Bug#974184: python3-siconos: mechanics-tools tests fail with h5py 3.1

[Drew Parsons]

Package: python3-siconos
Version: 4.3.0+dfsg-2
Severity: normal

The mechanics-tools tests for siconos are failing with
python3-h5py 3.1.0-1exp1 from experimental.

The error message is

  ...
  [io.mechanics] step 600 of 600
  [io.mechanics] output in hdf5 file at step  600
  [io.mechanics] number of contacts 4 (detected) 4 (active at velocity level. approx)
  [io.mechanics] Numerics solver info at time :   3.000000 iterations =        8 precision = 8.160e-08
  [io.mechanics] 
  Excluding object IDs []
  Traceback (most recent call last):
    File "h5py/_debian_h5py_serial/h5o.pyx", line 302, in h5py._debian_h5py_serial.h5o.cb_obj_simple
    File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/group.py", line 591, in proxy
      return func(name, self[name])
    File "/usr/bin/siconos_filter", line 156, in visitor
      ds[range(len(time_idx)),:] = obj[time_idx,:]
    File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper
    File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper
    File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line 910, in __setitem__
      selection = sel.select(self.shape, args, dataset=self)
    File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/selections.py", line 82, in select
      return selector.make_selection(args)
    File "h5py/_debian_h5py_serial/_selector.pyx", line 272, in h5py._debian_h5py_serial._selector.Selector.make_selection
    File "h5py/_debian_h5py_serial/_selector.pyx", line 213, in h5py._debian_h5py_serial._selector.Selector.apply_args
  TypeError: Simple selection can't process range(0, 1556)
  
  The above exception was the direct cause of the following exception:
  
  Traceback (most recent call last):
    File "/usr/bin/siconos_filter", line 234, in <module>
      io_in.visititems(CopyVisitor(
    File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/group.py", line 592, in visititems
      return h5o.visit(self.id, proxy)
    File "h5py/_debian_h5py_serial/_objects.pyx", line 54, in h5py._debian_h5py_serial._objects.with_phil.wrapper
    File "h5py/_debian_h5py_serial/_objects.pyx", line 55, in h5py._debian_h5py_serial._objects.with_phil.wrapper
  SystemError: <built-in function visit> returned a result with an error set
  ASSERT:Unknown failure encountered running a test


Full log at https://ci.debian.net/packages/s/siconos/unstable/amd64/
https://ci.debian.net/data/autopkgtest/unstable/amd64/s/siconos/8011428/log.gz




-- System Information:
Debian Release: bullseye/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 5.9.0-1-amd64 (SMP w/8 CPU threads)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE=en_AU:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages python3-siconos depends on:
ii  libboost-serialization1.71.0  1.71.0-7+b1
ii  libbullet3.06                 3.06+dfsg-3
ii  libc6                         2.31-4
ii  libcxsparse3                  1:5.8.1+dfsg-2
ii  libfclib0                     3.1.0+dfsg-2
ii  libgcc-s1                     10.2.0-16
pn  libsiconos-control6           <none>
pn  libsiconos-io6                <none>
pn  libsiconos-kernel6            <none>
pn  libsiconos-mechanics6         <none>
pn  libsiconos-numerics6          <none>
ii  libstdc++6                    10.2.0-16
ii  python3                       3.8.6-1
ii  python3-numpy                 1:1.19.4-1
pn  siconos                       <none>

python3-siconos recommends no packages.

python3-siconos suggests no packages.