[Debian-med-packaging] Bug#974178: python3-biom-format: debci tests fail: Object of type bytes is not JSON serializable

[Drew Parsons]

Package: python3-biom-format
Version: 2.1.9-2
Severity: normal

debci tests for python3-biom-format are show test error triggered by
python3-h5py 3.1.0-1exp1 from experimental.

The odd thing is that the error trace does not directly refer to h5py,
it's a json problem:

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/biom/assets/exercise_api.py", line 95, in <module>
    out.write(table.to_json('rc-testing'))
  File "/usr/lib/python3/dist-packages/biom/table.py", line 4720, in to_json
    dumps(samp[1]), dumps(samp[2])))
  File "/usr/lib/python3.8/json/__init__.py", line 231, in dumps
    return _default_encoder.encode(obj)
  File "/usr/lib/python3.8/json/encoder.py", line 199, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib/python3.8/json/encoder.py", line 257, in iterencode
    return _iterencode(o, 0)
  File "/usr/lib/python3.8/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type bytes is not JSON serializable


Full error log at
https://ci.debian.net/packages/p/python-biom-format/unstable/amd64/
https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-biom-format/8093113/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-biom-format depends on:
ii  cython3                             0.29.21-3
ii  libc6                               2.31-4
ii  python3                             3.8.6-1
ii  python3-click                       7.1.2-1
ii  python3-future                      0.18.2-4
ii  python3-h5py                        3.1.0-1exp1
ii  python3-h5py-serial                 3.1.0-1exp1
ii  python3-numpy [python3-numpy-abi9]  1:1.19.4-1
ii  python3-pandas                      1.1.4+dfsg-1
ii  python3-scipy                       1.5.3-2
ii  python3-six                         1.15.0-2

python3-biom-format recommends no packages.

Versions of packages python3-biom-format suggests:
pn  python-biom-format-doc  <none>