Fix warnings, use keyword args where possible

[rly]

Use the just released HDMF 3.3.1. Note that HDMF 3.3 introduces warnings when positional arguments are used in subclasses of many base types. This PR replaces positional args with keyword args in source code and tests throughout. Fix #1189

Also remove old-style super() calls and calls to call_docval_func

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[codecov]

Codecov Report

Merging #1484 (1bde866) into dev (728e0ac) will increase coverage by 0.03%.
The diff coverage is 95.43%.

@@            Coverage Diff             @@
##              dev    #1484      +/-   ##
==========================================
+ Coverage   78.24%   78.27%   +0.03%     
==========================================
  Files          37       37              
  Lines        2799     2757      -42     
  Branches      473      486      +13     
==========================================
- Hits         2190     2158      -32     
+ Misses        524      518       -6     
+ Partials       85       81       -4     

Impacted Files	Coverage Δ
src/pynwb/io/ophys.py	45.45% <0.00%> (ø)
src/pynwb/io/base.py	58.62% <50.00%> (ø)
src/pynwb/__init__.py	76.64% <80.00%> (ø)
src/pynwb/spec.py	89.07% <83.33%> (ø)
src/pynwb/ophys.py	94.20% <91.30%> (-1.14%)	⬇️
src/pynwb/file.py	87.56% <93.93%> (-0.07%)	⬇️
src/pynwb/base.py	100.00% <100.00%> (+4.76%)	⬆️
src/pynwb/behavior.py	100.00% <100.00%> (ø)
src/pynwb/core.py	65.85% <100.00%> (ø)
src/pynwb/device.py	100.00% <100.00%> (ø)
... and 11 more

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[rly]

This looks like a really big PR, but no functionality has changed.

This PR does not introduce warnings for using positional arguments for most NWB neurodata type classes, but sets the foundation for it. That change will be in the next minor release.

A minor bug was fixed in src/pynwb/io/epoch.py

There is still a warning about the length of data not matching the length of timestamps when an ImageSeries is created where an external file is used and timestamps are provided. In this case, a placeholder 'data' is set with shape (0,0,0). Again, this is a case where ImageSeries, when not used to store data in the data field breaks inheritance rules and causes headache. I think we should revisit creation of a new neurodata type that is just for external file backed ImageSeries. See also NeurodataWithoutBorders/nwb-schema#481 and #1220 and #1274