ERROR: a bytes-like object is required, not 'str' (h5py v3.0.0)

[GuidoBartoli]

In the latest months I successfully used silx for many data analysis projects and it worked like a charm.

I'm using it in the standard Python + Virtual Environment scenario, but yesterday I had to reinstall it from scratch and when I opened a previously working HDF5 file I received the following error:

a bytes-like object is required, not 'str'   File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/hdf5/Hdf5TreeModel.py", line 520, in data
    return node.dataDescription(role)
  File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/hdf5/Hdf5Item.py", line 564, in dataDescription
    kind, _label = self.__getDataDescription()
  File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/hdf5/Hdf5Item.py", line 558, in __getDataDescription
    self.__description = self.__computeDataDescription()
  File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/hdf5/Hdf5Item.py", line 527, in __computeDataDescription
    return DescriptionType.VALUE, self._getFormatter().humanReadableValue(self.obj)
  File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/hdf5/Hdf5Formatter.py", line 110, in humanReadableValue
    text = self.__formatter.toString(numpy_object, dtype=dataset.dtype)
  File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/data/TextFormatter.py", line 299, in toString
    text = [self.toString(d, dtype) for d in data]
  File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/data/TextFormatter.py", line 299, in <listcomp>
    text = [self.toString(d, dtype) for d in data]
  File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/data/TextFormatter.py", line 302, in toString
    text = self.__formatH5pyObject(data, dtype)
  File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/data/TextFormatter.py", line 270, in __formatH5pyObject
    return self.__formatText(data)
  File "/home/bartoli/.virtualenvs/ml/lib/python3.8/site-packages/silx/gui/data/TextFormatter.py", line 200, in __formatText
    text = "\"%s\"" % text.replace("\\", "\\\\").replace("\"", "\\\"")

After a bit of investigation, I found that requirements.txt of silx install the latest version of h5py that 3 days ago was bumped to v3.0.0 and that is the cause of this error. Forcing the installation of the previous v2.10.0 of h5py solves that.

While waiting for an update of silx compatibility against the latest version of h5py, this problem can be solved by adding the line h5py==2.10.0 in requirements.txt.

Can anybody else reproduce this?

Thanks

[GuidoBartoli]

Sorry for the duplicate issue, I just found out that #3240 could solve this problem.

[t20100]

Thanks for the report!

PR #3240 has been merged, but it's most probably not yet enough to fix all issues related to h5py v3.

[t20100]

Here is a quick&dirty fix:

silx/gui/data/TextFormatter.py l198:

    def __formatText(self, text):
        if self.__useQuoteForText:
            if isinstance(text, (bytes, numpy.bytes_)):
                text = text.decode('utf-8')
            text = "\"%s\"" % text.replace("\\", "\\\\").replace("\"", "\\\"")
        return text