Orange Table-specific HDF5Reader

[stuart-cls]

Issue

Enable saving/loading the Orange Table data structure from the binary HDF5 container.
Based on the implementation used in the dask branch, but with the dask parts removed.

Related: #6356

Description of changes

• Add HDF5Reader with both read and write_file methods.
• Add round-trip test for HDF5Reader
• Add h5py to requirements
• Use existing .metadata sidecar file to store table.attributes if present.

Includes

• Code changes
• Tests
• Documentation

[stuart-cls]

It might be better to put some attribute in the HDF5 to explicitly identify it as coming from Orange (could also specify which version) rather than just sniffing for "domain". This would improve discoverability, which is always an issue for HDF5 files.

[markotoplak]

Yes, absolutely. We should have an ID field and probably also a version identifier. Do you know how HDF5 files usually do it?

[stuart-cls]

I added some attributes to the root following the NeXus convention (creator, Orange_version, HDF5_Version, h5py_version) Weird capitalization of "HDF5_Version" is apparently intentional.

[stuart-cls]

I couldn't find a satisfactory solution to the .attributes problem (for the use case I care about) so I re-used the .metadata sidecar files for now, which is better than nothing.

[codecov]

Codecov Report

Attention: Patch coverage is 93.67089% with 5 lines in your changes are missing coverage. Please review.

Project coverage is 88.21%. Comparing base (5ada6c4) to head (63c71b3).
Report is 21 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #6791   +/-   ##
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  Coverage   88.20%   88.21%           
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  Files         327      327           
  Lines       71223    71301   +78     
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+ Hits        62825    62900   +75     
- Misses       8398     8401    +3     

[markotoplak]

Comments from @stuart-cls (from his email, just so that they do not get lost):

• Table.attributes -> I could try again to properly store this in the HDF5, instead of the .metadata sidecar. I got stuck trying to get the round-trip on a visible image to work :)
• Compatibility with dask branch: both opening files saved with that branch, and updating the branch to be compatible.