test_iterload[nc] in test_trajectory.py
=================================== FAILURES ===================================
______________________________ test_iterload[nc] _______________________________
write_traj = TrajObj(fobj=<class 'mdtraj.formats.netcdf.NetCDFTrajectoryFile'>,
fext='nc', fn='/tmp/pytest-of-sbuild/pytest-1/test_iterload_nc_0/traj.nc')
get_fn = <function get_fn.<locals>._get_fn at 0x7fb7a81a4860>
monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7fb7a8126a50>
def test_iterload(write_traj, get_fn, monkeypatch):
if write_traj.fext == "dtr":
pytest.xfail("This is broken with dtr")
def test_base(write_traj, get_fn):
t_ref = md.load(get_fn("frame0.h5"))[:20]
if write_traj.fext in ("ncrst", "rst7"):
pytest.skip("Only 1 frame per file format")
t_ref.save(write_traj.fn)
for stride in [1, 2, 3]:
loaded = md.load(write_traj.fn, top=t_ref, stride=stride)
iterloaded = functools.reduce(
lambda a, b: a.join(b),
md.iterload(write_traj.fn, top=t_ref, stride=stride,
chunk=6),
)
eq(loaded.xyz, iterloaded.xyz)
eq(loaded.time, iterloaded.time)
eq(loaded.unitcell_angles, iterloaded.unitcell_angles)
eq(loaded.unitcell_lengths, iterloaded.unitcell_lengths)
if write_traj.fext in ("nc"):
# Running with scipy
with monkeypatch.context() as m:
m.setitem(sys.modules, "netCDF4", None)
test_base(write_traj, get_fn)
> test_base(write_traj, get_fn)
tests/test_trajectory.py:662:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_trajectory.py:647: in test_base
iterloaded = functools.reduce(
mdtraj/core/trajectory.py:625: in iterload
traj = f.read_as_traj(
mdtraj/formats/netcdf.py:237: in read_as_traj
xyz, time, cell_lengths, cell_angles = self.read(
mdtraj/formats/netcdf.py:341: in read
coordinates = self._handle.variables["coordinates"][
src/netCDF4/_netCDF4.pyx:5107: in netCDF4._netCDF4.Variable.__getitem__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E IndexError: index exceeds dimension bounds
src/netCDF4/_netCDF4.pyx:6079: IndexError
= 1 failed, 986 passed, 103 skipped, 24 deselected, 61 xfailed, 1 warning in
114.21s (0:01:54) =
Reported upstream
https://github.com/mdtraj/mdtraj/issues/2142
--- End Message ---
--- Begin Message ---
Source: mdtraj
Source-Version: 1.11.1.post1-3
Done: Drew Parsons <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 03 Mar 2026 20:05:08 +0100
Source: mdtraj
Architecture: source
Version: 1.11.1.post1-3
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 1129346
Changes:
mdtraj (1.11.1.post1-3) unstable; urgency=medium
.
* debian patch fix_netcdf_PR2143.patch applies upstream PR#2143 to
fix use of libnetcdf when handling of netcdf files.
Reenable test_iterload[nc]. Closes: #1129346
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